A B C D E F G H I J K L M N O P Q R S T U V W X Y 

A

AboutInterconnect - Class in org.ecocean.interconnect
 
AboutInterconnect() - Constructor for class org.ecocean.interconnect.AboutInterconnect
 
AbstractTag - Class in org.ecocean.tag
 
AbstractTag() - Constructor for class org.ecocean.tag.AbstractTag
 
accept(File) - Method in class org.ecocean.interconnect.ImageFileFilter
Return true if this file should be shown in the directory pane, false if it shouldn't.
AcceptDialog - Class in org.ecocean.interconnect
 
AcceptDialog(CompareResults, String, String) - Constructor for class org.ecocean.interconnect.AcceptDialog
 
AcceptDialog.OptionListener - Class in org.ecocean.interconnect
An ActionListener that listens to the check box.
AcceptDialog.OptionListener() - Constructor for class org.ecocean.interconnect.AcceptDialog.OptionListener
 
acceptedUserAgreement - Variable in class org.ecocean.User
 
ACOUSTIC_TAG_ID - Static variable in class org.ecocean.servlet.EncounterSetTags
 
ACOUSTIC_TAG_SERIAL - Static variable in class org.ecocean.servlet.EncounterSetTags
 
acousticTag - Variable in class org.ecocean.Encounter
 
AcousticTag - Class in org.ecocean.tag
 
AcousticTag() - Constructor for class org.ecocean.tag.AcousticTag
 
AcousticTag(String, String) - Constructor for class org.ecocean.tag.AcousticTag
 
action - Variable in class org.ecocean.ImageProcessor
 
actionPerformed(ActionEvent) - Method in class org.ecocean.grid.WorkApplet3.scanAppletActionListener
 
actionPerformed(ActionEvent) - Method in class org.ecocean.interconnect.AboutInterconnect
 
actionPerformed(ActionEvent) - Method in class org.ecocean.interconnect.AcceptDialog
 
actionPerformed(ActionEvent) - Method in class org.ecocean.interconnect.AcceptDialog.OptionListener
 
actionPerformed(ActionEvent) - Method in class org.ecocean.interconnect.CompareResults
 
actionPerformed(ActionEvent) - Method in class org.ecocean.interconnect.GetEncounterNumber
 
actionPerformed(ActionEvent) - Method in class org.ecocean.interconnect.InsertDatabase
 
actionPerformed(ActionEvent) - Method in class org.ecocean.interconnect.InsertDatabase.OptionListener
 
actionPerformed(ActionEvent) - Method in class org.ecocean.interconnect.Interconnect.SharkMenu
 
actionPerformed(ActionEvent) - Method in class org.ecocean.interconnect.SharkIdentification
 
actionPerformed(ActionEvent) - Method in class org.ecocean.interconnect.ShowResults
 
add(double, double) - Method in class org.ecocean.interconnect.FingerPrint
 
addATOMEntry(String, String, String, File, String) - Static method in class org.ecocean.servlet.ServletUtilities
 
addClick(double, double) - Method in class org.ecocean.interconnect.SharkPanel
 
addComments(String) - Method in class org.ecocean.Encounter
Adds additional comments about the encounter
addComments(String) - Method in class org.ecocean.MarkedIndividual
Adds any general comments recorded for this MarkedIndividual as a whole.
addComments(String) - Method in class org.ecocean.Occurrence
Adds any general comments recorded for this Occurrence as a whole.
addDataFile(String) - Method in class org.ecocean.MarkedIndividual
Adds a satellite tag data file for this MarkedIndividual.
addEmails(Vector) - Method in class org.ecocean.servlet.export.EncounterSearchExportEmailAddresses
 
addEncounter(Encounter) - Method in class org.ecocean.MarkedIndividual
Adds a new encounter to this MarkedIndividual.
addEncounter(Encounter) - Method in class org.ecocean.Occurrence
 
addExtension(String) - Method in class org.ecocean.interconnect.ImageFileFilter
Adds a filetype "dot" extension to filter against.
addGeneticAnalysis(GeneticAnalysis) - Method in class org.ecocean.genetics.TissueSample
 
addHistories(Vector<MarkedIndividual>, int, HttpServletRequest, DateTime[], DateTime[]) - Method in class org.ecocean.servlet.export.SimpleCMROutput
 
addInterestedResearcher(String) - Method in class org.ecocean.Encounter
 
addInterestedResearcher(String) - Method in class org.ecocean.MarkedIndividual
 
additionalImageNames - Variable in class org.ecocean.Encounter
 
addKeyword(Keyword) - Method in class org.ecocean.SinglePhotoVideo
 
addLocus(Locus) - Method in class org.ecocean.genetics.MicrosatelliteMarkersAnalysis
 
addMarkedIndividual(MarkedIndividual) - Method in class org.ecocean.Shepherd
Adds a new shark to the database
addMeasurement(Measurement) - Method in class org.ecocean.Encounter
 
addMetalTag(MetalTag) - Method in class org.ecocean.Encounter
 
addNode(String, String) - Method in class org.ecocean.grid.ScanTask
 
addPair(Map, int, double, int, Pair) - Method in class com.reijns.I3S.FingerPrint
Adds the distance and array index reference between two points in two different FingerPrints.
addResult(ScanWorkItemResult) - Method in class org.ecocean.grid.ScanTask
 
addRSSEntry(String, String, String, File) - Static method in class org.ecocean.servlet.ServletUtilities
 
addSinglePhotoVideo(SinglePhotoVideo) - Method in class org.ecocean.Encounter
 
addTissueSample(TissueSample) - Method in class org.ecocean.Encounter
 
addWorkItem(ScanWorkItem) - Method in class org.ecocean.grid.GridManager
 
addWorkItem(ScanWorkItem) - Method in class org.ecocean.grid.ScanTask
 
adjustedMatchValue - Variable in class org.ecocean.grid.MatchObject
 
adopterAddress - Variable in class org.ecocean.Adoption
 
adopterEmail - Variable in class org.ecocean.Adoption
 
adopterImage - Variable in class org.ecocean.Adoption
 
adopterName - Variable in class org.ecocean.Adoption
 
adopterQuote - Variable in class org.ecocean.Adoption
 
Adoption - Class in org.ecocean
COmment
Adoption(String, String, String, String, String) - Constructor for class org.ecocean.Adoption
 
AdoptionAction - Class in org.ecocean.servlet
 
AdoptionAction() - Constructor for class org.ecocean.servlet.AdoptionAction
 
adoptionEndDate - Variable in class org.ecocean.Adoption
 
adoptionManager - Variable in class org.ecocean.Adoption
 
adoptionStartDate - Variable in class org.ecocean.Adoption
 
adoptionType - Variable in class org.ecocean.Adoption
 
affiliation - Variable in class org.ecocean.User
 
Affine - Class in com.reijns.I3S
 
Affine() - Constructor for class com.reijns.I3S.Affine
 
afterExecute(AppletWorkItemThread, Throwable) - Method in class org.ecocean.grid.SharkGridThreadPoolExecutor
 
allele(int) - Method in class org.ecocean.genetics.HFStatistics
 
allele0 - Variable in class org.ecocean.genetics.Locus
 
allele1 - Variable in class org.ecocean.genetics.Locus
 
allele2 - Variable in class org.ecocean.genetics.Locus
 
allele3 - Variable in class org.ecocean.genetics.Locus
 
alleleFrequencyPerPopulation(int, int) - Method in class org.ecocean.genetics.FStatistics
 
alleleFrequencyPerPopulation(int, int) - Method in class org.ecocean.genetics.HFStatistics
 
alleleFrequencyTotal(int) - Method in class org.ecocean.genetics.FStatistics
 
alleleFrequencyTotal(int) - Method in class org.ecocean.genetics.HFStatistics
 
alleleLengths - Variable in class org.ecocean.genetics.distance.Ind2IndDistance
 
alleleRepSize - Variable in class org.ecocean.genetics.distance.Ind2IndDistance
 
alleleValue(int) - Method in class org.ecocean.genetics.FStatistics
 
alleleValue(int) - Method in class org.ecocean.genetics.HFStatistics
 
AllocVectors(int[][], int[]) - Static method in class org.ecocean.genetics.distance.MyFuns
 
AllocVectors(int[][][], int[]) - Static method in class org.ecocean.genetics.distance.MyFuns
 
AllocVectors(double[][], int[]) - Static method in class org.ecocean.genetics.distance.MyFuns
 
AllocVectors(double[][][], int[]) - Static method in class org.ecocean.genetics.distance.MyFuns
 
allowAdoptions(String) - Static method in class org.ecocean.CommonConfiguration
This configuration option defines whether adoptions of MarkedIndividual or encounter objects are allowed.
allowNicknames(String) - Static method in class org.ecocean.CommonConfiguration
This configuration option defines whether nicknames are allowed for MarkedIndividual entries.
alternateid - Variable in class org.ecocean.MarkedIndividual
 
alternateSampleID - Variable in class org.ecocean.genetics.TissueSample
 
analyses - Variable in class org.ecocean.genetics.TissueSample
 
analysisID - Variable in class org.ecocean.genetics.GeneticAnalysis
 
analysisType - Variable in class org.ecocean.genetics.GeneticAnalysis
 
appendEmailRemoveHashString(HttpServletRequest, String, String, String) - Static method in class org.ecocean.CommonConfiguration
 
AppletHeartbeatThread - Class in org.ecocean.grid
COmment
AppletHeartbeatThread(String, int, String, String) - Constructor for class org.ecocean.grid.AppletHeartbeatThread
Constructor to create a new thread object
appletID - Variable in class org.ecocean.grid.AppletHeartbeatThread
 
AppletSwingWorker<V> - Class in org.ecocean.grid
An abstract class that you subclass to perform GUI-related work in a dedicated thread.
AppletSwingWorker() - Constructor for class org.ecocean.grid.AppletSwingWorker
Creates new SwingWorker with default executor.
AppletSwingWorker(Executor) - Constructor for class org.ecocean.grid.AppletSwingWorker
Creates new SwingWorker with specified executor.
appletVersion - Variable in class org.ecocean.grid.GridManager
 
AppletWorkItemThread - Class in org.ecocean.grid
Test comment
AppletWorkItemThread(ScanWorkItem, Vector) - Constructor for class org.ecocean.grid.AppletWorkItemThread
Constructor to create a new thread object
approved - Variable in class org.ecocean.Encounter
 
area - Variable in class org.ecocean.Spot
 
arg - Variable in class org.ecocean.ImageProcessor
 
argosPttNumber - Variable in class org.ecocean.tag.SatelliteTag
 
assignToMarkedIndividual(String) - Method in class org.ecocean.Encounter
 
asUrl(Encounter, String) - Method in class org.ecocean.SinglePhotoVideo
 
augMat - Variable in class com.reijns.I3S.LinSys
 
averageLengthInYear(int) - Method in class org.ecocean.MarkedIndividual
Deprecated. 
averageMeasuredLengthInYear(int, boolean) - Method in class org.ecocean.MarkedIndividual
Deprecated. 
avgLengthInPeriod(int, int, int, int) - Method in class org.ecocean.MarkedIndividual
Deprecated. 

B

backSub() - Method in class com.reijns.I3S.LinSys
 
BareBonesBrowserLaunch - Class in org.ecocean.interconnect
 
BareBonesBrowserLaunch() - Constructor for class org.ecocean.interconnect.BareBonesBrowserLaunch
 
beginDBTransaction() - Method in class org.ecocean.Shepherd
Opens the database up for information retrieval, storage, and removal
behavior - Variable in class org.ecocean.Encounter
 
belongsToMarkedIndividual - Variable in class org.ecocean.grid.EncounterLite
 
best - Variable in class com.reijns.I3S.Compare
 
bgImg - Variable in class org.ecocean.interconnect.BothSharks
 
bidirectional - Variable in class org.ecocean.social.Relationship
 
BiologicalMeasurement - Class in org.ecocean.genetics
 
BiologicalMeasurement() - Constructor for class org.ecocean.genetics.BiologicalMeasurement
 
BiologicalMeasurement(String, String, String, String, Double, String, String) - Constructor for class org.ecocean.genetics.BiologicalMeasurement
 
BIOLOGICALMEASUREMENT - Static variable in class org.ecocean.Util
 
BIOLOGICALMEASUREMENTUNITS - Static variable in class org.ecocean.Util
 
blocked(Vector, HttpServletRequest) - Static method in class org.ecocean.Encounter
 
bmp - Static variable in class org.ecocean.interconnect.Utils
 
BothSharks - Class in org.ecocean.interconnect
 
BothSharks(String, String, Point2D[], Point2D[], int[], double) - Constructor for class org.ecocean.interconnect.BothSharks
 
buf - Variable in class org.ecocean.interconnect.CopyFile
 
buildUI(Container) - Method in class org.ecocean.interconnect.Interconnect
 
BYTES_DOWNLOAD - Static variable in class org.ecocean.servlet.export.EncounterSearchExportEmailAddresses
 
BYTES_DOWNLOAD - Static variable in class org.ecocean.servlet.export.EncounterSearchExportExcelFile
 
BYTES_DOWNLOAD - Static variable in class org.ecocean.servlet.export.EncounterSearchExportGeneGISFormat
 
BYTES_DOWNLOAD - Static variable in class org.ecocean.servlet.export.EncounterSearchExportKML
 
BYTES_DOWNLOAD - Static variable in class org.ecocean.servlet.export.EncounterSearchExportShapefile
 
BYTES_DOWNLOAD - Static variable in class org.ecocean.servlet.export.GenalexExportCodominantMSDataBySize
 
BYTES_DOWNLOAD - Static variable in class org.ecocean.servlet.export.KinalyzerExport
 
BYTES_DOWNLOAD - Static variable in class org.ecocean.servlet.export.SimpleCMROutput
 
BYTES_DOWNLOAD - Static variable in class org.ecocean.servlet.export.SOCPROGExport
 

C

C - Variable in class org.ecocean.grid.GridManager
 
C - Variable in class org.ecocean.grid.ScanWorkItem
 
C - Variable in class org.ecocean.grid.SpotTriangle
 
cacheOff() - Static method in class org.ecocean.genetics.distance.Distances
 
cacheOn() - Static method in class org.ecocean.genetics.distance.Distances
 
calcAffine(double, double, double, double, double, double, double, double, double, double, double, double, double[]) - Static method in class com.reijns.I3S.Affine
 
calcDisplayFactor() - Method in class org.ecocean.interconnect.SharkPanel
 
calculate(int[], int[], int) - Static method in class org.ecocean.genetics.distance.DistSAD
 
calculate(int[], int[]) - Method in class org.ecocean.genetics.distance.DistWAD
 
calculate(int[], int[]) - Method in class org.ecocean.genetics.distance.Ind2IndDistance
 
CalendarXMLServer - Class in org.ecocean.servlet
Returns the results of an encounter search request in XML for display in a calendar.
CalendarXMLServer() - Constructor for class org.ecocean.servlet.CalendarXMLServer
 
CalendarXMLServer2 - Class in org.ecocean.servlet
 
CalendarXMLServer2() - Constructor for class org.ecocean.servlet.CalendarXMLServer2
 
cancel(boolean) - Method in class org.ecocean.grid.AppletSwingWorker
Attempts to cancel execution of this task.
canCollaborate(String, String, String) - Static method in class org.ecocean.security.Collaboration
 
canUserAccess(HttpServletRequest) - Method in class org.ecocean.Encounter
 
canUserAccess(HttpServletRequest) - Method in class org.ecocean.MarkedIndividual
 
canUserAccess(HttpServletRequest) - Method in class org.ecocean.Occurrence
 
canUserAccessEncounter(Encounter, HttpServletRequest) - Static method in class org.ecocean.security.Collaboration
 
canUserAccessMarkedIndividual(MarkedIndividual, HttpServletRequest) - Static method in class org.ecocean.security.Collaboration
 
canUserAccessOccurrence(Occurrence, HttpServletRequest) - Static method in class org.ecocean.security.Collaboration
 
catalogNumber - Variable in class org.ecocean.Encounter
 
catalogSex - Variable in class org.ecocean.grid.I3SMatchObject
 
catalogSex - Variable in class org.ecocean.grid.MatchObject
 
centroidX - Variable in class org.ecocean.Spot
 
centroidX - Variable in class org.ecocean.SuperSpot
 
centroidY - Variable in class org.ecocean.Spot
 
centroidY - Variable in class org.ecocean.SuperSpot
 
checkFileType(DataInputStream) - Method in class com.reijns.I3S.FgpFileOpen
Checks to see if the file is of the FGP file type by checking the file header.
checkin(int) - Method in class org.ecocean.grid.GridNode
 
checkinResult(ScanWorkItemResult) - Method in class org.ecocean.grid.GridManager
 
checkoutTimeout - Variable in class org.ecocean.grid.GridManager
 
chooser - Static variable in class org.ecocean.interconnect.Interconnect
 
cleanFileName(String) - Static method in class org.ecocean.servlet.ServletUtilities
 
cleanup() - Method in class org.ecocean.grid.GridCleanupThread
 
cleanup() - Method in class org.ecocean.grid.ScanTaskCleanupThread
 
cleanupOldNodes() - Method in class org.ecocean.grid.GridManager
 
clearCache() - Static method in class org.ecocean.genetics.distance.Distances
 
clockwise - Variable in class org.ecocean.grid.SpotTriangle
 
close() - Method in class com.reijns.I3S.Compare
 
close() - Method in class org.ecocean.interconnect.LogFile
 
close() - Method in class org.ecocean.interconnect.SharkPanel
 
closeCompare() - Method in class org.ecocean.interconnect.SharkPanel
 
closeDBTransaction() - Method in class org.ecocean.Shepherd
Closes a PersistenceManager
closeFile(InputStream) - Method in class com.reijns.I3S.FgpFileOpen
Closes the FGP opened as any InputStream decendent.
closeOnExit() - Method in class org.ecocean.interconnect.SharkPanel
 
cnt - Variable in class com.reijns.I3S.Compare
 
cnt - Variable in class com.reijns.I3S.FingerPrint
 
Collaborate - Class in org.ecocean.servlet
 
Collaborate() - Constructor for class org.ecocean.servlet.Collaborate
 
Collaboration - Class in org.ecocean.security
a Collaboration is a defined, two-way relationship between two Users.
Collaboration() - Constructor for class org.ecocean.security.Collaboration
 
Collaboration(String, String) - Constructor for class org.ecocean.security.Collaboration
 
collaborationBetweenUsers(String, String, String) - Static method in class org.ecocean.security.Collaboration
 
collaborationLockHtml(ArrayList<Collaboration>) - Method in class org.ecocean.Encounter
 
collaborationLockHtml(HttpServletRequest) - Method in class org.ecocean.MarkedIndividual
 
collaborationsForCurrentUser(HttpServletRequest) - Static method in class org.ecocean.security.Collaboration
 
collaborationsForCurrentUser(HttpServletRequest, String) - Static method in class org.ecocean.security.Collaboration
 
collaborationsForUser(String, String) - Static method in class org.ecocean.security.Collaboration
 
collaborationsForUser(String, String, String) - Static method in class org.ecocean.security.Collaboration
 
collectionCode - Variable in class org.ecocean.DataCollectionEvent
 
collectionID - Variable in class org.ecocean.DataCollectionEvent
 
com.reijns.I3S - package com.reijns.I3S
 
combinations(int, int) - Method in class org.ecocean.servlet.ScanTaskHandler
 
command - Variable in class org.ecocean.ImageProcessor
 
comment - Variable in class org.ecocean.interconnect.FingerPrint
 
comments - Variable in class org.ecocean.MarkedIndividual
 
comments - Variable in class org.ecocean.Occurrence
 
commitDBTransaction() - Method in class org.ecocean.Shepherd
Commits (makes permanent) any changes made to an open database
commitDBTransaction(String) - Method in class org.ecocean.Shepherd
Commits (makes permanent) any changes made to an open database
COMMON_CONFIGURATION_PROPERTIES - Static variable in class org.ecocean.CommonConfiguration
 
CommonConfiguration - Class in org.ecocean
 
CommonConfiguration() - Constructor for class org.ecocean.CommonConfiguration
 
Compare - Class in com.reijns.I3S
 
Compare(FingerPrint) - Constructor for class com.reijns.I3S.Compare
 
Compare(FingerPrint[]) - Constructor for class com.reijns.I3S.Compare
 
compare(Object, Object) - Method in class org.ecocean.EncounterDateComparator
 
compare(Object, Object) - Method in class org.ecocean.genetics.distance.DistanceComparator
 
compare(Object, Object) - Method in class org.ecocean.grid.I3SMatchComparator
 
compare(Object, Object) - Method in class org.ecocean.grid.MatchComparator
 
compare(Object, Object) - Method in class org.ecocean.grid.NewI3SMatchComparator
 
compare(Object, Object) - Method in class org.ecocean.grid.RComparator
 
compare(Object, Object) - Method in class org.ecocean.grid.ScoreComparator
 
compare(Object, Object) - Method in class org.ecocean.IndividualOccurrenceNumComparator
 
CompareResults - Class in org.ecocean.interconnect
 
CompareResults(SharkPanel, String, String, Point2D[], Point2D[], Point2D[], Point2D[], int[], double) - Constructor for class org.ecocean.interconnect.CompareResults
 
compareTwo(FingerPrint, FingerPrint, Map, boolean) - Method in class com.reijns.I3S.Compare
Compares an unknown visitor FingerPrint to a prior encountered FingerPrint.
compareWithDatabase(StringBuffer, boolean) - Method in class org.ecocean.interconnect.SharkPanel
 
comparisons - Variable in class org.ecocean.grid.WorkApplet3
 
comparisons - Variable in class org.ecocean.grid.WorkApplet3.runWIScan
 
comparisons - Variable in class org.ecocean.grid.WorkApplet3.scanAppletActionListener
 
computeAngle(double[], double[], double[]) - Static method in class org.ecocean.grid.Geometry
Find the angle between three points.
computeCrossProduct(double[], double[]) - Static method in class org.ecocean.grid.Geometry
Compute the cross product (a vector) of two vectors.
computeDotProduct(double[], double[]) - Static method in class org.ecocean.grid.Geometry
Compute the dot product (a scalar) between two vectors.
computePointOnLine(double[], double[], double) - Static method in class org.ecocean.grid.Geometry
Find the point on the line p0,p1 [x,y,z] a given fraction from p0.
computePointOnLine(double, double, double, double, double) - Static method in class org.ecocean.grid.Geometry
Find the point on the line defined by x0,y0,x1,y1 a given fraction from x0,y0.
computePolygonArea(double[], double[]) - Static method in class org.ecocean.grid.Geometry
Compute the area of the specfied polygon.
computePolygonArea(double[]) - Static method in class org.ecocean.grid.Geometry
Compute the area of the specfied polygon.
computePolygonCentroid(double[], double[]) - Static method in class org.ecocean.grid.Geometry
Compute centorid (center of gravity) of specified polygon.
constrain(Container, Component, int, int, int, int, int, int, double, double, int, int, int, int) - Static method in class org.ecocean.genetics.distance.MyFuns
 
constrain(Container, Component, int, int, int, int, int, int) - Static method in class org.ecocean.genetics.distance.MyFuns
 
constrain(Container, Component, int, int, int, int) - Static method in class org.ecocean.genetics.distance.MyFuns
 
constrain(Container, Component, int, int, int, int, int, int, int, int) - Static method in class org.ecocean.genetics.distance.MyFuns
 
construct() - Method in class org.ecocean.grid.AppletSwingWorker
Computes the value to be returned by the get method.
construct() - Method in class org.ecocean.grid.WorkApplet3.gridSwingWorker
 
containsNode(String) - Method in class org.ecocean.grid.GridManager
 
containsSpot(Spot) - Method in class org.ecocean.grid.SpotTriangle
 
context - Variable in class org.ecocean.grid.FalseMatchCreationThread
 
context - Variable in class org.ecocean.grid.GridCleanupThread
 
context - Variable in class org.ecocean.grid.ScanWorkItemCreationThread
 
context - Variable in class org.ecocean.grid.TuningTaskCreationThread
 
context - Variable in class org.ecocean.ImageProcessor
 
context - Variable in class org.ecocean.NotificationMailer
 
context - Variable in class org.ecocean.Role
 
ContextConfiguration - Class in org.ecocean
 
ContextConfiguration() - Constructor for class org.ecocean.ContextConfiguration
 
CONTEXTS_PROPERTIES - Static variable in class org.ecocean.ContextConfiguration
 
contourY - Variable in class org.ecocean.Spot
 
control - Variable in class com.reijns.I3S.FingerPrint
 
convertStreamToString(FileInputStream) - Method in class org.ecocean.servlet.EncounterSetPatterningPassport
Converts given InputStream to a String
coords - Static variable in class org.ecocean.Util
 
copyData(double[], double[], double[]) - Method in class org.ecocean.interconnect.FingerPrint
 
CopyFile - Class in org.ecocean.interconnect
 
CopyFile(String, String) - Constructor for class org.ecocean.interconnect.CopyFile
 
copyrightOwner - Variable in class org.ecocean.SinglePhotoVideo
 
copyrightStatement - Variable in class org.ecocean.SinglePhotoVideo
 
correspondingEncounterNumber - Variable in class org.ecocean.DataCollectionEvent
correspondingEncounterNumber species which Encounter instance this data collection even corresponds with
correspondingEncounterNumber - Variable in class org.ecocean.genetics.GeneticAnalysis
 
correspondingEncounterNumber - Variable in class org.ecocean.Story
 
correspondingMarkedIndividualID - Variable in class org.ecocean.Story
 
correspondingOccurrenceID - Variable in class org.ecocean.Story
 
correspondingSocialUnitName - Variable in class org.ecocean.Story
 
correspondingStoryID - Variable in class org.ecocean.SinglePhotoVideo
 
correspondingThumbnailSinglePhotoVideo - Variable in class org.ecocean.Story
 
correspondingUsername - Variable in class org.ecocean.SinglePhotoVideo
 
cosineAtVertex1 - Variable in class org.ecocean.grid.SpotTriangle
 
CountCharsInString(String, char) - Static method in class org.ecocean.genetics.distance.MyFuns
 
CountFieldsInString(String) - Static method in class org.ecocean.genetics.distance.MyFuns
 
countourX - Variable in class org.ecocean.Spot
 
country - Variable in class org.ecocean.Encounter
 
countSharedAlleles(int[], int[], int) - Static method in class org.ecocean.genetics.distance.Ind2IndDistance
 
countUnsharedAlleles(int[], int[], int) - Static method in class org.ecocean.genetics.distance.DistSAD
 
cr - Static variable in class org.ecocean.interconnect.AcceptDialog
 
cr - Static variable in class org.ecocean.interconnect.SharkIdentification
 
create(String, String) - Static method in class org.ecocean.security.Collaboration
 
createArrow(int[], int[], double, double, double) - Static method in class org.ecocean.grid.Geometry
Create the geometry of an arrow.
createArrow(int, int, int, int, double, double, double) - Static method in class org.ecocean.grid.Geometry
Create geometry for an arrow along the specified line and with tip at x1,y1.
createCircle(int, int, int) - Static method in class org.ecocean.grid.Geometry
Create geometry for a circle.
createCircle(double, double, double) - Static method in class org.ecocean.grid.Geometry
Create geometry for a circle.
createEllipse(int[], int[]) - Static method in class org.ecocean.grid.Geometry
Return the geometry of an ellipse based on its four top points.
createEllipse(int, int, int, int) - Static method in class org.ecocean.grid.Geometry
Create the geometry for an unrotated, unskewed ellipse.
createEllipse(double, double, double, double) - Static method in class org.ecocean.grid.Geometry
Create the geometry for an unrotated, unskewed ellipse.
createFeatureType(String) - Static method in class org.ecocean.servlet.export.EncounterSearchExportShapefile
Here is how you can use a SimpleFeatureType builder to create the schema for your shapefile dynamically.
createMenuBar() - Method in class org.ecocean.interconnect.Interconnect.SharkMenu
 
createRectangle(int, int, int, int) - Static method in class org.ecocean.grid.Geometry
Create geometry for a rectangle.
createRectangle(double, double, double, double) - Static method in class org.ecocean.grid.Geometry
Create geometry for a rectangle.
createSector(int, int, int, int, double, double) - Static method in class org.ecocean.grid.Geometry
Create the geometry of a sector of an ellipse.
createSector(int, int, int, double, double) - Static method in class org.ecocean.grid.Geometry
Create the geometry of a sector of a circle.
createStar(int, int, int, int, int) - Static method in class org.ecocean.grid.Geometry
Create geometry of a star.
createStar(double, double, double, double, int) - Static method in class org.ecocean.grid.Geometry
Create geometry of a star.
createThem() - Method in class org.ecocean.grid.FalseMatchCreationThread
 
createThem() - Method in class org.ecocean.grid.ScanWorkItemCreationThread
 
createThem() - Method in class org.ecocean.grid.TuningTaskCreationThread
 
createTime - Variable in class org.ecocean.grid.ScanWorkItem
 
createToken(ServletRequest, ServletResponse) - Method in class org.ecocean.security.WildbookBasicHttpAuthenticationFilter
 
createVector(double[], double[]) - Static method in class org.ecocean.grid.Geometry
Construct the vector specified by two points.
creationDeletionThreadQueueSize - Variable in class org.ecocean.grid.GridManager
 
CrossProd - Variable in class org.ecocean.grid.SpotTriangle
 
cursor - Variable in class org.ecocean.interconnect.SharkPanel
 

D

D12 - Variable in class org.ecocean.grid.SpotTriangle
 
D13 - Variable in class org.ecocean.grid.SpotTriangle
 
D23 - Variable in class org.ecocean.grid.SpotTriangle
 
d_clear() - Method in class org.ecocean.genetics.HFStatistics
 
d_flag - Variable in class org.ecocean.genetics.FStatistics
 
d_flag - Variable in class org.ecocean.genetics.HFStatistics
 
d_genotypes - Variable in class org.ecocean.genetics.FStatistics
 
d_genotypes - Variable in class org.ecocean.genetics.HFStatistics
 
d_init() - Method in class org.ecocean.genetics.FStatistics
 
d_init() - Method in class org.ecocean.genetics.HFStatistics
 
d_numberOfGenotypes - Variable in class org.ecocean.genetics.FStatistics
 
d_numberOfGenotypes - Variable in class org.ecocean.genetics.HFStatistics
 
d_populationLabels - Variable in class org.ecocean.genetics.FStatistics
 
d_populationLabels - Variable in class org.ecocean.genetics.HFStatistics
 
d_reserved - Variable in class org.ecocean.genetics.FStatistics
 
d_reserved - Variable in class org.ecocean.genetics.HFStatistics
 
DataCollectionEvent - Class in org.ecocean
 
DataCollectionEvent() - Constructor for class org.ecocean.DataCollectionEvent
 
DataCollectionEvent(String, String) - Constructor for class org.ecocean.DataCollectionEvent
 
DataCollectionEvent(String, String, HttpServletRequest) - Constructor for class org.ecocean.DataCollectionEvent
 
dataCollectionEventID - Variable in class org.ecocean.DataCollectionEvent
 
dataDir(String, String) - Static method in class org.ecocean.servlet.ServletUtilities
 
dataDir(String, String, String) - Static method in class org.ecocean.servlet.ServletUtilities
 
dataFiles - Variable in class org.ecocean.MarkedIndividual
 
datasetID - Variable in class org.ecocean.DataCollectionEvent
 
datasetName - Variable in class org.ecocean.DataCollectionEvent
 
date - Variable in class org.ecocean.grid.EncounterLite
 
date - Variable in class org.ecocean.grid.I3SMatchObject
 
date - Variable in class org.ecocean.grid.MatchObject
 
dateInMilliseconds - Variable in class org.ecocean.Encounter
 
dateInMilliseconds - Variable in class org.ecocean.User
 
dateTimeCreated - Variable in class org.ecocean.MarkedIndividual
 
dateTimeCreated - Variable in class org.ecocean.Occurrence
 
dateTimeCreated - Variable in class org.ecocean.security.Collaboration
 
day - Variable in class org.ecocean.Encounter
 
DBL_INIT - Static variable in class com.reijns.I3S.Point2D
 
decimalLatitude - Variable in class org.ecocean.Encounter
 
decimalLongitude - Variable in class org.ecocean.Encounter
 
DeleteAdoption - Class in org.ecocean.servlet
 
DeleteAdoption() - Constructor for class org.ecocean.servlet.DeleteAdoption
 
DeleteAllDataPermanently - Class in org.ecocean.servlet
 
DeleteAllDataPermanently() - Constructor for class org.ecocean.servlet.DeleteAllDataPermanently
 
deleteOldScans(String, String) - Method in class org.ecocean.servlet.InterconnectSubmitSpots
 
deleteOnFinish - Variable in class org.ecocean.grid.ScanTask
 
description - Variable in class org.ecocean.interconnect.ImageFileFilter
 
destroy() - Method in class org.ecocean.servlet.StrutsUTF8Filter
 
Dij - Variable in class org.ecocean.grid.SpotTriangle
 
Dik - Variable in class org.ecocean.grid.SpotTriangle
 
dir(String) - Method in class org.ecocean.Encounter
 
dir(String, String) - Static method in class org.ecocean.Encounter
 
dir(File, String) - Static method in class org.ecocean.Encounter
 
dir - Variable in class org.ecocean.interconnect.AcceptDialog
 
display - Variable in class org.ecocean.Util.OptionDesc
 
dispose() - Method in class org.ecocean.interconnect.AcceptDialog
 
dispose() - Method in class org.ecocean.interconnect.CompareResults
 
dispose() - Method in class org.ecocean.interconnect.GetEncounterNumber
 
dispose() - Method in class org.ecocean.interconnect.InsertDatabase
 
dispose() - Method in class org.ecocean.interconnect.SharkIdentification
 
dispose() - Method in class org.ecocean.interconnect.ShowResults
 
dispose() - Method in class org.ecocean.interconnect.Splash
 
dist - Variable in class com.reijns.I3S.Pair
 
distance(FingerPrint, Map, int) - Method in class com.reijns.I3S.FingerPrint
This caculates the distance and distance score comparing a FingerPrint object to a visitor FingerPrint object passed as parameter f.
distance(int, int, int, int, int, int) - Static method in class org.ecocean.grid.Geometry
Return distance bwetween the line defined by (x0,y0) and (x1,y1) and the point (x,y).
DistanceComparator - Class in org.ecocean.genetics.distance
 
DistanceComparator() - Constructor for class org.ecocean.genetics.distance.DistanceComparator
 
Distances - Class in org.ecocean.genetics.distance
 
Distances() - Constructor for class org.ecocean.genetics.distance.Distances
 
distFrom(float, float, float, float) - Method in class org.ecocean.MarkedIndividual
 
distinguishingScar - Variable in class org.ecocean.Encounter
 
distNames - Static variable in class org.ecocean.genetics.distance.Ind2IndDistance
 
DistSAD - Class in org.ecocean.genetics.distance
 
DistSAD() - Constructor for class org.ecocean.genetics.distance.DistSAD
 
DistWAD - Class in org.ecocean.genetics.distance
 
DistWAD() - Constructor for class org.ecocean.genetics.distance.DistWAD
 
Djk - Variable in class org.ecocean.grid.SpotTriangle
 
doAffine(double[]) - Method in class com.reijns.I3S.FingerPrint
 
doAffine(FingerPrint) - Method in class org.ecocean.grid.EncounterLite
 
doAffine() - Method in class org.ecocean.interconnect.SharkPanel
 
doesUserHaveAnyRoleInContext(String, String) - Method in class org.ecocean.Shepherd
 
doesUserHaveRole(String, String, String) - Method in class org.ecocean.Shepherd
 
doFilter(ServletRequest, ServletResponse, FilterChain) - Method in class org.ecocean.servlet.StrutsUTF8Filter
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.AdoptionAction
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.CalendarXMLServer
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.CalendarXMLServer2
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.Collaborate
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.DeleteAdoption
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.DeleteAllDataPermanently
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.DontTrack
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterAddComment
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterAddImage
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterAddSpotFile
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterApprove
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterDelete
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterForm
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterGetPatterningPassport
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterRemoveImage
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterRemoveSpots
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterRemoveTissueSample
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterResetDate
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterSetAlternateID
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterSetAsUnidentifiable
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterSetBehavior
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterSetCountry
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterSetDynamicProperty
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterSetGenusSpecies
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterSetGPS
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterSetIdentifiable
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterSetInformOthers
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterSetLifeStage
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterSetLivingStatus
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterSetLocation
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterSetLocationID
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterSetMatchedBy
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterSetMaximumDepth
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterSetMaximumElevation
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterSetMeasurements
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterSetOccurrenceRemarks
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterSetPatterningCode
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterSetPatterningPassport
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterSetScarring
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterSetSex
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterSetSize
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterSetState
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterSetSubmitterID
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterSetSubmitterPhotographerContactInfo
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterSetTapirLinkExposure
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterSetTissueSample
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterSetVerbatimEventDate
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.export.EncounterSearchExportEmailAddresses
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.export.EncounterSearchExportExcelFile
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.export.EncounterSearchExportGeneGISFormat
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.export.EncounterSearchExportKML
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.export.EncounterSearchExportShapefile
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.export.GenalexExportCodominantMSDataBySize
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.export.GenePopExport
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.export.GetIndividualSearchGoogleMapsPoints
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.export.IndividualSearchExportCapture
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.export.KinalyzerExport
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.export.SimpleCMROutput
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.export.SOCPROGExport
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.GridHeartbeatReceiver
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.importer.ImportSRGD
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.IndividualAddComment
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.IndividualAddEncounter
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.IndividualAddFile
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.IndividualCreate
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.IndividualRemoveDataFile
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.IndividualRemoveEncounter
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.IndividualSetAlternateID
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.IndividualSetNickName
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.IndividualSetSex
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.IndividualSetYearOfBirth
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.IndividualSetYearOfDeath
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.InterconnectSubmitSpots
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.JavascriptGlobals
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.KeywordHandler
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.LoginUser
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.LogoutUser
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.MassExposeGBIF
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.MassSetInformOthers
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.MassSetLocationCodeFromLocationString
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.MassSwapLocationCode
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.OccurrenceAddComment
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.OccurrenceAddEncounter
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.OccurrenceCreate
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.OccurrenceRemoveEncounter
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.OccurrenceSetGroupBehavior
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.OccurrenceSetIndividualCount
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.RelationshipCreate
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.RelationshipDelete
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.RemoveEmailAddress
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.ResurrectDeletedAdoption
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.ResurrectDeletedEncounter
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.ScanAppletSupport
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.ScanResultsServlet
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.ScanTaskHandler
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.ScanWorkItemResultsHandler
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.SinglePhotoVideoAddKeyword
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.SinglePhotoVideoRemoveKeyword
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.TissueSampleRemoveBiologicalMeasurement
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.TissueSampleRemoveHaplotype
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.TissueSampleRemoveMicrosatelliteMarkers
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.TissueSampleRemoveSexAnalysis
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.TissueSampleSetHaplotype
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.TissueSampleSetMeasurement
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.TissueSampleSetMicrosatelliteMarkers
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.TissueSampleSetSexAnalysis
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.TrackerFeed
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.TrackIt
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.UpdateEmailAddress
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.UserAddProfileImage
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.UserCreate
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.UserDelete
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.UserInfo
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.UserRemoveProfileImage
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.UserResetAcceptedUserAgreement
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.UserSelfUpdate
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.WriteOutScanTask
 
doGetAuthenticationInfo(AuthenticationToken) - Method in class org.ecocean.security.ShepherdRealm
 
doGetAuthorizationInfo(PrincipalCollection) - Method in class org.ecocean.security.ShepherdRealm
 
doIt() - Method in class org.ecocean.interconnect.CopyFile
 
done - Variable in class org.ecocean.grid.GridManager
 
done - Variable in class org.ecocean.grid.ScanWorkItem
 
doneContains(ScanWorkItemResult) - Method in class org.ecocean.grid.GridManager
 
doNotSetLocalHaplotypeReflection(String) - Method in class org.ecocean.MarkedIndividual
DO NOT SET DIRECTLY!!
DontTrack - Class in org.ecocean.servlet
 
DontTrack() - Constructor for class org.ecocean.servlet.DontTrack
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.AdoptionAction
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.CalendarXMLServer
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.CalendarXMLServer2
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.Collaborate
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.DeleteAdoption
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.DeleteAllDataPermanently
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.DontTrack
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterAddComment
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterAddImage
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterAddSpotFile
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterApprove
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterDelete
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterForm
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterGetPatterningPassport
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterRemoveImage
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterRemoveSpots
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterRemoveTissueSample
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterResetDate
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterSetAlternateID
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterSetAsUnidentifiable
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterSetBehavior
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterSetCountry
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterSetDynamicProperty
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterSetGenusSpecies
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterSetGPS
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterSetIdentifiable
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterSetInformOthers
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterSetLifeStage
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterSetLivingStatus
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterSetLocation
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterSetLocationID
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterSetMatchedBy
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterSetMaximumDepth
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterSetMaximumElevation
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterSetMeasurements
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterSetOccurrenceRemarks
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterSetPatterningCode
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterSetPatterningPassport
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterSetReleaseDate
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterSetScarring
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterSetSex
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterSetSize
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterSetState
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterSetSubmitterID
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterSetSubmitterPhotographerContactInfo
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterSetTags
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterSetTapirLinkExposure
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterSetTissueSample
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.EncounterSetVerbatimEventDate
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.export.EncounterSearchExportEmailAddresses
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.export.EncounterSearchExportExcelFile
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.export.EncounterSearchExportGeneGISFormat
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.export.EncounterSearchExportKML
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.export.EncounterSearchExportShapefile
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.export.GenalexExportCodominantMSDataBySize
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.export.GenePopExport
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.export.GetIndividualSearchGoogleMapsPoints
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.export.IndividualSearchExportCapture
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.export.KinalyzerExport
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.export.SimpleCMROutput
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.export.SOCPROGExport
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.GridHeartbeatReceiver
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.importer.ImportSRGD
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.IndividualAddComment
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.IndividualAddEncounter
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.IndividualAddFile
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.IndividualCreate
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.IndividualRemoveDataFile
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.IndividualRemoveEncounter
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.IndividualSetAlternateID
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.IndividualSetNickName
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.IndividualSetSex
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.IndividualSetYearOfBirth
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.IndividualSetYearOfDeath
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.InterconnectSubmitSpots
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.JavascriptGlobals
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.KeywordHandler
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.LoginUser
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.LogoutUser
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.MassExposeGBIF
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.MassSetInformOthers
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.MassSetLocationCodeFromLocationString
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.MassSwapLocationCode
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.OccurrenceAddComment
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.OccurrenceAddEncounter
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.OccurrenceCreate
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.OccurrenceRemoveEncounter
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.OccurrenceSetGroupBehavior
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.OccurrenceSetIndividualCount
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.RelationshipCreate
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.RelationshipDelete
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.RemoveEmailAddress
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.ResurrectDeletedAdoption
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.ResurrectDeletedEncounter
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.ScanAppletSupport
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.ScanResultsServlet
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.ScanTaskHandler
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.ScanWorkItemResultsHandler
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.SinglePhotoVideoAddKeyword
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.SinglePhotoVideoRemoveKeyword
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.TissueSampleRemoveBiologicalMeasurement
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.TissueSampleRemoveHaplotype
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.TissueSampleRemoveMicrosatelliteMarkers
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.TissueSampleRemoveSexAnalysis
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.TissueSampleSetHaplotype
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.TissueSampleSetMeasurement
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.TissueSampleSetMicrosatelliteMarkers
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.TissueSampleSetSexAnalysis
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.TrackerFeed
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.TrackIt
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.UpdateEmailAddress
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.UserAddProfileImage
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.UserCreate
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.UserDelete
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.UserInfo
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.UserRemoveProfileImage
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.UserResetAcceptedUserAgreement
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.UserSelfUpdate
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.WriteOutScanTask
 
dorsal1 - Variable in class org.ecocean.interconnect.SharkPanel
 
dorsal2 - Variable in class org.ecocean.interconnect.SharkPanel
 
dotSelection - Variable in class org.ecocean.interconnect.SharkPanel
 
doVisualComparison(int, double) - Method in class org.ecocean.interconnect.SharkPanel
 
dwcDateAdded - Variable in class org.ecocean.Encounter
 
dwcImageURL - Variable in class org.ecocean.Encounter
 
Dxl - Variable in class org.ecocean.grid.SpotTriangle
 
Dxs - Variable in class org.ecocean.grid.SpotTriangle
 
Dyl - Variable in class org.ecocean.grid.SpotTriangle
 
dynamicProperties - Variable in class org.ecocean.Encounter
 
dynamicProperties - Variable in class org.ecocean.MarkedIndividual
 
Dys - Variable in class org.ecocean.grid.SpotTriangle
 

E

elim(int, double, int, int) - Method in class com.reijns.I3S.LinSys
 
elipseWidth - Variable in class org.ecocean.Spot
 
ellipseAngle - Variable in class org.ecocean.Spot
 
ellipseHeight - Variable in class org.ecocean.Spot
 
emailAddress - Variable in class org.ecocean.User
 
empty() - Method in class org.ecocean.interconnect.Point2D
 
encounter - Variable in class org.ecocean.Adoption
 
Encounter - Class in org.ecocean
An encounter object stores the complete data for a single sighting/capture report.
Encounter() - Constructor for class org.ecocean.Encounter
empty constructor required by the JDO Enhancer
Encounter(int, int, int, int, String, String, String, String, String, List<SinglePhotoVideo>) - Constructor for class org.ecocean.Encounter
Use this constructor to add the minimum level of information for a new encounter The Vector additionalImages must be a Vector of Blob objects
EncounterAddComment - Class in org.ecocean.servlet
 
EncounterAddComment() - Constructor for class org.ecocean.servlet.EncounterAddComment
 
EncounterAddImage - Class in org.ecocean.servlet
Uploads a new image to the file system and associates the image with an Encounter record
EncounterAddImage() - Constructor for class org.ecocean.servlet.EncounterAddImage
 
EncounterAddSpotFile - Class in org.ecocean.servlet
This servlet allows the user to upload an extracted, processed patterning file that corresponds to a previously uploaded set of spots.
EncounterAddSpotFile() - Constructor for class org.ecocean.servlet.EncounterAddSpotFile
 
EncounterApprove - Class in org.ecocean.servlet
 
EncounterApprove() - Constructor for class org.ecocean.servlet.EncounterApprove
 
EncounterDateComparator - Class in org.ecocean
 
EncounterDateComparator() - Constructor for class org.ecocean.EncounterDateComparator
 
EncounterDateComparator(boolean) - Constructor for class org.ecocean.EncounterDateComparator
 
EncounterDelete - Class in org.ecocean.servlet
 
EncounterDelete() - Constructor for class org.ecocean.servlet.EncounterDelete
 
EncounterForm - Class in org.ecocean.servlet
Uploads a new image to the file system and associates the image with an Encounter record
EncounterForm() - Constructor for class org.ecocean.servlet.EncounterForm
 
EncounterGetPatterningPassport - Class in org.ecocean.servlet
 
EncounterGetPatterningPassport() - Constructor for class org.ecocean.servlet.EncounterGetPatterningPassport
 
encounterId - Variable in class org.ecocean.PatterningPassport
 
EncounterLite - Class in org.ecocean.grid
 
EncounterLite() - Constructor for class org.ecocean.grid.EncounterLite
 
EncounterLite(Encounter) - Constructor for class org.ecocean.grid.EncounterLite
 
encounterNumber - Variable in class org.ecocean.grid.EncounterLite
 
encounterNumber - Variable in class org.ecocean.grid.I3SMatchObject
 
encounterNumber - Variable in class org.ecocean.grid.MatchObject
 
encounterNumber - Variable in class org.ecocean.grid.ScanWorkItemCreationThread
 
EncounterQueryProcessor - Class in org.ecocean
 
EncounterQueryProcessor() - Constructor for class org.ecocean.EncounterQueryProcessor
 
EncounterQueryResult - Class in org.ecocean
 
EncounterQueryResult(Vector<Encounter>, String, String) - Constructor for class org.ecocean.EncounterQueryResult
 
EncounterRemoveImage - Class in org.ecocean.servlet
 
EncounterRemoveImage() - Constructor for class org.ecocean.servlet.EncounterRemoveImage
 
EncounterRemoveSpots - Class in org.ecocean.servlet
 
EncounterRemoveSpots() - Constructor for class org.ecocean.servlet.EncounterRemoveSpots
 
EncounterRemoveTissueSample - Class in org.ecocean.servlet
 
EncounterRemoveTissueSample() - Constructor for class org.ecocean.servlet.EncounterRemoveTissueSample
 
EncounterResetDate - Class in org.ecocean.servlet
 
EncounterResetDate() - Constructor for class org.ecocean.servlet.EncounterResetDate
 
encounters - Variable in class org.ecocean.MarkedIndividual
 
encounters - Variable in class org.ecocean.Occurrence
 
EncounterSearchExportEmailAddresses - Class in org.ecocean.servlet.export
 
EncounterSearchExportEmailAddresses() - Constructor for class org.ecocean.servlet.export.EncounterSearchExportEmailAddresses
 
EncounterSearchExportExcelFile - Class in org.ecocean.servlet.export
 
EncounterSearchExportExcelFile() - Constructor for class org.ecocean.servlet.export.EncounterSearchExportExcelFile
 
EncounterSearchExportGeneGISFormat - Class in org.ecocean.servlet.export
 
EncounterSearchExportGeneGISFormat() - Constructor for class org.ecocean.servlet.export.EncounterSearchExportGeneGISFormat
 
EncounterSearchExportKML - Class in org.ecocean.servlet.export
 
EncounterSearchExportKML() - Constructor for class org.ecocean.servlet.export.EncounterSearchExportKML
 
EncounterSearchExportShapefile - Class in org.ecocean.servlet.export
 
EncounterSearchExportShapefile() - Constructor for class org.ecocean.servlet.export.EncounterSearchExportShapefile
 
EncounterSetAlternateID - Class in org.ecocean.servlet
 
EncounterSetAlternateID() - Constructor for class org.ecocean.servlet.EncounterSetAlternateID
 
EncounterSetAsUnidentifiable - Class in org.ecocean.servlet
 
EncounterSetAsUnidentifiable() - Constructor for class org.ecocean.servlet.EncounterSetAsUnidentifiable
 
EncounterSetBehavior - Class in org.ecocean.servlet
 
EncounterSetBehavior() - Constructor for class org.ecocean.servlet.EncounterSetBehavior
 
EncounterSetCountry - Class in org.ecocean.servlet
 
EncounterSetCountry() - Constructor for class org.ecocean.servlet.EncounterSetCountry
 
EncounterSetDynamicProperty - Class in org.ecocean.servlet
 
EncounterSetDynamicProperty() - Constructor for class org.ecocean.servlet.EncounterSetDynamicProperty
 
EncounterSetGenusSpecies - Class in org.ecocean.servlet
 
EncounterSetGenusSpecies() - Constructor for class org.ecocean.servlet.EncounterSetGenusSpecies
 
EncounterSetGPS - Class in org.ecocean.servlet
 
EncounterSetGPS() - Constructor for class org.ecocean.servlet.EncounterSetGPS
 
EncounterSetIdentifiable - Class in org.ecocean.servlet
 
EncounterSetIdentifiable() - Constructor for class org.ecocean.servlet.EncounterSetIdentifiable
 
EncounterSetInformOthers - Class in org.ecocean.servlet
 
EncounterSetInformOthers() - Constructor for class org.ecocean.servlet.EncounterSetInformOthers
 
EncounterSetLifeStage - Class in org.ecocean.servlet
 
EncounterSetLifeStage() - Constructor for class org.ecocean.servlet.EncounterSetLifeStage
 
EncounterSetLivingStatus - Class in org.ecocean.servlet
 
EncounterSetLivingStatus() - Constructor for class org.ecocean.servlet.EncounterSetLivingStatus
 
EncounterSetLocation - Class in org.ecocean.servlet
 
EncounterSetLocation() - Constructor for class org.ecocean.servlet.EncounterSetLocation
 
EncounterSetLocationID - Class in org.ecocean.servlet
 
EncounterSetLocationID() - Constructor for class org.ecocean.servlet.EncounterSetLocationID
 
EncounterSetMatchedBy - Class in org.ecocean.servlet
 
EncounterSetMatchedBy() - Constructor for class org.ecocean.servlet.EncounterSetMatchedBy
 
EncounterSetMaximumDepth - Class in org.ecocean.servlet
 
EncounterSetMaximumDepth() - Constructor for class org.ecocean.servlet.EncounterSetMaximumDepth
 
EncounterSetMaximumElevation - Class in org.ecocean.servlet
 
EncounterSetMaximumElevation() - Constructor for class org.ecocean.servlet.EncounterSetMaximumElevation
 
EncounterSetMeasurements - Class in org.ecocean.servlet
 
EncounterSetMeasurements() - Constructor for class org.ecocean.servlet.EncounterSetMeasurements
 
EncounterSetMeasurements.RequestEventValues - Class in org.ecocean.servlet
 
EncounterSetMeasurements.RequestEventValues(String, String, Double, String, String) - Constructor for class org.ecocean.servlet.EncounterSetMeasurements.RequestEventValues
 
EncounterSetOccurrenceRemarks - Class in org.ecocean.servlet
 
EncounterSetOccurrenceRemarks() - Constructor for class org.ecocean.servlet.EncounterSetOccurrenceRemarks
 
EncounterSetPatterningCode - Class in org.ecocean.servlet
 
EncounterSetPatterningCode() - Constructor for class org.ecocean.servlet.EncounterSetPatterningCode
 
EncounterSetPatterningPassport - Class in org.ecocean.servlet
Populates a patterning passport for a specific image/mediafile encounterId mediaId
EncounterSetPatterningPassport() - Constructor for class org.ecocean.servlet.EncounterSetPatterningPassport
 
EncounterSetReleaseDate - Class in org.ecocean.servlet
 
EncounterSetReleaseDate() - Constructor for class org.ecocean.servlet.EncounterSetReleaseDate
 
EncounterSetScarring - Class in org.ecocean.servlet
 
EncounterSetScarring() - Constructor for class org.ecocean.servlet.EncounterSetScarring
 
EncounterSetSex - Class in org.ecocean.servlet
 
EncounterSetSex() - Constructor for class org.ecocean.servlet.EncounterSetSex
 
EncounterSetSize - Class in org.ecocean.servlet
 
EncounterSetSize() - Constructor for class org.ecocean.servlet.EncounterSetSize
 
EncounterSetState - Class in org.ecocean.servlet
 
EncounterSetState() - Constructor for class org.ecocean.servlet.EncounterSetState
 
EncounterSetSubmitterID - Class in org.ecocean.servlet
 
EncounterSetSubmitterID() - Constructor for class org.ecocean.servlet.EncounterSetSubmitterID
 
EncounterSetSubmitterPhotographerContactInfo - Class in org.ecocean.servlet
 
EncounterSetSubmitterPhotographerContactInfo() - Constructor for class org.ecocean.servlet.EncounterSetSubmitterPhotographerContactInfo
 
EncounterSetTags - Class in org.ecocean.servlet
 
EncounterSetTags() - Constructor for class org.ecocean.servlet.EncounterSetTags
 
EncounterSetTapirLinkExposure - Class in org.ecocean.servlet
 
EncounterSetTapirLinkExposure() - Constructor for class org.ecocean.servlet.EncounterSetTapirLinkExposure
 
EncounterSetTissueSample - Class in org.ecocean.servlet
 
EncounterSetTissueSample() - Constructor for class org.ecocean.servlet.EncounterSetTissueSample
 
EncounterSetVerbatimEventDate - Class in org.ecocean.servlet
 
EncounterSetVerbatimEventDate() - Constructor for class org.ecocean.servlet.EncounterSetVerbatimEventDate
 
encounterUrl - Variable in class org.ecocean.PatterningPassport
 
endTime - Variable in class org.ecocean.grid.ScanTask
 
endTime - Variable in class org.ecocean.social.Relationship
 
epsilon - Variable in class org.ecocean.grid.GridManager
 
epsilon - Variable in class org.ecocean.grid.ScanWorkItem
 
equals(double, double, double) - Static method in class org.ecocean.grid.Geometry
Check if two double precision numbers are "equal", i.e.
equals(double, double) - Static method in class org.ecocean.grid.Geometry
Check if two double precision numbers are "equal", i.e.
errMsg - Static variable in class org.ecocean.interconnect.BareBonesBrowserLaunch
 
ERROR_PROPERTY_MAX_LENGTH_EXCEEDED - Static variable in class org.ecocean.servlet.EncounterForm
 
eventEndDate - Variable in class org.ecocean.DataCollectionEvent
 
eventID - Variable in class org.ecocean.Encounter
 
eventRemarks - Variable in class org.ecocean.DataCollectionEvent
 
eventStartDate - Variable in class org.ecocean.DataCollectionEvent
 
excl - Variable in class org.ecocean.interconnect.SharkPanel
 
execute() - Method in class org.ecocean.grid.ScanWorkItem
Executes the work to be done on the remote node.
executeComparison() - Method in class org.ecocean.grid.AppletWorkItemThread
 
EXECUTOR - Static variable in class org.ecocean.grid.AppletSwingWorker
Default executor.
executor - Variable in class org.ecocean.grid.AppletSwingWorker
Executor instance.
exhaustiveSearch(FingerPrint, Map) - Method in class com.reijns.I3S.Compare
Finds the best matching FingerPrint compared to unknown, starting with a known FingerPrint fp, and trys to correct for affine translation differences between unknown and fp, and will returns the best matching affine translation back in private parameter encountered.
existingEncounter - Variable in class org.ecocean.grid.ScanWorkItem
 
exit() - Static method in class org.ecocean.interconnect.Interconnect
 
ext - Variable in class org.ecocean.interconnect.AcceptDialog
 
ext - Variable in class org.ecocean.interconnect.GetImageFile
 
ext - Variable in class org.ecocean.interconnect.InsertDatabase
 
ext - Variable in class org.ecocean.interconnect.SharkIdentification
 
extendLine(double[], double[], double, double) - Static method in class org.ecocean.grid.Geometry
Extend a given line segment to a specified length.
extendLine(double[], double[], double) - Static method in class org.ecocean.grid.Geometry
Extend a given line segment to a given length and holding the first point of the line as fixed.
extension() - Method in class org.ecocean.interconnect.LogFile
 

F

factor - Variable in class org.ecocean.interconnect.SharkPanel
 
FalseMatchCreationThread - Class in org.ecocean.grid
 
FalseMatchCreationThread(int, String, String) - Constructor for class org.ecocean.grid.FalseMatchCreationThread
Constructor to create a new thread object
feretAngle - Variable in class org.ecocean.Spot
 
feretCenterX - Variable in class org.ecocean.Spot
 
feretCenterY - Variable in class org.ecocean.Spot
 
feretHeight - Variable in class org.ecocean.Spot
 
feretWidth - Variable in class org.ecocean.Spot
 
ffound - Variable in class org.ecocean.interconnect.AcceptDialog
 
ffound - Variable in class org.ecocean.interconnect.CompareResults
 
ffound - Variable in class org.ecocean.interconnect.SharkIdentification
 
FgpFileOpen - Class in com.reijns.I3S
 
FgpFileOpen() - Constructor for class com.reijns.I3S.FgpFileOpen
 
fieldNotes - Variable in class org.ecocean.DataCollectionEvent
 
fieldNumber - Variable in class org.ecocean.DataCollectionEvent
 
file - Variable in class org.ecocean.interconnect.ImagePreview
 
filename - Variable in class org.ecocean.interconnect.FingerPrint
 
filename - Static variable in class org.ecocean.interconnect.Interconnect.SharkMenu
 
filename - Variable in class org.ecocean.SinglePhotoVideo
 
files - Variable in class org.ecocean.interconnect.ShowResults
 
fileSaved - Variable in class org.ecocean.interconnect.SharkPanel
 
filters - Variable in class org.ecocean.interconnect.ImageFileFilter
 
fim - Variable in class org.ecocean.interconnect.ShowImagePane
 
fImg - Variable in class org.ecocean.interconnect.InsertDatabase
 
finalize(WritableWorkbook) - Method in class org.ecocean.servlet.WriteOutScanTask
 
find(FingerPrint, FingerPrint[], int, boolean, TreeMap) - Method in class com.reijns.I3S.Compare
Finds the best score for an unknown visitor FingerPrint from an array of encountered FingerPrints (loaded into the Compare Class at construction).
findBiologicalMeasurementDescs(String, String) - Static method in class org.ecocean.Util
 
findCollaborationWithUser(String, ArrayList) - Static method in class org.ecocean.security.Collaboration
 
findDataCollectionEvent(Class<T>, String) - Method in class org.ecocean.Shepherd
 
findGeneticAnalysis(Class<T>, String) - Method in class org.ecocean.Shepherd
 
findLabel(String, String, String) - Static method in class org.ecocean.Util
 
findLinePolygonIntersections(double[], double[], double, double, double, double) - Static method in class org.ecocean.grid.Geometry
Find the intersections between a polygon and a straight line.
findLineSegmentIntersection(double, double, double, double, double, double, double, double, double[]) - Static method in class org.ecocean.grid.Geometry
Compute the intersection between two line segments, or two lines of infinite length.
findMax(int, int) - Method in class com.reijns.I3S.LinSys
 
findMeasurementDescs(String, String) - Static method in class org.ecocean.Util
 
findMeasurementOfType(String) - Method in class org.ecocean.Encounter
 
findMetalTag(Util.MetalTagDesc, Encounter) - Static method in class org.ecocean.Util
Find the MetalTag instance belonging to an Encounter that is described by the MetalTagDesc.
findMetalTagDescs(String, String) - Static method in class org.ecocean.Util
 
findMetalTagForLocation(String) - Method in class org.ecocean.Encounter
 
findPair(Map, double, int) - Method in class com.reijns.I3S.FingerPrint
Find the matching pair object with the same soure FingerPrint point index
findPolygonExtent(double[], double[], double[], double[], double[], double[]) - Static method in class org.ecocean.grid.Geometry
Find the 3D extent of a polyline.
findPolygonExtent(int[], int[], int[], int[]) - Static method in class org.ecocean.grid.Geometry
Find the extent of a polygon.
findPolygonPosition(int[], int[], double, int[]) - Static method in class org.ecocean.grid.Geometry
Return the x,y position at distance "length" into the given polyline.
findRequestEventValues(HttpServletRequest, int) - Method in class org.ecocean.servlet.EncounterSetMeasurements
 
findResourceOnFileSystem(String) - Static method in class org.ecocean.servlet.ServletUtilities
 
findSamplingProtocols(String, String) - Static method in class org.ecocean.Util
Returns a map of sampling protocols, where the key is the name of protocol, and the value is the user-friendly, localized label.
findSatelliteTagNames(String) - Static method in class org.ecocean.Util
 
FingerPrint - Class in com.reijns.I3S
 
FingerPrint() - Constructor for class com.reijns.I3S.FingerPrint
 
FingerPrint(Point2D[], Point2D[]) - Constructor for class com.reijns.I3S.FingerPrint
 
FingerPrint(Point2D[], Point2D[], Point2D[]) - Constructor for class com.reijns.I3S.FingerPrint
 
FingerPrint(FingerPrint) - Constructor for class com.reijns.I3S.FingerPrint
 
FingerPrint - Class in org.ecocean.interconnect
 
FingerPrint() - Constructor for class org.ecocean.interconnect.FingerPrint
 
finished - Variable in class org.ecocean.grid.AppletHeartbeatThread
 
finished() - Method in class org.ecocean.grid.AppletSwingWorker
Called on the event dispatching thread (not on the worker thread) after the construct method has returned.
finished - Variable in class org.ecocean.grid.FalseMatchCreationThread
 
finished - Variable in class org.ecocean.grid.ScanTaskCleanupThread
 
finished - Variable in class org.ecocean.grid.ScanWorkItemCreationThread
 
finished - Variable in class org.ecocean.grid.TuningTaskCreationThread
 
finished() - Method in class org.ecocean.grid.WorkApplet3.gridSwingWorker
 
firstAllele(int) - Method in class org.ecocean.genetics.FStatistics
 
fname - Static variable in class org.ecocean.interconnect.LogFile
 
forig - Variable in class org.ecocean.interconnect.AcceptDialog
 
forig - Variable in class org.ecocean.interconnect.CompareResults
 
forig - Variable in class org.ecocean.interconnect.SharkIdentification
 
found - Variable in class org.ecocean.interconnect.AcceptDialog
 
found - Variable in class org.ecocean.interconnect.BothSharks
 
found - Variable in class org.ecocean.interconnect.SharkIdentification
 
found - Variable in class org.ecocean.interconnect.SpotCloud
 
foundImg - Variable in class org.ecocean.interconnect.BothSharks
 
fpa - Variable in class com.reijns.I3S.Compare
 
FPCMP - Static variable in class com.reijns.I3S.Compare
The Comparator method class for sorting in the find method.
fpfile - Variable in class org.ecocean.interconnect.SharkPanel
 
fpIn - Variable in class org.ecocean.interconnect.InsertDatabase
 
fpp - Variable in class com.reijns.I3S.FingerPrint
FingerPrint Protected and Private Variables Comments: Moving from a file based system to a database system, so all references to file based serialization has been removed.
frame - Static variable in class org.ecocean.interconnect.AboutInterconnect
 
frame - Static variable in class org.ecocean.interconnect.AcceptDialog
 
frame - Static variable in class org.ecocean.interconnect.CompareResults
 
frame - Variable in class org.ecocean.interconnect.GetEncounterNumber
 
frame - Static variable in class org.ecocean.interconnect.InsertDatabase
 
frame - Static variable in class org.ecocean.interconnect.Interconnect
 
frame - Static variable in class org.ecocean.interconnect.SharkIdentification
 
frame - Static variable in class org.ecocean.interconnect.ShowResults
 
frame - Variable in class org.ecocean.interconnect.Splash
 
from - Variable in class org.ecocean.NotificationMailer
 
FStatistics - Class in org.ecocean.genetics
 
FStatistics(int) - Constructor for class org.ecocean.genetics.FStatistics
 
fullDescription - Variable in class org.ecocean.interconnect.ImageFileFilter
 
fullFileSystemPath - Variable in class org.ecocean.SinglePhotoVideo
 
fullName - Variable in class org.ecocean.User
 
funnyIP(double[][], double[][], double[][], int[]) - Static method in class org.ecocean.genetics.distance.Distances
 
fw - Static variable in class org.ecocean.interconnect.LogFile
 

G

gaussElim() - Method in class com.reijns.I3S.LinSys
 
gaussj(double[][], int, double[][], int) - Static method in class com.reijns.I3S.Affine
 
gaussJordanElim1() - Method in class com.reijns.I3S.LinSys
 
gaussJordanElim2() - Method in class com.reijns.I3S.LinSys
 
GenalexExportCodominantMSDataBySize - Class in org.ecocean.servlet.export
 
GenalexExportCodominantMSDataBySize() - Constructor for class org.ecocean.servlet.export.GenalexExportCodominantMSDataBySize
 
GenePopExport - Class in org.ecocean.servlet.export
 
GenePopExport() - Constructor for class org.ecocean.servlet.export.GenePopExport
 
generateEncounterNumber() - Method in class org.ecocean.Encounter
 
generateSystem() - Method in class com.reijns.I3S.LinSys
 
generateUUID() - Static method in class org.ecocean.Util
 
GeneticAnalysis - Class in org.ecocean.genetics
 
GeneticAnalysis() - Constructor for class org.ecocean.genetics.GeneticAnalysis
Empty constructor required for JDO processing.
GeneticAnalysis(String, String, String, String) - Constructor for class org.ecocean.genetics.GeneticAnalysis
 
genotypeFrequencyPerPopulation(int, int, int) - Method in class org.ecocean.genetics.FStatistics
 
genotypeFrequencyTotal(int, int) - Method in class org.ecocean.genetics.FStatistics
 
genus - Variable in class org.ecocean.Encounter
 
Geometry - Class in org.ecocean.grid
Collection of geometry utility methods.
Geometry() - Constructor for class org.ecocean.grid.Geometry
 
get() - Method in class org.ecocean.grid.AppletSwingWorker
Waits if necessary for this task to complete, and then returns its result.
get(long, TimeUnit) - Method in class org.ecocean.grid.AppletSwingWorker
Waits if necessary for at most the given time for this task to complete, and then returns its result, if available.
getAcceptedUserAgreement() - Method in class org.ecocean.User
 
getAcousticTag() - Method in class org.ecocean.Encounter
 
getAcousticTag(HashMap) - Method in class org.ecocean.servlet.EncounterForm
 
getAdditionalImageNames() - Method in class org.ecocean.Encounter
Returns the file names of all images taken for this encounter.
getAdjustedMatchValue() - Method in class org.ecocean.grid.MatchObject
 
getAdopterAddress() - Method in class org.ecocean.Adoption
 
getAdopterEmail() - Method in class org.ecocean.Adoption
 
getAdopterEmailsForMarkedIndividual(Query, String) - Method in class org.ecocean.Shepherd
 
getAdopterImage() - Method in class org.ecocean.Adoption
 
getAdopterName() - Method in class org.ecocean.Adoption
 
getAdopterQuote() - Method in class org.ecocean.Adoption
 
getAdoption(String) - Method in class org.ecocean.Shepherd
 
getAdoptionDeepCopy(String) - Method in class org.ecocean.Shepherd
 
getAdoptionEndDate() - Method in class org.ecocean.Adoption
 
getAdoptionManager() - Method in class org.ecocean.Adoption
 
getAdoptionStartDate() - Method in class org.ecocean.Adoption
 
getAdoptionType() - Method in class org.ecocean.Adoption
 
getAffiliation() - Method in class org.ecocean.User
 
getAll(Shepherd) - Method in class org.ecocean.servlet.EncounterGetPatterningPassport
 
getAllAdoptionsForEncounter(String) - Method in class org.ecocean.Shepherd
 
getAllAdoptionsForMarkedIndividual(String, String) - Method in class org.ecocean.Shepherd
 
getAllAdoptionsNoQuery() - Method in class org.ecocean.Shepherd
 
getAllAdoptionsWithQuery(Query) - Method in class org.ecocean.Shepherd
 
getAllAlternateIDs() - Method in class org.ecocean.MarkedIndividual
 
getAllAppliedKeywordNames(Shepherd) - Method in class org.ecocean.MarkedIndividual
 
getAllAssignedUsers() - Method in class org.ecocean.MarkedIndividual
 
getAllAssignedUsers() - Method in class org.ecocean.Occurrence
 
getAllBehaviors() - Method in class org.ecocean.Shepherd
 
getAllCountries() - Method in class org.ecocean.Shepherd
 
getAllele(int) - Method in class org.ecocean.genetics.Locus
 
getAllele0() - Method in class org.ecocean.genetics.Locus
 
getAllele1() - Method in class org.ecocean.genetics.Locus
 
getAllele2() - Method in class org.ecocean.genetics.Locus
 
getAllele3() - Method in class org.ecocean.genetics.Locus
 
getAlleleIndex(int) - Method in class org.ecocean.genetics.FStatistics
 
getAlleleIndex(int) - Method in class org.ecocean.genetics.HFStatistics
 
getAllelesHTMLString() - Method in class org.ecocean.genetics.MicrosatelliteMarkersAnalysis
 
getAlleleValuesForLocus(String) - Method in class org.ecocean.MarkedIndividual
 
getAllEmailsToUpdate() - Method in class org.ecocean.MarkedIndividual
Obtains the email addresses of all submitters, photographs, and others to notify.
getAllEncounters() - Method in class org.ecocean.Shepherd
Retrieves any all approved encounters that are stored in the database
getAllEncounters(Query) - Method in class org.ecocean.Shepherd
 
getAllEncounters(Query, Map<String, Object>) - Method in class org.ecocean.Shepherd
 
getAllEncounters(String) - Method in class org.ecocean.Shepherd
Retrieves all encounters that are stored in the database in the order specified by the input String
getAllEncounters(Query, String) - Method in class org.ecocean.Shepherd
 
getAllEncounters(String, String) - Method in class org.ecocean.Shepherd
Retrieves a filtered list of encounters that are stored in the database in the order specified by the input String
getAllEncountersNoFilter() - Method in class org.ecocean.Shepherd
 
getAllEncountersNoFilter(String, String) - Method in class org.ecocean.Shepherd
 
getAllEncountersNoFilterAsVector() - Method in class org.ecocean.Shepherd
 
getAllEncountersNoFilterReturnQuery(String, String) - Method in class org.ecocean.Shepherd
 
getAllEncountersNoQuery() - Method in class org.ecocean.Shepherd
 
getAllGeneticSexes() - Method in class org.ecocean.Shepherd
 
getAllGenuses() - Method in class org.ecocean.Shepherd
 
getAllHaplotypes() - Method in class org.ecocean.Shepherd
 
getAllKeywords() - Method in class org.ecocean.Shepherd
 
getAllKeywords(Query) - Method in class org.ecocean.Shepherd
 
getAllLifeStages() - Method in class org.ecocean.Shepherd
 
getAllLocationIDs() - Method in class org.ecocean.Shepherd
 
getAllLoci() - Method in class org.ecocean.Shepherd
 
getAllMarkedIndividuals() - Method in class org.ecocean.Shepherd
Retrieves an Iterator of all the sharks in the database
getAllMarkedIndividuals(Query) - Method in class org.ecocean.Shepherd
 
getAllMarkedIndividuals(Query, String) - Method in class org.ecocean.Shepherd
Retrieves an Iterator of all the sharks in the database, ordered according to the input String
getAllMarkedIndividuals(Query, String, Map<String, Object>) - Method in class org.ecocean.Shepherd
 
getAllMarkedIndividualsFromLocationID(String) - Method in class org.ecocean.Shepherd
 
getAllMarkedIndividualsInCommunity(String) - Method in class org.ecocean.Shepherd
 
getAllOccurrences(Query) - Method in class org.ecocean.Shepherd
 
getAllOccurrences() - Method in class org.ecocean.Shepherd
 
getAllOccurrencesForMarkedIndividual(Query, String) - Method in class org.ecocean.Shepherd
 
getAllOtherIndividualsOccurringWithMarkedIndividual(String) - Method in class org.ecocean.Shepherd
 
getAllPatterningCodes() - Method in class org.ecocean.Shepherd
 
getAllRecordedBy() - Method in class org.ecocean.Shepherd
 
getAllRelatedMedia() - Method in class org.ecocean.Occurrence
 
getAllRelationships(Shepherd) - Method in class org.ecocean.MarkedIndividual
 
getAllRelationshipsForCommunity(String) - Method in class org.ecocean.Shepherd
 
getAllRelationshipsForMarkedIndividual(String) - Method in class org.ecocean.Shepherd
 
getAllRoleNames() - Method in class org.ecocean.Shepherd
 
getAllRoleNamesForMarkedIndividual(String) - Method in class org.ecocean.Shepherd
 
getAllRoles() - Method in class org.ecocean.Shepherd
 
getAllRolesForUser(String) - Method in class org.ecocean.Shepherd
 
getAllRolesForUserAsString(String) - Method in class org.ecocean.Shepherd
 
getAllRolesForUserInContext(String, String) - Method in class org.ecocean.Shepherd
 
getAllScanTasksNoQuery() - Method in class org.ecocean.Shepherd
 
getAllScanWorkItemsNoQuery() - Method in class org.ecocean.Shepherd
 
getAllSinglePhotoVideo() - Method in class org.ecocean.MarkedIndividual
 
getAllSinglePhotoVideo(Query) - Method in class org.ecocean.Shepherd
 
getAllSinglePhotoVideosForEncounter(String) - Method in class org.ecocean.Shepherd
 
getAllSinglePhotoVideosNoQuery() - Method in class org.ecocean.Shepherd
 
getAllSocialUnitNames() - Method in class org.ecocean.Shepherd
 
getAllSocialUnitsForMarkedIndividual(String) - Method in class org.ecocean.Shepherd
 
getAllSpecificEpithets() - Method in class org.ecocean.Shepherd
 
getAllTissueSamples() - Method in class org.ecocean.MarkedIndividual
 
getAllTissueSamplesForEncounter(String) - Method in class org.ecocean.Shepherd
 
getAllUnidentifiableEncounters(Query) - Method in class org.ecocean.Shepherd
Retrieves all encounters that are stored in the database but which have been rejected for the visual database
getAllUnidentifiableEncounters(Query, String) - Method in class org.ecocean.Shepherd
Retrieves all encounters that are stored in the database but which have been rejected for the visual database in the order identified by the input String
getAllUserEmailAddressesForLocationID(String, String) - Method in class org.ecocean.Shepherd
 
getAllUsernames() - Method in class org.ecocean.Shepherd
 
getAllUsers() - Method in class org.ecocean.Shepherd
 
getAllUsersForMarkedIndividual(MarkedIndividual) - Method in class org.ecocean.Shepherd
 
getAllUsersForMarkedIndividual(String) - Method in class org.ecocean.Shepherd
 
getAllUsersForOccurrence(Occurrence) - Method in class org.ecocean.Shepherd
 
getAllUsersForOccurrence(String) - Method in class org.ecocean.Shepherd
 
getAllValuesForDynamicProperty(String) - Method in class org.ecocean.MarkedIndividual
 
getAllVerbatimEventDates() - Method in class org.ecocean.Shepherd
 
getAlternateID() - Method in class org.ecocean.Encounter
 
getAlternateID() - Method in class org.ecocean.MarkedIndividual
 
getAlternateSampleID() - Method in class org.ecocean.genetics.TissueSample
 
getAnalysisID() - Method in class org.ecocean.genetics.GeneticAnalysis
 
getAnalysisType() - Method in class org.ecocean.genetics.GeneticAnalysis
 
getApproved() - Method in class org.ecocean.Encounter
 
getArea() - Method in class org.ecocean.Spot
Retrieves the area in pixels of the thresholded spot.
getArgosPttNumber() - Method in class org.ecocean.tag.SatelliteTag
 
getAssignedUsername() - Method in class org.ecocean.Encounter
 
getAutoEmailAddress(String) - Static method in class org.ecocean.CommonConfiguration
 
getAvailableScanWorkItems(Query, int, long) - Method in class org.ecocean.Shepherd
 
getAvailableScanWorkItems(Query, int, String, long) - Method in class org.ecocean.Shepherd
 
getAverageBiologicalMeasurementInPeriod(int, int, int, int, String) - Method in class org.ecocean.MarkedIndividual
 
getAverageMeasurementInPeriod(int, int, int, int, String) - Method in class org.ecocean.MarkedIndividual
 
getBehavior() - Method in class org.ecocean.Encounter
 
getBidirectional() - Method in class org.ecocean.social.Relationship
 
getBiologicalMeasurement(String) - Method in class org.ecocean.Encounter
 
getBiologicalMeasurement(String) - Method in class org.ecocean.genetics.TissueSample
 
getBiologicalMeasurement(String, String, String) - Method in class org.ecocean.Shepherd
 
getBiologicalMeasurements() - Method in class org.ecocean.genetics.TissueSample
 
getC(String) - Static method in class org.ecocean.CommonConfiguration
 
getCachedGPSCoordinates(boolean, String) - Static method in class org.ecocean.Util
 
getCatalogNumber() - Method in class org.ecocean.Encounter
 
getCentroidX() - Method in class org.ecocean.Spot
Retrieves the X coordinate of the centroid found for the thresholded blob that represents this spot in the original image.
getCentroidX() - Method in class org.ecocean.SuperSpot
 
getCentroidY() - Method in class org.ecocean.Spot
Retrieves the Y coordinate of the centroid found for the thresholded blob that represents this spot in the original image.
getCentroidY() - Method in class org.ecocean.SuperSpot
 
getCheckoutTimeout() - Method in class org.ecocean.grid.GridManager
 
getClone() - Method in class org.ecocean.Encounter
 
getClone() - Method in class org.ecocean.Spot
 
getCnt() - Method in class com.reijns.I3S.Compare
 
getCnt() - Method in class com.reijns.I3S.FingerPrint
 
getCnt() - Method in class org.ecocean.interconnect.FingerPrint
 
getCollectionCode() - Method in class org.ecocean.DataCollectionEvent
 
getCollectionID() - Method in class org.ecocean.DataCollectionEvent
 
getCollisionRatePercentage() - Method in class org.ecocean.grid.GridManager
 
getColorCode(String, String) - Method in class org.ecocean.genetics.MitochondrialDNAAnalysis
 
getComment() - Method in class org.ecocean.interconnect.FingerPrint
 
getComments() - Method in class org.ecocean.Encounter
Returns any submitted comments about scarring on the shark.
getComments() - Method in class org.ecocean.MarkedIndividual
Returns any additional, general comments recorded for this MarkedIndividual as a whole.
getComments() - Method in class org.ecocean.Occurrence
Returns any additional, general comments recorded for this Occurrence as a whole.
getCommunity(String) - Method in class org.ecocean.Shepherd
 
getCompletedWork() - Method in class org.ecocean.grid.GridManager
 
getConnection(String, String, int, String, int) - Method in class org.ecocean.grid.WorkApplet3
 
getConnection(String, String, int, String, int) - Method in class org.ecocean.grid.WorkAppletHeadless
 
getConnection() - Static method in class org.ecocean.servlet.ServletUtilities
 
getContext() - Method in class org.ecocean.Role
 
getContext(HttpServletRequest) - Static method in class org.ecocean.servlet.ServletUtilities
 
getContextDomainNames(String) - Static method in class org.ecocean.ContextConfiguration
 
getContextNames() - Static method in class org.ecocean.ContextConfiguration
 
getContextsProperties() - Static method in class org.ecocean.ContextConfiguration
 
getContextsProperties() - Static method in class org.ecocean.ShepherdProperties
 
getCopyrightOwner() - Method in class org.ecocean.SinglePhotoVideo
 
getCopyrightStatement() - Method in class org.ecocean.SinglePhotoVideo
 
getCorrespondingEncounterNumber() - Method in class org.ecocean.DataCollectionEvent
 
getCorrespondingEncounterNumber() - Method in class org.ecocean.genetics.GeneticAnalysis
 
getCorrespondingEncounterNumber() - Method in class org.ecocean.Story
 
getCorrespondingHaplotypePairsForMarkedIndividuals(Shepherd) - Method in class org.ecocean.Occurrence
 
getCorrespondingMarkedIndividualID() - Method in class org.ecocean.Story
 
getCorrespondingOccurrenceID() - Method in class org.ecocean.Story
 
getCorrespondingSocialUnitName() - Method in class org.ecocean.Story
 
getCorrespondingStoryID() - Method in class org.ecocean.SinglePhotoVideo
 
getCorrespondingThumbnailSinglePhotoVideo() - Method in class org.ecocean.Story
 
getCorrespondingUsername() - Method in class org.ecocean.SinglePhotoVideo
 
getCountry() - Method in class org.ecocean.Encounter
 
getCreateTime() - Method in class org.ecocean.grid.ScanWorkItem
 
getCreationDeletionThreadQueueSize() - Method in class org.ecocean.grid.GridManager
 
getCSSURLLocation(HttpServletRequest, String) - Static method in class org.ecocean.CommonConfiguration
 
getDataCollectionEventID() - Method in class org.ecocean.DataCollectionEvent
 
getDataDirectoryName(String) - Static method in class org.ecocean.CommonConfiguration
 
getDataDirForContext(String) - Static method in class org.ecocean.ContextConfiguration
 
getDataFiles() - Method in class org.ecocean.MarkedIndividual
Returns the complete Vector of stored satellite tag data files for this MarkedIndividual.
getDatasetID() - Method in class org.ecocean.DataCollectionEvent
 
getDatasetName() - Method in class org.ecocean.DataCollectionEvent
 
getDate() - Method in class org.ecocean.Encounter
Returns the date of this encounter.
getDate() - Method in class org.ecocean.grid.EncounterLite
 
getDate() - Method in class org.ecocean.grid.MatchObject
 
getDate() - Static method in class org.ecocean.servlet.ServletUtilities
 
getDateInMilliseconds() - Method in class org.ecocean.Encounter
 
getDateInMilliseconds() - Method in class org.ecocean.User
 
getDateSortedEncounters(boolean) - Method in class org.ecocean.MarkedIndividual
 
getDateSortedEncounters() - Method in class org.ecocean.MarkedIndividual
 
getDateSortedEncounters(boolean) - Method in class org.ecocean.Occurrence
 
getDateTimeCreated() - Method in class org.ecocean.MarkedIndividual
 
getDateTimeCreated() - Method in class org.ecocean.Occurrence
 
getDateTimeCreated() - Method in class org.ecocean.security.Collaboration
 
getDay() - Method in class org.ecocean.Encounter
 
getDBLocation(String) - Static method in class org.ecocean.CommonConfiguration
 
getDecimalLatitude() - Method in class org.ecocean.Encounter
 
getDecimalLatitudeAsDouble() - Method in class org.ecocean.Encounter
 
getDecimalLongitude() - Method in class org.ecocean.Encounter
 
getDecimalLongitudeAsDouble() - Method in class org.ecocean.Encounter
 
getDefaultContext() - Static method in class org.ecocean.ContextConfiguration
 
getDeleteOnFinish() - Method in class org.ecocean.grid.ScanTask
 
getDepth() - Method in class org.ecocean.Encounter
Returns the recorded depth of this encounter.
getDepthAsDouble() - Method in class org.ecocean.Encounter
 
getDescription() - Method in class org.ecocean.interconnect.ImageFileFilter
Returns the human readable description of this filter.
getDescription(File) - Method in class org.ecocean.interconnect.ImageFileView
 
getDisplay() - Method in class org.ecocean.Util.OptionDesc
 
getDisplayCountry() - Method in class org.ecocean.grid.GridNode
 
getDist() - Method in class com.reijns.I3S.Pair
 
getDistanceOuput(String[], String[], boolean, boolean, String, String, String) - Static method in class org.ecocean.genetics.distance.ShareDst
 
getDistinguishingScar() - Method in class org.ecocean.Encounter
Returns the String holding specific location data used for searching
getDistMeasure(int) - Static method in class org.ecocean.genetics.distance.Ind2IndDistance
 
getDoneSize() - Method in class org.ecocean.grid.GridManager
 
getDorsal1() - Method in class org.ecocean.interconnect.SharkPanel
 
getDorsal2() - Method in class org.ecocean.interconnect.SharkPanel
 
getDWCDateAdded() - Method in class org.ecocean.Encounter
 
getDWCDateLastModified() - Method in class org.ecocean.Encounter
 
getDWCDateLastModified() - Method in class org.ecocean.Occurrence
 
getDWCDecimalLatitude() - Method in class org.ecocean.Encounter
 
getDWCDecimalLongitude() - Method in class org.ecocean.Encounter
 
getDWCGlobalUniqueIdentifier() - Method in class org.ecocean.Encounter
 
getDynamicProperties() - Method in class org.ecocean.Encounter
 
getDynamicProperties() - Method in class org.ecocean.MarkedIndividual
 
getDynamicPropertyValue(String) - Method in class org.ecocean.Encounter
 
getDynamicPropertyValue(String) - Method in class org.ecocean.MarkedIndividual
 
getEarliestSightingTime() - Method in class org.ecocean.MarkedIndividual
 
getEarliestSightingYear() - Method in class org.ecocean.MarkedIndividual
 
getEarliestSightingYear() - Method in class org.ecocean.Shepherd
 
getEmailAddress() - Method in class org.ecocean.User
 
getEncounter() - Method in class org.ecocean.Adoption
 
getEncounter(int) - Method in class org.ecocean.MarkedIndividual
Returns the specified encounter, where the encounter numbers range from 0 to n-1, where n is the total number of encounters stored for this MarkedIndividual.
getEncounter(Shepherd, HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.ScanAppletSupport
 
getEncounter(String) - Method in class org.ecocean.Shepherd
 
getEncounter(MarkedIndividual, int) - Method in class org.ecocean.Shepherd
Returns the ith numbered encounter for a shark
getEncounterDeepCopy(String) - Method in class org.ecocean.Shepherd
 
getEncounterId() - Method in class org.ecocean.PatterningPassport
 
getEncounterNumber() - Method in class org.ecocean.Encounter
Returns the unique encounter identifier number for this encounter.
getEncounterNumber() - Method in class org.ecocean.grid.EncounterLite
 
getEncounterNumber() - Method in class org.ecocean.grid.MatchObject
 
GetEncounterNumber - Class in org.ecocean.interconnect
 
GetEncounterNumber(SharkPanel, StringBuffer, String, int, String) - Constructor for class org.ecocean.interconnect.GetEncounterNumber
 
getEncounters() - Method in class org.ecocean.MarkedIndividual
Returns the complete Vector of stored encounters for this MarkedIndividual.
getEncounters() - Method in class org.ecocean.Occurrence
 
getEncountersByAlternateID(String) - Method in class org.ecocean.Shepherd
 
getEncountersWithHashedEmailAddress(String) - Method in class org.ecocean.Shepherd
 
getEncountersWithSpotData(Shepherd, HttpServletRequest, HttpServletResponse) - Method in class org.ecocean.servlet.ScanAppletSupport
 
getEncounterUrl() - Method in class org.ecocean.PatterningPassport
 
getEndTime() - Method in class org.ecocean.grid.ScanTask
 
getEndTime() - Method in class org.ecocean.social.Relationship
 
getEpsilon(String) - Static method in class org.ecocean.CommonConfiguration
 
getEvaluation() - Method in class org.ecocean.grid.I3SMatchObject
DONT NEED THESE - I think...
getEvaluation() - Method in class org.ecocean.grid.MatchObject
 
getEventEndDate() - Method in class org.ecocean.DataCollectionEvent
 
getEventID() - Method in class org.ecocean.Encounter
 
getEventRemarks() - Method in class org.ecocean.DataCollectionEvent
 
getEventStartDate() - Method in class org.ecocean.DataCollectionEvent
 
getExecutor() - Method in class org.ecocean.grid.AppletSwingWorker
Returns executor to be used when worker is started.
getExecutorService() - Static method in class org.ecocean.grid.SharkGridThreadExecutorService
 
getExecutorService() - Static method in class org.ecocean.MailThreadExecutorService
 
getEXIFDataFromJPEGAsHTML(File) - Static method in class org.ecocean.Util
 
getExistingEncNumber() - Method in class org.ecocean.grid.ScanWorkItem
 
getExistingEncounterLite() - Method in class org.ecocean.grid.ScanWorkItem
 
getExtension(File) - Method in class org.ecocean.interconnect.ImageFileFilter
Return the extension portion of the file's name .
getExtension(File) - Static method in class org.ecocean.interconnect.Utils
 
getF() - Method in class org.ecocean.genetics.FStatistics
 
getf() - Method in class org.ecocean.genetics.FStatistics
 
GetFgpFiles(File, Collection) - Method in class com.reijns.I3S.FgpFileOpen
This method is called when "f" is a folder.
getFieldNotes() - Method in class org.ecocean.DataCollectionEvent
 
getFieldNumber() - Method in class org.ecocean.DataCollectionEvent
 
getFile() - Method in class org.ecocean.SinglePhotoVideo
Returns the photo or video represented by this object as a java.io.File This is a convenience method.
getFileName() - Method in class org.ecocean.interconnect.FingerPrint
 
getFilename() - Method in class org.ecocean.SinglePhotoVideo
 
getFileSaved() - Method in class org.ecocean.interconnect.SharkPanel
 
getFomattedMSMarkersString(String[]) - Method in class org.ecocean.MarkedIndividual
 
getFooter(String) - Static method in class org.ecocean.servlet.ServletUtilities
 
getFpp(int) - Method in class com.reijns.I3S.FingerPrint
 
getFullFileSystemPath() - Method in class org.ecocean.SinglePhotoVideo
 
getFullName() - Method in class org.ecocean.User
 
getGeneticAnalyses() - Method in class org.ecocean.genetics.TissueSample
 
getGeneticAnalysis(String, String, String) - Method in class org.ecocean.Shepherd
 
getGeneticAnalysis(String, String, String, String) - Method in class org.ecocean.Shepherd
 
getGeneticSex() - Method in class org.ecocean.Encounter
A convenience method that returns the first genetic sex found in the TissueSamples for this Encounter.
getGeneticSex() - Method in class org.ecocean.MarkedIndividual
 
getGenus() - Method in class org.ecocean.Encounter
 
getGenusSpecies() - Method in class org.ecocean.MarkedIndividual
Returns the first genus-species pair found in the Encounter objects for this MarkedIndividual.
getGlobalUniqueIdentifierPrefix(String) - Static method in class org.ecocean.CommonConfiguration
 
getGoing(JProgressBar, JLabel, JLabel) - Method in class org.ecocean.grid.WorkApplet3.runWIScan
 
getGoing() - Method in class org.ecocean.grid.WorkAppletHeadless
 
getGoogleMapsKey(String) - Static method in class org.ecocean.CommonConfiguration
 
getGoogleSearchKey(String) - Static method in class org.ecocean.CommonConfiguration
 
getGPSLatitude() - Method in class org.ecocean.Encounter
 
getGPSLongitude() - Method in class org.ecocean.Encounter
 
getGridManager() - Static method in class org.ecocean.grid.GridManagerFactory
 
getGridNode(String) - Method in class org.ecocean.grid.GridManager
 
getGrothC() - Method in class org.ecocean.grid.GridManager
 
getGrothEpsilon() - Method in class org.ecocean.grid.GridManager
 
getGrothMaxTriangleRotation() - Method in class org.ecocean.grid.GridManager
 
getGrothR() - Method in class org.ecocean.grid.GridManager
 
getGrothSecondRun() - Method in class org.ecocean.grid.GridManager
 
getGrothSizelim() - Method in class org.ecocean.grid.GridManager
 
getGroupBehavior() - Method in class org.ecocean.Occurrence
 
getGroupSize() - Method in class org.ecocean.grid.GridManager
 
getHaplotype() - Method in class org.ecocean.Encounter
A convenience method that returns the first haplotype found in the TissueSamples for this Encounter.
getHaplotype() - Method in class org.ecocean.genetics.MitochondrialDNAAnalysis
 
getHaplotype() - Method in class org.ecocean.MarkedIndividual
Returns the first haplotype found in the Encounter objects for this MarkedIndividual.
getHashedInformOthers() - Method in class org.ecocean.Encounter
 
getHashedPhotographerEmail() - Method in class org.ecocean.Encounter
 
getHashedSubmitterEmail() - Method in class org.ecocean.Encounter
 
getHashOfEmailString(String) - Static method in class org.ecocean.Encounter
 
getHeader(HttpServletRequest) - Static method in class org.ecocean.servlet.ServletUtilities
 
getHighestEncounterSpot() - Method in class org.ecocean.grid.MatchObject
 
getHighestRightSpot() - Method in class org.ecocean.Encounter
 
getHighestRightSpot() - Method in class org.ecocean.grid.EncounterLite
 
getHighestSharkSpot() - Method in class org.ecocean.grid.MatchObject
 
getHighestSpot() - Method in class org.ecocean.Encounter
 
getHighestSpot() - Method in class org.ecocean.grid.EncounterLite
 
getHour() - Method in class org.ecocean.Encounter
 
getHTMLAuthor(String) - Static method in class org.ecocean.CommonConfiguration
 
getHTMLDescription(String) - Static method in class org.ecocean.CommonConfiguration
 
getHTMLKeywords(String) - Static method in class org.ecocean.CommonConfiguration
 
getHTMLShortcutIcon(String) - Static method in class org.ecocean.CommonConfiguration
 
getHTMLString() - Method in class org.ecocean.DataCollectionEvent
 
getHTMLString() - Method in class org.ecocean.genetics.BiologicalMeasurement
 
getHTMLString() - Method in class org.ecocean.genetics.GeneticAnalysis
 
getHTMLString() - Method in class org.ecocean.genetics.Locus
 
getHTMLString() - Method in class org.ecocean.genetics.MicrosatelliteMarkersAnalysis
 
getHTMLString() - Method in class org.ecocean.genetics.MitochondrialDNAAnalysis
 
getHTMLString() - Method in class org.ecocean.genetics.SexAnalysis
 
getHTMLString() - Method in class org.ecocean.genetics.TissueSample
 
getHTMLTitle(String) - Static method in class org.ecocean.CommonConfiguration
 
getI3SMatchValue() - Method in class org.ecocean.grid.I3SMatchObject
 
getI3SMatchValue() - Method in class org.ecocean.grid.MatchObject
 
getI3SResult() - Method in class org.ecocean.grid.ScanWorkItem
 
getI3SResult() - Method in class org.ecocean.grid.ScanWorkItemResult
 
getIcon(File) - Method in class org.ecocean.interconnect.ImageFileView
 
getID() - Method in class org.ecocean.Adoption
 
getId() - Method in class org.ecocean.security.Collaboration
 
getId() - Method in class org.ecocean.tag.AbstractTag
 
getID4AvailableScanWorkItems(Query, int, long, boolean) - Method in class org.ecocean.Shepherd
 
getID4AvailableScanWorkItems(String, Query, int, long, boolean) - Method in class org.ecocean.Shepherd
 
getIdentificationRemarks() - Method in class org.ecocean.Encounter
 
getIdNumber() - Method in class org.ecocean.tag.AcousticTag
 
getImageExtension() - Method in class org.ecocean.interconnect.GetImageFile
 
GetImageFile - Class in org.ecocean.interconnect
 
GetImageFile(String) - Constructor for class org.ecocean.interconnect.GetImageFile
 
getImages() - Method in class org.ecocean.Encounter
 
getImageString() - Method in class org.ecocean.interconnect.GetImageFile
 
getIncompleteWork() - Method in class org.ecocean.grid.GridManager
 
getIndexedValues(String, String) - Static method in class org.ecocean.CommonConfiguration
 
getIndexname() - Method in class org.ecocean.Keyword
 
getIndexNumberForValue(String, String, String) - Static method in class org.ecocean.CommonConfiguration
 
getIndividualCount() - Method in class org.ecocean.Occurrence
 
getIndividualID() - Method in class org.ecocean.Encounter
 
getIndividualID() - Method in class org.ecocean.MarkedIndividual
 
getIndividualName() - Method in class org.ecocean.grid.I3SMatchObject
 
getIndividualName() - Method in class org.ecocean.grid.MatchObject
 
GetIndividualSearchGoogleMapsPoints - Class in org.ecocean.servlet.export
 
GetIndividualSearchGoogleMapsPoints() - Constructor for class org.ecocean.servlet.export.GetIndividualSearchGoogleMapsPoints
 
getInformOthers() - Method in class org.ecocean.Encounter
 
getInstitutionCode() - Method in class org.ecocean.DataCollectionEvent
 
getInstitutionID() - Method in class org.ecocean.DataCollectionEvent
 
getInterestedResearchers() - Method in class org.ecocean.Encounter
 
getInterestedResearchers() - Method in class org.ecocean.MarkedIndividual
 
getIPTURL(String) - Static method in class org.ecocean.CommonConfiguration
 
getJDOQLRepresentation() - Method in class org.ecocean.EncounterQueryResult
 
getJDOQLRepresentation() - Method in class org.ecocean.MarkedIndividualQueryResult
 
getKeyword(String) - Method in class org.ecocean.Shepherd
 
getKeywordDeepCopy(String) - Method in class org.ecocean.Shepherd
 
getKeywords() - Method in class org.ecocean.SinglePhotoVideo
 
getKeywordsInCommon(String, String) - Method in class org.ecocean.Shepherd
 
getLabel() - Method in class org.ecocean.Util.MeasurementDesc
 
getLanguageCode(HttpServletRequest) - Static method in class org.ecocean.servlet.ServletUtilities
 
getLastCheckin() - Method in class org.ecocean.grid.GridNode
 
getLastCheckout() - Method in class org.ecocean.grid.GridNode
 
getLastEstimatedSize() - Method in class org.ecocean.MarkedIndividual
 
getLastHeartbeat() - Method in class org.ecocean.grid.GridNode
 
getLastLogin() - Method in class org.ecocean.User
 
getLastLoginAsDateString() - Method in class org.ecocean.User
 
getLastMonthOfSightingYear(int) - Method in class org.ecocean.Shepherd
 
getLastSightingYear() - Method in class org.ecocean.Shepherd
 
getLatitudeAsDouble() - Method in class org.ecocean.Encounter
 
getLeftmostRightSpot() - Method in class org.ecocean.Encounter
 
getLeftmostRightSpot() - Method in class org.ecocean.grid.EncounterLite
 
getLeftmostSpot() - Method in class org.ecocean.Encounter
 
getLeftmostSpot() - Method in class org.ecocean.grid.EncounterLite
 
getLeftReferenceSpots() - Method in class org.ecocean.Encounter
 
getLeftReferenceSpots() - Method in class org.ecocean.grid.EncounterLite
 
getLifeStage() - Method in class org.ecocean.Encounter
 
getLivingStatus() - Method in class org.ecocean.Encounter
 
getLocalizedSamplingProtocol(String, String, String) - Static method in class org.ecocean.Util
 
getLocation() - Method in class org.ecocean.Encounter
Returns the recorded location of this encounter.
getLocation() - Method in class org.ecocean.tag.MetalTag
 
getLocation() - Method in class org.ecocean.Util.MetalTagDesc
 
getLocationCode() - Method in class org.ecocean.Encounter
Returns the String holding specific location data used for searching
getLocationID() - Method in class org.ecocean.Encounter
 
getLocationID() - Method in class org.ecocean.Occurrence
This method simply iterates through the encounters for the occurrence and returns the first Encounter.locationID that it finds or returns null.
getLocationLabel() - Method in class org.ecocean.Util.MetalTagDesc
 
getLoci() - Method in class org.ecocean.genetics.MicrosatelliteMarkersAnalysis
 
getLocus(String) - Method in class org.ecocean.genetics.MicrosatelliteMarkersAnalysis
 
getLogEncounter(int) - Method in class org.ecocean.MarkedIndividual
 
getLogMBreakdown() - Method in class org.ecocean.grid.MatchObject
 
getLogMStdDev() - Method in class org.ecocean.grid.MatchObject
 
getLongitudeAsDouble() - Method in class org.ecocean.Encounter
 
getLowestRightSpot() - Method in class org.ecocean.Encounter
 
getLowestRightSpot() - Method in class org.ecocean.grid.EncounterLite
 
getLowestSpot() - Method in class org.ecocean.Encounter
 
getLowestSpot() - Method in class org.ecocean.grid.EncounterLite
 
getM1() - Method in class com.reijns.I3S.Pair
 
getM2() - Method in class com.reijns.I3S.Pair
 
getMailHost(String) - Static method in class org.ecocean.CommonConfiguration
 
getMap() - Method in class org.ecocean.grid.I3SMatchObject
 
getMap2() - Method in class org.ecocean.grid.MatchObject
 
getMarkedIndividual() - Method in class org.ecocean.Adoption
 
getMarkedIndividual(String) - Method in class org.ecocean.Shepherd
 
getMarkedIndividual1DirectionalDescriptor() - Method in class org.ecocean.social.Relationship
 
getMarkedIndividual2DirectionalDescriptor() - Method in class org.ecocean.social.Relationship
 
getMarkedIndividualCaseInsensitive(String) - Method in class org.ecocean.Shepherd
Provides a case-insensitive way to retrieve a MarkedIndividual.
getMarkedIndividualName1() - Method in class org.ecocean.social.Relationship
 
getMarkedIndividualName2() - Method in class org.ecocean.social.Relationship
 
getMarkedIndividualNamesForThisOccurrence() - Method in class org.ecocean.Occurrence
 
getMarkedIndividualRole1() - Method in class org.ecocean.social.Relationship
 
getMarkedIndividualRole2() - Method in class org.ecocean.social.Relationship
 
getMarkedIndividuals(Shepherd) - Method in class org.ecocean.social.SocialUnit
 
getMarkedIndividualsByAlternateID(String) - Method in class org.ecocean.Shepherd
 
getMarkedIndividualsByNickname(String) - Method in class org.ecocean.Shepherd
 
getMarkedIndividualThumbnails(HttpServletRequest, Iterator<MarkedIndividual>, int, int, String[]) - Method in class org.ecocean.Shepherd
 
getMatchedBy() - Method in class org.ecocean.Encounter
 
getMatchObjectsForTask(String) - Method in class org.ecocean.grid.GridManager
 
getMatchValue() - Method in class org.ecocean.grid.MatchObject
 
getMaxDistanceBetweenTwoSightings() - Method in class org.ecocean.MarkedIndividual
 
getMaximumDepthInMeters() - Method in class org.ecocean.Encounter
 
getMaximumElevationInMeters() - Method in class org.ecocean.Encounter
 
getMaxMediaSizeInMegabytes(String) - Static method in class org.ecocean.CommonConfiguration
 
getMaxNumYearsBetweenSightings() - Method in class org.ecocean.MarkedIndividual
 
getMaxTimeBetweenTwoSightings() - Method in class org.ecocean.MarkedIndividual
 
getMaxTriangleRotation(String) - Static method in class org.ecocean.CommonConfiguration
 
getMeasurement(String) - Method in class org.ecocean.Encounter
Returns the first measurement of the specified type
getMeasurements() - Method in class org.ecocean.Encounter
 
getMeasurements(HashMap, String, String) - Method in class org.ecocean.servlet.EncounterForm
 
getMeasurementType() - Method in class org.ecocean.genetics.BiologicalMeasurement
 
getMeasurementUnit() - Method in class org.ecocean.Encounter
 
getMeasureUnits() - Method in class org.ecocean.Encounter
Returns the units of the recorded size and depth of the shark for this encounter.
getMediaId() - Method in class org.ecocean.PatterningPassport
 
getMediaUrl() - Method in class org.ecocean.PatterningPassport
 
getMetalTagParamNames(HttpServletRequest) - Method in class org.ecocean.servlet.EncounterSetTags
 
getMetalTags() - Method in class org.ecocean.Encounter
 
getMetalTags(HashMap) - Method in class org.ecocean.servlet.EncounterForm
 
getMicrosatelliteMarkersAnalysis(String, String, String) - Method in class org.ecocean.Shepherd
 
getMinDistanceBetweenTwoMarkedIndividuals(MarkedIndividual) - Method in class org.ecocean.MarkedIndividual
 
getMinutes() - Method in class org.ecocean.Encounter
 
getMitochondrialDNAAnalysis(String, String, String) - Method in class org.ecocean.Shepherd
 
getMonth() - Method in class org.ecocean.Encounter
 
getMyVertexOneRotationInRadians() - Method in class org.ecocean.grid.SpotTriangle
 
getName(int) - Static method in class org.ecocean.genetics.distance.Ind2IndDistance
 
getName() - Method in class org.ecocean.genetics.Locus
 
getName(File) - Method in class org.ecocean.interconnect.ImageFileView
 
getName() - Method in class org.ecocean.MarkedIndividual
Returns the user-input name of the MarkedIndividual, which is also used as an Index in the FastObjects database
getName() - Method in class org.ecocean.tag.SatelliteTag
 
getName() - Method in class org.ecocean.Util.OptionDesc
 
getNameForContext(String) - Static method in class org.ecocean.ContextConfiguration
 
getNewEncNumber() - Method in class org.ecocean.grid.ScanWorkItem
 
getNewEncounterLite() - Method in class org.ecocean.grid.ScanWorkItem
 
getNewSex() - Method in class org.ecocean.grid.MatchObject
 
getNewSubmissionEmail(String) - Static method in class org.ecocean.CommonConfiguration
 
getNewX() - Method in class org.ecocean.grid.VertexPointMatch
 
getNewY() - Method in class org.ecocean.grid.VertexPointMatch
 
getNextEncounterCatalogNumber() - Method in class org.ecocean.Shepherd
 
getNextEncounterNumber() - Method in class org.ecocean.Shepherd
 
getNextGroupSize(GridNode) - Method in class org.ecocean.grid.GridManager
 
getNextGroupSize(long, int) - Method in class org.ecocean.grid.GridNode
 
getNextWorkItemGroup(long, int) - Method in class org.ecocean.grid.ScanTask
 
getNice() - Method in class org.ecocean.grid.ScanWorkItem
 
getNickName() - Method in class org.ecocean.MarkedIndividual
 
getNickNamer() - Method in class org.ecocean.MarkedIndividual
 
getNodeIdentifier() - Method in class org.ecocean.grid.GridNode
 
getNodeIdentifiers() - Method in class org.ecocean.grid.ScanTask
 
getNodeLocations() - Method in class org.ecocean.grid.ScanTask
 
getNodes() - Method in class org.ecocean.grid.GridManager
 
getNodeTimeout() - Method in class org.ecocean.grid.GridManager
 
getNodeTimes() - Method in class org.ecocean.grid.ScanTask
 
getNotes() - Method in class org.ecocean.Adoption
 
getNotes() - Method in class org.ecocean.User
 
getNotificationsWidgetHtml(HttpServletRequest) - Static method in class org.ecocean.security.Collaboration
 
getNumAdoptions() - Method in class org.ecocean.Shepherd
 
getNumAllowedNodes() - Method in class org.ecocean.grid.GridManager
 
getNumAnalyses() - Method in class org.ecocean.genetics.TissueSample
 
getNumApprovedEncounters() - Method in class org.ecocean.Shepherd
 
getNumberEncounters() - Method in class org.ecocean.Occurrence
 
getNumberRightTrainableEncounters() - Method in class org.ecocean.MarkedIndividual
 
getNumberTrainableEncounters() - Method in class org.ecocean.MarkedIndividual
 
getNumCollisions() - Method in class org.ecocean.grid.GridManager
 
getNumCollisions() - Method in class org.ecocean.grid.ScanTask
 
getNumComparisons() - Method in class org.ecocean.grid.GridNode
 
getNumComparisons() - Method in class org.ecocean.grid.ScanTask
 
getNumCompletedWorkItems() - Method in class org.ecocean.grid.GridManager
 
getNumContributingNodes() - Method in class org.ecocean.grid.ScanTask
 
getNumCooccurrencesBetweenTwoMarkedIndividual(String, String) - Method in class org.ecocean.Shepherd
 
getNumEncounters() - Method in class org.ecocean.Shepherd
 
getNumEncounters(String) - Method in class org.ecocean.Shepherd
 
getNumEncountersWithSpotData(boolean) - Method in class org.ecocean.Shepherd
 
getNumKeywords() - Method in class org.ecocean.Shepherd
 
getNumMarkedIndividuals() - Method in class org.ecocean.Shepherd
 
getNumMarkedIndividualThumbnails(Iterator<MarkedIndividual>, String[]) - Method in class org.ecocean.Shepherd
 
getNumMeasures() - Static method in class org.ecocean.genetics.distance.Ind2IndDistance
 
getNumNodes() - Method in class org.ecocean.grid.GridManager
 
getNumProcessors() - Method in class org.ecocean.grid.GridManager
 
getNumRejectedEncounters() - Method in class org.ecocean.Shepherd
 
getNumRightSpots() - Method in class org.ecocean.Encounter
 
getNumScanTasks() - Method in class org.ecocean.Shepherd
 
getNumSpots() - Method in class org.ecocean.Encounter
Returns the number of spots in the cropped image stored for this encounter.
getNumSpots() - Method in class org.ecocean.grid.ScanTask
 
getNumTasks(String) - Method in class org.ecocean.grid.GridManager
 
getNumThumbnails(Iterator, String[]) - Method in class org.ecocean.Shepherd
 
getNumThumbnails(Vector) - Method in class org.ecocean.Shepherd
Returns the number of acceptable images/videos in the enter Iterator.
getNumUnapprovedEncounters() - Method in class org.ecocean.Shepherd
 
getNumUnfinishedScanTasks() - Method in class org.ecocean.Shepherd
 
getNumUnidentifiableEncounters() - Method in class org.ecocean.Shepherd
 
getNumUnidentifiableEncountersForMarkedIndividual(String) - Method in class org.ecocean.Shepherd
 
getNumUserEncounters(String) - Method in class org.ecocean.Shepherd
 
getNumUsers() - Method in class org.ecocean.Shepherd
 
getNumWorkItems(String) - Method in class org.ecocean.grid.GridManager
 
getNumWorkItems() - Method in class org.ecocean.grid.ScanTask
 
getNumWorkItemsAndResults() - Method in class org.ecocean.grid.GridManager
 
getNumWorkItemsComplete() - Method in class org.ecocean.grid.ScanTask
 
getNumWorkItemsCompleteForTask(String) - Method in class org.ecocean.grid.GridManager
 
getNumWorkItemsIncompleteForTask(String) - Method in class org.ecocean.grid.GridManager
 
getOccurrence(String) - Method in class org.ecocean.Shepherd
 
getOccurrenceForEncounter(String) - Method in class org.ecocean.Shepherd
 
getOccurrenceID() - Method in class org.ecocean.Encounter
 
getOccurrenceID() - Method in class org.ecocean.Occurrence
 
getOccurrenceIDsForMarkedIndividual(String) - Method in class org.ecocean.Shepherd
 
getOccurrenceRemarks() - Method in class org.ecocean.Encounter
 
getOKExposeViaTapirLink() - Method in class org.ecocean.Encounter
 
getOldAdditionalImageNames() - Method in class org.ecocean.Encounter
 
getOldX() - Method in class org.ecocean.grid.VertexPointMatch
 
getOldY() - Method in class org.ecocean.grid.VertexPointMatch
 
getOtherCatalogNumbers() - Method in class org.ecocean.Encounter
 
getPairCnt() - Method in class com.reijns.I3S.FingerPrint
 
getPairs(Query, int) - Method in class org.ecocean.Shepherd
 
getParam(HttpServletRequest, String) - Method in class org.ecocean.servlet.EncounterSetTags
 
getParameterInfo() - Method in class org.ecocean.genetics.distance.ShareDst
 
getPassportDataXml(String) - Method in class org.ecocean.PatterningPassport
 
getPassword() - Method in class org.ecocean.User
 
getPasswordForUser(String) - Method in class org.ecocean.security.ShepherdRealm
 
getPatterningCode() - Method in class org.ecocean.Encounter
 
getPatterningCode() - Method in class org.ecocean.MarkedIndividual
Returns the patterning type evident on this MarkedIndividual instance.
getPatterningPassport() - Method in class org.ecocean.SinglePhotoVideo
 
getPatterningPassportFile() - Method in class org.ecocean.SinglePhotoVideo
 
getPatterningPassports() - Method in class org.ecocean.Shepherd
 
getPatterningPassportXmlUrl() - Method in class org.ecocean.PatterningPassport
 
getPelvic() - Method in class org.ecocean.interconnect.SharkPanel
 
getPercentComplete() - Method in class org.ecocean.grid.ScanTask
 
getPerMinuteRate() - Method in class org.ecocean.grid.GridManager
 
getPhoneNumber() - Method in class org.ecocean.User
 
getPhotographerAddress() - Method in class org.ecocean.Encounter
Returns the mailing address of the person who took the primaryImage this encounter.
getPhotographerEmail() - Method in class org.ecocean.Encounter
Returns the e-mail address of the person who took the primaryImage this encounter.
getPhotographerName() - Method in class org.ecocean.Encounter
Returns the name of the person who took the primaryImage this encounter.
getPhotographerPhone() - Method in class org.ecocean.Encounter
Returns the phone number of the person who took the primaryImage this encounter.
getPhysicalAddress() - Method in class org.ecocean.User
 
getPM() - Method in class org.ecocean.Shepherd
 
getPMF(String) - Static method in class org.ecocean.ShepherdPMF
 
getPointBreakdown() - Method in class org.ecocean.grid.MatchObject
 
getPoints(Collection, DataInputStream, String) - Method in class com.reijns.I3S.FgpFileOpen
Gets the points from the current FGP file.
getPoints() - Method in class org.ecocean.grid.VertexPointMatch
 
getPointsForBestMatch(SuperSpot[], double, double, double, double, double, boolean, boolean) - Method in class org.ecocean.grid.EncounterLite
 
getPopulationIndex(int) - Method in class org.ecocean.genetics.FStatistics
 
getPopulationIndex(int) - Method in class org.ecocean.genetics.HFStatistics
 
getPossibleTrainingIndividuals() - Method in class org.ecocean.Shepherd
Returns all of the names of the sharks that can be used for training purporses - i.e.
getPreferredSize() - Method in class org.ecocean.interconnect.Interconnect
 
getPreservationMethod() - Method in class org.ecocean.genetics.TissueSample
 
getProcessingLabContactDetails() - Method in class org.ecocean.genetics.GeneticAnalysis
 
getProcessingLabContactName() - Method in class org.ecocean.genetics.GeneticAnalysis
 
getProcessingLabName() - Method in class org.ecocean.genetics.GeneticAnalysis
 
getProcessingLabTaskID() - Method in class org.ecocean.genetics.GeneticAnalysis
 
getProcessingTime() - Method in class org.ecocean.grid.ScanTask
 
getProperties(String) - Static method in class org.ecocean.ShepherdProperties
 
getProperties(String, String) - Static method in class org.ecocean.ShepherdProperties
 
getProperties(String, String, String) - Static method in class org.ecocean.ShepherdProperties
 
getProperty(String, String) - Static method in class org.ecocean.CommonConfiguration
 
getPropertyNames(String) - Static method in class org.ecocean.CommonConfiguration
 
getQueryPrettyPrint() - Method in class org.ecocean.EncounterQueryResult
 
getQueryPrettyPrint() - Method in class org.ecocean.MarkedIndividualQueryResult
 
getR(String) - Static method in class org.ecocean.CommonConfiguration
 
getRandomAdoption() - Method in class org.ecocean.Shepherd
 
getRComments() - Method in class org.ecocean.Encounter
Returns any comments added by researchers
getReadableName() - Method in class org.ecocean.Keyword
 
getRealCnt() - Method in class com.reijns.I3S.Compare
 
getReceiveEmails() - Method in class org.ecocean.User
 
getRecordedBy() - Method in class org.ecocean.Encounter
 
getRelatedComments() - Method in class org.ecocean.social.Relationship
 
getRelatedSocialUnitName() - Method in class org.ecocean.social.Relationship
 
getRelationship(String, String, String) - Method in class org.ecocean.Shepherd
 
getRelationship(String, String, String, String, String) - Method in class org.ecocean.Shepherd
 
getRelationship(String, String, String, String, String, String) - Method in class org.ecocean.Shepherd
 
getReleaseDate() - Method in class org.ecocean.Encounter
 
getReleaseDateDONOTUSE() - Method in class org.ecocean.Encounter
 
getReleaseDateLong() - Method in class org.ecocean.Encounter
 
getRemainingWorkItemsForTask(String) - Method in class org.ecocean.grid.GridManager
 
getResult() - Method in class org.ecocean.EncounterQueryResult
 
getResult() - Method in class org.ecocean.grid.ScanWorkItem
 
getResult() - Method in class org.ecocean.grid.ScanWorkItemResult
 
getResult() - Method in class org.ecocean.MarkedIndividualQueryResult
 
getResultsForTask(String) - Method in class org.ecocean.grid.GridManager
 
getRightmostEncounterSpot() - Method in class org.ecocean.grid.MatchObject
 
getRightmostRightSpot() - Method in class org.ecocean.Encounter
 
getRightmostRightSpot() - Method in class org.ecocean.grid.EncounterLite
 
getRightmostSharkSpot() - Method in class org.ecocean.grid.MatchObject
 
getRightmostSpot() - Method in class org.ecocean.Encounter
 
getRightmostSpot() - Method in class org.ecocean.grid.EncounterLite
 
getRightPossibleTrainingIndividuals() - Method in class org.ecocean.Shepherd
 
getRightReferenceSpots() - Method in class org.ecocean.Encounter
 
getRightReferenceSpots() - Method in class org.ecocean.grid.EncounterLite
 
getRightSpotImageFileName() - Method in class org.ecocean.Encounter
 
getRightSpots() - Method in class org.ecocean.Encounter
 
getRightSpots() - Method in class org.ecocean.grid.EncounterLite
 
getRightTrainableEncounters() - Method in class org.ecocean.MarkedIndividual
 
getRole(String, String, String) - Method in class org.ecocean.Shepherd
 
getRolename() - Method in class org.ecocean.Role
 
getRoleNamesForUserInContext(String, String) - Method in class org.ecocean.security.ShepherdRealm
 
getSalt() - Static method in class org.ecocean.servlet.ServletUtilities
 
getSalt() - Method in class org.ecocean.User
 
getSampleID() - Method in class org.ecocean.genetics.GeneticAnalysis
 
getSampleID() - Method in class org.ecocean.genetics.TissueSample
 
getSamplingEffort() - Method in class org.ecocean.DataCollectionEvent
 
getSamplingProtocol() - Method in class org.ecocean.DataCollectionEvent
 
getSamplingProtocol() - Method in class org.ecocean.genetics.BiologicalMeasurement
 
getSatelliteTag() - Method in class org.ecocean.Encounter
 
getSatelliteTag(HashMap) - Method in class org.ecocean.servlet.EncounterForm
 
getScanTask(String) - Method in class org.ecocean.Shepherd
 
getScanTaskLimit() - Method in class org.ecocean.grid.GridManager
 
getScore() - Method in class com.reijns.I3S.FingerPrint
 
getScores() - Method in class org.ecocean.grid.MatchObject
 
getSequentialPropertyValues(String, String) - Static method in class org.ecocean.CommonConfiguration
 
getSerialNumber() - Method in class org.ecocean.tag.AcousticTag
 
getSerialNumber() - Method in class org.ecocean.tag.SatelliteTag
 
getSeriesCode() - Method in class org.ecocean.MarkedIndividual
 
getSex() - Method in class org.ecocean.Encounter
Returns the recorded sex of the shark in this encounter.
getSex() - Method in class org.ecocean.genetics.SexAnalysis
 
getSex() - Method in class org.ecocean.grid.MatchObject
 
getSex() - Method in class org.ecocean.MarkedIndividual
Returns the sex of this MarkedIndividual.
getSexAnalysis(String, String, String) - Method in class org.ecocean.Shepherd
 
getSharkPanel() - Method in class org.ecocean.interconnect.CompareResults
 
getShortDate() - Method in class org.ecocean.Encounter
 
getSide() - Method in class org.ecocean.interconnect.SharkPanel
 
getSinglePhotoVideo() - Method in class org.ecocean.Encounter
 
getSinglePhotoVideo(String) - Method in class org.ecocean.Shepherd
 
getSize() - Method in class org.ecocean.Encounter
Returns the recorded length of the shark for this encounter.
getSize() - Method in class org.ecocean.grid.MatchObject
 
getSizeAsDouble() - Method in class org.ecocean.Encounter
 
getSizeGuess() - Method in class org.ecocean.Encounter
Returns the String discussing how the size of this animal was approximated.
getSizelim(String) - Static method in class org.ecocean.CommonConfiguration
 
getSocialUnitName() - Method in class org.ecocean.social.SocialUnit
 
getSortedUserEncounters(Query, String) - Method in class org.ecocean.Shepherd
 
getSpecificEpithet() - Method in class org.ecocean.Encounter
 
getSpotImageFileName() - Method in class org.ecocean.Encounter
 
getSpots() - Method in class org.ecocean.Encounter
Returns an array of all of the superSpots for this encounter.
getSpots() - Method in class org.ecocean.grid.EncounterLite
 
getSpots() - Method in class org.ecocean.interconnect.SharkPanel
 
getStartTime() - Method in class org.ecocean.grid.ScanTask
 
getStartTime() - Method in class org.ecocean.grid.ScanWorkItem
Returns the startTime of the workItem.
getStartTime() - Method in class org.ecocean.social.Relationship
 
getState() - Method in class org.ecocean.Encounter
 
getState() - Method in class org.ecocean.security.Collaboration
 
getStorageLabID() - Method in class org.ecocean.genetics.TissueSample
 
getStoryID() - Method in class org.ecocean.Story
 
getStoryMediaURL() - Method in class org.ecocean.Story
 
getStoryTellerEmail() - Method in class org.ecocean.Story
 
getStoryTellerName() - Method in class org.ecocean.Story
 
getStoryText() - Method in class org.ecocean.Story
 
getSubmitter() - Method in class org.ecocean.grid.ScanTask
 
getSubmitterAddress() - Method in class org.ecocean.Encounter
Returns the mailing address of the person who submitted this encounter data.
getSubmitterEmail() - Method in class org.ecocean.Encounter
Returns the e-mail address of the person who submitted this encounter data
getSubmitterID() - Method in class org.ecocean.Encounter
 
getSubmitterName() - Method in class org.ecocean.Encounter
Returns the name of the person who submitted this encounter data.
getSubmitterOrganization() - Method in class org.ecocean.Encounter
 
getSubmitterPhone() - Method in class org.ecocean.Encounter
Returns the phone number of the person who submitted this encounter data.
getSubmitterProject() - Method in class org.ecocean.Encounter
 
getSuperHTMLString() - Method in class org.ecocean.genetics.BiologicalMeasurement
 
getSuperHTMLString() - Method in class org.ecocean.genetics.MicrosatelliteMarkersAnalysis
 
getSuperHTMLString() - Method in class org.ecocean.genetics.MitochondrialDNAAnalysis
 
getSuperHTMLString() - Method in class org.ecocean.genetics.SexAnalysis
 
getSupportedAppletVersion() - Method in class org.ecocean.grid.GridManager
 
getT1() - Method in class org.ecocean.genetics.HFStatistics
 
getT2() - Method in class org.ecocean.genetics.HFStatistics
 
getTagNumber() - Method in class org.ecocean.tag.MetalTag
 
getTapirLinkURL(String) - Static method in class org.ecocean.CommonConfiguration
 
getTaskID() - Method in class org.ecocean.grid.MatchObject
 
getTaskIdentifier() - Method in class org.ecocean.grid.ScanWorkItem
 
getText(String) - Static method in class org.ecocean.servlet.ServletUtilities
 
getTheSpot() - Method in class org.ecocean.SuperSpot
Returns the central spot which the neighboring spots surround
getTheta() - Method in class org.ecocean.genetics.FStatistics
 
getTheta() - Method in class org.ecocean.genetics.HFStatistics
 
getThreeLeftFiducialPoints() - Method in class org.ecocean.Encounter
 
getThreeLeftFiducialPoints() - Method in class org.ecocean.grid.EncounterLite
 
getThreeRightFiducialPoints() - Method in class org.ecocean.Encounter
 
getThreeRightFiducialPoints() - Method in class org.ecocean.grid.EncounterLite
 
getThumbnails(HttpServletRequest, Iterator, int, int, String[]) - Method in class org.ecocean.Shepherd
 
getTimeOfBirth() - Method in class org.ecocean.MarkedIndividual
 
getTimeofDeath() - Method in class org.ecocean.MarkedIndividual
 
getTimestampOfLastUpdate() - Method in class org.ecocean.PatterningPassport
 
getTissueSample(String, String) - Method in class org.ecocean.Shepherd
 
getTissueSamples() - Method in class org.ecocean.Encounter
 
getTissueType() - Method in class org.ecocean.genetics.TissueSample
 
getToDoSize() - Method in class org.ecocean.grid.GridManager
 
getTotalWorkItemsInTask() - Method in class org.ecocean.grid.ScanWorkItem
 
getTrainableEncounters() - Method in class org.ecocean.MarkedIndividual
 
getTriangleCentroidX() - Method in class org.ecocean.grid.SpotTriangle
 
getTriangleCentroidY() - Method in class org.ecocean.grid.SpotTriangle
 
getType() - Method in class org.ecocean.DataCollectionEvent
 
getType() - Static method in class org.ecocean.genetics.BiologicalMeasurement
 
getType() - Method in class org.ecocean.social.Relationship
 
getType() - Method in class org.ecocean.Util.MeasurementDesc
 
getTypeDescription(File) - Method in class org.ecocean.interconnect.ImageFileView
 
getUnapprovedEncounters(Query) - Method in class org.ecocean.Shepherd
Retrieves all new encounters that are stored in the database but which have been approved for public viewing in the visual database
getUnapprovedEncounters(Query, String) - Method in class org.ecocean.Shepherd
 
getUnassignedEncounters() - Method in class org.ecocean.Shepherd
Retrieves any unassigned encounters that are stored in the database - but not yet analyzed - to see whether they represent new or already persistent sharks
getUnassignedEncountersIncludingUnapproved() - Method in class org.ecocean.Shepherd
 
getUnassignedEncountersIncludingUnapproved(Query) - Method in class org.ecocean.Shepherd
 
getUnidentifiable() - Method in class org.ecocean.Encounter
 
getUnidentifiableEncounters() - Method in class org.ecocean.MarkedIndividual
public Encounter[] getDateSortedEncounters(boolean includeLogEncounters) { return getDateSortedEncounters(); }
getUnidentifiableEncountersForMarkedIndividual(String) - Method in class org.ecocean.Shepherd
 
getUniqueNumber() - Method in class org.ecocean.grid.ScanTask
Returns the unique number for this workItem.
getUniqueNumber() - Method in class org.ecocean.grid.ScanWorkItem
Returns the unique number for this workItem.
getUniqueNumberTask() - Method in class org.ecocean.grid.ScanWorkItemResult
 
getUniqueNumberWorkItem() - Method in class org.ecocean.grid.ScanWorkItemResult
Returns the unique number for this workItem.
getUniqueNumberWorkItemResult() - Method in class org.ecocean.grid.ScanWorkItemResult
 
getUniqueWorkItems(Shepherd, Vector, HttpServletRequest, Query, int, long, boolean, int, int, GridManager) - Method in class org.ecocean.servlet.ScanAppletSupport
 
getUniqueWorkItemsGeneric(boolean, GridManager, GridNode, Shepherd, Vector, HttpServletRequest, int, long, boolean, int, int) - Method in class org.ecocean.servlet.ScanAppletSupport
 
getUnits() - Method in class org.ecocean.genetics.BiologicalMeasurement
 
getUnits() - Method in class org.ecocean.Measurement
 
getUnits() - Method in class org.ecocean.Util.MeasurementDesc
 
getUnitsLabel() - Method in class org.ecocean.Util.MeasurementDesc
 
getURLLocation(HttpServletRequest) - Static method in class org.ecocean.CommonConfiguration
 
getURLToFooterGraphic(String) - Static method in class org.ecocean.CommonConfiguration
 
getURLToMastheadGraphic(String) - Static method in class org.ecocean.CommonConfiguration
 
getUser() - Method in class org.ecocean.grid.ScanTask
 
getUser(String) - Method in class org.ecocean.Shepherd
 
getUserEncounters(Query, String) - Method in class org.ecocean.Shepherd
 
getUserID() - Method in class org.ecocean.User
 
getUserImage() - Method in class org.ecocean.User
 
getUsername() - Method in class org.ecocean.Role
 
getUsername() - Method in class org.ecocean.User
 
getUsername1() - Method in class org.ecocean.security.Collaboration
 
getUsername2() - Method in class org.ecocean.security.Collaboration
 
getUserProject() - Method in class org.ecocean.User
 
getUserStatement() - Method in class org.ecocean.User
 
getUserURL() - Method in class org.ecocean.User
 
getVal(HashMap, String) - Method in class org.ecocean.servlet.AdoptionAction
 
getVal(HashMap, String) - Method in class org.ecocean.servlet.EncounterForm
 
getVallele() - Method in class org.ecocean.genetics.FStatistics
 
getValue() - Method in class org.ecocean.genetics.BiologicalMeasurement
 
getValue() - Method in class org.ecocean.Measurement
 
getVerbatimEventDate() - Method in class org.ecocean.Encounter
 
getVerbatimLocality() - Method in class org.ecocean.Encounter
 
getVersion() - Static method in class org.ecocean.ContextConfiguration
 
getVertex(int) - Method in class org.ecocean.grid.SpotTriangle
 
getVindividual() - Method in class org.ecocean.genetics.FStatistics
 
getVpopulation() - Method in class org.ecocean.genetics.FStatistics
 
getWebappsDir() - Method in class org.ecocean.PatterningPassport
 
getWI4MO(ScanWorkItemResult, ArrayList<ScanWorkItem>) - Method in class org.ecocean.servlet.WriteOutScanTask
 
getWikiLocation(String) - Static method in class org.ecocean.CommonConfiguration
 
getWorkItem(String) - Method in class org.ecocean.grid.GridManager
 
getWorkItem(String) - Method in class org.ecocean.grid.ScanTask
 
getWorkItemGroup(Shepherd, HttpServletRequest, HttpServletResponse, GridManager) - Method in class org.ecocean.servlet.ScanAppletSupport
 
getWorkItems(int) - Method in class org.ecocean.grid.GridManager
 
getWorkItemsCompleteInTask() - Method in class org.ecocean.grid.ScanWorkItem
 
getWorkItemUniqueNumber() - Method in class org.ecocean.grid.MatchObject
 
getWriteThis() - Method in class org.ecocean.grid.ScanTask
 
getX() - Method in class com.reijns.I3S.Point2D
Point2D Public Methods

Comments: Normally getter methods bend Encapsulation, but since the Point2D class can be considered as only a Value Object access to the data is required by the processor objects.

getY() - Method in class com.reijns.I3S.Point2D
 
getYear() - Method in class org.ecocean.Encounter
 
gif - Static variable in class org.ecocean.interconnect.Utils
 
gifIcon - Variable in class org.ecocean.interconnect.ImageFileView
 
gm - Variable in class org.ecocean.grid.FalseMatchCreationThread
 
gm - Static variable in class org.ecocean.grid.GridManagerFactory
 
gm - Variable in class org.ecocean.grid.ScanWorkItemCreationThread
 
gm - Variable in class org.ecocean.grid.TuningTaskCreationThread
 
go - Variable in class org.ecocean.grid.WorkApplet3.scanAppletActionListener
 
gpsLatitude - Variable in class org.ecocean.Encounter
 
gpsLongitude - Variable in class org.ecocean.Encounter
 
gravCenterX - Variable in class org.ecocean.Spot
 
gravCenterY - Variable in class org.ecocean.Spot
 
GridCleanupThread - Class in org.ecocean.grid
 
GridCleanupThread(String) - Constructor for class org.ecocean.grid.GridCleanupThread
Constructor to create a new thread object
GridHeartbeatReceiver - Class in org.ecocean.servlet
 
GridHeartbeatReceiver() - Constructor for class org.ecocean.servlet.GridHeartbeatReceiver
 
GridManager - Class in org.ecocean.grid
 
GridManager() - Constructor for class org.ecocean.grid.GridManager
 
GridManagerFactory - Class in org.ecocean.grid
 
GridManagerFactory() - Constructor for class org.ecocean.grid.GridManagerFactory
 
GridNode - Class in org.ecocean.grid
 
GridNode(HttpServletRequest, int) - Constructor for class org.ecocean.grid.GridNode
 
gridStatsRefreshPeriod - Variable in class org.ecocean.grid.GridManager
 
groupBehavior - Variable in class org.ecocean.Occurrence
 
groupSize - Variable in class org.ecocean.grid.GridManager
 
groupSize - Variable in class org.ecocean.grid.GridNode
 
guid - Variable in class org.ecocean.Encounter
 

H

haploColorProps - Static variable in class org.ecocean.genetics.MitochondrialDNAAnalysis
 
haplotype - Variable in class org.ecocean.genetics.MitochondrialDNAAnalysis
 
hasAllele(Integer) - Method in class org.ecocean.genetics.Locus
 
hasBiologicalMeasurement(String) - Method in class org.ecocean.Encounter
 
hasFinished() - Method in class org.ecocean.grid.ScanTask
Returns whether all of the work of this Task has been completed by remote nodes.
hasGeneticSex() - Method in class org.ecocean.MarkedIndividual
 
hash - Variable in class org.ecocean.genetics.distance.HashTokenizer
 
hashAndSaltPassword(String, String) - Static method in class org.ecocean.servlet.ServletUtilities
 
hashedInformOthers - Variable in class org.ecocean.Encounter
 
hashedPhotographerEmail - Variable in class org.ecocean.Encounter
 
hashedSubmitterEmail - Variable in class org.ecocean.Encounter
 
HashTokenizer - Class in org.ecocean.genetics.distance
 
HashTokenizer(String, String) - Constructor for class org.ecocean.genetics.distance.HashTokenizer
 
HashTokenizer(String) - Constructor for class org.ecocean.genetics.distance.HashTokenizer
 
hasKeyword(Keyword) - Method in class org.ecocean.Encounter
 
hasLeftSpotImage() - Method in class org.ecocean.Encounter
 
hasLocus(String) - Method in class org.ecocean.genetics.MicrosatelliteMarkersAnalysis
 
hasLocus(String) - Method in class org.ecocean.MarkedIndividual
 
hasLocusAndAllele(String, Integer) - Method in class org.ecocean.MarkedIndividual
 
hasMadeFirstCheckin - Variable in class org.ecocean.grid.GridNode
 
hasMatchedPair(Spot, Spot) - Method in class org.ecocean.grid.MatchedPoints
 
hasMeasurement(String) - Method in class org.ecocean.Encounter
 
hasMeasurement(String) - Method in class org.ecocean.genetics.TissueSample
 
hasMeasurements() - Method in class org.ecocean.Encounter
 
hasMeasurements() - Method in class org.ecocean.genetics.TissueSample
 
hasMsMarkers() - Method in class org.ecocean.MarkedIndividual
 
hasRightSpotImage - Variable in class org.ecocean.Encounter
 
hasRightSpotImage() - Method in class org.ecocean.Encounter
 
hasSinglePhotoVideoByFileName(String) - Method in class org.ecocean.Encounter
 
hasSpotImage - Variable in class org.ecocean.Encounter
 
hasStarted() - Method in class org.ecocean.grid.ScanTask
 
hb - Variable in class org.ecocean.grid.WorkApplet3
 
hb - Variable in class org.ecocean.grid.WorkAppletHeadless
 
heartbeatThread - Variable in class org.ecocean.grid.AppletHeartbeatThread
 
height - Variable in class org.ecocean.ImageProcessor
 
HFStatistics - Class in org.ecocean.genetics
 
HFStatistics(int) - Constructor for class org.ecocean.genetics.HFStatistics
 
HIDDEN_FILE - Static variable in class org.ecocean.interconnect.ImageFileFilter
 
host - Variable in class org.ecocean.NotificationMailer
 
hour - Variable in class org.ecocean.Encounter
 

I

i - Variable in class org.ecocean.grid.WorkApplet3
 
i3sDataDir - Variable in class org.ecocean.interconnect.InsertDatabase
 
i3sDataDir - Variable in class org.ecocean.interconnect.SharkPanel
 
i3sIcon - Variable in class org.ecocean.interconnect.ImageFileView
 
I3SMatchComparator - Class in org.ecocean.grid
 
I3SMatchComparator() - Constructor for class org.ecocean.grid.I3SMatchComparator
 
I3SMatchObject - Class in org.ecocean.grid
matchObject is a temporary object used by the shepherd class to store unordered match values
I3SMatchObject() - Constructor for class org.ecocean.grid.I3SMatchObject
 
I3SMatchObject(String, double, String, String, String, double, TreeMap, double) - Constructor for class org.ecocean.grid.I3SMatchObject
 
i3sMatchValue - Variable in class org.ecocean.grid.MatchObject
 
i3sResult - Variable in class org.ecocean.grid.ScanWorkItem
 
i3sResult - Variable in class org.ecocean.grid.ScanWorkItemResult
 
i3sScan(EncounterLite, boolean) - Method in class org.ecocean.grid.EncounterLite
This method allows us to use the I3S match algorithm as well.
i3sWriteThis(Shepherd, MatchObject[], String, String, String, String, boolean, double, String) - Method in class org.ecocean.servlet.WriteOutScanTask
 
id - Variable in class org.ecocean.Adoption
 
id - Variable in class org.ecocean.security.Collaboration
 
id - Variable in class org.ecocean.servlet.EncounterSetMeasurements.RequestEventValues
 
id - Variable in class org.ecocean.tag.AbstractTag
 
identificationRemarks - Variable in class org.ecocean.Encounter
 
identifyShark - Variable in class org.ecocean.interconnect.CompareResults
 
identity - Variable in class org.ecocean.interconnect.SharkIdentification
 
idNumber - Variable in class org.ecocean.tag.AcousticTag
 
ih - Variable in class org.ecocean.interconnect.SharkPanel
 
image - Variable in class org.ecocean.grid.WorkApplet3.ImagePanel
 
ImageFileFilter - Class in org.ecocean.interconnect
A convenience implementation of FileFilter that filters out all files except for those type extensions that it knows about.
ImageFileFilter() - Constructor for class org.ecocean.interconnect.ImageFileFilter
Creates a file filter.
ImageFileFilter(String) - Constructor for class org.ecocean.interconnect.ImageFileFilter
Creates a file filter that accepts files with the given extension.
ImageFileFilter(String, String) - Constructor for class org.ecocean.interconnect.ImageFileFilter
Creates a file filter that accepts the given file type.
ImageFileFilter(String[]) - Constructor for class org.ecocean.interconnect.ImageFileFilter
Creates a file filter from the given string array.
ImageFileFilter(String[], String) - Constructor for class org.ecocean.interconnect.ImageFileFilter
Creates a file filter from the given string array and description.
ImageFileView - Class in org.ecocean.interconnect
 
ImageFileView() - Constructor for class org.ecocean.interconnect.ImageFileView
 
imageOp() - Method in class org.ecocean.interconnect.SharkPanel
 
ImagePreview - Class in org.ecocean.interconnect
 
ImagePreview(JFileChooser) - Constructor for class org.ecocean.interconnect.ImagePreview
 
ImageProcessor - Class in org.ecocean
Does actual comparison processing of batch-uploaded images.
ImageProcessor(String, String, int, int, String, String, String) - Constructor for class org.ecocean.ImageProcessor
 
ImageProcessor.Phase - Enum in org.ecocean
Enumeration representing possible processing phases.
ImageProcessor.Phase() - Constructor for enum org.ecocean.ImageProcessor.Phase
 
ImageProcessor.Status - Enum in org.ecocean
Enumeration representing possible status values for the batch processor.
ImageProcessor.Status() - Constructor for enum org.ecocean.ImageProcessor.Status
 
images - Variable in class org.ecocean.Encounter
 
images - Variable in class org.ecocean.NotificationMailer
 
imageSourcePath - Variable in class org.ecocean.ImageProcessor
 
imageTargetPath - Variable in class org.ecocean.ImageProcessor
 
imfilter - Variable in class org.ecocean.interconnect.Interconnect
 
img - Static variable in class org.ecocean.interconnect.AboutInterconnect
 
img - Variable in class org.ecocean.interconnect.SharkPanel
 
img - Variable in class org.ecocean.interconnect.ShowImagePane
 
img - Variable in class org.ecocean.interconnect.Splash
 
ImportSRGD - Class in org.ecocean.servlet.importer
Uploads an SRGD CSV file for data import
ImportSRGD() - Constructor for class org.ecocean.servlet.importer.ImportSRGD
 
in - Variable in class org.ecocean.interconnect.CopyFile
 
incrementCompletedWorkItems(int) - Method in class org.ecocean.grid.GridManager
 
Ind2IndDistance - Class in org.ecocean.genetics.distance
 
Ind2IndDistance() - Constructor for class org.ecocean.genetics.distance.Ind2IndDistance
 
indexname - Variable in class org.ecocean.Keyword
 
individual - Variable in class org.ecocean.Adoption
 
IndividualAddComment - Class in org.ecocean.servlet
 
IndividualAddComment() - Constructor for class org.ecocean.servlet.IndividualAddComment
 
IndividualAddEncounter - Class in org.ecocean.servlet
 
IndividualAddEncounter() - Constructor for class org.ecocean.servlet.IndividualAddEncounter
 
IndividualAddFile - Class in org.ecocean.servlet
 
IndividualAddFile() - Constructor for class org.ecocean.servlet.IndividualAddFile
 
individualCount - Variable in class org.ecocean.Occurrence
 
IndividualCreate - Class in org.ecocean.servlet
 
IndividualCreate() - Constructor for class org.ecocean.servlet.IndividualCreate
 
individualID - Variable in class org.ecocean.Encounter
 
individualID - Variable in class org.ecocean.MarkedIndividual
 
individualLabel(int) - Method in class org.ecocean.genetics.FStatistics
 
individualLabel(int) - Method in class org.ecocean.genetics.HFStatistics
 
individualName - Variable in class org.ecocean.grid.I3SMatchObject
 
individualName - Variable in class org.ecocean.grid.MatchObject
 
IndividualOccurrenceNumComparator - Class in org.ecocean
 
IndividualOccurrenceNumComparator() - Constructor for class org.ecocean.IndividualOccurrenceNumComparator
 
IndividualQueryProcessor - Class in org.ecocean
 
IndividualQueryProcessor() - Constructor for class org.ecocean.IndividualQueryProcessor
 
IndividualRemoveDataFile - Class in org.ecocean.servlet
 
IndividualRemoveDataFile() - Constructor for class org.ecocean.servlet.IndividualRemoveDataFile
 
IndividualRemoveEncounter - Class in org.ecocean.servlet
 
IndividualRemoveEncounter() - Constructor for class org.ecocean.servlet.IndividualRemoveEncounter
 
IndividualSearchExportCapture - Class in org.ecocean.servlet.export
 
IndividualSearchExportCapture() - Constructor for class org.ecocean.servlet.export.IndividualSearchExportCapture
 
IndividualSetAlternateID - Class in org.ecocean.servlet
 
IndividualSetAlternateID() - Constructor for class org.ecocean.servlet.IndividualSetAlternateID
 
IndividualSetNickName - Class in org.ecocean.servlet
 
IndividualSetNickName() - Constructor for class org.ecocean.servlet.IndividualSetNickName
 
IndividualSetSex - Class in org.ecocean.servlet
 
IndividualSetSex() - Constructor for class org.ecocean.servlet.IndividualSetSex
 
IndividualSetYearOfBirth - Class in org.ecocean.servlet
 
IndividualSetYearOfBirth() - Constructor for class org.ecocean.servlet.IndividualSetYearOfBirth
 
IndividualSetYearOfDeath - Class in org.ecocean.servlet
 
IndividualSetYearOfDeath() - Constructor for class org.ecocean.servlet.IndividualSetYearOfDeath
 
informInterestedIndividualParties(HttpServletRequest, String, String, String) - Static method in class org.ecocean.servlet.ServletUtilities
 
informInterestedParties(HttpServletRequest, String, String, String) - Static method in class org.ecocean.servlet.ServletUtilities
 
informothers - Variable in class org.ecocean.Encounter
 
init() - Method in class org.ecocean.genetics.distance.ShareDst
 
init() - Method in class org.ecocean.grid.WorkApplet3
 
init(ServletConfig) - Method in class org.ecocean.servlet.AdoptionAction
 
init(ServletConfig) - Method in class org.ecocean.servlet.CalendarXMLServer
 
init(ServletConfig) - Method in class org.ecocean.servlet.CalendarXMLServer2
 
init(ServletConfig) - Method in class org.ecocean.servlet.Collaborate
 
init(ServletConfig) - Method in class org.ecocean.servlet.DeleteAdoption
 
init(ServletConfig) - Method in class org.ecocean.servlet.DeleteAllDataPermanently
 
init(ServletConfig) - Method in class org.ecocean.servlet.DontTrack
 
init(ServletConfig) - Method in class org.ecocean.servlet.EncounterAddComment
 
init(ServletConfig) - Method in class org.ecocean.servlet.EncounterAddImage
 
init(ServletConfig) - Method in class org.ecocean.servlet.EncounterAddSpotFile
 
init(ServletConfig) - Method in class org.ecocean.servlet.EncounterApprove
 
init(ServletConfig) - Method in class org.ecocean.servlet.EncounterDelete
 
init(ServletConfig) - Method in class org.ecocean.servlet.EncounterForm
 
init(ServletConfig) - Method in class org.ecocean.servlet.EncounterGetPatterningPassport
 
init(ServletConfig) - Method in class org.ecocean.servlet.EncounterRemoveImage
 
init(ServletConfig) - Method in class org.ecocean.servlet.EncounterRemoveSpots
 
init(ServletConfig) - Method in class org.ecocean.servlet.EncounterRemoveTissueSample
 
init(ServletConfig) - Method in class org.ecocean.servlet.EncounterResetDate
 
init(ServletConfig) - Method in class org.ecocean.servlet.EncounterSetAlternateID
 
init(ServletConfig) - Method in class org.ecocean.servlet.EncounterSetAsUnidentifiable
 
init(ServletConfig) - Method in class org.ecocean.servlet.EncounterSetBehavior
 
init(ServletConfig) - Method in class org.ecocean.servlet.EncounterSetCountry
 
init(ServletConfig) - Method in class org.ecocean.servlet.EncounterSetDynamicProperty
 
init(ServletConfig) - Method in class org.ecocean.servlet.EncounterSetGenusSpecies
 
init(ServletConfig) - Method in class org.ecocean.servlet.EncounterSetGPS
 
init(ServletConfig) - Method in class org.ecocean.servlet.EncounterSetIdentifiable
 
init(ServletConfig) - Method in class org.ecocean.servlet.EncounterSetInformOthers
 
init(ServletConfig) - Method in class org.ecocean.servlet.EncounterSetLifeStage
 
init(ServletConfig) - Method in class org.ecocean.servlet.EncounterSetLivingStatus
 
init(ServletConfig) - Method in class org.ecocean.servlet.EncounterSetLocation
 
init(ServletConfig) - Method in class org.ecocean.servlet.EncounterSetLocationID
 
init(ServletConfig) - Method in class org.ecocean.servlet.EncounterSetMatchedBy
 
init(ServletConfig) - Method in class org.ecocean.servlet.EncounterSetMaximumDepth
 
init(ServletConfig) - Method in class org.ecocean.servlet.EncounterSetMaximumElevation
 
init(ServletConfig) - Method in class org.ecocean.servlet.EncounterSetOccurrenceRemarks
 
init(ServletConfig) - Method in class org.ecocean.servlet.EncounterSetPatterningCode
 
init(ServletConfig) - Method in class org.ecocean.servlet.EncounterSetPatterningPassport
 
init(ServletConfig) - Method in class org.ecocean.servlet.EncounterSetScarring
 
init(ServletConfig) - Method in class org.ecocean.servlet.EncounterSetSex
 
init(ServletConfig) - Method in class org.ecocean.servlet.EncounterSetSize
 
init(ServletConfig) - Method in class org.ecocean.servlet.EncounterSetState
 
init(ServletConfig) - Method in class org.ecocean.servlet.EncounterSetSubmitterID
 
init(ServletConfig) - Method in class org.ecocean.servlet.EncounterSetSubmitterPhotographerContactInfo
 
init(ServletConfig) - Method in class org.ecocean.servlet.EncounterSetTapirLinkExposure
 
init(ServletConfig) - Method in class org.ecocean.servlet.EncounterSetTissueSample
 
init(ServletConfig) - Method in class org.ecocean.servlet.EncounterSetVerbatimEventDate
 
init(ServletConfig) - Method in class org.ecocean.servlet.export.EncounterSearchExportEmailAddresses
 
init(ServletConfig) - Method in class org.ecocean.servlet.export.EncounterSearchExportExcelFile
 
init(ServletConfig) - Method in class org.ecocean.servlet.export.EncounterSearchExportGeneGISFormat
 
init(ServletConfig) - Method in class org.ecocean.servlet.export.EncounterSearchExportKML
 
init(ServletConfig) - Method in class org.ecocean.servlet.export.EncounterSearchExportShapefile
 
init(ServletConfig) - Method in class org.ecocean.servlet.export.GenalexExportCodominantMSDataBySize
 
init(ServletConfig) - Method in class org.ecocean.servlet.export.GenePopExport
 
init(ServletConfig) - Method in class org.ecocean.servlet.export.GetIndividualSearchGoogleMapsPoints
 
init(ServletConfig) - Method in class org.ecocean.servlet.export.IndividualSearchExportCapture
 
init(ServletConfig) - Method in class org.ecocean.servlet.export.KinalyzerExport
 
init(ServletConfig) - Method in class org.ecocean.servlet.export.SimpleCMROutput
 
init(ServletConfig) - Method in class org.ecocean.servlet.export.SOCPROGExport
 
init(ServletConfig) - Method in class org.ecocean.servlet.GridHeartbeatReceiver
 
init(ServletConfig) - Method in class org.ecocean.servlet.importer.ImportSRGD
 
init(ServletConfig) - Method in class org.ecocean.servlet.IndividualAddComment
 
init(ServletConfig) - Method in class org.ecocean.servlet.IndividualAddEncounter
 
init(ServletConfig) - Method in class org.ecocean.servlet.IndividualAddFile
 
init(ServletConfig) - Method in class org.ecocean.servlet.IndividualCreate
 
init(ServletConfig) - Method in class org.ecocean.servlet.IndividualRemoveDataFile
 
init(ServletConfig) - Method in class org.ecocean.servlet.IndividualRemoveEncounter
 
init(ServletConfig) - Method in class org.ecocean.servlet.IndividualSetAlternateID
 
init(ServletConfig) - Method in class org.ecocean.servlet.IndividualSetNickName
 
init(ServletConfig) - Method in class org.ecocean.servlet.IndividualSetSex
 
init(ServletConfig) - Method in class org.ecocean.servlet.IndividualSetYearOfBirth
 
init(ServletConfig) - Method in class org.ecocean.servlet.IndividualSetYearOfDeath
 
init(ServletConfig) - Method in class org.ecocean.servlet.InterconnectSubmitSpots
 
init(ServletConfig) - Method in class org.ecocean.servlet.JavascriptGlobals
 
init(ServletConfig) - Method in class org.ecocean.servlet.KeywordHandler
 
init(ServletConfig) - Method in class org.ecocean.servlet.MassExposeGBIF
 
init(ServletConfig) - Method in class org.ecocean.servlet.MassSetInformOthers
 
init(ServletConfig) - Method in class org.ecocean.servlet.MassSetLocationCodeFromLocationString
 
init(ServletConfig) - Method in class org.ecocean.servlet.MassSwapLocationCode
 
init(ServletConfig) - Method in class org.ecocean.servlet.OccurrenceAddComment
 
init(ServletConfig) - Method in class org.ecocean.servlet.OccurrenceAddEncounter
 
init(ServletConfig) - Method in class org.ecocean.servlet.OccurrenceCreate
 
init(ServletConfig) - Method in class org.ecocean.servlet.OccurrenceRemoveEncounter
 
init(ServletConfig) - Method in class org.ecocean.servlet.OccurrenceSetGroupBehavior
 
init(ServletConfig) - Method in class org.ecocean.servlet.OccurrenceSetIndividualCount
 
init(ServletConfig) - Method in class org.ecocean.servlet.RelationshipCreate
 
init(ServletConfig) - Method in class org.ecocean.servlet.RelationshipDelete
 
init(ServletConfig) - Method in class org.ecocean.servlet.RemoveEmailAddress
 
init(ServletConfig) - Method in class org.ecocean.servlet.ResurrectDeletedAdoption
 
init(ServletConfig) - Method in class org.ecocean.servlet.ResurrectDeletedEncounter
 
init(ServletConfig) - Method in class org.ecocean.servlet.ScanAppletSupport
 
init(ServletConfig) - Method in class org.ecocean.servlet.ScanResultsServlet
 
init(ServletConfig) - Method in class org.ecocean.servlet.ScanTaskHandler
 
init(ServletConfig) - Method in class org.ecocean.servlet.ScanWorkItemResultsHandler
 
init(ServletConfig) - Method in class org.ecocean.servlet.SinglePhotoVideoAddKeyword
 
init(ServletConfig) - Method in class org.ecocean.servlet.SinglePhotoVideoRemoveKeyword
 
init(FilterConfig) - Method in class org.ecocean.servlet.StrutsUTF8Filter
 
init(ServletConfig) - Method in class org.ecocean.servlet.TissueSampleRemoveBiologicalMeasurement
 
init(ServletConfig) - Method in class org.ecocean.servlet.TissueSampleRemoveHaplotype
 
init(ServletConfig) - Method in class org.ecocean.servlet.TissueSampleRemoveMicrosatelliteMarkers
 
init(ServletConfig) - Method in class org.ecocean.servlet.TissueSampleRemoveSexAnalysis
 
init(ServletConfig) - Method in class org.ecocean.servlet.TissueSampleSetHaplotype
 
init(ServletConfig) - Method in class org.ecocean.servlet.TissueSampleSetMicrosatelliteMarkers
 
init(ServletConfig) - Method in class org.ecocean.servlet.TissueSampleSetSexAnalysis
 
init(ServletConfig) - Method in class org.ecocean.servlet.TrackerFeed
 
init(ServletConfig) - Method in class org.ecocean.servlet.TrackIt
 
init(ServletConfig) - Method in class org.ecocean.servlet.UpdateEmailAddress
 
init(ServletConfig) - Method in class org.ecocean.servlet.UserAddProfileImage
 
init(ServletConfig) - Method in class org.ecocean.servlet.UserCreate
 
init(ServletConfig) - Method in class org.ecocean.servlet.UserDelete
 
init(ServletConfig) - Method in class org.ecocean.servlet.UserInfo
 
init(ServletConfig) - Method in class org.ecocean.servlet.UserRemoveProfileImage
 
init(ServletConfig) - Method in class org.ecocean.servlet.UserResetAcceptedUserAgreement
 
init(ServletConfig) - Method in class org.ecocean.servlet.UserSelfUpdate
 
init(ServletConfig) - Method in class org.ecocean.servlet.WriteOutScanTask
 
initCompare() - Method in class org.ecocean.interconnect.SharkPanel
 
initialize(String) - Static method in class org.ecocean.CommonConfiguration
 
initialize() - Static method in class org.ecocean.ContextConfiguration
 
initializeColorCodes(String) - Static method in class org.ecocean.genetics.MitochondrialDNAAnalysis
 
InsertDatabase - Class in org.ecocean.interconnect
 
InsertDatabase(SharkPanel, String, String) - Constructor for class org.ecocean.interconnect.InsertDatabase
 
InsertDatabase.OptionListener - Class in org.ecocean.interconnect
An ActionListener that listens to the check box.
InsertDatabase.OptionListener() - Constructor for class org.ecocean.interconnect.InsertDatabase.OptionListener
 
insertInDatabase(StringBuffer) - Method in class org.ecocean.interconnect.SharkPanel
 
insertInDB - Variable in class org.ecocean.interconnect.CompareResults
 
institutionCode - Variable in class org.ecocean.DataCollectionEvent
 
institutionID - Variable in class org.ecocean.DataCollectionEvent
 
Interconnect - Class in org.ecocean.interconnect
 
Interconnect() - Constructor for class org.ecocean.interconnect.Interconnect
 
Interconnect.SharkMenu - Class in org.ecocean.interconnect
 
Interconnect.SharkMenu() - Constructor for class org.ecocean.interconnect.Interconnect.SharkMenu
 
InterconnectSubmitSpots - Class in org.ecocean.servlet
 
InterconnectSubmitSpots() - Constructor for class org.ecocean.servlet.InterconnectSubmitSpots
 
interestedResearchers - Variable in class org.ecocean.Encounter
 
interestedResearchers - Variable in class org.ecocean.MarkedIndividual
 
ipAddress - Variable in class org.ecocean.grid.GridNode
 
ipAddress() - Method in class org.ecocean.grid.GridNode
 
isAcceptableImageFile(String) - Static method in class org.ecocean.Shepherd
 
isAcceptableVideoFile(String) - Method in class org.ecocean.Shepherd
 
isAdoption(String) - Method in class org.ecocean.Shepherd
 
isApproved() - Method in class org.ecocean.Encounter
 
isAssignedToMarkedIndividual() - Method in class org.ecocean.Encounter
 
isBetween(int, int, int) - Static method in class org.ecocean.grid.Geometry
Return true if c is between a and b.
isBetween(double, double, double) - Static method in class org.ecocean.grid.Geometry
Return true if c is between a and b.
isBlank(String) - Method in class org.ecocean.ImageProcessor
 
isCancelled() - Method in class org.ecocean.grid.AppletSwingWorker
Returns true if this task was cancelled before it completed normally.
isCatalogEditable(String) - Static method in class org.ecocean.CommonConfiguration
This configuration option defines whether users can edit this catalog.
isCheckedOut(long) - Method in class org.ecocean.grid.ScanWorkItem
Returns true if a node is currently working on this object.
isCommunity(String) - Method in class org.ecocean.Shepherd
 
isDeceased() - Method in class org.ecocean.MarkedIndividual
 
isDescribedByPhotoKeyword(Keyword) - Method in class org.ecocean.MarkedIndividual
 
isDone() - Method in class org.ecocean.grid.AppletSwingWorker
Returns true if this task completed.
isDone() - Method in class org.ecocean.grid.ScanWorkItem
 
isEncounter(String) - Method in class org.ecocean.Shepherd
 
isExtensionListInDescription() - Method in class org.ecocean.interconnect.ImageFileFilter
Returns whether the extension list (.jpg, .gif, etc) should show up in the human readable description.
isFinished() - Method in class org.ecocean.grid.AppletHeartbeatThread
 
isFinished() - Method in class org.ecocean.grid.FalseMatchCreationThread
 
isFinished() - Method in interface org.ecocean.grid.ISharkGridThread
 
isFinished - Variable in class org.ecocean.grid.ScanTask
 
isFinished() - Method in class org.ecocean.grid.ScanTaskCleanupThread
 
isFinished() - Method in class org.ecocean.grid.ScanWorkItemCreationThread
 
isFinished() - Method in class org.ecocean.grid.TuningTaskCreationThread
 
isGeneticAnalysis(String, String, String, String) - Method in class org.ecocean.Shepherd
 
isGridSpaceAvailable(HttpServletRequest, boolean) - Method in class org.ecocean.grid.GridManager
 
ISharkGridThread - Interface in org.ecocean.grid
A thread interface
isInAllowedPosition(String) - Method in class org.ecocean.grid.GridManager
 
isIntegratedWithWildMe(String) - Static method in class org.ecocean.CommonConfiguration
 
isKeyword(String) - Method in class org.ecocean.Shepherd
 
isLineIntersectingLine(int, int, int, int, int, int, int, int) - Static method in class org.ecocean.grid.Geometry
Check if two line segments intersects.
isLineIntersectingRectangle(int, int, int, int, int, int, int, int) - Static method in class org.ecocean.grid.Geometry
Check if a specified line intersects a specified rectangle.
isMarkedIndividual(String) - Method in class org.ecocean.Shepherd
 
isMemberOf(String) - Method in class org.ecocean.Keyword
 
isOccurrence(String) - Method in class org.ecocean.Shepherd
 
isPointInsidePolygon(double[], double[], double, double) - Static method in class org.ecocean.grid.Geometry
Check if a given point is inside a given (complex) polygon.
isPointInsidePolygon(int[], int[], int, int) - Static method in class org.ecocean.grid.Geometry
Check if a given point is inside a given polygon.
isPointInsideRectangle(int, int, int, int, int, int) - Static method in class org.ecocean.grid.Geometry
Check if a specified point is inside a specified rectangle.
isPolygonIntersectingRectangle(int[], int[], int, int, int, int) - Static method in class org.ecocean.grid.Geometry
Check if a specified polygon intersects a specified rectangle.
isPolylineIntersectingRectangle(int[], int[], int, int, int, int) - Static method in class org.ecocean.grid.Geometry
Check if a specified polyline intersects a specified rectangle.
isRelationship(String, String, String, String, String, boolean) - Method in class org.ecocean.Shepherd
 
isRelationship(String, String, String, String, String, String, boolean) - Method in class org.ecocean.Shepherd
 
isRightScan() - Method in class org.ecocean.grid.ScanWorkItem
 
isScanTask(String) - Method in class org.ecocean.Shepherd
 
isSinglePhotoVideo(String) - Method in class org.ecocean.Shepherd
 
isTargeted() - Method in class org.ecocean.grid.GridNode
 
isTissueSample(String, String) - Method in class org.ecocean.Shepherd
 
isTraversable(File) - Method in class org.ecocean.interconnect.ImageFileView
 
isUserAuthorizedForEncounter(Encounter, HttpServletRequest) - Static method in class org.ecocean.servlet.ServletUtilities
 
isUserAuthorizedForIndividual(MarkedIndividual, HttpServletRequest) - Static method in class org.ecocean.servlet.ServletUtilities
 
isUserAuthorizedForOccurrence(Occurrence, HttpServletRequest) - Static method in class org.ecocean.servlet.ServletUtilities
 
isUsernameAnonymous(String) - Static method in class org.ecocean.User
 
isUUID(String) - Static method in class org.ecocean.Util
 
Item1 - Variable in class org.ecocean.interconnect.Interconnect.SharkMenu
 
Item1_1 - Variable in class org.ecocean.interconnect.Interconnect.SharkMenu
 
Item1_2 - Variable in class org.ecocean.interconnect.Interconnect.SharkMenu
 
Item1_3 - Variable in class org.ecocean.interconnect.Interconnect.SharkMenu
 
Item1_4 - Variable in class org.ecocean.interconnect.Interconnect.SharkMenu
 
Item1_5 - Variable in class org.ecocean.interconnect.Interconnect.SharkMenu
 
Item1_6 - Variable in class org.ecocean.interconnect.Interconnect.SharkMenu
 
Item1_7 - Variable in class org.ecocean.interconnect.Interconnect.SharkMenu
 
Item2 - Variable in class org.ecocean.interconnect.Interconnect.SharkMenu
 
Item2_2 - Variable in class org.ecocean.interconnect.Interconnect.SharkMenu
 
Item3 - Variable in class org.ecocean.interconnect.Interconnect.SharkMenu
 
Item3_1 - Variable in class org.ecocean.interconnect.Interconnect.SharkMenu
 
Item3_2 - Variable in class org.ecocean.interconnect.Interconnect.SharkMenu
 
Item3_3 - Variable in class org.ecocean.interconnect.Interconnect.SharkMenu
 
Item4 - Variable in class org.ecocean.interconnect.Interconnect.SharkMenu
 
Item4_1 - Variable in class org.ecocean.interconnect.Interconnect.SharkMenu
 
Item5 - Variable in class org.ecocean.interconnect.Interconnect.SharkMenu
 
Item5_1 - Variable in class org.ecocean.interconnect.Interconnect.SharkMenu
 
itemStateChanged(ItemEvent) - Method in class org.ecocean.interconnect.Interconnect.SharkMenu
 
iw - Variable in class org.ecocean.interconnect.SharkPanel
 

J

JavascriptGlobals - Class in org.ecocean.servlet
 
JavascriptGlobals() - Constructor for class org.ecocean.servlet.JavascriptGlobals
 
jdoqlRepresentation - Variable in class org.ecocean.EncounterQueryResult
 
jdoqlRepresentation - Variable in class org.ecocean.MarkedIndividualQueryResult
 
jpeg - Static variable in class org.ecocean.interconnect.Utils
 
jpg - Static variable in class org.ecocean.interconnect.Utils
 
jpgIcon - Variable in class org.ecocean.interconnect.ImageFileView
 
JprevXfreqs - Static variable in class org.ecocean.genetics.distance.Distances
 
JprevYfreqs - Static variable in class org.ecocean.genetics.distance.Distances
 
Jx - Static variable in class org.ecocean.genetics.distance.Distances
 
Jxy - Static variable in class org.ecocean.genetics.distance.Distances
 
Jy - Static variable in class org.ecocean.genetics.distance.Distances
 

K

Keyword - Class in org.ecocean
 
Keyword() - Constructor for class org.ecocean.Keyword
empty constructor required by JDO Enhancer
Keyword(String) - Constructor for class org.ecocean.Keyword
 
KeywordHandler - Class in org.ecocean.servlet
 
KeywordHandler() - Constructor for class org.ecocean.servlet.KeywordHandler
 
keywords - Variable in class org.ecocean.SinglePhotoVideo
 
killShowResultsWindow() - Method in class org.ecocean.interconnect.SharkPanel
 
KinalyzerExport - Class in org.ecocean.servlet.export
 
KinalyzerExport() - Constructor for class org.ecocean.servlet.export.KinalyzerExport
 

L

label - Variable in class org.ecocean.Util.MeasurementDesc
 
largestRun - Variable in class org.ecocean.Spot
 
lastCheckin - Variable in class org.ecocean.grid.GridNode
 
lastCheckout - Variable in class org.ecocean.grid.GridNode
 
lastGridStatsQuery - Variable in class org.ecocean.grid.GridManager
 
lastHeartbeat - Variable in class org.ecocean.grid.GridNode
 
lastLogin - Variable in class org.ecocean.User
 
lastSearchExhaustive - Variable in class org.ecocean.interconnect.SharkPanel
 
leftReferenceSpots - Variable in class org.ecocean.Encounter
 
leftReferenceSpotsX - Variable in class org.ecocean.grid.EncounterLite
 
leftReferenceSpotsY - Variable in class org.ecocean.grid.EncounterLite
 
length(double[]) - Static method in class org.ecocean.grid.Geometry
Return the length of a vector.
length(double[], double[]) - Static method in class org.ecocean.grid.Geometry
Compute distance between two points.
length(int, int, int, int) - Static method in class org.ecocean.grid.Geometry
Compute the length of the line from (x0,y0) to (x1,y1)
length(double, double, double, double) - Static method in class org.ecocean.grid.Geometry
Compute the length of the line from (x0,y0) to (x1,y1)
length(int[], int[], boolean) - Static method in class org.ecocean.grid.Geometry
Compute the length of a polyline.
lifeStage - Variable in class org.ecocean.Encounter
 
lim22CenterX - Variable in class org.ecocean.Spot
 
lim22CenterY - Variable in class org.ecocean.Spot
 
lim22Height - Variable in class org.ecocean.Spot
 
lim22Width - Variable in class org.ecocean.Spot
 
lim45CenterX - Variable in class org.ecocean.Spot
 
lim45CenterY - Variable in class org.ecocean.Spot
 
lim45Height - Variable in class org.ecocean.Spot
 
lim45Width - Variable in class org.ecocean.Spot
 
lim68CenterX - Variable in class org.ecocean.Spot
 
lim68CenterY - Variable in class org.ecocean.Spot
 
lim68Height - Variable in class org.ecocean.Spot
 
lim68Width - Variable in class org.ecocean.Spot
 
limitCenterX - Variable in class org.ecocean.Spot
 
limitCenterY - Variable in class org.ecocean.Spot
 
limitHeight - Variable in class org.ecocean.Spot
 
limitWidth - Variable in class org.ecocean.Spot
 
LinSys - Class in com.reijns.I3S
 
LinSys(int, int) - Constructor for class com.reijns.I3S.LinSys
 
LinSys.MatRow - Class in com.reijns.I3S
 
LinSys.MatRow() - Constructor for class com.reijns.I3S.LinSys.MatRow
 
list - Variable in class org.ecocean.interconnect.ShowResults
 
livingStatus - Variable in class org.ecocean.Encounter
 
loadImage() - Method in class org.ecocean.interconnect.ImagePreview
 
loadIndividual(int, int, int) - Method in class org.ecocean.genetics.FStatistics
 
loadIndividual(int, int) - Method in class org.ecocean.genetics.HFStatistics
 
loadOverrideProps(String) - Static method in class org.ecocean.CommonConfiguration
 
loadOverrideProps(String) - Static method in class org.ecocean.ShepherdPMF
 
loadOverrideProps(String, String, String) - Static method in class org.ecocean.ShepherdProperties
 
loadProps(String) - Static method in class org.ecocean.CommonConfiguration
 
loadProps() - Static method in class org.ecocean.ContextConfiguration
 
loadSpots(DataInputStream, int, Point2D[]) - Method in class com.reijns.I3S.FgpFileOpen
Reads in all the spots (x,y coordinate points) from a file.
localContext - Variable in class org.ecocean.Shepherd
 
locale - Variable in class org.ecocean.grid.GridNode
 
localHaplotypeReflection - Variable in class org.ecocean.MarkedIndividual
 
location - Variable in class org.ecocean.tag.MetalTag
 
location - Variable in class org.ecocean.Util.MetalTagDesc
 
locationID - Variable in class org.ecocean.Encounter
 
locationLabel - Variable in class org.ecocean.Util.MetalTagDesc
 
loci - Variable in class org.ecocean.genetics.MicrosatelliteMarkersAnalysis
 
Locus - Class in org.ecocean.genetics
 
Locus() - Constructor for class org.ecocean.genetics.Locus
 
Locus(String, Integer, Integer) - Constructor for class org.ecocean.genetics.Locus
Convenience constructor for diploid organisms.
Locus(String, ArrayList<Integer>) - Constructor for class org.ecocean.genetics.Locus
 
LogFile - Class in org.ecocean.interconnect
 
LogFile(String) - Constructor for class org.ecocean.interconnect.LogFile
 
LoginUser - Class in org.ecocean.servlet
Uses JSecurity to authenticate a user If user can be authenticated successfully forwards user to /secure/index.jsp If user cannot be authenticated then forwards user to the /login.jsp which will display an error message
LoginUser() - Constructor for class org.ecocean.servlet.LoginUser
 
logMbreakdown - Variable in class org.ecocean.grid.MatchObject
 
LogoutUser - Class in org.ecocean.servlet
Use JSecurity to logout the current user
LogoutUser() - Constructor for class org.ecocean.servlet.LogoutUser
 
logPerimeter - Variable in class org.ecocean.grid.SpotTriangle
 

M

m - Variable in class com.reijns.I3S.LinSys
 
m1 - Variable in class com.reijns.I3S.Pair
 
m2 - Variable in class com.reijns.I3S.Pair
 
mailerObject - Variable in class org.ecocean.NotificationMailer
 
mailList - Variable in class org.ecocean.servlet.AdoptionAction
 
MailThreadExecutorService - Class in org.ecocean
 
MailThreadExecutorService() - Constructor for class org.ecocean.MailThreadExecutorService
 
main(String[]) - Static method in class org.ecocean.grid.WorkApplet3
 
main(String[]) - Static method in class org.ecocean.grid.WorkAppletHeadless
 
main(String[]) - Static method in class org.ecocean.interconnect.Interconnect
 
makeNewPassportXml(String) - Method in class org.ecocean.PatterningPassport
 
map - Variable in class org.ecocean.grid.I3SMatchObject
 
MarkedIndividual - Class in org.ecocean
A MarkedIndividual object stores the complete encounter data for a single marked individual in a mark-recapture study.
MarkedIndividual(String, Encounter) - Constructor for class org.ecocean.MarkedIndividual
 
MarkedIndividual() - Constructor for class org.ecocean.MarkedIndividual
empty constructor used by JDO Enhancer - DO NOT USE
markedIndividual1DirectionalDescriptor - Variable in class org.ecocean.social.Relationship
 
markedIndividual2DirectionalDescriptor - Variable in class org.ecocean.social.Relationship
 
markedIndividualName1 - Variable in class org.ecocean.social.Relationship
 
markedIndividualName2 - Variable in class org.ecocean.social.Relationship
 
MarkedIndividualQueryResult - Class in org.ecocean
 
MarkedIndividualQueryResult(Vector<MarkedIndividual>, String, String) - Constructor for class org.ecocean.MarkedIndividualQueryResult
 
markedIndividualRole1 - Variable in class org.ecocean.social.Relationship
 
markedIndividualRole2 - Variable in class org.ecocean.social.Relationship
 
MassExposeGBIF - Class in org.ecocean.servlet
Exposes all approved encounters to the GBIF.
MassExposeGBIF() - Constructor for class org.ecocean.servlet.MassExposeGBIF
 
MassSetInformOthers - Class in org.ecocean.servlet
 
MassSetInformOthers() - Constructor for class org.ecocean.servlet.MassSetInformOthers
 
MassSetLocationCodeFromLocationString - Class in org.ecocean.servlet
 
MassSetLocationCodeFromLocationString() - Constructor for class org.ecocean.servlet.MassSetLocationCodeFromLocationString
 
MassSwapLocationCode - Class in org.ecocean.servlet
 
MassSwapLocationCode() - Constructor for class org.ecocean.servlet.MassSwapLocationCode
 
MatchComparator - Class in org.ecocean.grid
 
MatchComparator() - Constructor for class org.ecocean.grid.MatchComparator
 
MatchedPoints - Class in org.ecocean.grid
 
MatchedPoints() - Constructor for class org.ecocean.grid.MatchedPoints
 
matches - Static variable in class org.ecocean.Shepherd
 
MatchObject - Class in org.ecocean.grid
matchObject is a temporary object used by the shepherd class to store unordered match values tests
MatchObject() - Constructor for class org.ecocean.grid.MatchObject
 
MatchObject(String, double, double, int, ArrayList, String, String, double[], String, String, double) - Constructor for class org.ecocean.grid.MatchObject
 
MatchObject(String, double, int, String) - Constructor for class org.ecocean.grid.MatchObject
 
matchValue - Variable in class org.ecocean.grid.I3SMatchObject
 
matchValue - Variable in class org.ecocean.grid.MatchObject
 
matrix - Variable in class org.ecocean.interconnect.SharkPanel
 
MatrixToString(double[][], int, int) - Static method in class org.ecocean.genetics.distance.MyFuns
 
MatrixToString(double[][], int, int, String, String) - Static method in class org.ecocean.genetics.distance.MyFuns
 
MatrixToString(double[][], int, int, String, String, boolean) - Static method in class org.ecocean.genetics.distance.MyFuns
 
MatrixToString(int[][], int) - Static method in class org.ecocean.genetics.distance.MyFuns
 
MatrixToString(int[][], int, String, String) - Static method in class org.ecocean.genetics.distance.MyFuns
 
MatrixToString(int[][], int, String, String, boolean) - Static method in class org.ecocean.genetics.distance.MyFuns
 
Max(int[]) - Static method in class org.ecocean.genetics.distance.MyFuns
 
Max(double[]) - Static method in class org.ecocean.genetics.distance.MyFuns
 
max(double, double, double, double) - Static method in class org.ecocean.grid.Geometry
Return largest of four numbers.
MAX_SPOT_CNT - Static variable in class org.ecocean.interconnect.SharkPanel
 
maxCode - Variable in class org.ecocean.genetics.distance.HashTokenizer
 
maxGroupSize - Variable in class org.ecocean.grid.GridManager
 
maximumDepthInMeters - Variable in class org.ecocean.Encounter
 
maximumElevationInMeters - Variable in class org.ecocean.Encounter
 
maxNumWorkItems - Variable in class org.ecocean.grid.TuningTaskCreationThread
 
maxTriangleRotation - Variable in class org.ecocean.grid.GridManager
 
maxTriangleRotation - Variable in class org.ecocean.grid.ScanWorkItem
 
maxYearsBetweenResightings - Variable in class org.ecocean.MarkedIndividual
 
Measurement - Class in org.ecocean
 
Measurement() - Constructor for class org.ecocean.Measurement
 
Measurement(String, String, Double, String, String) - Constructor for class org.ecocean.Measurement
 
MEASUREMENT - Static variable in class org.ecocean.Util
 
MEASUREMENT_NAME - Static variable in class org.ecocean.servlet.EncounterSetMeasurements
 
MEASUREMENT_NAME - Static variable in class org.ecocean.servlet.TissueSampleSetMeasurement
 
measurements - Variable in class org.ecocean.Encounter
 
measurementType - Variable in class org.ecocean.genetics.BiologicalMeasurement
 
measurementUnit - Variable in class org.ecocean.Encounter
 
mediaId - Variable in class org.ecocean.PatterningPassport
 
mediaUrl - Variable in class org.ecocean.PatterningPassport
 
mess - Variable in class org.ecocean.interconnect.GetEncounterNumber
 
message - Variable in class org.ecocean.NotificationMailer
 
METAL_TAG_LOCATION - Static variable in class org.ecocean.Util
 
METAL_TAG_PARAM_START - Static variable in class org.ecocean.servlet.EncounterSetTags
 
MetalTag - Class in org.ecocean.tag
 
MetalTag(String, String) - Constructor for class org.ecocean.tag.MetalTag
 
MetalTag() - Constructor for class org.ecocean.tag.MetalTag
 
metalTags - Variable in class org.ecocean.Encounter
 
MicrosatelliteMarkersAnalysis - Class in org.ecocean.genetics
 
MicrosatelliteMarkersAnalysis() - Constructor for class org.ecocean.genetics.MicrosatelliteMarkersAnalysis
 
MicrosatelliteMarkersAnalysis(String, String, String) - Constructor for class org.ecocean.genetics.MicrosatelliteMarkersAnalysis
 
MicrosatelliteMarkersAnalysis(String, String, String, ArrayList<Locus>) - Constructor for class org.ecocean.genetics.MicrosatelliteMarkersAnalysis
 
min(double, double, double, double) - Static method in class org.ecocean.grid.Geometry
Return smallest of four numbers.
MIN_SPOT_CNT - Static variable in class org.ecocean.interconnect.SharkPanel
 
minutes - Variable in class org.ecocean.Encounter
 
MitochondrialDNAAnalysis - Class in org.ecocean.genetics
 
MitochondrialDNAAnalysis() - Constructor for class org.ecocean.genetics.MitochondrialDNAAnalysis
 
MitochondrialDNAAnalysis(String, String, String, String) - Constructor for class org.ecocean.genetics.MitochondrialDNAAnalysis
 
modified - Variable in class org.ecocean.Encounter
 
modified - Variable in class org.ecocean.Occurrence
 
month - Variable in class org.ecocean.Encounter
 
mouseClicked(MouseEvent) - Method in class org.ecocean.interconnect.SharkPanel.MouseClickListener
 
mouseClicked(MouseEvent) - Method in class org.ecocean.interconnect.ShowResults.MouseClickListener
 
mousePressed(MouseEvent) - Method in class org.ecocean.interconnect.ShowResults.MouseClickListener
 
mouseReleased(MouseEvent) - Method in class org.ecocean.interconnect.ShowResults.MouseClickListener
 
multiply(double, int) - Method in class com.reijns.I3S.LinSys
 
multiply(double, int, int) - Method in class com.reijns.I3S.LinSys
 
MuprevXfreqs - Static variable in class org.ecocean.genetics.distance.Distances
 
MuprevYfreqs - Static variable in class org.ecocean.genetics.distance.Distances
 
Mux - Static variable in class org.ecocean.genetics.distance.Distances
 
Muy - Static variable in class org.ecocean.genetics.distance.Distances
 
MyFuns - Class in org.ecocean.genetics.distance
 
MyFuns() - Constructor for class org.ecocean.genetics.distance.MyFuns
 
myShepherd - Variable in class org.ecocean.servlet.UpdateEmailAddress
 

N

n - Variable in class com.reijns.I3S.LinSys
 
name - Variable in class com.reijns.I3S.FingerPrint
 
name - Variable in class org.ecocean.genetics.Locus
 
name - Variable in class org.ecocean.tag.SatelliteTag
 
name - Variable in class org.ecocean.Util.OptionDesc
 
NbRuns - Variable in class org.ecocean.Spot
 
newEncounter - Variable in class org.ecocean.grid.ScanWorkItem
 
NewI3SMatchComparator - Class in org.ecocean.grid
 
NewI3SMatchComparator() - Constructor for class org.ecocean.grid.NewI3SMatchComparator
 
newSex - Variable in class org.ecocean.grid.I3SMatchObject
 
newSex - Variable in class org.ecocean.grid.MatchObject
 
newX - Variable in class org.ecocean.grid.VertexPointMatch
 
newY - Variable in class org.ecocean.grid.VertexPointMatch
 
nextTokenCode() - Method in class org.ecocean.genetics.distance.HashTokenizer
 
nice - Variable in class org.ecocean.grid.ScanWorkItem
 
nickName - Variable in class org.ecocean.MarkedIndividual
 
nickNamer - Variable in class org.ecocean.MarkedIndividual
 
noCache - Static variable in class org.ecocean.genetics.distance.Distances
 
NODE_NAME_ID - Static variable in class org.ecocean.PatterningPassport
 
nodeIdentifier - Variable in class org.ecocean.grid.GridNode
 
nodeIdentifiers - Variable in class org.ecocean.grid.ScanTask
 
nodeLocations - Variable in class org.ecocean.grid.ScanTask
 
nodes - Variable in class org.ecocean.grid.GridManager
 
nodeTimeout - Variable in class org.ecocean.grid.GridManager
 
nodeTimes - Variable in class org.ecocean.grid.ScanTask
 
NormalizeVectors(double[]) - Static method in class org.ecocean.genetics.distance.MyFuns
 
NormalizeVectors(double[][]) - Static method in class org.ecocean.genetics.distance.MyFuns
 
NormalizeVectors(double[][][]) - Static method in class org.ecocean.genetics.distance.MyFuns
 
normspots - Variable in class org.ecocean.interconnect.FingerPrint
 
normspots - Variable in class org.ecocean.interconnect.SharkPanel
 
notes - Variable in class org.ecocean.Adoption
 
notes - Variable in class org.ecocean.User
 
NotificationMailer - Class in org.ecocean
 
NotificationMailer(String, String, String, String, String, Vector, String) - Constructor for class org.ecocean.NotificationMailer
Constructor to create a new shepherd thread object
NR_OF_MATCHES - Static variable in class org.ecocean.interconnect.SharkPanel
 
nrpairs - Variable in class org.ecocean.interconnect.BothSharks
 
nrpairs - Variable in class org.ecocean.interconnect.ShowResults
 
nukeAllSpots() - Method in class org.ecocean.Encounter
 
nullThread() - Method in class org.ecocean.grid.AppletWorkItemThread
 
numAdded - Variable in class org.ecocean.grid.TuningTaskCreationThread
 
numAlleleCopies - Variable in class org.ecocean.genetics.distance.Ind2IndDistance
 
numAllowedNodes - Variable in class org.ecocean.grid.GridManager
 
numberEncounters - Variable in class org.ecocean.MarkedIndividual
 
numberOfAlleles() - Method in class org.ecocean.genetics.FStatistics
 
numberOfAlleles() - Method in class org.ecocean.genetics.HFStatistics
 
numberOfGenotypes() - Method in class org.ecocean.genetics.FStatistics
 
numberOfGenotypes() - Method in class org.ecocean.genetics.HFStatistics
 
numberOfPopulations() - Method in class org.ecocean.genetics.FStatistics
 
numberOfPopulations() - Method in class org.ecocean.genetics.HFStatistics
 
numCollisions - Variable in class org.ecocean.grid.GridManager
 
numCollisions - Variable in class org.ecocean.grid.ScanTask
 
numComparisons - Variable in class org.ecocean.grid.GridNode
 
numComparisons - Variable in class org.ecocean.grid.ScanTask
 
numComparisons - Variable in class org.ecocean.grid.WorkApplet3
 
numComparisons - Variable in class org.ecocean.grid.WorkAppletHeadless
 
numCompletedWorkItems - Variable in class org.ecocean.grid.GridManager
 
numFalseComparisons - Variable in class org.ecocean.grid.FalseMatchCreationThread
 
numMatches - Variable in class org.ecocean.grid.WorkApplet3
 
numMatches - Variable in class org.ecocean.grid.WorkAppletHeadless
 
numPopulations - Variable in class org.ecocean.genetics.FStatistics
 
numPopulations - Variable in class org.ecocean.genetics.HFStatistics
 
numProcessors - Variable in class org.ecocean.grid.AppletHeartbeatThread
 
numProcessors - Variable in class org.ecocean.grid.GridNode
 
numScanTasks - Variable in class org.ecocean.grid.GridManager
 
numScanWorkItems - Variable in class org.ecocean.grid.GridManager
 
numSpots - Variable in class org.ecocean.grid.ScanTask
 
numSpotsLeft - Variable in class org.ecocean.Encounter
 
numSpotsRight - Variable in class org.ecocean.Encounter
 
numTriangles - Variable in class org.ecocean.grid.MatchObject
 
numUnidentifiableEncounters - Variable in class org.ecocean.MarkedIndividual
 

O

Occurrence - Class in org.ecocean
Whereas an Encounter is meant to represent one MarkedIndividual at one point in time and space, an Occurrence is meant to represent several Encounters that occur in a natural grouping (e.g., a pod of dolphins).
Occurrence() - Constructor for class org.ecocean.Occurrence
 
Occurrence(String, Encounter) - Constructor for class org.ecocean.Occurrence
Class constructor.
OccurrenceAddComment - Class in org.ecocean.servlet
 
OccurrenceAddComment() - Constructor for class org.ecocean.servlet.OccurrenceAddComment
 
OccurrenceAddEncounter - Class in org.ecocean.servlet
 
OccurrenceAddEncounter() - Constructor for class org.ecocean.servlet.OccurrenceAddEncounter
 
OccurrenceCreate - Class in org.ecocean.servlet
 
OccurrenceCreate() - Constructor for class org.ecocean.servlet.OccurrenceCreate
 
occurrenceID - Variable in class org.ecocean.Encounter
 
occurrenceID - Variable in class org.ecocean.Occurrence
 
occurrenceRemarks - Variable in class org.ecocean.Encounter
 
OccurrenceRemoveEncounter - Class in org.ecocean.servlet
 
OccurrenceRemoveEncounter() - Constructor for class org.ecocean.servlet.OccurrenceRemoveEncounter
 
OccurrenceSetGroupBehavior - Class in org.ecocean.servlet
 
OccurrenceSetGroupBehavior() - Constructor for class org.ecocean.servlet.OccurrenceSetGroupBehavior
 
OccurrenceSetIndividualCount - Class in org.ecocean.servlet
 
OccurrenceSetIndividualCount() - Constructor for class org.ecocean.servlet.OccurrenceSetIndividualCount
 
okExposeViaTapirLink - Variable in class org.ecocean.Encounter
 
oldX - Variable in class org.ecocean.grid.VertexPointMatch
 
oldY - Variable in class org.ecocean.grid.VertexPointMatch
 
OpenFgpFile(File, Collection) - Method in class com.reijns.I3S.FgpFileOpen
Opens a file, checks to see if it is a FGP file, and if it is, loads the spots point pattern and addes it as a FingerPrint object to Collection fp.
openURL(String) - Static method in class org.ecocean.interconnect.BareBonesBrowserLaunch
 
org.ecocean - package org.ecocean
 
org.ecocean.genetics - package org.ecocean.genetics
 
org.ecocean.genetics.distance - package org.ecocean.genetics.distance
 
org.ecocean.grid - package org.ecocean.grid
 
org.ecocean.interconnect - package org.ecocean.interconnect
 
org.ecocean.security - package org.ecocean.security
 
org.ecocean.servlet - package org.ecocean.servlet
 
org.ecocean.servlet.export - package org.ecocean.servlet.export
 
org.ecocean.servlet.importer - package org.ecocean.servlet.importer
 
org.ecocean.social - package org.ecocean.social
 
org.ecocean.tag - package org.ecocean.tag
 
orig - Variable in class com.reijns.I3S.FingerPrint
 
orig - Variable in class org.ecocean.interconnect.AcceptDialog
 
orig - Variable in class org.ecocean.interconnect.BothSharks
 
orig - Variable in class org.ecocean.interconnect.SharkIdentification
 
orig - Variable in class org.ecocean.interconnect.SpotCloud
 
origdir - Variable in class org.ecocean.interconnect.SharkIdentification
 
origImg - Variable in class org.ecocean.interconnect.BothSharks
 
otherCatalogNumbers - Variable in class org.ecocean.Encounter
 
out - Variable in class org.ecocean.interconnect.CopyFile
 

P

padDecimal(String, int, int) - Static method in class org.ecocean.genetics.distance.MyFuns
 
padLeft(String, int) - Static method in class org.ecocean.genetics.distance.MyFuns
 
padRight(String, int) - Static method in class org.ecocean.genetics.distance.MyFuns
 
paint(Graphics2D, double, int, int, boolean, String, String, String) - Method in class org.ecocean.interconnect.FingerPrint
 
paintComponent(Graphics) - Method in class org.ecocean.grid.WorkApplet3.ImagePanel
 
paintComponent(Graphics) - Method in class org.ecocean.interconnect.AboutInterconnect
 
paintComponent(Graphics) - Method in class org.ecocean.interconnect.BothSharks
 
paintComponent(Graphics) - Method in class org.ecocean.interconnect.ImagePreview
 
paintComponent(Graphics) - Method in class org.ecocean.interconnect.SharkPanel
 
paintComponent(Graphics) - Method in class org.ecocean.interconnect.ShowImagePane
 
paintComponent(Graphics) - Method in class org.ecocean.interconnect.Splash
 
paintComponent(Graphics) - Method in class org.ecocean.interconnect.SpotCloud
 
paintImage(Graphics2D, Image, Point2D[], int) - Method in class org.ecocean.interconnect.BothSharks
 
paintImage(Graphics2D) - Method in class org.ecocean.interconnect.ShowImagePane
 
Pair - Class in com.reijns.I3S
test
Pair() - Constructor for class com.reijns.I3S.Pair
 
paircnt - Variable in class com.reijns.I3S.FingerPrint
 
pairs - Variable in class org.ecocean.interconnect.SpotCloud
 
participatesInTheseLocationIDs() - Method in class org.ecocean.MarkedIndividual
 
participatesInTheseVerbatimEventDates() - Method in class org.ecocean.MarkedIndividual
 
passportDataXml - Variable in class org.ecocean.PatterningPassport
 
password - Variable in class org.ecocean.User
 
patterningCode - Variable in class org.ecocean.Encounter
 
patterningCode - Variable in class org.ecocean.MarkedIndividual
 
PatterningPassport - Class in org.ecocean
 
PatterningPassport() - Constructor for class org.ecocean.PatterningPassport
 
patterningPassport - Variable in class org.ecocean.SinglePhotoVideo
 
patterningPassportXmlUrl - Variable in class org.ecocean.PatterningPassport
 
pelvic - Variable in class org.ecocean.interconnect.SharkPanel
 
phase - Variable in class org.ecocean.ImageProcessor
Current phase of the batch processor.
phoneNumber - Variable in class org.ecocean.User
 
photographerAddress - Variable in class org.ecocean.Encounter
 
photographerEmail - Variable in class org.ecocean.Encounter
 
photographerName - Variable in class org.ecocean.Encounter
 
photographerPhone - Variable in class org.ecocean.Encounter
 
photos - Variable in class org.ecocean.Keyword
 
physicalAddress - Variable in class org.ecocean.User
 
pixelMax - Variable in class org.ecocean.Spot
 
pixelMin - Variable in class org.ecocean.Spot
 
pixGrayAvg - Variable in class org.ecocean.Spot
 
pixGrayVar - Variable in class org.ecocean.Spot
 
ploidy - Variable in class org.ecocean.genetics.distance.Ind2IndDistance
 
ploidy - Static variable in class org.ecocean.genetics.distance.ShareDst
 
pm - Variable in class org.ecocean.Shepherd
 
pmfs - Static variable in class org.ecocean.ShepherdPMF
 
png - Static variable in class org.ecocean.interconnect.Utils
 
Point2D - Class in com.reijns.I3S
 
Point2D() - Constructor for class com.reijns.I3S.Point2D
Point2D Constructor

Comments: Second constructor method added.

Point2D(double, double) - Constructor for class com.reijns.I3S.Point2D
 
Point2D(Point2D) - Constructor for class com.reijns.I3S.Point2D
 
Point2D - Class in org.ecocean.interconnect
To do: - Clicking in image convert to image coordinates instead of window coordinates - Keyboard listener for ctrl-s *
Point2D() - Constructor for class org.ecocean.interconnect.Point2D
 
Point2D(double, double) - Constructor for class org.ecocean.interconnect.Point2D
 
pointBreakdown - Variable in class org.ecocean.grid.MatchObject
 
pointDistance(FingerPrint, int, int) - Method in class com.reijns.I3S.FingerPrint
Finds the distance between a point in the local fpp[] array and that in a test FingerPrint class.
Points - Variable in class org.ecocean.grid.MatchObject
 
points - Variable in class org.ecocean.grid.VertexPointMatch
 
Pop2PopDistDa(double[][], double[][]) - Static method in class org.ecocean.genetics.distance.Distances
 
Pop2PopDistDm(double[][], double[][]) - Static method in class org.ecocean.genetics.distance.Distances
 
Pop2PopDistDmu(double[][], double[][], double[][], int[]) - Static method in class org.ecocean.genetics.distance.Distances
 
Pop2PopDistDs(double[][], double[][]) - Static method in class org.ecocean.genetics.distance.Distances
 
Pop2PopDistDsw(double[][], double[][], double[][], int[]) - Static method in class org.ecocean.genetics.distance.Distances
 
Pop2PopDistRst(double[][], double[][], double[][], int[]) - Static method in class org.ecocean.genetics.distance.Distances
 
populationFrequency(int) - Method in class org.ecocean.genetics.FStatistics
 
populationFrequency(int) - Method in class org.ecocean.genetics.HFStatistics
 
populationLabel(int) - Method in class org.ecocean.genetics.FStatistics
 
populationLabel(int) - Method in class org.ecocean.genetics.HFStatistics
 
popup - Variable in class org.ecocean.interconnect.ShowResults.MouseClickListener
 
potentialMatches - Variable in class org.ecocean.grid.WorkApplet3
 
potentialMatches - Variable in class org.ecocean.grid.WorkApplet3.runWIScan
 
potentialMatches - Variable in class org.ecocean.grid.WorkApplet3.scanAppletActionListener
 
preferredSize - Variable in class org.ecocean.interconnect.Interconnect
 
preservationMethod - Variable in class org.ecocean.genetics.TissueSample
 
preventCrossSiteScriptingAttacks(String) - Static method in class org.ecocean.servlet.ServletUtilities
 
previous - Static variable in class org.ecocean.interconnect.Interconnect.SharkMenu
 
print(Graphics2D, double, double, int, int, int) - Method in class org.ecocean.interconnect.FingerPrint
 
printComment(Graphics2D, int, int) - Method in class org.ecocean.interconnect.FingerPrint
 
printMat() - Method in class com.reijns.I3S.LinSys
 
printSoln() - Method in class com.reijns.I3S.LinSys
 
processAcousticTagFilter(HttpServletRequest, StringBuffer) - Static method in class org.ecocean.EncounterQueryProcessor
 
processAcousticTagFilter(HttpServletRequest, StringBuffer) - Static method in class org.ecocean.IndividualQueryProcessor
 
processAlleles() - Method in class org.ecocean.genetics.FStatistics
 
processAlleles() - Method in class org.ecocean.genetics.HFStatistics
 
processFile(File, Collection) - Method in class com.reijns.I3S.FgpFileOpen
Checks the path provided for FGP files.
processHeartbeat(HttpServletRequest) - Method in class org.ecocean.grid.GridManager
 
processingLabContactDetails - Variable in class org.ecocean.genetics.GeneticAnalysis
 
processingLabContactName - Variable in class org.ecocean.genetics.GeneticAnalysis
 
processingLabName - Variable in class org.ecocean.genetics.GeneticAnalysis
 
processingLabTaskID - Variable in class org.ecocean.genetics.GeneticAnalysis
 
processLeftReferenceSpots(ArrayList<SuperSpot>) - Method in class org.ecocean.grid.EncounterLite
 
processLeftSpots(ArrayList<SuperSpot>) - Method in class org.ecocean.grid.EncounterLite
 
processPopulations() - Method in class org.ecocean.genetics.FStatistics
 
processPopulations() - Method in class org.ecocean.genetics.HFStatistics
 
processQuery(Shepherd, HttpServletRequest, String) - Static method in class org.ecocean.EncounterQueryProcessor
 
processQuery(Shepherd, HttpServletRequest, String) - Static method in class org.ecocean.IndividualQueryProcessor
 
processRightReferenceSpots(ArrayList<SuperSpot>) - Method in class org.ecocean.grid.EncounterLite
 
processRightSpots(ArrayList<SuperSpot>) - Method in class org.ecocean.grid.EncounterLite
 
processSatelliteTagFilter(HttpServletRequest, StringBuffer) - Static method in class org.ecocean.EncounterQueryProcessor
 
processSatelliteTagFilter(HttpServletRequest, StringBuffer) - Static method in class org.ecocean.IndividualQueryProcessor
 
processTagFilters(HttpServletRequest, StringBuffer) - Static method in class org.ecocean.EncounterQueryProcessor
 
propertyChange(PropertyChangeEvent) - Method in class org.ecocean.interconnect.ImagePreview
 
props - Static variable in class org.ecocean.ContextConfiguration
 
props - Variable in class org.ecocean.grid.ScanWorkItem
 
props - Variable in class org.ecocean.NotificationMailer
 
props2 - Variable in class org.ecocean.grid.FalseMatchCreationThread
 
props2 - Variable in class org.ecocean.grid.ScanWorkItemCreationThread
 
props2 - Variable in class org.ecocean.grid.TuningTaskCreationThread
 
propsSize - Static variable in class org.ecocean.ContextConfiguration
 

Q

queryPrettyPrint - Variable in class org.ecocean.EncounterQueryResult
 
queryPrettyPrint - Variable in class org.ecocean.MarkedIndividualQueryResult
 
queryStringBuilder(HttpServletRequest, StringBuffer, Map<String, Object>) - Static method in class org.ecocean.EncounterQueryProcessor
 
queryStringBuilder(HttpServletRequest, StringBuffer, Map<String, Object>) - Static method in class org.ecocean.IndividualQueryProcessor
 
QuickSort(int[], int, int) - Static method in class org.ecocean.genetics.distance.MyFuns
19 Feb 1996: Fixed to avoid infinite loop discoved by Paul Haberli.
QuickSort(int[]) - Static method in class org.ecocean.genetics.distance.MyFuns
 
QuickSort(double[], int, int) - Static method in class org.ecocean.genetics.distance.MyFuns
 
QuickSort(double[]) - Static method in class org.ecocean.genetics.distance.MyFuns
 
quote(String) - Static method in class org.ecocean.Util
 

R

R - Variable in class org.ecocean.grid.GridManager
 
R - Variable in class org.ecocean.grid.ScanWorkItem
 
R - Variable in class org.ecocean.grid.SpotTriangle
 
r2 - Variable in class org.ecocean.grid.SpotTriangle
 
r3 - Variable in class org.ecocean.grid.SpotTriangle
 
ran - Variable in class org.ecocean.servlet.AdoptionAction
 
ratioLong2Short - Variable in class org.ecocean.grid.SpotTriangle
 
RComparator - Class in org.ecocean.grid
 
RComparator() - Constructor for class org.ecocean.grid.RComparator
 
read(String, Collection) - Method in class com.reijns.I3S.FgpFileOpen
Public method to read in all the available FGP files in the supplied PathName.
read(String, StringBuffer) - Method in class org.ecocean.interconnect.FingerPrint
 
readableName - Variable in class org.ecocean.Keyword
 
readFile(StringBuffer) - Method in class org.ecocean.interconnect.CopyFile
 
readFingerprint(StringBuffer) - Method in class org.ecocean.interconnect.SharkPanel
 
readInSystem() - Method in class com.reijns.I3S.LinSys
 
realcnt - Variable in class com.reijns.I3S.Compare
 
recalcJ(double[][], double[][]) - Static method in class org.ecocean.genetics.distance.Distances
 
recalcMu(double[][], double[][], double[][]) - Static method in class org.ecocean.genetics.distance.Distances
 
recalcW(double[][], double[][], double[][], int[]) - Static method in class org.ecocean.genetics.distance.Distances
 
receiveEmails - Variable in class org.ecocean.User
 
receiveObject(ObjectInputStream) - Static method in class org.ecocean.servlet.ScanResultsServlet
 
receiveObject(ObjectInputStream) - Static method in class org.ecocean.servlet.ScanWorkItemResultsHandler
 
recordedBy - Variable in class org.ecocean.Encounter
 
reduceString(String) - Method in class org.ecocean.interconnect.AcceptDialog
 
refPoint1 - Variable in class org.ecocean.interconnect.FingerPrint
 
refPoint2 - Variable in class org.ecocean.interconnect.FingerPrint
 
refPoint3 - Variable in class org.ecocean.interconnect.FingerPrint
 
refPointsOk() - Method in class org.ecocean.interconnect.FingerPrint
 
refresh() - Static method in class org.ecocean.ContextConfiguration
 
refreshAssetFormats(String, String) - Method in class org.ecocean.Encounter
 
refreshAssetFormats(String, String, SinglePhotoVideo, boolean) - Method in class org.ecocean.Encounter
 
RefreshDate() - Method in class org.ecocean.User
 
registerHeartbeat() - Method in class org.ecocean.grid.GridNode
 
relatedComments - Variable in class org.ecocean.social.Relationship
 
relatedSocialUnitName - Variable in class org.ecocean.social.Relationship
 
Relationship - Class in org.ecocean.social
Representing a dyadic social relationship
Relationship() - Constructor for class org.ecocean.social.Relationship
 
Relationship(String, String, String, String, String, String) - Constructor for class org.ecocean.social.Relationship
 
Relationship(String, String, String, String, String) - Constructor for class org.ecocean.social.Relationship
 
Relationship(String, String, String) - Constructor for class org.ecocean.social.Relationship
 
RelationshipCreate - Class in org.ecocean.servlet
 
RelationshipCreate() - Constructor for class org.ecocean.servlet.RelationshipCreate
 
RelationshipDelete - Class in org.ecocean.servlet
 
RelationshipDelete() - Constructor for class org.ecocean.servlet.RelationshipDelete
 
releaseDate - Variable in class org.ecocean.Encounter
 
releaseDateLong - Variable in class org.ecocean.Encounter
 
removeAllCompletedWorkItems() - Method in class org.ecocean.grid.GridManager
 
removeAllWorkItems() - Method in class org.ecocean.grid.GridManager
 
removeCompletedWorkItemsForTask(String) - Method in class org.ecocean.grid.GridManager
 
removeDataFile(String) - Method in class org.ecocean.MarkedIndividual
Removes a satellite tag data file for this MarkedIndividual.
removeDynamicProperty(String) - Method in class org.ecocean.Encounter
 
removeDynamicProperty(String) - Method in class org.ecocean.MarkedIndividual
 
RemoveEmailAddress - Class in org.ecocean.servlet
 
RemoveEmailAddress() - Constructor for class org.ecocean.servlet.RemoveEmailAddress
 
removeEncounter(Encounter) - Method in class org.ecocean.MarkedIndividual
Removes an encounter from this MarkedIndividual.
removeEncounter(Encounter) - Method in class org.ecocean.Occurrence
 
removeGeneticAnalysis(GeneticAnalysis) - Method in class org.ecocean.genetics.TissueSample
 
removeGeneticAnalysis(int) - Method in class org.ecocean.genetics.TissueSample
 
removeInterestedResearcher(String) - Method in class org.ecocean.Encounter
 
removeInterestedResearcher(String) - Method in class org.ecocean.MarkedIndividual
 
removeKeyword(int) - Method in class org.ecocean.SinglePhotoVideo
 
removeKeyword(Keyword) - Method in class org.ecocean.SinglePhotoVideo
 
removeLocus(Locus) - Method in class org.ecocean.genetics.MicrosatelliteMarkersAnalysis
 
removeLocus(int) - Method in class org.ecocean.genetics.MicrosatelliteMarkersAnalysis
 
removeLogEncounter(Encounter) - Method in class org.ecocean.MarkedIndividual
 
removeMeasurement(int) - Method in class org.ecocean.Encounter
 
removeMeasurement(Measurement) - Method in class org.ecocean.Encounter
 
removeMetalTag(MetalTag) - Method in class org.ecocean.Encounter
 
removeNearest(double, double) - Method in class org.ecocean.interconnect.FingerPrint
 
removeNearestClick(double, double) - Method in class org.ecocean.interconnect.SharkPanel
 
removeRightSpots() - Method in class org.ecocean.Encounter
 
removeSinglePhotoVideo(int) - Method in class org.ecocean.Encounter
 
removeSinglePhotoVideo(SinglePhotoVideo) - Method in class org.ecocean.Encounter
 
removeSpots() - Method in class org.ecocean.Encounter
Removes any spot data
removeTissueSample(int) - Method in class org.ecocean.Encounter
 
removeTissueSample(TissueSample) - Method in class org.ecocean.Encounter
 
removeWorkItem(String) - Method in class org.ecocean.grid.GridManager
 
removeWorkItemsForTask(String) - Method in class org.ecocean.grid.GridManager
 
reportCollision() - Method in class org.ecocean.grid.GridManager
 
reportCollision() - Method in class org.ecocean.grid.ScanTask
 
researcherComments - Variable in class org.ecocean.Encounter
 
reset() - Method in class com.reijns.I3S.Compare
 
reset() - Method in class org.ecocean.interconnect.FingerPrint
 
reset() - Method in class org.ecocean.interconnect.Point2D
 
resetAbstractClassParameters(HttpServletRequest) - Method in class org.ecocean.DataCollectionEvent
 
resetDateInMilliseconds() - Method in class org.ecocean.Encounter
 
resetMaxNumYearsBetweenSightings() - Method in class org.ecocean.MarkedIndividual
 
resetScore() - Method in class com.reijns.I3S.FingerPrint
 
result - Variable in class org.ecocean.EncounterQueryResult
 
result - Variable in class org.ecocean.grid.ScanWorkItem
 
result - Variable in class org.ecocean.grid.ScanWorkItemResult
 
result - Variable in class org.ecocean.MarkedIndividualQueryResult
 
results - Variable in class org.ecocean.grid.AppletWorkItemThread
 
results - Variable in class org.ecocean.interconnect.SharkPanel
 
ResurrectDeletedAdoption - Class in org.ecocean.servlet
 
ResurrectDeletedAdoption() - Constructor for class org.ecocean.servlet.ResurrectDeletedAdoption
 
ResurrectDeletedEncounter - Class in org.ecocean.servlet
 
ResurrectDeletedEncounter() - Constructor for class org.ecocean.servlet.ResurrectDeletedEncounter
 
returnEncountersWithGPSData() - Method in class org.ecocean.MarkedIndividual
 
returnEncountersWithGPSData(boolean, boolean, String) - Method in class org.ecocean.MarkedIndividual
 
returnEncountersWithGPSData(boolean, boolean, String) - Method in class org.ecocean.Occurrence
 
reverse - Variable in class org.ecocean.EncounterDateComparator
If reverse is true, encounters will be sorted with earliest to most recent.
rightReferenceSpots - Variable in class org.ecocean.Encounter
 
rightReferenceSpotsX - Variable in class org.ecocean.grid.EncounterLite
 
rightReferenceSpotsY - Variable in class org.ecocean.grid.EncounterLite
 
rightScan - Variable in class org.ecocean.grid.ScanWorkItem
 
rightSide - Variable in class org.ecocean.grid.FalseMatchCreationThread
 
rightSide - Variable in class org.ecocean.grid.ScanWorkItemCreationThread
 
rightSide - Variable in class org.ecocean.grid.TuningTaskCreationThread
 
rightSpotImageFileName - Variable in class org.ecocean.Encounter
 
rightSpots - Variable in class org.ecocean.Encounter
 
rightSpotsX - Variable in class org.ecocean.grid.EncounterLite
 
rightSpotsY - Variable in class org.ecocean.grid.EncounterLite
 
Role - Class in org.ecocean
User stores information about a contact/user.
Role() - Constructor for class org.ecocean.Role
 
Role(String, String) - Constructor for class org.ecocean.Role
 
rolename - Variable in class org.ecocean.Role
 
rollbackDBTransaction() - Method in class org.ecocean.Shepherd
Undoes any changes made to an open database.
rootURL - Variable in class org.ecocean.grid.AppletHeartbeatThread
 
run() - Method in class org.ecocean.grid.AppletHeartbeatThread
main method of the heartbeat thread
run() - Method in class org.ecocean.grid.AppletSwingWorker
Runs this task.
run() - Method in class org.ecocean.grid.AppletWorkItemThread
 
run() - Method in class org.ecocean.grid.FalseMatchCreationThread
main method of the shepherd thread
run() - Method in class org.ecocean.grid.GridCleanupThread
main method of the shepherd thread
run() - Method in class org.ecocean.grid.ScanTaskCleanupThread
main method of the shepherd thread
run() - Method in class org.ecocean.grid.ScanWorkItem
 
run() - Method in class org.ecocean.grid.ScanWorkItemCreationThread
main method of the shepherd thread
run() - Method in class org.ecocean.grid.TuningTaskCreationThread
main method of the shepherd thread
run() - Method in class org.ecocean.grid.WorkApplet3.runWIScan
 
run() - Method in class org.ecocean.ImageProcessor
 
run() - Method in class org.ecocean.NotificationMailer
main method of the shepherd thread

S

s - Variable in class org.ecocean.interconnect.GetImageFile
 
s1 - Variable in class org.ecocean.interconnect.BothSharks
 
s1 - Variable in class org.ecocean.interconnect.SpotCloud
 
S2 - Variable in class org.ecocean.grid.SpotTriangle
 
s2 - Variable in class org.ecocean.interconnect.BothSharks
 
s2 - Variable in class org.ecocean.interconnect.SpotCloud
 
s_alleleFrequenciesPerPopulation - Variable in class org.ecocean.genetics.FStatistics
 
s_alleleFrequenciesPerPopulation - Variable in class org.ecocean.genetics.HFStatistics
 
s_alleleFrequenciesTotal - Variable in class org.ecocean.genetics.FStatistics
 
s_alleleFrequenciesTotal - Variable in class org.ecocean.genetics.HFStatistics
 
s_alleleValueMapping - Variable in class org.ecocean.genetics.FStatistics
 
s_alleleValueMapping - Variable in class org.ecocean.genetics.HFStatistics
 
s_clear() - Method in class org.ecocean.genetics.FStatistics
 
s_clear() - Method in class org.ecocean.genetics.HFStatistics
 
s_compute() - Method in class org.ecocean.genetics.FStatistics
 
s_compute() - Method in class org.ecocean.genetics.HFStatistics
 
s_flag - Variable in class org.ecocean.genetics.FStatistics
 
s_flag - Variable in class org.ecocean.genetics.HFStatistics
 
s_genotypeFrequenciesPerPopulation - Variable in class org.ecocean.genetics.FStatistics
 
s_genotypeFrequenciesTotal - Variable in class org.ecocean.genetics.FStatistics
 
s_init() - Method in class org.ecocean.genetics.FStatistics
 
s_init() - Method in class org.ecocean.genetics.HFStatistics
 
s_numberOfAlleles - Variable in class org.ecocean.genetics.FStatistics
 
s_numberOfAlleles - Variable in class org.ecocean.genetics.HFStatistics
 
s_numberOfPopulations - Variable in class org.ecocean.genetics.FStatistics
 
s_numberOfPopulations - Variable in class org.ecocean.genetics.HFStatistics
 
s_populationFrequencies - Variable in class org.ecocean.genetics.FStatistics
 
s_populationFrequencies - Variable in class org.ecocean.genetics.HFStatistics
 
s_populationLabelMapping - Variable in class org.ecocean.genetics.FStatistics
 
s_populationLabelMapping - Variable in class org.ecocean.genetics.HFStatistics
 
SAD - Static variable in class org.ecocean.genetics.distance.Ind2IndDistance
 
salt - Variable in class org.ecocean.User
 
sameSide(double, double, double, double, double, double, double, double) - Static method in class org.ecocean.grid.Geometry
Check if two points are on the same side of a given line.
sameSide(int, int, int, int, int, int, int, int) - Static method in class org.ecocean.grid.Geometry
Check if two points are on the same side of a given line.
sampleID - Variable in class org.ecocean.genetics.GeneticAnalysis
 
sampleID - Variable in class org.ecocean.genetics.TissueSample
 
samplingEffort - Variable in class org.ecocean.DataCollectionEvent
 
samplingProtocol - Variable in class org.ecocean.DataCollectionEvent
 
samplingProtocol - Variable in class org.ecocean.genetics.BiologicalMeasurement
 
samplingProtocol - Variable in class org.ecocean.servlet.EncounterSetMeasurements.RequestEventValues
 
SATELLITE_TAG_ARGOS_PTT_NUMBER - Static variable in class org.ecocean.servlet.EncounterSetTags
 
SATELLITE_TAG_NAME - Static variable in class org.ecocean.servlet.EncounterSetTags
 
SATELLITE_TAG_NAME - Static variable in class org.ecocean.Util
 
SATELLITE_TAG_SERIAL - Static variable in class org.ecocean.servlet.EncounterSetTags
 
satelliteTag - Variable in class org.ecocean.Encounter
 
SatelliteTag - Class in org.ecocean.tag
 
SatelliteTag() - Constructor for class org.ecocean.tag.SatelliteTag
 
SatelliteTag(String, String, String) - Constructor for class org.ecocean.tag.SatelliteTag
 
saveResultsPrompt() - Static method in class org.ecocean.interconnect.Interconnect
 
scale() - Method in class org.ecocean.interconnect.BothSharks
 
scale() - Method in class org.ecocean.interconnect.SpotCloud
 
scaleTo(String, int, int, String) - Method in class org.ecocean.SinglePhotoVideo
 
scaleToWatermark(String, int, int, String, String) - Method in class org.ecocean.SinglePhotoVideo
 
ScanAppletSupport - Class in org.ecocean.servlet
 
ScanAppletSupport() - Constructor for class org.ecocean.servlet.ScanAppletSupport
 
ScanResultsServlet - Class in org.ecocean.servlet
 
ScanResultsServlet() - Constructor for class org.ecocean.servlet.ScanResultsServlet
 
ScanTask - Class in org.ecocean.grid
A scanTask is...
ScanTask() - Constructor for class org.ecocean.grid.ScanTask
empty constructor required by JDO Enhancer.
ScanTask(Shepherd, String, Properties, String, boolean) - Constructor for class org.ecocean.grid.ScanTask
Use this constructor for new Groth scanTasks.
ScanTaskCleanupThread - Class in org.ecocean.grid
 
ScanTaskCleanupThread(String) - Constructor for class org.ecocean.grid.ScanTaskCleanupThread
Constructor to create a new thread object test
ScanTaskHandler - Class in org.ecocean.servlet
 
ScanTaskHandler() - Constructor for class org.ecocean.servlet.ScanTaskHandler
 
scanTaskLimit - Variable in class org.ecocean.grid.GridManager
 
ScanWorkItem - Class in org.ecocean.grid
A class description...
ScanWorkItem() - Constructor for class org.ecocean.grid.ScanWorkItem
empty constructor required by JDO Enhancer.
ScanWorkItem(Encounter, Encounter, String, String, Properties) - Constructor for class org.ecocean.grid.ScanWorkItem
 
ScanWorkItemCreationThread - Class in org.ecocean.grid
 
ScanWorkItemCreationThread(String, boolean, String, boolean, String) - Constructor for class org.ecocean.grid.ScanWorkItemCreationThread
Constructor to create a new thread object
ScanWorkItemResult - Class in org.ecocean.grid
An encounter object stores the complete data for a single sighting.
ScanWorkItemResult() - Constructor for class org.ecocean.grid.ScanWorkItemResult
empty constructor required by JDO Enhancer.
ScanWorkItemResult(String, String, MatchObject) - Constructor for class org.ecocean.grid.ScanWorkItemResult
 
ScanWorkItemResultsHandler - Class in org.ecocean.servlet
 
ScanWorkItemResultsHandler() - Constructor for class org.ecocean.servlet.ScanWorkItemResultsHandler
 
score - Variable in class com.reijns.I3S.FingerPrint
 
score - Variable in class org.ecocean.interconnect.BothSharks
 
score - Variable in class org.ecocean.interconnect.SpotCloud
 
ScoreComparator - Class in org.ecocean.grid
 
ScoreComparator() - Constructor for class org.ecocean.grid.ScoreComparator
 
scores - Variable in class org.ecocean.grid.MatchObject
 
scores - Variable in class org.ecocean.interconnect.ShowResults
 
secondAllele(int) - Method in class org.ecocean.genetics.FStatistics
 
secondGrothPass(SuperSpot[], SuperSpot[], double, double, double, double, double) - Method in class org.ecocean.grid.EncounterLite
 
secondRun - Variable in class org.ecocean.grid.GridManager
 
secondRun - Variable in class org.ecocean.grid.ScanWorkItem
 
securityEnabled(String) - Static method in class org.ecocean.security.Collaboration
 
SELECT_FROM_ORG_ECOCEAN_ENCOUNTER_WHERE - Static variable in class org.ecocean.EncounterQueryProcessor
 
SELECT_FROM_ORG_ECOCEAN_INDIVIDUAL_WHERE - Static variable in class org.ecocean.IndividualQueryProcessor
 
selectImage() - Static method in class org.ecocean.interconnect.Interconnect
 
send2library(StringBuffer, String) - Method in class org.ecocean.interconnect.SharkPanel
 
sendEmailNotifications(String) - Static method in class org.ecocean.CommonConfiguration
 
sendHeartbeat(String) - Method in class org.ecocean.grid.AppletHeartbeatThread
 
sendIt(String, String, String, String, String, Vector) - Method in class org.ecocean.NotificationMailer
 
sendObject(ObjectOutputStream, Object) - Method in class org.ecocean.grid.WorkApplet3
 
sendObject(ObjectOutputStream, Object) - Method in class org.ecocean.grid.WorkAppletHeadless
 
sendObject(HttpServletResponse, Object) - Method in class org.ecocean.servlet.ScanAppletSupport
 
serialNumber - Variable in class org.ecocean.tag.AcousticTag
 
serialNumber - Variable in class org.ecocean.tag.SatelliteTag
 
serialVersionUID - Static variable in class com.reijns.I3S.Pair
 
serialVersionUID - Static variable in class com.reijns.I3S.Point2D
 
serialVersionUID - Static variable in class org.ecocean.Adoption
 
serialVersionUID - Static variable in class org.ecocean.DataCollectionEvent
 
serialVersionUID - Static variable in class org.ecocean.Encounter
 
serialVersionUID - Static variable in class org.ecocean.genetics.BiologicalMeasurement
 
serialVersionUID - Static variable in class org.ecocean.genetics.GeneticAnalysis
 
serialVersionUID - Static variable in class org.ecocean.genetics.Locus
 
serialVersionUID - Static variable in class org.ecocean.genetics.MicrosatelliteMarkersAnalysis
 
serialVersionUID - Static variable in class org.ecocean.genetics.MitochondrialDNAAnalysis
 
serialVersionUID - Static variable in class org.ecocean.genetics.SexAnalysis
 
serialVersionUID - Static variable in class org.ecocean.genetics.TissueSample
 
serialVersionUID - Static variable in class org.ecocean.grid.EncounterLite
 
serialVersionUID - Static variable in class org.ecocean.grid.I3SMatchObject
 
serialVersionUID - Static variable in class org.ecocean.grid.MatchObject
 
serialVersionUID - Static variable in class org.ecocean.grid.ScanTask
 
serialVersionUID - Static variable in class org.ecocean.grid.ScanWorkItem
 
serialVersionUID - Static variable in class org.ecocean.grid.ScanWorkItemResult
 
serialVersionUID - Static variable in class org.ecocean.grid.SpotTriangle
 
serialVersionUID - Static variable in class org.ecocean.grid.VertexPointMatch
 
serialVersionUID - Static variable in class org.ecocean.Measurement
 
serialVersionUID - Static variable in class org.ecocean.Occurrence
 
serialVersionUID - Static variable in class org.ecocean.PatterningPassport
 
serialVersionUID - Static variable in class org.ecocean.Role
 
serialVersionUID - Static variable in class org.ecocean.security.Collaboration
 
serialVersionUID - Static variable in class org.ecocean.servlet.LoginUser
 
serialVersionUID - Static variable in class org.ecocean.servlet.LogoutUser
 
serialVersionUID - Static variable in class org.ecocean.SinglePhotoVideo
 
serialVersionUID - Static variable in class org.ecocean.social.Relationship
 
serialVersionUID - Static variable in class org.ecocean.social.SocialUnit
 
serialVersionUID - Static variable in class org.ecocean.Spot
 
serialVersionUID - Static variable in class org.ecocean.Story
 
serialVersionUID - Static variable in class org.ecocean.SuperSpot
 
serialVersionUID - Static variable in class org.ecocean.User
 
seriesCode - Variable in class org.ecocean.MarkedIndividual
 
servletContext - Variable in class org.ecocean.ImageProcessor
ServletContext for web application, to allow access to resources.
ServletUtilities - Class in org.ecocean.servlet
 
ServletUtilities() - Constructor for class org.ecocean.servlet.ServletUtilities
 
session - Variable in class org.ecocean.NotificationMailer
 
setAcceptedUserAgreement(boolean) - Method in class org.ecocean.User
 
setAcousticTag(AcousticTag) - Method in class org.ecocean.Encounter
 
setAdopterAddress(String) - Method in class org.ecocean.Adoption
 
setAdopterEmail(String) - Method in class org.ecocean.Adoption
 
setAdopterImage(String) - Method in class org.ecocean.Adoption
 
setAdopterName(String) - Method in class org.ecocean.Adoption
 
setAdopterQuote(String) - Method in class org.ecocean.Adoption
 
setAdoptionEndDate(String) - Method in class org.ecocean.Adoption
 
setAdoptionManager(String) - Method in class org.ecocean.Adoption
 
setAdoptionStartDate(String) - Method in class org.ecocean.Adoption
 
setAdoptionType(String) - Method in class org.ecocean.Adoption
 
setAffiliation(String) - Method in class org.ecocean.User
 
setAlleleLengths(int[][]) - Method in class org.ecocean.genetics.distance.Ind2IndDistance
 
setAlternateID(String) - Method in class org.ecocean.Encounter
 
setAlternateID(String) - Method in class org.ecocean.MarkedIndividual
 
setAlternateSampleID(String) - Method in class org.ecocean.genetics.TissueSample
 
setAnalysisType(String) - Method in class org.ecocean.genetics.GeneticAnalysis
 
setArgosPttNumber(String) - Method in class org.ecocean.tag.SatelliteTag
 
setBehavior(String) - Method in class org.ecocean.Encounter
 
setBidirectional(Boolean) - Method in class org.ecocean.social.Relationship
 
setCatalogNumber(String) - Method in class org.ecocean.Encounter
 
setCentroidX(double) - Method in class org.ecocean.SuperSpot
 
setCentroidY(double) - Method in class org.ecocean.SuperSpot
 
setCheckoutTimeout(long) - Method in class org.ecocean.grid.GridManager
 
setCollectionCode(String) - Method in class org.ecocean.DataCollectionEvent
 
setCollectionID(String) - Method in class org.ecocean.DataCollectionEvent
 
setComments(String) - Method in class org.ecocean.Encounter
Sets the initially submitted comments about markings and additional details on the shark.
setContext(String) - Method in class org.ecocean.Role
 
setCopyrightOwner(String) - Method in class org.ecocean.SinglePhotoVideo
 
setCopyrightStatement(String) - Method in class org.ecocean.SinglePhotoVideo
 
setCorrespondingEncounterNumber(String) - Method in class org.ecocean.DataCollectionEvent
 
setCorrespondingEncounterNumber(String) - Method in class org.ecocean.Story
 
setCorrespondingMarkedIndividualID(String) - Method in class org.ecocean.Story
 
setCorrespondingOccurrenceID(String) - Method in class org.ecocean.Story
 
setCorrespondingSocialUnitName(String) - Method in class org.ecocean.Story
 
setCorrespondingStoryID(String) - Method in class org.ecocean.SinglePhotoVideo
 
setCorrespondingThumbnailSinglePhotoVideo(SinglePhotoVideo) - Method in class org.ecocean.Story
 
setCorrespondingUsername(String) - Method in class org.ecocean.SinglePhotoVideo
 
setCountry(String) - Method in class org.ecocean.Encounter
 
setDataCollectionEventID(String) - Method in class org.ecocean.DataCollectionEvent
 
setDatasetID(String) - Method in class org.ecocean.DataCollectionEvent
 
setDatasetName(String) - Method in class org.ecocean.DataCollectionEvent
 
setDateLastModified(Encounter) - Method in class org.ecocean.servlet.EncounterAddComment
 
setDateLastModified(Encounter) - Method in class org.ecocean.servlet.EncounterApprove
 
setDateLastModified(Encounter) - Method in class org.ecocean.servlet.EncounterDelete
 
setDateLastModified(Encounter) - Method in class org.ecocean.servlet.EncounterRemoveSpots
 
setDateLastModified(Encounter) - Method in class org.ecocean.servlet.EncounterResetDate
 
setDateLastModified(Encounter) - Method in class org.ecocean.servlet.EncounterSetAsUnidentifiable
 
setDateLastModified(Encounter) - Method in class org.ecocean.servlet.EncounterSetBehavior
 
setDateLastModified(Encounter) - Method in class org.ecocean.servlet.EncounterSetDynamicProperty
 
setDateLastModified(Encounter) - Method in class org.ecocean.servlet.EncounterSetGPS
 
setDateLastModified(Encounter) - Method in class org.ecocean.servlet.EncounterSetIdentifiable
 
setDateLastModified(Encounter) - Method in class org.ecocean.servlet.EncounterSetLocation
 
setDateLastModified(Encounter) - Method in class org.ecocean.servlet.EncounterSetLocationID
 
setDateLastModified(Encounter) - Method in class org.ecocean.servlet.EncounterSetMaximumDepth
 
setDateLastModified(Encounter) - Method in class org.ecocean.servlet.EncounterSetMaximumElevation
 
setDateLastModified(Encounter) - Method in class org.ecocean.servlet.EncounterSetOccurrenceRemarks
 
setDateLastModified(Encounter) - Method in class org.ecocean.servlet.EncounterSetScarring
 
setDateLastModified(Encounter) - Method in class org.ecocean.servlet.EncounterSetSex
 
setDateLastModified(Encounter) - Method in class org.ecocean.servlet.EncounterSetSize
 
setDateLastModified(Encounter) - Method in class org.ecocean.servlet.EncounterSetState
 
setDateLastModified(Encounter) - Method in class org.ecocean.servlet.EncounterSetSubmitterPhotographerContactInfo
 
setDateLastModified(Encounter) - Method in class org.ecocean.servlet.IndividualAddEncounter
 
setDateLastModified(Encounter) - Method in class org.ecocean.servlet.IndividualCreate
 
setDateLastModified(Encounter) - Method in class org.ecocean.servlet.IndividualRemoveEncounter
 
setDateLastModified(Occurrence) - Method in class org.ecocean.servlet.OccurrenceAddComment
 
setDateLastModified(Encounter) - Method in class org.ecocean.servlet.OccurrenceAddEncounter
 
setDateLastModified(Encounter) - Method in class org.ecocean.servlet.OccurrenceCreate
 
setDateLastModified(Encounter) - Method in class org.ecocean.servlet.OccurrenceRemoveEncounter
 
setDateLastModified(Occurrence) - Method in class org.ecocean.servlet.OccurrenceSetGroupBehavior
 
setDateLastModified(Occurrence) - Method in class org.ecocean.servlet.OccurrenceSetIndividualCount
 
setDateTimeCreated(String) - Method in class org.ecocean.MarkedIndividual
 
setDateTimeCreated(String) - Method in class org.ecocean.Occurrence
 
setDateTimeCreated(long) - Method in class org.ecocean.security.Collaboration
 
setDateTimeCreated() - Method in class org.ecocean.security.Collaboration
 
setDay(int) - Method in class org.ecocean.Encounter
 
setDecimalLatitude(Double) - Method in class org.ecocean.Encounter
 
setDecimalLongitude(Double) - Method in class org.ecocean.Encounter
 
setDeleteOnFinish(boolean) - Method in class org.ecocean.grid.ScanTask
 
setDepth(Double) - Method in class org.ecocean.Encounter
Sets the recorded depth of this encounter.
setDescription(String) - Method in class org.ecocean.interconnect.ImageFileFilter
Sets the human readable description of this filter.
setDistinguishingScar(String) - Method in class org.ecocean.Encounter
Sets the String holding scarring information for the encounter
setDone(boolean) - Method in class org.ecocean.grid.ScanWorkItem
 
setDWCDateAdded(String) - Method in class org.ecocean.Encounter
 
setDWCDateLastModified(String) - Method in class org.ecocean.Encounter
 
setDWCDateLastModified(String) - Method in class org.ecocean.Occurrence
 
setDWCDecimalLatitude(double) - Method in class org.ecocean.Encounter
 
setDWCDecimalLatitude(Double) - Method in class org.ecocean.Encounter
 
setDWCDecimalLongitude(double) - Method in class org.ecocean.Encounter
 
setDWCGlobalUniqueIdentifier(String) - Method in class org.ecocean.Encounter
 
setDWCImageURL(String) - Method in class org.ecocean.Encounter
 
setDynamicProperty(String, String) - Method in class org.ecocean.Encounter
 
setDynamicProperty(String, String) - Method in class org.ecocean.MarkedIndividual
 
setEmailAddress(String) - Method in class org.ecocean.User
 
setEncounter(String) - Method in class org.ecocean.Adoption
 
setEncounterId(String) - Method in class org.ecocean.PatterningPassport
 
setEncounterNumber(String) - Method in class org.ecocean.Encounter
Sets the unique encounter identifier to be usd with this encounter.
setEncounters(ArrayList<Encounter>) - Method in class org.ecocean.Occurrence
 
setEncounterUrl(String) - Method in class org.ecocean.PatterningPassport
 
setEndTime(long) - Method in class org.ecocean.grid.ScanTask
 
setEndTime(long) - Method in class org.ecocean.social.Relationship
 
setEventEndDate(String) - Method in class org.ecocean.DataCollectionEvent
 
setEventID(String) - Method in class org.ecocean.Encounter
 
setEventRemarks(String) - Method in class org.ecocean.DataCollectionEvent
 
setEventStartDate(String) - Method in class org.ecocean.DataCollectionEvent
 
setExecutor(Executor) - Method in class org.ecocean.grid.AppletSwingWorker
Sets executor to be used when worker is started.
setExistingEncounter(EncounterLite) - Method in class org.ecocean.grid.ScanWorkItem
 
setExtensionListInDescription(boolean) - Method in class org.ecocean.interconnect.ImageFileFilter
Determines whether the extension list (.jpg, .gif, etc) should show up in the human readable description.
setFieldNotes(String) - Method in class org.ecocean.DataCollectionEvent
 
setFieldNumber(String) - Method in class org.ecocean.DataCollectionEvent
 
setFilename(String) - Method in class org.ecocean.SinglePhotoVideo
 
setFinished(boolean) - Method in class org.ecocean.grid.AppletHeartbeatThread
 
setFinished(boolean) - Method in class org.ecocean.grid.ScanTask
 
setFullFileSystemPath(String) - Method in class org.ecocean.SinglePhotoVideo
 
setFullName(String) - Method in class org.ecocean.User
 
setGenus(String) - Method in class org.ecocean.Encounter
 
setGPSLatitude(String) - Method in class org.ecocean.Encounter
 
setGPSLongitude(String) - Method in class org.ecocean.Encounter
 
setGroupBehavior(String) - Method in class org.ecocean.Occurrence
 
setGroupSize(int) - Method in class org.ecocean.grid.GridManager
 
setGroupSize(int) - Method in class org.ecocean.grid.GridNode
 
setHaplotype(String) - Method in class org.ecocean.genetics.MitochondrialDNAAnalysis
 
setHour(int) - Method in class org.ecocean.Encounter
 
setI3SValues(Vector, double) - Method in class org.ecocean.grid.MatchObject
 
setID(String) - Method in class org.ecocean.Adoption
 
setId() - Method in class org.ecocean.security.Collaboration
 
setId(String) - Method in class org.ecocean.tag.AbstractTag
 
setIdentificationRemarks(String) - Method in class org.ecocean.Encounter
 
setIdNumber(String) - Method in class org.ecocean.tag.AcousticTag
 
setIndividual(String) - Method in class org.ecocean.Adoption
 
setIndividualCount(Integer) - Method in class org.ecocean.Occurrence
 
setIndividualID(String) - Method in class org.ecocean.Encounter
 
setIndividualID(String) - Method in class org.ecocean.MarkedIndividual
 
setInformOthers(String) - Method in class org.ecocean.Encounter
 
setInstitutionCode(String) - Method in class org.ecocean.DataCollectionEvent
 
setInstitutionID(String) - Method in class org.ecocean.DataCollectionEvent
 
setLastCheckout(long) - Method in class org.ecocean.grid.GridNode
 
setLastLogin(long) - Method in class org.ecocean.User
 
setLeftReferenceSpots(ArrayList<SuperSpot>) - Method in class org.ecocean.Encounter
 
setLifeStage(String) - Method in class org.ecocean.Encounter
 
setLivingStatus(String) - Method in class org.ecocean.Encounter
 
setLocation(String) - Method in class org.ecocean.Encounter
 
setLocation(String) - Method in class org.ecocean.tag.MetalTag
 
setLocationCode(String) - Method in class org.ecocean.Encounter
A legacy method replaced by setLocationID(...).
setLocationID(String) - Method in class org.ecocean.Encounter
 
setLoci(ArrayList<Locus>) - Method in class org.ecocean.genetics.MicrosatelliteMarkersAnalysis
 
setMarkedIndividual1DirectionalDescriptor(String) - Method in class org.ecocean.social.Relationship
 
setMarkedIndividual2DirectionalDescriptor(String) - Method in class org.ecocean.social.Relationship
 
setMarkedIndividualName1(String) - Method in class org.ecocean.social.Relationship
 
setMarkedIndividualName2(String) - Method in class org.ecocean.social.Relationship
 
setMarkedIndividualRole1(String) - Method in class org.ecocean.social.Relationship
 
setMarkedIndividualRole2(String) - Method in class org.ecocean.social.Relationship
 
setMatchedBy(String) - Method in class org.ecocean.Encounter
 
setMaxGroupSize(int) - Method in class org.ecocean.grid.GridManager
 
setMaximumDepthInMeters(Double) - Method in class org.ecocean.Encounter
 
setMaximumElevationInMeters(Double) - Method in class org.ecocean.Encounter
 
setMeasurementType(String) - Method in class org.ecocean.genetics.BiologicalMeasurement
 
setMeasureUnits(String) - Method in class org.ecocean.Encounter
Sets the units of the recorded size and depth of the shark for this encounter.
setMediaId(String) - Method in class org.ecocean.PatterningPassport
 
setMediaUrl(String) - Method in class org.ecocean.PatterningPassport
 
setMinutes(String) - Method in class org.ecocean.Encounter
 
setMonth(int) - Method in class org.ecocean.Encounter
 
setName(String) - Method in class org.ecocean.genetics.Locus
 
setName(String) - Method in class org.ecocean.MarkedIndividual
 
setName(String) - Method in class org.ecocean.tag.SatelliteTag
 
setNewEncounter(EncounterLite) - Method in class org.ecocean.grid.ScanWorkItem
 
setNice(int) - Method in class org.ecocean.grid.ScanWorkItem
 
setNickName(String) - Method in class org.ecocean.MarkedIndividual
Sets the nickname of the MarkedIndividual.
setNickNamer(String) - Method in class org.ecocean.MarkedIndividual
 
setNodeTimeout(long) - Method in class org.ecocean.grid.GridManager
 
setNotes(String) - Method in class org.ecocean.Adoption
 
setNotes(String) - Method in class org.ecocean.User
 
setNumAllowedNodes(int) - Method in class org.ecocean.grid.GridManager
 
setNumComparisons(int) - Method in class org.ecocean.grid.ScanTask
 
setNumLeftSpots(int) - Method in class org.ecocean.Encounter
 
setNumRightSpots(int) - Method in class org.ecocean.Encounter
 
setOccurrenceID(String) - Method in class org.ecocean.Encounter
 
setOccurrenceRemarks(String) - Method in class org.ecocean.Encounter
 
setOKExposeViaTapirLink(boolean) - Method in class org.ecocean.Encounter
 
setOtherCatalogNumbers(String) - Method in class org.ecocean.Encounter
 
setPairCnt(int) - Method in class com.reijns.I3S.FingerPrint
 
setPassportDataXml(String, String) - Method in class org.ecocean.PatterningPassport
 
setPassportForMediaObject(String, String, File, String) - Method in class org.ecocean.servlet.EncounterSetPatterningPassport
 
setPassword(String) - Method in class org.ecocean.User
 
setPatterningCode(String) - Method in class org.ecocean.Encounter
 
setPatterningCode(String) - Method in class org.ecocean.MarkedIndividual
Sets the patterning type evident on this MarkedIndividual instance.
setPatterningPassport(PatterningPassport) - Method in class org.ecocean.SinglePhotoVideo
 
setPatterningPassportXmlUrl(String) - Method in class org.ecocean.PatterningPassport
 
setPhoneNumber(String) - Method in class org.ecocean.User
 
setPhotographerAddress(String) - Method in class org.ecocean.Encounter
Sets the mailing address of the person who took the primaryImage this encounter.
setPhotographerEmail(String) - Method in class org.ecocean.Encounter
Sets the e-mail address of the person who took the primaryImage this encounter.
setPhotographerName(String) - Method in class org.ecocean.Encounter
Sets the name of the person who took the primaryImage this encounter.
setPhotographerPhone(String) - Method in class org.ecocean.Encounter
Sets the phone number of the person who took the primaryImage this encounter.
setPhysicalAddress(String) - Method in class org.ecocean.User
 
setPloidy(int) - Method in class org.ecocean.genetics.distance.Ind2IndDistance
 
setPreservationMethod(String) - Method in class org.ecocean.genetics.TissueSample
 
setProcessingLabContactDetails(String) - Method in class org.ecocean.genetics.GeneticAnalysis
 
setProcessingLabContactName(String) - Method in class org.ecocean.genetics.GeneticAnalysis
 
setProcessingLabName(String) - Method in class org.ecocean.genetics.GeneticAnalysis
 
setProcessingLabTaskID(String) - Method in class org.ecocean.genetics.GeneticAnalysis
 
setRange(Query, int, int, int) - Static method in class org.ecocean.servlet.ServletUtilities
 
setReadableName(String) - Method in class org.ecocean.Keyword
 
setReceiveEmails(boolean) - Method in class org.ecocean.User
 
setRecordedBy(String) - Method in class org.ecocean.Encounter
 
setRelatedComments(String) - Method in class org.ecocean.social.Relationship
 
setRelatedSocialUnitName(String) - Method in class org.ecocean.social.Relationship
 
setReleaseDate(Long) - Method in class org.ecocean.Encounter
 
setRepSize(int) - Method in class org.ecocean.genetics.distance.Ind2IndDistance
 
setResult(MatchObject) - Method in class org.ecocean.grid.ScanWorkItem
 
setRightReferenceSpots(ArrayList<SuperSpot>) - Method in class org.ecocean.Encounter
 
setRightSpotImageFileName(String) - Method in class org.ecocean.Encounter
 
setRightSpots(ArrayList<SuperSpot>) - Method in class org.ecocean.Encounter
 
setRolename(String) - Method in class org.ecocean.Role
 
setSalt(String) - Method in class org.ecocean.User
 
setSamplingEffort(String) - Method in class org.ecocean.DataCollectionEvent
 
setSamplingProtocol(String) - Method in class org.ecocean.DataCollectionEvent
 
setSamplingProtocol(String) - Method in class org.ecocean.genetics.BiologicalMeasurement
 
setSatelliteTag(SatelliteTag) - Method in class org.ecocean.Encounter
 
setScanTaskLimit(int) - Method in class org.ecocean.grid.GridManager
 
setScore(double) - Method in class com.reijns.I3S.FingerPrint
Sets the total distance score for all the points in this class compared to another FingerPrint class passed in via the distance method.
setSerialNumber(String) - Method in class org.ecocean.tag.AcousticTag
 
setSerialNumber(String) - Method in class org.ecocean.tag.SatelliteTag
 
setSeriesCode(String) - Method in class org.ecocean.MarkedIndividual
 
setSex(String) - Method in class org.ecocean.Encounter
Sets the recorded sex of the shark in this encounter.
setSex(String) - Method in class org.ecocean.genetics.SexAnalysis
 
setSex(String) - Method in class org.ecocean.MarkedIndividual
Sets the sex of this MarkedIndividual.
setSide(String) - Method in class org.ecocean.interconnect.SharkPanel
 
setSize(Double) - Method in class org.ecocean.Encounter
Sets the recorded length of the shark for this encounter.
setSizeGuess(String) - Method in class org.ecocean.Encounter
Sets the String documenting how the size of this animal was approximated.
setSocialUnitName(String) - Method in class org.ecocean.social.SocialUnit
 
setSpecificEpithet(String) - Method in class org.ecocean.Encounter
 
setSpotImageFileName(String) - Method in class org.ecocean.Encounter
 
setSpots(Point2D[], Point2D[], Point2D[]) - Method in class com.reijns.I3S.FingerPrint
 
setSpots(ArrayList<SuperSpot>) - Method in class org.ecocean.Encounter
Returns an array of all of the superSpots for this encounter.
setStarted(boolean) - Method in class org.ecocean.grid.ScanTask
 
setStartTime(long) - Method in class org.ecocean.grid.ScanWorkItem
Sets the startTime of this workItem.
setStartTime(long) - Method in class org.ecocean.social.Relationship
 
setState(String) - Method in class org.ecocean.Encounter
 
setState(String) - Method in class org.ecocean.security.Collaboration
 
setStorageLabID(String) - Method in class org.ecocean.genetics.TissueSample
 
setStoryID(String) - Method in class org.ecocean.Story
 
setStoryMediaURL(String) - Method in class org.ecocean.Story
 
setStoryTellerEmail(String) - Method in class org.ecocean.Story
 
setStoryTellerName(String) - Method in class org.ecocean.Story
 
setStoryText(String) - Method in class org.ecocean.Story
 
setSubmitter(String) - Method in class org.ecocean.grid.ScanTask
 
setSubmitterAddress(String) - Method in class org.ecocean.Encounter
Sets the mailing address of the person who submitted this encounter data.
setSubmitterEmail(String) - Method in class org.ecocean.Encounter
 
setSubmitterID(String) - Method in class org.ecocean.Encounter
 
setSubmitterName(String) - Method in class org.ecocean.Encounter
 
setSubmitterOrganization(String) - Method in class org.ecocean.Encounter
 
setSubmitterPhone(String) - Method in class org.ecocean.Encounter
Sets the phone number of the person who submitted this encounter data.
setSubmitterProject(String) - Method in class org.ecocean.Encounter
 
setTagNumber(String) - Method in class org.ecocean.tag.MetalTag
 
setTaskID(String) - Method in class org.ecocean.grid.MatchObject
 
setTimeOfBirth(long) - Method in class org.ecocean.MarkedIndividual
 
setTimeOfDeath(long) - Method in class org.ecocean.MarkedIndividual
 
setTissueType(String) - Method in class org.ecocean.genetics.TissueSample
 
setTotalWorkItemsInTask(int) - Method in class org.ecocean.grid.ScanWorkItem
 
setType(String) - Method in class org.ecocean.social.Relationship
 
setUser(String) - Method in class org.ecocean.grid.ScanTask
 
setUserID(long) - Method in class org.ecocean.User
 
setUserImage(SinglePhotoVideo) - Method in class org.ecocean.User
 
setUsername(String) - Method in class org.ecocean.Role
 
setUsername(String) - Method in class org.ecocean.User
 
setUsername1(String) - Method in class org.ecocean.security.Collaboration
 
setUsername2(String) - Method in class org.ecocean.security.Collaboration
 
setUserProject(String) - Method in class org.ecocean.User
 
setUserStatement(String) - Method in class org.ecocean.User
 
setUserURL(String) - Method in class org.ecocean.User
 
setValue(Double) - Method in class org.ecocean.genetics.BiologicalMeasurement
 
setValue(Double) - Method in class org.ecocean.Measurement
 
setVerbatimEventDate(String) - Method in class org.ecocean.Encounter
 
setVerbatimLocality(String) - Method in class org.ecocean.Encounter
 
setWebappsDir(File) - Method in class org.ecocean.PatterningPassport
 
setWorkItems(Vector) - Method in class org.ecocean.grid.ScanTask
 
setWorkItemsCompleteInTask(int) - Method in class org.ecocean.grid.ScanWorkItem
 
setWorkItemUniqueNumber(String) - Method in class org.ecocean.grid.MatchObject
 
setX(double) - Method in class com.reijns.I3S.Point2D
 
setY(double) - Method in class com.reijns.I3S.Point2D
 
setYear(int) - Method in class org.ecocean.Encounter
 
sex - Variable in class org.ecocean.Encounter
The following attributes are described in the Darwin Core quick reference at: http://rs.tdwg.org/dwc/terms/#dcterms:type

Wherever possible, this class will be extended with Darwin Core attributes for greater adoption of the standard.

sex - Variable in class org.ecocean.genetics.SexAnalysis
 
sex - Variable in class org.ecocean.grid.EncounterLite
 
sex - Variable in class org.ecocean.MarkedIndividual
 
SexAnalysis - Class in org.ecocean.genetics
 
SexAnalysis() - Constructor for class org.ecocean.genetics.SexAnalysis
 
SexAnalysis(String, String, String, String) - Constructor for class org.ecocean.genetics.SexAnalysis
 
ShareDst - Class in org.ecocean.genetics.distance
 
ShareDst(String) - Constructor for class org.ecocean.genetics.distance.ShareDst
 
SharkGridThreadExecutorService - Class in org.ecocean.grid
 
SharkGridThreadExecutorService() - Constructor for class org.ecocean.grid.SharkGridThreadExecutorService
 
SharkGridThreadPoolExecutor - Class in org.ecocean.grid
 
SharkGridThreadPoolExecutor(int, int) - Constructor for class org.ecocean.grid.SharkGridThreadPoolExecutor
 
SharkIdentification - Class in org.ecocean.interconnect
 
SharkIdentification(CompareResults, String, String) - Constructor for class org.ecocean.interconnect.SharkIdentification
 
SharkPanel - Class in org.ecocean.interconnect
 
SharkPanel(String) - Constructor for class org.ecocean.interconnect.SharkPanel
 
SharkPanel.MouseClickListener - Class in org.ecocean.interconnect
 
SharkPanel.MouseClickListener() - Constructor for class org.ecocean.interconnect.SharkPanel.MouseClickListener
 
sharpen - Variable in class org.ecocean.interconnect.SharkPanel
 
sharpened - Variable in class org.ecocean.interconnect.SharkPanel
 
Shepherd - Class in org.ecocean
Shepherd is the main information retrieval, processing, and persistence class to be used for all shepherd project applications.
Shepherd(String) - Constructor for class org.ecocean.Shepherd
Constructor to create a new shepherd thread object
ShepherdPMF - Class in org.ecocean
 
ShepherdPMF() - Constructor for class org.ecocean.ShepherdPMF
 
ShepherdProperties - Class in org.ecocean
 
ShepherdProperties() - Constructor for class org.ecocean.ShepherdProperties
 
ShepherdRealm - Class in org.ecocean.security
 
ShepherdRealm() - Constructor for class org.ecocean.security.ShepherdRealm
 
showAcousticTag(String) - Static method in class org.ecocean.CommonConfiguration
 
showButton - Variable in class org.ecocean.interconnect.ShowResults
 
showCategory(String, String) - Static method in class org.ecocean.CommonConfiguration
 
showEXIFData(String) - Static method in class org.ecocean.CommonConfiguration
This configuration option defines whether users can edit this catalog.
ShowImagePane - Class in org.ecocean.interconnect
 
ShowImagePane(String) - Constructor for class org.ecocean.interconnect.ShowImagePane
 
showMeasurements(String) - Static method in class org.ecocean.CommonConfiguration
 
showMetalTags(String) - Static method in class org.ecocean.CommonConfiguration
 
showProperty(String, String) - Static method in class org.ecocean.CommonConfiguration
 
showReleaseDate(String) - Static method in class org.ecocean.CommonConfiguration
 
showRes - Static variable in class org.ecocean.interconnect.SharkPanel
 
ShowResults - Class in org.ecocean.interconnect
 
ShowResults(SharkPanel, String[], double[], int[]) - Constructor for class org.ecocean.interconnect.ShowResults
 
ShowResults.MouseClickListener - Class in org.ecocean.interconnect
 
ShowResults.MouseClickListener() - Constructor for class org.ecocean.interconnect.ShowResults.MouseClickListener
 
showSatelliteTag(String) - Static method in class org.ecocean.CommonConfiguration
 
showUsersToPublic(String) - Static method in class org.ecocean.CommonConfiguration
This configuration option defines whether information about User objects associated with Encounters and MarkedIndividuals will be displayed to web site viewers.
side - Variable in class org.ecocean.interconnect.GetEncounterNumber
 
side - Variable in class org.ecocean.interconnect.SharkPanel
 
sidesSightedInPeriod(int, int, int, int, int, int, String) - Method in class org.ecocean.MarkedIndividual
 
sideURLAddition - Variable in class org.ecocean.interconnect.GetEncounterNumber
 
sigmaX - Variable in class org.ecocean.Spot
 
sigmaXX - Variable in class org.ecocean.Spot
 
sigmaXY - Variable in class org.ecocean.Spot
 
sigmaY - Variable in class org.ecocean.Spot
 
sigmaYY - Variable in class org.ecocean.Spot
 
SimpleCMROutput - Class in org.ecocean.servlet.export
 
SimpleCMROutput() - Constructor for class org.ecocean.servlet.export.SimpleCMROutput
 
SinglePhotoVideo - Class in org.ecocean
 
SinglePhotoVideo() - Constructor for class org.ecocean.SinglePhotoVideo
Empty constructor required for JDO persistence
SinglePhotoVideo(String, String, String) - Constructor for class org.ecocean.SinglePhotoVideo
 
SinglePhotoVideo(String, File) - Constructor for class org.ecocean.SinglePhotoVideo
 
SinglePhotoVideo(Encounter, FileItem, String, String) - Constructor for class org.ecocean.SinglePhotoVideo
 
SinglePhotoVideoAddKeyword - Class in org.ecocean.servlet
 
SinglePhotoVideoAddKeyword() - Constructor for class org.ecocean.servlet.SinglePhotoVideoAddKeyword
 
SinglePhotoVideoRemoveKeyword - Class in org.ecocean.servlet
 
SinglePhotoVideoRemoveKeyword() - Constructor for class org.ecocean.servlet.SinglePhotoVideoRemoveKeyword
 
size - Variable in class org.ecocean.Encounter
 
size - Variable in class org.ecocean.grid.EncounterLite
 
size - Variable in class org.ecocean.grid.I3SMatchObject
 
size - Variable in class org.ecocean.grid.MatchObject
 
size - Variable in class org.ecocean.interconnect.CopyFile
 
size_guess - Variable in class org.ecocean.Encounter
 
Sizelim - Variable in class org.ecocean.grid.GridManager
 
Sizelim - Variable in class org.ecocean.grid.ScanWorkItem
 
SocialUnit - Class in org.ecocean.social
 
SocialUnit() - Constructor for class org.ecocean.social.SocialUnit
 
SocialUnit(String) - Constructor for class org.ecocean.social.SocialUnit
 
socialUnitName - Variable in class org.ecocean.social.SocialUnit
 
SOCPROGExport - Class in org.ecocean.servlet.export
 
SOCPROGExport() - Constructor for class org.ecocean.servlet.export.SOCPROGExport
 
sortMapByDoubleValue(Map) - Static method in class org.ecocean.genetics.distance.MyFuns
 
sp - Static variable in class org.ecocean.interconnect.CompareResults
 
sp - Variable in class org.ecocean.interconnect.GetEncounterNumber
 
sp - Variable in class org.ecocean.interconnect.InsertDatabase
 
sp - Static variable in class org.ecocean.interconnect.Interconnect
 
sp - Variable in class org.ecocean.interconnect.ShowResults
 
spaces - Static variable in class org.ecocean.genetics.distance.MyFuns
 
specificEpithet - Variable in class org.ecocean.Encounter
 
Splash - Class in org.ecocean.interconnect
 
Splash() - Constructor for class org.ecocean.interconnect.Splash
 
Spot - Class in org.ecocean
spot stores the data for a single blob(spot) thresholded by the EasyObject library from a cropped digital image of a whale shark encounter.
Spot() - Constructor for class org.ecocean.Spot
empty constructor required by JDO Enhancer.
Spot(int, double, double) - Constructor for class org.ecocean.Spot
This constructor is for initial testing only - REMOVE ME AND REPLACE WITH A CONSTRUCTOR THAT REQUIRES ALL DATA
SpotCloud - Class in org.ecocean.interconnect
 
SpotCloud(String, String, Point2D[], Point2D[], int[], double) - Constructor for class org.ecocean.interconnect.SpotCloud
 
spotcnt - Variable in class org.ecocean.interconnect.FingerPrint
 
spotcnt - Variable in class org.ecocean.interconnect.GetEncounterNumber
 
spotcnt - Variable in class org.ecocean.interconnect.SharkPanel
 
spotImageFileName - Variable in class org.ecocean.Encounter
 
spots - Variable in class org.ecocean.Encounter
 
spots - Variable in class org.ecocean.interconnect.FingerPrint
 
spots - Variable in class org.ecocean.interconnect.SharkPanel
 
spotsX - Variable in class org.ecocean.grid.EncounterLite
 
spotsY - Variable in class org.ecocean.grid.EncounterLite
 
SpotTriangle - Class in org.ecocean.grid
 
SpotTriangle(Spot, Spot, Spot, double) - Constructor for class org.ecocean.grid.SpotTriangle
 
standard_deviation(double[]) - Method in class org.ecocean.Encounter
 
start() - Method in class org.ecocean.grid.AppletSwingWorker
Submits this worker to executor for execution.
start - Variable in class org.ecocean.grid.WorkApplet3.scanAppletActionListener
 
started - Variable in class org.ecocean.grid.AppletSwingWorker
true if start method was called.
started - Variable in class org.ecocean.grid.ScanTask
 
startTime - Variable in class org.ecocean.grid.GridNode
 
startTime - Variable in class org.ecocean.grid.ScanTask
 
startTime - Variable in class org.ecocean.grid.ScanWorkItem
 
startTime - Variable in class org.ecocean.social.Relationship
 
state - Variable in class org.ecocean.Encounter
 
state - Variable in class org.ecocean.security.Collaboration
 
STATE_APPROVED - Static variable in class org.ecocean.security.Collaboration
 
STATE_INITIALIZED - Static variable in class org.ecocean.security.Collaboration
 
STATE_REJECTED - Static variable in class org.ecocean.security.Collaboration
 
status - Variable in class org.ecocean.grid.WorkApplet3.runWIScan
 
status - Variable in class org.ecocean.grid.WorkApplet3.scanAppletActionListener
 
status - Variable in class org.ecocean.grid.WorkApplet3
 
status - Variable in class org.ecocean.ImageProcessor
Current status of the batch processor.
storageLabID - Variable in class org.ecocean.genetics.TissueSample
 
storeNewAdoption(Adoption, String) - Method in class org.ecocean.Shepherd
 
storeNewCollaboration(Collaboration) - Method in class org.ecocean.Shepherd
 
storeNewEncounter(Encounter, String) - Method in class org.ecocean.Shepherd
Stores a new, unassigned encounter in the database for later retrieval and analysis.
storeNewKeyword(Keyword) - Method in class org.ecocean.Shepherd
 
storeNewMarkedIndividual(MarkedIndividual) - Method in class org.ecocean.Shepherd
 
storeNewOccurrence(Occurrence) - Method in class org.ecocean.Shepherd
 
storeNewTask(ScanTask) - Method in class org.ecocean.Shepherd
 
Story - Class in org.ecocean
 
Story() - Constructor for class org.ecocean.Story
empty constructor required by JDO Enhancer
Story(String) - Constructor for class org.ecocean.Story
 
storyID - Variable in class org.ecocean.Story
 
storyMediaURL - Variable in class org.ecocean.Story
 
storyTellerEmail - Variable in class org.ecocean.Story
 
storyTellerName - Variable in class org.ecocean.Story
 
storyText - Variable in class org.ecocean.Story
 
StringToDoubles(String) - Static method in class org.ecocean.genetics.distance.MyFuns
 
StringToHashCodes(String) - Static method in class org.ecocean.genetics.distance.MyFuns
 
StringToHashCodes(int[], String, boolean) - Static method in class org.ecocean.genetics.distance.MyFuns
 
StringToHashCodes(int[][], String, boolean) - Static method in class org.ecocean.genetics.distance.MyFuns
 
StringToHashCodes(int[][][], String, boolean) - Static method in class org.ecocean.genetics.distance.MyFuns
 
StringToHashCodes(int[], HashTokenizer, boolean) - Static method in class org.ecocean.genetics.distance.MyFuns
 
StringToInts(String) - Static method in class org.ecocean.genetics.distance.MyFuns
 
StringToNumbers(int[], String, boolean) - Static method in class org.ecocean.genetics.distance.MyFuns
 
StringToNumbers(int[][], String, boolean) - Static method in class org.ecocean.genetics.distance.MyFuns
 
StringToNumbers(int[][][], String, boolean) - Static method in class org.ecocean.genetics.distance.MyFuns
 
StringToNumbers(int[], StringTokenizer, boolean) - Static method in class org.ecocean.genetics.distance.MyFuns
 
StringToNumbers(double[], String, boolean) - Static method in class org.ecocean.genetics.distance.MyFuns
 
StringToNumbers(double[][], String, boolean) - Static method in class org.ecocean.genetics.distance.MyFuns
 
StringToNumbers(double[][][], String, boolean) - Static method in class org.ecocean.genetics.distance.MyFuns
 
StringToNumbers(double[], StringTokenizer, boolean) - Static method in class org.ecocean.genetics.distance.MyFuns
 
StrutsUTF8Filter - Class in org.ecocean.servlet
 
StrutsUTF8Filter() - Constructor for class org.ecocean.servlet.StrutsUTF8Filter
 
subdir() - Method in class org.ecocean.Encounter
 
subdir(String) - Static method in class org.ecocean.Encounter
 
subject - Variable in class org.ecocean.NotificationMailer
 
submitter - Variable in class org.ecocean.grid.ScanTask
 
submitterAddress - Variable in class org.ecocean.Encounter
 
submitterEmail - Variable in class org.ecocean.Encounter
 
submitterID - Variable in class org.ecocean.Encounter
 
submitterOrganization - Variable in class org.ecocean.Encounter
 
submitterPhone - Variable in class org.ecocean.Encounter
 
submitterProject - Variable in class org.ecocean.Encounter
 
Sum(int[]) - Static method in class org.ecocean.genetics.distance.MyFuns
 
Sum(double[]) - Static method in class org.ecocean.genetics.distance.MyFuns
 
Sum(double[][]) - Static method in class org.ecocean.genetics.distance.MyFuns
 
SumProduct(double[], double[]) - Static method in class org.ecocean.genetics.distance.MyFuns
 
SumProduct(double[][], double[][]) - Static method in class org.ecocean.genetics.distance.MyFuns
 
SumSquares(double[]) - Static method in class org.ecocean.genetics.distance.MyFuns
 
SumSquares(double[][]) - Static method in class org.ecocean.genetics.distance.MyFuns
 
SuperSpot - Class in org.ecocean
superSpot stores the data for a single spot.
SuperSpot() - Constructor for class org.ecocean.SuperSpot
empty constructor used by JDO Enhancer - DO NOT USE
SuperSpot(Spot) - Constructor for class org.ecocean.SuperSpot
the constructor to be used for quick and dirty pattern matching in encounter.filterTrianglesByCentroidPatternMatching()
SuperSpot(double, double) - Constructor for class org.ecocean.SuperSpot
 
swap(int, int) - Method in class com.reijns.I3S.LinSys
 
swi - Variable in class org.ecocean.grid.AppletWorkItemThread
 

T

tagNumber - Variable in class org.ecocean.tag.MetalTag
 
targeted - Variable in class org.ecocean.grid.GridNode
 
task - Variable in class org.ecocean.grid.AppletSwingWorker
Calls the construct method to compute the result, then invokes the finished method on the event dispatch thread.
taskID - Variable in class org.ecocean.grid.FalseMatchCreationThread
 
taskID - Variable in class org.ecocean.grid.MatchObject
 
taskID - Variable in class org.ecocean.grid.ScanTaskCleanupThread
 
taskID - Variable in class org.ecocean.grid.ScanWorkItem
 
taskID - Variable in class org.ecocean.grid.ScanWorkItemCreationThread
 
taskID - Variable in class org.ecocean.grid.TuningTaskCreationThread
 
tC2 - Variable in class org.ecocean.grid.SpotTriangle
 
tempSuperSpot - Static variable in class org.ecocean.servlet.IndividualAddFile
 
text - Variable in class org.ecocean.NotificationMailer
 
tf - Variable in class org.ecocean.interconnect.AcceptDialog
 
tf - Variable in class org.ecocean.interconnect.SharkIdentification
 
tfDir - Variable in class org.ecocean.interconnect.GetEncounterNumber
 
tfDir - Variable in class org.ecocean.interconnect.InsertDatabase
 
tfFile - Variable in class org.ecocean.interconnect.InsertDatabase
 
thisURLRoot - Static variable in class org.ecocean.grid.WorkApplet3
 
thisURLRoot - Static variable in class org.ecocean.grid.WorkAppletHeadless
 
thrd - Variable in class org.ecocean.grid.WorkApplet3.runWIScan
 
threadCleanupObject - Variable in class org.ecocean.grid.GridCleanupThread
 
threadCleanupObject - Variable in class org.ecocean.grid.ScanTaskCleanupThread
 
threadCreationObject - Variable in class org.ecocean.grid.FalseMatchCreationThread
 
threadCreationObject - Variable in class org.ecocean.grid.ScanWorkItemCreationThread
 
threadCreationObject - Variable in class org.ecocean.grid.TuningTaskCreationThread
 
threadHandler - Variable in class org.ecocean.grid.WorkApplet3
 
threadHandler - Variable in class org.ecocean.grid.WorkAppletHeadless
 
threadObject - Variable in class org.ecocean.grid.AppletWorkItemThread
 
threadPool - Static variable in class org.ecocean.grid.SharkGridThreadExecutorService
 
THRESHOLD - Static variable in class com.reijns.I3S.LinSys
 
throwAwayAdoption(Adoption) - Method in class org.ecocean.Shepherd
 
throwAwayEncounter(Encounter) - Method in class org.ecocean.Shepherd
Removes an encounter from the database.
throwAwayGeneticAnalysis(GeneticAnalysis) - Method in class org.ecocean.Shepherd
 
throwAwayKeyword(Keyword) - Method in class org.ecocean.Shepherd
 
throwAwayMarkedIndividual(MarkedIndividual) - Method in class org.ecocean.Shepherd
Removes a marked individual from the database.
throwAwayMicrosatelliteMarkersAnalysis(MicrosatelliteMarkersAnalysis) - Method in class org.ecocean.Shepherd
 
throwAwayOccurrence(Occurrence) - Method in class org.ecocean.Shepherd
 
throwAwaySuperSpotArray(SuperSpot[]) - Method in class org.ecocean.Shepherd
 
throwAwayTask(ScanTask) - Method in class org.ecocean.Shepherd
 
throwAwayTissueSample(TissueSample) - Method in class org.ecocean.Shepherd
 
thrown - Variable in class org.ecocean.ImageProcessor
Throwable instance produced by the batch processor (if any).
thumbnail - Variable in class org.ecocean.interconnect.ImagePreview
 
tif - Static variable in class org.ecocean.interconnect.Utils
 
tiff - Static variable in class org.ecocean.interconnect.Utils
 
timeOfBirth - Variable in class org.ecocean.MarkedIndividual
 
timeOfDeath - Variable in class org.ecocean.MarkedIndividual
 
timestampOfLastUpdate - Variable in class org.ecocean.PatterningPassport
 
TissueSample - Class in org.ecocean.genetics
 
TissueSample() - Constructor for class org.ecocean.genetics.TissueSample
Empty constructor required for JDO persistence.
TissueSample(String, String) - Constructor for class org.ecocean.genetics.TissueSample
 
TissueSample(String, String, HttpServletRequest) - Constructor for class org.ecocean.genetics.TissueSample
 
TissueSampleRemoveBiologicalMeasurement - Class in org.ecocean.servlet
 
TissueSampleRemoveBiologicalMeasurement() - Constructor for class org.ecocean.servlet.TissueSampleRemoveBiologicalMeasurement
 
TissueSampleRemoveHaplotype - Class in org.ecocean.servlet
 
TissueSampleRemoveHaplotype() - Constructor for class org.ecocean.servlet.TissueSampleRemoveHaplotype
 
TissueSampleRemoveMicrosatelliteMarkers - Class in org.ecocean.servlet
 
TissueSampleRemoveMicrosatelliteMarkers() - Constructor for class org.ecocean.servlet.TissueSampleRemoveMicrosatelliteMarkers
 
TissueSampleRemoveSexAnalysis - Class in org.ecocean.servlet
 
TissueSampleRemoveSexAnalysis() - Constructor for class org.ecocean.servlet.TissueSampleRemoveSexAnalysis
 
tissueSamples - Variable in class org.ecocean.Encounter
 
TissueSampleSetHaplotype - Class in org.ecocean.servlet
 
TissueSampleSetHaplotype() - Constructor for class org.ecocean.servlet.TissueSampleSetHaplotype
 
TissueSampleSetMeasurement - Class in org.ecocean.servlet
 
TissueSampleSetMeasurement() - Constructor for class org.ecocean.servlet.TissueSampleSetMeasurement
 
TissueSampleSetMicrosatelliteMarkers - Class in org.ecocean.servlet
 
TissueSampleSetMicrosatelliteMarkers() - Constructor for class org.ecocean.servlet.TissueSampleSetMicrosatelliteMarkers
 
TissueSampleSetSexAnalysis - Class in org.ecocean.servlet
 
TissueSampleSetSexAnalysis() - Constructor for class org.ecocean.servlet.TissueSampleSetSexAnalysis
 
tissueType - Variable in class org.ecocean.genetics.TissueSample
 
to - Variable in class org.ecocean.NotificationMailer
 
toDo - Variable in class org.ecocean.grid.GridManager
 
toDoContains(ScanWorkItem) - Method in class org.ecocean.grid.GridManager
 
toggleDotSelection() - Method in class org.ecocean.interconnect.SharkPanel
 
toggleSharpen() - Method in class org.ecocean.interconnect.SharkPanel
 
toleranceInCosineAtVertex1 - Variable in class org.ecocean.grid.SpotTriangle
 
toleranceRatioLong2Short - Variable in class org.ecocean.grid.SpotTriangle
 
toString() - Method in class com.reijns.I3S.LinSys.MatRow
 
totalEncounters() - Method in class org.ecocean.MarkedIndividual
Returns the total number of submitted encounters for this MarkedIndividual
totalLogEncounters() - Method in class org.ecocean.MarkedIndividual
 
totalTimeSinceStart - Variable in class org.ecocean.grid.GridNode
 
totalWorkItemsInTask - Variable in class org.ecocean.grid.ScanWorkItem
 
tR2 - Variable in class org.ecocean.grid.SpotTriangle
 
TrackerFeed - Class in org.ecocean.servlet
 
TrackerFeed() - Constructor for class org.ecocean.servlet.TrackerFeed
 
TrackIt - Class in org.ecocean.servlet
 
TrackIt() - Constructor for class org.ecocean.servlet.TrackIt
 
transmitToURL - Variable in class org.ecocean.interconnect.GetEncounterNumber
 
transmitToURL - Static variable in class org.ecocean.interconnect.Interconnect
 
Transpose(double[][]) - Static method in class org.ecocean.genetics.distance.MyFuns
 
Transpose(int[][]) - Static method in class org.ecocean.genetics.distance.MyFuns
 
Transpose12(double[][][]) - Static method in class org.ecocean.genetics.distance.MyFuns
 
trimDecimal(String, int) - Static method in class org.ecocean.genetics.distance.MyFuns
 
TuningTaskCreationThread - Class in org.ecocean.grid
 
TuningTaskCreationThread(String, boolean, int, String) - Constructor for class org.ecocean.grid.TuningTaskCreationThread
Constructor to create a new thread object
type - Variable in class org.ecocean.DataCollectionEvent
 
type - Static variable in class org.ecocean.genetics.BiologicalMeasurement
 
type - Static variable in class org.ecocean.genetics.MicrosatelliteMarkersAnalysis
 
type - Static variable in class org.ecocean.genetics.MitochondrialDNAAnalysis
 
type - Static variable in class org.ecocean.genetics.SexAnalysis
 
type - Static variable in class org.ecocean.genetics.TissueSample
 
type - Variable in class org.ecocean.servlet.EncounterSetMeasurements.RequestEventValues
 
type - Static variable in class org.ecocean.SinglePhotoVideo
 
type - Variable in class org.ecocean.social.Relationship
 
type - Variable in class org.ecocean.Util.MeasurementDesc
 
TYPE_UNKNOWN - Static variable in class org.ecocean.interconnect.ImageFileFilter
 

U

unidentifiable - Variable in class org.ecocean.Encounter
 
unidentifiableEncounters - Variable in class org.ecocean.MarkedIndividual
 
uniqueNum - Variable in class org.ecocean.grid.ScanTask
 
uniqueNum - Variable in class org.ecocean.grid.ScanWorkItem
 
uniqueNumTask - Variable in class org.ecocean.grid.ScanWorkItemResult
 
uniqueNumWI - Variable in class org.ecocean.grid.ScanWorkItemResult
 
units - Variable in class org.ecocean.genetics.BiologicalMeasurement
 
units - Variable in class org.ecocean.Measurement
 
units - Variable in class org.ecocean.servlet.EncounterSetMeasurements.RequestEventValues
 
units - Variable in class org.ecocean.Util.MeasurementDesc
 
UNITS - Static variable in class org.ecocean.Util
 
unitsLabel - Variable in class org.ecocean.Util.MeasurementDesc
 
updateDatabase() - Method in class org.ecocean.interconnect.SharkPanel
 
UpdateEmailAddress - Class in org.ecocean.servlet
 
UpdateEmailAddress() - Constructor for class org.ecocean.servlet.UpdateEmailAddress
 
updateGridStats(String) - Method in class org.ecocean.grid.GridManager
 
updateImage(String, StringBuffer) - Method in class org.ecocean.interconnect.SharkPanel
 
updateJdoqlVariableDeclaration(String, String) - Static method in class org.ecocean.EncounterQueryProcessor
 
updateJdoqlVariableDeclaration(String, String) - Static method in class org.ecocean.IndividualQueryProcessor
 
updateParametersDeclaration(String, String) - Static method in class org.ecocean.EncounterQueryProcessor
 
updateParametersDeclaration(String, String) - Static method in class org.ecocean.IndividualQueryProcessor
 
updateTimeStamp() - Method in class org.ecocean.PatterningPassport
 
UPLOAD_DIRECTORY - Variable in class org.ecocean.servlet.AdoptionAction
 
UPLOAD_DIRECTORY - Variable in class org.ecocean.servlet.EncounterForm
 
useExtensionsInDescription - Variable in class org.ecocean.interconnect.ImageFileFilter
 
user - Variable in class org.ecocean.grid.ScanTask
 
User - Class in org.ecocean
User stores information about a contact/user.
User() - Constructor for class org.ecocean.User
 
User(String, String, String, String, String, String) - Constructor for class org.ecocean.User
 
User(String, String, String) - Constructor for class org.ecocean.User
 
UserAddProfileImage - Class in org.ecocean.servlet
Uploads a new image to the file system and associates the image with an Encounter record
UserAddProfileImage() - Constructor for class org.ecocean.servlet.UserAddProfileImage
 
UserCreate - Class in org.ecocean.servlet
 
UserCreate() - Constructor for class org.ecocean.servlet.UserCreate
 
UserDelete - Class in org.ecocean.servlet
 
UserDelete() - Constructor for class org.ecocean.servlet.UserDelete
 
userID - Variable in class org.ecocean.User
 
userImage - Variable in class org.ecocean.User
 
UserInfo - Class in org.ecocean.servlet
 
UserInfo() - Constructor for class org.ecocean.servlet.UserInfo
 
username - Variable in class org.ecocean.Role
 
username - Variable in class org.ecocean.User
 
username1 - Variable in class org.ecocean.security.Collaboration
 
username2 - Variable in class org.ecocean.security.Collaboration
 
userProject - Variable in class org.ecocean.User
 
UserRemoveProfileImage - Class in org.ecocean.servlet
 
UserRemoveProfileImage() - Constructor for class org.ecocean.servlet.UserRemoveProfileImage
 
UserResetAcceptedUserAgreement - Class in org.ecocean.servlet
 
UserResetAcceptedUserAgreement() - Constructor for class org.ecocean.servlet.UserResetAcceptedUserAgreement
 
UserSelfUpdate - Class in org.ecocean.servlet
 
UserSelfUpdate() - Constructor for class org.ecocean.servlet.UserSelfUpdate
 
userStatement - Variable in class org.ecocean.User
 
userURL - Variable in class org.ecocean.User
 
useSpotPatternRecognition(String) - Static method in class org.ecocean.CommonConfiguration
This configuration option defines whether the spot pattern recognition software embedded in the framework is used for the species under study.
useTapirLinkURL(String) - Static method in class org.ecocean.CommonConfiguration
This configuration option defines whether a pre-installed TapirLink provider will be used in conjunction with this database to expose mark-recapture data to biodiversity frameworks, such as the GBIF.
Util - Class in org.ecocean
 
Util() - Constructor for class org.ecocean.Util
 
Util.MeasurementDesc - Class in org.ecocean
 
Util.MeasurementDesc(String, String, String, String) - Constructor for class org.ecocean.Util.MeasurementDesc
 
Util.MetalTagDesc - Class in org.ecocean
 
Util.MetalTagDesc(String, String) - Constructor for class org.ecocean.Util.MetalTagDesc
 
Util.OptionDesc - Class in org.ecocean
 
Util.OptionDesc(String, String) - Constructor for class org.ecocean.Util.OptionDesc
 
Utils - Class in org.ecocean.interconnect
 
Utils() - Constructor for class org.ecocean.interconnect.Utils
 

V

v1 - Variable in class org.ecocean.grid.