public class MarkedIndividual extends Object implements Serializable
MarkedIndividual
object stores the complete encounter
data for a single marked individual in a mark-recapture study.
Encounters
are added to MarkedIndividual objects as multiple encounters are associated with
known marked individuals.
Encounter, Shepherd
,
Serialized FormModifier and Type | Field and Description |
---|---|
private String |
alternateid |
private String |
comments |
private Vector |
dataFiles |
private String |
dateTimeCreated |
private String |
dynamicProperties |
private Vector |
encounters |
private String |
individualID |
private Vector |
interestedResearchers |
private String |
localHaplotypeReflection |
private int |
maxYearsBetweenResightings |
private String |
nickName |
private String |
nickNamer |
private int |
numberEncounters |
private int |
numUnidentifiableEncounters |
private String |
patterningCode |
private String |
seriesCode |
private String |
sex |
private long |
timeOfBirth |
private long |
timeOfDeath |
private Vector |
unidentifiableEncounters |
Constructor and Description |
---|
MarkedIndividual()
empty constructor used by JDO Enhancer - DO NOT USE
|
MarkedIndividual(String individualID,
Encounter enc) |
Modifier and Type | Method and Description |
---|---|
void |
addComments(String newComments)
Adds any general comments recorded for this MarkedIndividual as a whole.
|
void |
addDataFile(String dataFile)
Adds a satellite tag data file for this MarkedIndividual.
|
boolean |
addEncounter(Encounter newEncounter)
Adds a new encounter to this MarkedIndividual.
|
void |
addInterestedResearcher(String email) |
double |
averageLengthInYear(int year)
Deprecated.
|
double |
averageMeasuredLengthInYear(int year,
boolean allowGuideGuess)
Deprecated.
|
double |
avgLengthInPeriod(int m_startYear,
int m_startMonth,
int m_endYear,
int m_endMonth)
Deprecated.
|
boolean |
canUserAccess(javax.servlet.http.HttpServletRequest request) |
String |
collaborationLockHtml(javax.servlet.http.HttpServletRequest request) |
float |
distFrom(float lat1,
float lng1,
float lat2,
float lng2) |
void |
doNotSetLocalHaplotypeReflection(String myHaplo)
DO NOT SET DIRECTLY!!
|
String |
getAllAlternateIDs() |
ArrayList<Keyword> |
getAllAppliedKeywordNames(Shepherd myShepherd) |
ArrayList<String> |
getAllAssignedUsers() |
ArrayList<Integer> |
getAlleleValuesForLocus(String locus) |
ArrayList |
getAllEmailsToUpdate()
Obtains the email addresses of all submitters, photographs, and others to notify.
|
ArrayList<Relationship> |
getAllRelationships(Shepherd myShepherd) |
ArrayList<SinglePhotoVideo> |
getAllSinglePhotoVideo() |
ArrayList<TissueSample> |
getAllTissueSamples() |
ArrayList<String> |
getAllValuesForDynamicProperty(String propertyName) |
String |
getAlternateID() |
Double |
getAverageBiologicalMeasurementInPeriod(int m_startYear,
int m_startMonth,
int m_endYear,
int m_endMonth,
String measurementType) |
Double |
getAverageMeasurementInPeriod(int m_startYear,
int m_startMonth,
int m_endYear,
int m_endMonth,
String measurementType) |
String |
getComments()
Returns any additional, general comments recorded for this MarkedIndividual as a whole.
|
Vector |
getDataFiles()
Returns the complete Vector of stored satellite tag data files for this MarkedIndividual.
|
Encounter[] |
getDateSortedEncounters() |
Encounter[] |
getDateSortedEncounters(boolean reverse) |
String |
getDateTimeCreated() |
String |
getDynamicProperties() |
String |
getDynamicPropertyValue(String name) |
long |
getEarliestSightingTime() |
int |
getEarliestSightingYear() |
Encounter |
getEncounter(int i)
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.
|
Vector |
getEncounters()
Returns the complete Vector of stored encounters for this MarkedIndividual.
|
String |
getFomattedMSMarkersString(String[] loci) |
String |
getGeneticSex() |
String |
getGenusSpecies()
Returns the first genus-species pair found in the Encounter objects for this MarkedIndividual.
|
String |
getHaplotype()
Returns the first haplotype found in the Encounter objects for this MarkedIndividual.
|
String |
getIndividualID() |
Vector |
getInterestedResearchers() |
double |
getLastEstimatedSize() |
Encounter |
getLogEncounter(int i) |
Float |
getMaxDistanceBetweenTwoSightings() |
int |
getMaxNumYearsBetweenSightings() |
long |
getMaxTimeBetweenTwoSightings() |
Float |
getMinDistanceBetweenTwoMarkedIndividuals(MarkedIndividual otherIndy) |
String |
getName()
Returns the user-input name of the MarkedIndividual, which is also used as an Index in the FastObjects database
|
String |
getNickName() |
String |
getNickNamer() |
int |
getNumberRightTrainableEncounters() |
int |
getNumberTrainableEncounters() |
String |
getPatterningCode()
Returns the patterning type evident on this MarkedIndividual instance.
|
Vector |
getRightTrainableEncounters() |
String |
getSeriesCode() |
String |
getSex()
Returns the sex of this MarkedIndividual.
|
long |
getTimeOfBirth() |
long |
getTimeofDeath() |
Vector |
getTrainableEncounters() |
Vector |
getUnidentifiableEncounters()
public Encounter[] getDateSortedEncounters(boolean includeLogEncounters) {
return getDateSortedEncounters();
}
|
boolean |
hasGeneticSex() |
boolean |
hasLocus(String locus) |
boolean |
hasLocusAndAllele(String locus,
Integer alleleValue) |
boolean |
hasMsMarkers() |
boolean |
isDeceased() |
boolean |
isDescribedByPhotoKeyword(Keyword word) |
ArrayList<String> |
participatesInTheseLocationIDs() |
ArrayList<String> |
participatesInTheseVerbatimEventDates() |
void |
removeDataFile(String dataFile)
Removes a satellite tag data file for this MarkedIndividual.
|
void |
removeDynamicProperty(String name) |
boolean |
removeEncounter(Encounter getRidOfMe)
Removes an encounter from this MarkedIndividual.
|
void |
removeInterestedResearcher(String email) |
void |
removeLogEncounter(Encounter enc) |
void |
resetMaxNumYearsBetweenSightings() |
Vector |
returnEncountersWithGPSData() |
Vector |
returnEncountersWithGPSData(boolean useLocales,
boolean reverseOrder,
String context) |
void |
setAlternateID(String newID) |
void |
setDateTimeCreated(String time) |
void |
setDynamicProperty(String name,
String value) |
void |
setIndividualID(String newName) |
void |
setName(String newName) |
void |
setNickName(String newName)
Sets the nickname of the MarkedIndividual.
|
void |
setNickNamer(String newNamer) |
void |
setPatterningCode(String newCode)
Sets the patterning type evident on this MarkedIndividual instance.
|
void |
setSeriesCode(String newCode) |
void |
setSex(String newSex)
Sets the sex of this MarkedIndividual.
|
void |
setTimeOfBirth(long newTime) |
void |
setTimeOfDeath(long newTime) |
String |
sidesSightedInPeriod(int m_startYear,
int m_startMonth,
int m_startDay,
int m_endYear,
int m_endMonth,
int m_endDay,
String locCode) |
int |
totalEncounters()
Returns the total number of submitted encounters for this MarkedIndividual
|
int |
totalLogEncounters() |
boolean |
wasSightedByUser(String user) |
boolean |
wasSightedInLocationCode(String locationCode) |
boolean |
wasSightedInMonth(int year,
int month) |
boolean |
wasSightedInPeriod(int m_startYear,
int m_startMonth,
int m_endYear,
int m_endMonth) |
boolean |
wasSightedInPeriod(int m_startYear,
int m_startMonth,
int m_startDay,
int m_endYear,
int m_endMonth,
int m_endDay) |
boolean |
wasSightedInPeriod(int m_startYear,
int m_startMonth,
int m_startDay,
int m_endYear,
int m_endMonth,
int m_endDay,
String locCode) |
boolean |
wasSightedInPeriodLeftOnly(int m_startYear,
int m_startMonth,
int m_endYear,
int m_endMonth) |
boolean |
wasSightedInVerbatimEventDate(String ved) |
boolean |
wasSightedInYear(int year) |
boolean |
wasSightedInYear(int year,
String locCode) |
boolean |
wasSightedInYearLeftTagsOnly(int year,
String locCode) |
private String individualID
private String alternateid
private String comments
private String sex
private String seriesCode
private String nickName
private String nickNamer
private Vector encounters
private Vector unidentifiableEncounters
private Vector dataFiles
private int numberEncounters
private int numUnidentifiableEncounters
private Vector interestedResearchers
private String dateTimeCreated
private String localHaplotypeReflection
private String dynamicProperties
private String patterningCode
private int maxYearsBetweenResightings
private long timeOfBirth
private long timeOfDeath
public MarkedIndividual()
public boolean addEncounter(Encounter newEncounter)
newEncounter
- the new encounter
to addShepherd.commitDBTransaction()
public boolean removeEncounter(Encounter getRidOfMe)
getRidOfMe
- the encounter
to remove from this MarkedIndividualShepherd.commitDBTransaction()
public int totalEncounters()
public int totalLogEncounters()
public Vector returnEncountersWithGPSData()
public Vector returnEncountersWithGPSData(boolean useLocales, boolean reverseOrder, String context)
public boolean isDeceased()
public boolean wasSightedInYear(int year)
public boolean wasSightedInYear(int year, String locCode)
public boolean wasSightedInYearLeftTagsOnly(int year, String locCode)
public double averageLengthInYear(int year)
public double averageMeasuredLengthInYear(int year, boolean allowGuideGuess)
public boolean isDescribedByPhotoKeyword(Keyword word)
public boolean wasSightedInMonth(int year, int month)
public boolean wasSightedInPeriod(int m_startYear, int m_startMonth, int m_endYear, int m_endMonth)
public boolean wasSightedInPeriod(int m_startYear, int m_startMonth, int m_startDay, int m_endYear, int m_endMonth, int m_endDay, String locCode)
public boolean wasSightedInPeriod(int m_startYear, int m_startMonth, int m_startDay, int m_endYear, int m_endMonth, int m_endDay)
public boolean wasSightedInPeriodLeftOnly(int m_startYear, int m_startMonth, int m_endYear, int m_endMonth)
public String getName()
public String getIndividualID()
public String getNickName()
public String getNickNamer()
public void setNickName(String newName)
public void setNickNamer(String newNamer)
public void setName(String newName)
public void setIndividualID(String newName)
public Encounter getEncounter(int i)
i
- the specified encounter number, where i=0...(n-1)public Encounter getLogEncounter(int i)
public Vector getEncounters()
Vector
public Encounter[] getDateSortedEncounters(boolean reverse)
public Encounter[] getDateSortedEncounters()
public Vector getUnidentifiableEncounters()
public String getComments()
public void addComments(String newComments)
public Vector getDataFiles()
Vector
public String getSex()
public void setSex(String newSex)
public double getLastEstimatedSize()
public boolean wasSightedInLocationCode(String locationCode)
public ArrayList<String> participatesInTheseVerbatimEventDates()
public boolean wasSightedInVerbatimEventDate(String ved)
public boolean wasSightedByUser(String user)
public int getMaxNumYearsBetweenSightings()
public int getEarliestSightingYear()
public long getEarliestSightingTime()
public String getSeriesCode()
public Vector getInterestedResearchers()
public void addInterestedResearcher(String email)
public void removeInterestedResearcher(String email)
public void setSeriesCode(String newCode)
public void addDataFile(String dataFile)
dataFile
- the satellite tag data file to be addedpublic void removeDataFile(String dataFile)
dataFile
- The satellite data file, as a String, to be removed.public int getNumberTrainableEncounters()
public int getNumberRightTrainableEncounters()
public Vector getTrainableEncounters()
public Vector getRightTrainableEncounters()
public double avgLengthInPeriod(int m_startYear, int m_startMonth, int m_endYear, int m_endMonth)
public Double getAverageMeasurementInPeriod(int m_startYear, int m_startMonth, int m_endYear, int m_endMonth, String measurementType)
public Double getAverageBiologicalMeasurementInPeriod(int m_startYear, int m_startMonth, int m_endYear, int m_endMonth, String measurementType)
public String getDateTimeCreated()
public void setDateTimeCreated(String time)
public void setAlternateID(String newID)
public String getAlternateID()
public String getAllAlternateIDs()
public String getDynamicProperties()
public void removeDynamicProperty(String name)
public ArrayList<TissueSample> getAllTissueSamples()
public ArrayList<SinglePhotoVideo> getAllSinglePhotoVideo()
public ArrayList<String> getAllValuesForDynamicProperty(String propertyName)
public String getPatterningCode()
public void setPatterningCode(String newCode)
public void resetMaxNumYearsBetweenSightings()
public String sidesSightedInPeriod(int m_startYear, int m_startMonth, int m_startDay, int m_endYear, int m_endMonth, int m_endDay, String locCode)
public String getGenusSpecies()
public String getHaplotype()
public String getGeneticSex()
public boolean hasLocus(String locus)
public boolean hasMsMarkers()
public boolean hasGeneticSex()
public ArrayList getAllEmailsToUpdate()
public void removeLogEncounter(Encounter enc)
public float distFrom(float lat1, float lng1, float lat2, float lng2)
public Float getMaxDistanceBetweenTwoSightings()
public long getMaxTimeBetweenTwoSightings()
public void doNotSetLocalHaplotypeReflection(String myHaplo)
myDepth
- public long getTimeOfBirth()
public long getTimeofDeath()
public void setTimeOfBirth(long newTime)
public void setTimeOfDeath(long newTime)
public ArrayList<Relationship> getAllRelationships(Shepherd myShepherd)
public Float getMinDistanceBetweenTwoMarkedIndividuals(MarkedIndividual otherIndy)
public boolean canUserAccess(javax.servlet.http.HttpServletRequest request)
public String collaborationLockHtml(javax.servlet.http.HttpServletRequest request)
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