MarkedIndividual (Unnamed - org.ecocean:wildbook:war:5.1.0-RELEASE 5.1.0-RELEASE API)

java.lang.Object
- org.ecocean.MarkedIndividual

All Implemented Interfaces:

Serializable
```
public class MarkedIndividual
extends Object
implements Serializable
```
A 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.

Version:

2.0

Author:

Jason Holmberg

See Also:
Encounter, Shepherd, Serialized Form

Field Summary

Fields
Modifier 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 Summary

Constructors
Constructor and Description

MarkedIndividual()
empty constructor used by JDO Enhancer - DO NOT USE

MarkedIndividual(String individualID, Encounter enc)

Constructors
Constructor and Description
`MarkedIndividual()` empty constructor used by JDO Enhancer - DO NOT USE
`MarkedIndividual(String individualID, Encounter enc)`

Method Summary

Methods
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)`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

individualID
```
private String individualID
```

alternateid
```
private String alternateid
```

comments
```
private String comments
```

sex
```
private String sex
```

seriesCode
```
private String seriesCode
```

nickName
```
private String nickName
```

nickNamer
```
private String nickNamer
```

encounters
```
private Vector encounters
```

unidentifiableEncounters

private Vector unidentifiableEncounters

dataFiles
```
private Vector dataFiles
```

numberEncounters
```
private int numberEncounters
```

numUnidentifiableEncounters

private int numUnidentifiableEncounters

interestedResearchers
```
private Vector interestedResearchers
```

dateTimeCreated
```
private String dateTimeCreated
```

localHaplotypeReflection

private String localHaplotypeReflection

dynamicProperties
```
private String dynamicProperties
```

patterningCode
```
private String patterningCode
```

maxYearsBetweenResightings
```
private int maxYearsBetweenResightings
```

timeOfBirth
```
private long timeOfBirth
```

timeOfDeath
```
private long timeOfDeath
```

Constructor Detail

MarkedIndividual

public MarkedIndividual(String individualID,
                Encounter enc)

MarkedIndividual
```
public MarkedIndividual()
```
empty constructor used by JDO Enhancer - DO NOT USE

Method Detail

addEncounter
```
public boolean addEncounter(Encounter newEncounter)
```
Adds a new encounter to this MarkedIndividual.

Parameters:
newEncounter - the new encounter to add

Returns:
true for successful addition, false for unsuccessful - Note: this change must still be committed for it to be stored in the database
See Also:
Shepherd.commitDBTransaction()

removeEncounter
```
public boolean removeEncounter(Encounter getRidOfMe)
```
Removes an encounter from this MarkedIndividual.

Parameters:
getRidOfMe - the encounter to remove from this MarkedIndividual

Returns:
true for successful removal, false for unsuccessful - Note: this change must still be committed for it to be stored in the database
See Also:
Shepherd.commitDBTransaction()

totalEncounters
```
public int totalEncounters()
```
Returns the total number of submitted encounters for this MarkedIndividual

Returns:
the total number of encounters recorded for this MarkedIndividual

totalLogEncounters
```
public int totalLogEncounters()
```

returnEncountersWithGPSData

public Vector returnEncountersWithGPSData()

returnEncountersWithGPSData

public Vector returnEncountersWithGPSData(boolean useLocales,
                                 boolean reverseOrder,
                                 String context)

isDeceased
```
public boolean isDeceased()
```

wasSightedInYear

public boolean wasSightedInYear(int year)

wasSightedInYear

public boolean wasSightedInYear(int year,
                       String locCode)

wasSightedInYearLeftTagsOnly

public boolean wasSightedInYearLeftTagsOnly(int year,
                                   String locCode)

averageLengthInYear

public double averageLengthInYear(int year)

Deprecated.

averageMeasuredLengthInYear

public double averageMeasuredLengthInYear(int year,
                                 boolean allowGuideGuess)

Deprecated.

isDescribedByPhotoKeyword

public boolean isDescribedByPhotoKeyword(Keyword word)

wasSightedInMonth

public boolean wasSightedInMonth(int year,
                        int month)

wasSightedInPeriod

public boolean wasSightedInPeriod(int m_startYear,
                         int m_startMonth,
                         int m_endYear,
                         int m_endMonth)

wasSightedInPeriod

public boolean wasSightedInPeriod(int m_startYear,
                         int m_startMonth,
                         int m_startDay,
                         int m_endYear,
                         int m_endMonth,
                         int m_endDay,
                         String locCode)

wasSightedInPeriod

public boolean wasSightedInPeriod(int m_startYear,
                         int m_startMonth,
                         int m_startDay,
                         int m_endYear,
                         int m_endMonth,
                         int m_endDay)

wasSightedInPeriodLeftOnly

public boolean wasSightedInPeriodLeftOnly(int m_startYear,
                                 int m_startMonth,
                                 int m_endYear,
                                 int m_endMonth)

getName
```
public String getName()
```
Returns the user-input name of the MarkedIndividual, which is also used as an Index in the FastObjects database

Returns:
the name of the MarkedIndividual as a String

getIndividualID
```
public String getIndividualID()
```

getNickName
```
public String getNickName()
```

getNickNamer
```
public String getNickNamer()
```

setNickName
```
public void setNickName(String newName)
```
Sets the nickname of the MarkedIndividual.

setNickNamer

public void setNickNamer(String newNamer)

setName
```
public void setName(String newName)
```

setIndividualID

public void setIndividualID(String newName)

getEncounter
```
public 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.

Parameters:
i - the specified encounter number, where i=0...(n-1)

Returns:
the encounter at position i in the stored Vector of encounters

getLogEncounter

public Encounter getLogEncounter(int i)

getEncounters
```
public Vector getEncounters()
```
Returns the complete Vector of stored encounters for this MarkedIndividual.

Returns:
a Vector of encounters
See Also:
Vector

getDateSortedEncounters

public Encounter[] getDateSortedEncounters(boolean reverse)

getDateSortedEncounters

public Encounter[] getDateSortedEncounters()

getUnidentifiableEncounters
```
public Vector getUnidentifiableEncounters()
```
public Encounter[] getDateSortedEncounters(boolean includeLogEncounters) { return getDateSortedEncounters(); }

getComments
```
public String getComments()
```
Returns any additional, general comments recorded for this MarkedIndividual as a whole.

Returns:
a String of comments

addComments
```
public void addComments(String newComments)
```
Adds any general comments recorded for this MarkedIndividual as a whole.

getDataFiles
```
public Vector getDataFiles()
```
Returns the complete Vector of stored satellite tag data files for this MarkedIndividual.

Returns:
a Vector of Files
See Also:
Vector

getSex
```
public String getSex()
```
Returns the sex of this MarkedIndividual.

Returns:
a String

setSex
```
public void setSex(String newSex)
```
Sets the sex of this MarkedIndividual.

getLastEstimatedSize
```
public double getLastEstimatedSize()
```

wasSightedInLocationCode

public boolean wasSightedInLocationCode(String locationCode)

participatesInTheseVerbatimEventDates

public ArrayList<String> participatesInTheseVerbatimEventDates()

participatesInTheseLocationIDs

public ArrayList<String> participatesInTheseLocationIDs()

wasSightedInVerbatimEventDate

public boolean wasSightedInVerbatimEventDate(String ved)

wasSightedByUser

public boolean wasSightedByUser(String user)

getMaxNumYearsBetweenSightings

public int getMaxNumYearsBetweenSightings()

getEarliestSightingYear
```
public int getEarliestSightingYear()
```

getEarliestSightingTime
```
public long getEarliestSightingTime()
```

getSeriesCode
```
public String getSeriesCode()
```

getInterestedResearchers

public Vector getInterestedResearchers()

addInterestedResearcher

public void addInterestedResearcher(String email)

removeInterestedResearcher

public void removeInterestedResearcher(String email)

setSeriesCode

public void setSeriesCode(String newCode)

addDataFile
```
public void addDataFile(String dataFile)
```
Adds a satellite tag data file for this MarkedIndividual.

Parameters:
dataFile - the satellite tag data file to be added

removeDataFile
```
public void removeDataFile(String dataFile)
```
Removes a satellite tag data file for this MarkedIndividual.

Parameters:
dataFile - The satellite data file, as a String, to be removed.

getNumberTrainableEncounters

public int getNumberTrainableEncounters()

getNumberRightTrainableEncounters

public int getNumberRightTrainableEncounters()

getTrainableEncounters

public Vector getTrainableEncounters()

getRightTrainableEncounters

public Vector getRightTrainableEncounters()

avgLengthInPeriod

public double avgLengthInPeriod(int m_startYear,
                       int m_startMonth,
                       int m_endYear,
                       int m_endMonth)

Deprecated.

getAverageMeasurementInPeriod

public Double getAverageMeasurementInPeriod(int m_startYear,
                                   int m_startMonth,
                                   int m_endYear,
                                   int m_endMonth,
                                   String measurementType)

getAverageBiologicalMeasurementInPeriod

public Double getAverageBiologicalMeasurementInPeriod(int m_startYear,
                                             int m_startMonth,
                                             int m_endYear,
                                             int m_endMonth,
                                             String measurementType)

getDateTimeCreated
```
public String getDateTimeCreated()
```

setDateTimeCreated

public void setDateTimeCreated(String time)

setAlternateID

public void setAlternateID(String newID)

getAlternateID
```
public String getAlternateID()
```

getAllAlternateIDs
```
public String getAllAlternateIDs()
```

getDynamicProperties
```
public String getDynamicProperties()
```

setDynamicProperty

public void setDynamicProperty(String name,
                      String value)

getDynamicPropertyValue

public String getDynamicPropertyValue(String name)

removeDynamicProperty

public void removeDynamicProperty(String name)

getAllAppliedKeywordNames

public ArrayList<Keyword> getAllAppliedKeywordNames(Shepherd myShepherd)

getAllTissueSamples

public ArrayList<TissueSample> getAllTissueSamples()

getAllSinglePhotoVideo

public ArrayList<SinglePhotoVideo> getAllSinglePhotoVideo()

getAllValuesForDynamicProperty

public ArrayList<String> getAllValuesForDynamicProperty(String propertyName)

getPatterningCode
```
public String getPatterningCode()
```
Returns the patterning type evident on this MarkedIndividual instance.

setPatterningCode
```
public void setPatterningCode(String newCode)
```
Sets the patterning type evident on this MarkedIndividual instance.

resetMaxNumYearsBetweenSightings

public void resetMaxNumYearsBetweenSightings()

sidesSightedInPeriod

public String sidesSightedInPeriod(int m_startYear,
                          int m_startMonth,
                          int m_startDay,
                          int m_endYear,
                          int m_endMonth,
                          int m_endDay,
                          String locCode)

getGenusSpecies
```
public String getGenusSpecies()
```
Returns the first genus-species pair found in the Encounter objects for this MarkedIndividual.

Returns:
a String if found or null if no genus-species pair is found

getHaplotype
```
public String getHaplotype()
```
Returns the first haplotype found in the Encounter objects for this MarkedIndividual.

Returns:
a String if found or null if no haplotype is found

getGeneticSex
```
public String getGeneticSex()
```

hasLocusAndAllele

public boolean hasLocusAndAllele(String locus,
                        Integer alleleValue)

getAlleleValuesForLocus

public ArrayList<Integer> getAlleleValuesForLocus(String locus)

hasLocus

public boolean hasLocus(String locus)

hasMsMarkers
```
public boolean hasMsMarkers()
```

hasGeneticSex
```
public boolean hasGeneticSex()
```

getAllEmailsToUpdate
```
public ArrayList getAllEmailsToUpdate()
```
Obtains the email addresses of all submitters, photographs, and others to notify.

Returns:
ArrayList of all emails to inform

removeLogEncounter

public void removeLogEncounter(Encounter enc)

distFrom

public float distFrom(float lat1,
             float lng1,
             float lat2,
             float lng2)

getMaxDistanceBetweenTwoSightings

public Float getMaxDistanceBetweenTwoSightings()

getMaxTimeBetweenTwoSightings

public long getMaxTimeBetweenTwoSightings()

getAllAssignedUsers

public ArrayList<String> getAllAssignedUsers()

doNotSetLocalHaplotypeReflection
```
public void doNotSetLocalHaplotypeReflection(String myHaplo)
```
DO NOT SET DIRECTLY!!

Parameters:
myDepth -

getTimeOfBirth
```
public long getTimeOfBirth()
```

getTimeofDeath
```
public long getTimeofDeath()
```

setTimeOfBirth

public void setTimeOfBirth(long newTime)

setTimeOfDeath

public void setTimeOfDeath(long newTime)

getAllRelationships

public ArrayList<Relationship> getAllRelationships(Shepherd myShepherd)

getFomattedMSMarkersString

public String getFomattedMSMarkersString(String[] loci)

getMinDistanceBetweenTwoMarkedIndividuals

public Float getMinDistanceBetweenTwoMarkedIndividuals(MarkedIndividual otherIndy)

canUserAccess

public boolean canUserAccess(javax.servlet.http.HttpServletRequest request)

collaborationLockHtml

public String collaborationLockHtml(javax.servlet.http.HttpServletRequest request)

Class MarkedIndividual

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

individualID

alternateid

comments

sex

seriesCode

nickName

nickNamer

encounters

unidentifiableEncounters

dataFiles

numberEncounters

numUnidentifiableEncounters

interestedResearchers

dateTimeCreated

localHaplotypeReflection

dynamicProperties

patterningCode

maxYearsBetweenResightings

timeOfBirth

timeOfDeath

Constructor Detail

MarkedIndividual

MarkedIndividual

Method Detail

addEncounter

removeEncounter

totalEncounters

totalLogEncounters

returnEncountersWithGPSData

returnEncountersWithGPSData

isDeceased

wasSightedInYear

wasSightedInYear

wasSightedInYearLeftTagsOnly

averageLengthInYear

averageMeasuredLengthInYear

isDescribedByPhotoKeyword

wasSightedInMonth

wasSightedInPeriod

wasSightedInPeriod

wasSightedInPeriod

wasSightedInPeriodLeftOnly

getName

getIndividualID

getNickName

getNickNamer

setNickName

setNickNamer

setName

setIndividualID

getEncounter

getLogEncounter

getEncounters

getDateSortedEncounters

getDateSortedEncounters

getUnidentifiableEncounters

getComments

addComments

getDataFiles

getSex

setSex

getLastEstimatedSize

wasSightedInLocationCode

participatesInTheseVerbatimEventDates

participatesInTheseLocationIDs

wasSightedInVerbatimEventDate

wasSightedByUser

getMaxNumYearsBetweenSightings

getEarliestSightingYear

getEarliestSightingTime

getSeriesCode

getInterestedResearchers

addInterestedResearcher

removeInterestedResearcher