Package tethys.species

Class DataBlockSpeciesManager<T extends PamDataUnit>

java.lang.Object

tethys.species.DataBlockSpeciesManager<T>

Direct Known Subclasses:

ClickBlockSpeciesManager, ClickEventSpeciesManager, ClickTrainSpeciesManager, DetectionGroupSpeciesManager, DLSpeciesManager, FixedSpeciesManager, FormsAnnotationSpeciesManager, GPLSpeciesManager, RoccaSpeciesManager, RWSpeciesManager, WhistleSpeciesManager, WslClassSpeciesManager

public abstract class DataBlockSpeciesManager<T extends PamDataUnit>
extends Object

Manage species conversion for a single datablock. there seem to be three types of manager:
1. Datablocks which have a totally free list of species codes, such as the click detector, or whistle classifier
1a. A slight variation on this is blocks which have a list and also a default for data units which aren't classified.
2. Datablocks which have a single type which may be unknown or partially known, but we want the possibility of overriding it. e.g. the whistle detector may default to odontocete, but may be overridden to a mysticete species.
3. Datablocks with no information, or where the list from (1.) is empty.

In all cases, we need to handle this reasonably sensibly. The code list is always the start of this and must always return something, even if it's 'unknown'.

Author:

dg50

Field Summary

Fields

Modifier and Type	Field	Description
static final String	unitType
static final String	UNKNOWNSPECIES

Constructor Summary

Constructors

Constructor	Description
DataBlockSpeciesManager(PamDataBlock<T> dataBlock)

Method Summary

Modifier and Type	Method	Description
String	checkSpeciesMapError()	Check the species map.
void	clearMap()	Used only in debug mode to clear the species map.
ArrayList<String>	getAllSpeciesCodes()	Get all PAMGuard species codes, which may come from the DataBlockSpeciesCodes object, or the defaultSpeciesCode, or the defaultDefaultSpecies name.
PamDataBlock<T>	getDataBlock()
DataBlockSpeciesMap	getDatablockSpeciesMap()
SpeciesMapItem	getDefaultDefaultSpecies()
String	getDefaultSpeciesCode()
PamDialogPanel	getDialogPanel(SpeciesManagerObserver speciesManagerObserver)	Return a (preferably) small dialog panel that can contain options for the species manager.
abstract String	getSpeciesCode(T dataUnit)	Gets a species string for a specific data unit, This is abstracted since different detectors store this in non standard ways.
abstract DataBlockSpeciesCodes	getSpeciesCodes()	Object that contains a list of species codes.
SpeciesMapItem	getSpeciesItem(T dataUnit)
ArrayList<String>	makeUniqueList(ArrayList<String> list)	Make sure all entries in an array list are unique.
void	setDatablockSpeciesMap(DataBlockSpeciesMap datablockSpeciesMap)
void	setDefaultDefaultSpecies(SpeciesMapItem defaultDefaultSpecies)
void	setDefaultSpeciesCode(String defaultName)
void	showSpeciesDialog()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details

UNKNOWNSPECIES

public static final String UNKNOWNSPECIES

See Also:

• Constant Field Values

unitType

public static final String unitType

See Also:

• Constant Field Values

Constructor Details

DataBlockSpeciesManager

public DataBlockSpeciesManager(PamDataBlock<T> dataBlock)

Method Details

getSpeciesCodes

public abstract DataBlockSpeciesCodes getSpeciesCodes()

Object that contains a list of species codes. This may be fluid between configurations and may change during a session, e.g. through the addition of a new click type or changes to the whistle classifier settings.

Returns:

object containing a list of species types.

getSpeciesCode

public abstract String getSpeciesCode(T dataUnit)

Gets a species string for a specific data unit, This is abstracted since different detectors store this in non standard ways. The result of this should be within the set provided by getSpeciesCodes() which can then be used in the DataBlockSpeciesMap to look up an itis code.

Parameters:

dataUnit -

Returns:

A species code for a specific data unit. May be null (e.g. for an unclassified click)

getSpeciesItem

public SpeciesMapItem getSpeciesItem(T dataUnit)

getAllSpeciesCodes

public ArrayList<String> getAllSpeciesCodes()

Get all PAMGuard species codes, which may come from the DataBlockSpeciesCodes object, or the defaultSpeciesCode, or the defaultDefaultSpecies name. Ideally, at least one of these should have something, or we'll stick in an "Unknown"

Returns:

makeUniqueList

public ArrayList<String> makeUniqueList(ArrayList<String> list)

Make sure all entries in an array list are unique.

Parameters:

list -

Returns:

updated list.

getDatablockSpeciesMap

public DataBlockSpeciesMap getDatablockSpeciesMap()

setDatablockSpeciesMap

public void setDatablockSpeciesMap(DataBlockSpeciesMap datablockSpeciesMap)

showSpeciesDialog

public void showSpeciesDialog()

getDataBlock

public PamDataBlock<T> getDataBlock()

Returns:

the dataBlock

getDefaultDefaultSpecies

public SpeciesMapItem getDefaultDefaultSpecies()

Returns:

the defaultSpecies

setDefaultDefaultSpecies

public void setDefaultDefaultSpecies(SpeciesMapItem defaultDefaultSpecies)

Parameters:

defaultSpecies - the defaultSpecies to set

getDefaultSpeciesCode

public String getDefaultSpeciesCode()

Returns:

the defaultName

setDefaultSpeciesCode

public void setDefaultSpeciesCode(String defaultName)

Parameters:

defaultName - the defaultName to set

checkSpeciesMapError

public String checkSpeciesMapError()

Check the species map. Only return null if every species code has a map item. Otherwise it's not safe to export.

Returns:

null if all codes have a lookup, otherwise some sort of useful error information

clearMap

public void clearMap()

Used only in debug mode to clear the species map. Just used while debugging so that I can check that it's easy to recreate the map and that dialogs don't go screwy when it's empty.

getDialogPanel

public PamDialogPanel getDialogPanel(SpeciesManagerObserver speciesManagerObserver)

Return a (preferably) small dialog panel that can contain options for the species manager.

Returns: