apollo.gui.synteny
Class CurationManager

java.lang.Object
  apollo.gui.synteny.CurationManager

public class CurationManager
extends java.lang.Object

Holds CurationState objects. Reflects current CompositeDataHolder. Should CurationManager also get in the link business and hold SyntenyLinkPanels as well? probably. Perhaps this should be broken into 2 (or 3) objects. The tracking of data adapters is handy for SyntenyAdapter - should maybe have the data adapter stuff in a dataadapter object - but might be hard to separate - maybe do with an interface?

Field Summary

protected static org.apache.log4j.Logger

logger

Method Summary

static GuiCurationState	getActiveCurationState()
GuiCurationState	getActiveCurState()
static Style	getActiveStyle()
CompositeDataHolder	getCompositeDataHolder()
Controller	getCurationController(int i) Convenience for getCurationState(i).getController()
static CurationManager	getCurationManager() Singleton - there should only be one curationState holder
java.lang.String	getCurationName(int i)
GuiCurationState	getCurationState(int i)
GuiCurationState	getCurStateForCurName(java.lang.String curationName) Returns null if no cur state with curationName (shouldnt happen)
ApolloDataAdapterI	getDataAdapter() data adapter could be composite(SyntenyAdapter) or single(the rest) depending on if we are multi or single curationState.
StatusBar	getStatusBar()
boolean	isActiveCurName(java.lang.String curName)
boolean	isMultiCuration() Whether we have more than one curationState or not
boolean	isSingleCuration()
int	numberOfCurations()
void	selectInputFeatures() If the input from dataadapter is a specific feature within the curation then select it.
void	setActiveCurState(GuiCurationState curationState)
void	setActiveCurState(java.lang.String curSetName)

Methods inherited from class java.lang.Object

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

Field Detail

logger

protected static final org.apache.log4j.Logger logger

Method Detail

getCurationManager

public static CurationManager getCurationManager()

Singleton - there should only be one curationState holder

getCompositeDataHolder

public CompositeDataHolder getCompositeDataHolder()

getDataAdapter

public ApolloDataAdapterI getDataAdapter()

data adapter could be composite(SyntenyAdapter) or single(the rest) depending on if we are multi or single curationState. It is the data adapter that produced the composite data holder(or the curation set that the composite data holder wraps) and can save the comp data holder (or its 1st cur set)

numberOfCurations

public int numberOfCurations()

isMultiCuration

public boolean isMultiCuration()

Whether we have more than one curationState or not

isSingleCuration

public boolean isSingleCuration()

getCurationState

public GuiCurationState getCurationState(int i)

getCurationName

public java.lang.String getCurationName(int i)

getStatusBar

public StatusBar getStatusBar()

getCurationController

public Controller getCurationController(int i)

Convenience for getCurationState(i).getController()

setActiveCurState

public void setActiveCurState(GuiCurationState curationState)

setActiveCurState

public void setActiveCurState(java.lang.String curSetName)

getActiveStyle

public static Style getActiveStyle()

getActiveCurationState

public static GuiCurationState getActiveCurationState()

getActiveCurState

public GuiCurationState getActiveCurState()

isActiveCurName

public boolean isActiveCurName(java.lang.String curName)

getCurStateForCurName

public GuiCurationState getCurStateForCurName(java.lang.String curationName)

Returns null if no cur state with curationName (shouldnt happen)

selectInputFeatures

public void selectInputFeatures()

If the input from dataadapter is a specific feature within the curation then select it. Presently only set up for DataInputType.GENE. If GENE then search for features with gene name and select them. This can be done for any input that is a subset of the whole curation set obvioulsy. Was a part of loadGUI(), had to break out as FileMenu._doLoad clears out selection after calling loadGUI().