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apollo.gui
Class SelectionSet  

java.lang.Object
  apollo.gui.SelectionSet

Direct Known Subclasses:

EvidenceSelectionSet

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public class SelectionSet

extends java.lang.Object

This is a convienience class for determining and making easily available which sets, transcripts and genes a group of features come from.

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Field Summary
(package private)  java.util.Vector	features           features contains only leaf features(descendants of sets)
(package private)  java.util.Vector	genes
private  java.util.Vector	originalFeatures           Vector of the original selection vector passed in, contains all different types of features.
(package private)  java.util.Vector	sets
(package private)  java.util.Vector	transcripts
(package private)  boolean	used

 

Constructor Summary

SelectionSet(Selection sel)

SelectionSet(Selection sel, apollo.gui.genomemap.ViewI v)

SelectionSet(java.util.Vector df)

 

Method Summary
private  void	addSeqFeature(apollo.datamodel.SeqFeatureI sf, java.util.Vector sets)
void	dump(java.lang.String desc)
private  java.util.Vector	findGenes(java.util.Vector tran)
private  java.util.Vector	findSeqFeatures(java.util.Vector features)
private  java.util.Vector	findSets(java.util.Vector features)           Goes through vector of features finding FeatureSets.
private  java.util.Vector	findTranscripts(java.util.Vector features)
apollo.datamodel.SeqFeatureI	getFeature(int index)
java.util.Vector	getFeatures()
apollo.datamodel.Transcript	getFirstFullySelectedTranscript()           Returns the first transcript in the selection that has all of its exons selected, if a Transcript is present that certainly qualifies.
apollo.datamodel.Gene	getGene(int index)
java.util.Vector	getGenes()
apollo.datamodel.FeatureSetI	getSet(int index)
java.util.Vector	getSets()
apollo.datamodel.Transcript	getTranscript(int index)
java.util.Vector	getTranscripts()           Return all transcript involved in selection, whether fully or partially selected.
boolean	getUsed()
void	init(java.util.Vector feat_vect)
void	setUsed(boolean state)

 

Methods inherited from class java.lang.Object

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

 

Field Detail

features

java.util.Vector features

features contains only leaf features(descendants of sets)

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sets

java.util.Vector sets

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transcripts

java.util.Vector transcripts

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genes

java.util.Vector genes

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originalFeatures

private java.util.Vector originalFeatures

Vector of the original selection vector passed in, contains all different types of features.

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used

boolean used

Constructor Detail

SelectionSet

public SelectionSet(java.util.Vector df)

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SelectionSet

public SelectionSet(Selection sel)

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SelectionSet

public SelectionSet(Selection sel,
                    apollo.gui.genomemap.ViewI v)

Method Detail

init

public void init(java.util.Vector feat_vect)

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getUsed

public boolean getUsed()

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setUsed

public void setUsed(boolean state)

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getFeatures

public java.util.Vector getFeatures()

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getFeature

public apollo.datamodel.SeqFeatureI getFeature(int index)

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getSets

public java.util.Vector getSets()

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getSet

public apollo.datamodel.FeatureSetI getSet(int index)

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getTranscripts

public java.util.Vector getTranscripts()

Return all transcript involved in selection, whether fully or partially selected.

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getTranscript

public apollo.datamodel.Transcript getTranscript(int index)

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getFirstFullySelectedTranscript

public apollo.datamodel.Transcript getFirstFullySelectedTranscript()

Returns the first transcript in the selection that has all of its exons selected, if a Transcript is present that certainly qualifies. This is not the same as getTranscript(0). The transcripts stored in SelectionSet do not have to be fully selected. So getTranscript(0) may return a multi-exon transcript that has only one of its exons selected. At present we only need the first fully selected trans (for AnnEd.moveExonsToTranscript). If in the future we need more than just this, this can be generalized.

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getGenes

public java.util.Vector getGenes()

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getGene

public apollo.datamodel.Gene getGene(int index)

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findTranscripts

private java.util.Vector findTranscripts(java.util.Vector features)

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findSeqFeatures

private java.util.Vector findSeqFeatures(java.util.Vector features)

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addSeqFeature

private void addSeqFeature(apollo.datamodel.SeqFeatureI sf,
                           java.util.Vector sets)

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findSets

private java.util.Vector findSets(java.util.Vector features)

Goes through vector of features finding FeatureSets. If features is a drawable it gets its model feature. If model feature is a FeatureSet adds it to return vector, if not adds parent, if not already added

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findGenes

private java.util.Vector findGenes(java.util.Vector tran)

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dump

public void dump(java.lang.String desc)

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SUMMARY:  JAVADOC |  SOURCE |  DOWNLOAD | NESTED | FIELD | CONSTR | METHOD	DETAIL: FIELD | CONSTR | METHOD

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