apollo.gui
Class Selection

java.lang.Object
  java.util.AbstractCollection<E>
      java.util.AbstractList<E>
          java.util.ArrayList
              apollo.util.FeatureList
                  apollo.gui.Selection

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, java.lang.Iterable, java.util.Collection, java.util.List, java.util.RandomAccess

public class Selection
extends FeatureList

Manages a selection of objects(a vector of SelectionItems), and for SelectableI's controls their selection state. A Selection may have both parent and child. getSelectionDescendedFromModel(SeqFeat,true) will filter out parent child redundnancies. This is used in AnnotationEditor

See Also:

Serialized Form

Field Summary

static int	FEATURE
static int	SET

Fields inherited from class apollo.util.FeatureList

logger

Fields inherited from class java.util.AbstractList

modCount

Constructor Summary

Selection()
Vector of SeqFeatureI data of SelectionItems, for convenience

Selection(FeatureList feats, java.lang.Object source)

Method Summary

void	add(FeatureList feats, java.lang.Object source)
void	add(FeatureList feats, java.lang.Object source, boolean deselectIfAlreadySelected)
void	add(Selection selection)
void	add(Selection selection, boolean deselectIfAlreadySelected)
void	add(SelectionItem item) I took out the boolean force, add is always an add and if its already it does nothing, in other words have it always be force == true, i dont think force==false was used at all Took out the return value of SelectionItem - dont think it was used.
void	add(SelectionItem item, boolean deselectIfAlreadySelected)
void	clear() This does deselection.
boolean	containsFeature(SeqFeatureI sf) Returns true if there is a SelectionItem in Selection with sf
FeatureList	getListDescendedFromModel(SeqFeatureI model, boolean check)
java.util.Vector	getSelected() Vector of SelectionItems
FeatureList	getSelectedData() Returns vector of selection items data of selection (SeqFeatureI's) change this to return FeatureList
SeqFeatureI	getSelectedData(int i) The data of the selection items is a SeqFeatureI, model not drawable
java.util.Vector	getSelectedVector()
java.util.HashSet	getSelectedVisualTypes() Returns a HashSet of Strings that is the unique set of visual types for the selection.
Selection	getSelectionDescendedFromModel(SeqFeatureI model) Return a sub-Selection of the current Selection that are descendants of SeqFeatureI model.
Selection	getSelectionDescendedFromModel(SeqFeatureI model, boolean checkForRedundantDescendants) Return a sub-Selection of the current Selection that are descendants of SeqFeatureI model.
SelectionItem	getSelectionItem(int i)
SelectionItem	getSelectionItem(SeqFeatureI sf)
void	removeFeature(SeqFeatureI feat)
int	size()

Methods inherited from class apollo.util.FeatureList

add, addAlignable, addAll, addAllFeatures, addFeature, addFeaturePair, addVector, cloneList, featureIterator, filterForFeaturePairs, first, getAlignable, getAllFeaturePairLeaves, getAllLeaves, getConsolidatedFeatures, getFeatsWithAlignments, getFeatsWithinRefSeqRegion, getFeature, getFeaturePair, getFeatWithName, getParents, getRangeOfWholeList, getUniqueHitNames, last, setAlignablesOnly, setDoUniqueCheck, setFeaturePairsOnly, sortByStart, toVector

Methods inherited from class java.util.ArrayList

add, addAll, addAll, clone, contains, ensureCapacity, get, indexOf, isEmpty, lastIndexOf, remove, remove, removeRange, set, toArray, toArray, trimToSize

Methods inherited from class java.util.AbstractList

equals, hashCode, iterator, listIterator, listIterator, subList

Methods inherited from class java.util.AbstractCollection

containsAll, removeAll, retainAll, toString

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.util.List

containsAll, equals, hashCode, iterator, listIterator, listIterator, removeAll, retainAll, subList

Field Detail

FEATURE

public static final int FEATURE

See Also:

Constant Field Values

SET

public static final int SET

See Also:

Constant Field Values

Constructor Detail

Selection

public Selection()

Vector of SeqFeatureI data of SelectionItems, for convenience

Selection

public Selection(FeatureList feats,
                 java.lang.Object source)

Method Detail

add

public void add(SelectionItem item)

I took out the boolean force, add is always an add and if its already it does nothing, in other words have it always be force == true, i dont think force==false was used at all Took out the return value of SelectionItem - dont think it was used. No longer checks if the new item descends from or is the ancestor of anything in the selection - too slow on big selections. This is done on demand with getSelectionDescendedFromModel(model,true)

add

public void add(SelectionItem item,
                boolean deselectIfAlreadySelected)

add

public void add(FeatureList feats,
                java.lang.Object source,
                boolean deselectIfAlreadySelected)

add

public void add(FeatureList feats,
                java.lang.Object source)

add

public void add(Selection selection,
                boolean deselectIfAlreadySelected)

add

public void add(Selection selection)

removeFeature

public void removeFeature(SeqFeatureI feat)

Overrides:

removeFeature in class FeatureList

getSelected

public java.util.Vector getSelected()

Vector of SelectionItems

getListDescendedFromModel

public FeatureList getListDescendedFromModel(SeqFeatureI model,
                                             boolean check)

getSelectionDescendedFromModel

public Selection getSelectionDescendedFromModel(SeqFeatureI model)

Return a sub-Selection of the current Selection that are descendants of SeqFeatureI model. This should replace getSelectionForSource as it is independent of which view the selection originally came from.

getSelectionDescendedFromModel

public Selection getSelectionDescendedFromModel(SeqFeatureI model,
                                                boolean checkForRedundantDescendants)

Return a sub-Selection of the current Selection that are descendants of SeqFeatureI model. This should replace getSelectionForSource as it is independent of which view the selection originally came from. If checkForRedundantDescendants is true then selection items whose parents/ancestors are already selected are filtered out. (Should the descend check be a separate method?) return a feat list?

containsFeature

public boolean containsFeature(SeqFeatureI sf)

Returns true if there is a SelectionItem in Selection with sf

getSelectedData

public FeatureList getSelectedData()

Returns vector of selection items data of selection (SeqFeatureI's) change this to return FeatureList

getSelectedVector

public java.util.Vector getSelectedVector()

getSelectedData

public SeqFeatureI getSelectedData(int i)

The data of the selection items is a SeqFeatureI, model not drawable

getSelectionItem

public SelectionItem getSelectionItem(int i)

getSelectionItem

public SelectionItem getSelectionItem(SeqFeatureI sf)

size

public int size()

Specified by:

size in interface java.util.Collection

Specified by:

size in interface java.util.List

Overrides:

size in class java.util.ArrayList

clear

public void clear()

This does deselection. deselect() is called on all the SelectionItems which handle deselection

Specified by:

clear in interface java.util.Collection

Specified by:

clear in interface java.util.List

Overrides:

clear in class java.util.ArrayList

getSelectedVisualTypes

public java.util.HashSet getSelectedVisualTypes()

Returns a HashSet of Strings that is the unique set of visual types for the selection. This is not the logical types. SeqFeature.getType returns the logical type. DetailInfo.getPropertyType maps the logical type to the visual type. The visual type is what is displayed in the evidence panel and tiers window. Should this take in strand? put this in FeatureList?