mesquite.lib
Class Associable

java.lang.Object
  mesquite.lib.Listened
      mesquite.lib.Attachable
          mesquite.lib.Associable

All Implemented Interfaces:

Annotatable, Commandable, HTMLDescribable, Listable, Listenable, Selectionable

Direct Known Subclasses:

AssociableWithSpecs, MesquiteTree

public abstract class Associable
extends Attachable
implements Commandable, Annotatable, Selectionable

A class that contains serially repeated parts, to each of which may be attached information. For example, a Tree contains many nodes, and information might be attached to each node. A Taxa contains taxons, a CharacterData contains characters, and so on. The purpose of this class is to coordinate this attached ("associated") information. Subclasses include FileElement (and thus CharacterData and Taxa) and Tree.

Field Summary

protected java.lang.String	comment
protected ObjectArray	comments The object array storing comments (e.g.
protected int	numParts
protected boolean	rememberDefaultOrder
protected Bits	selected The bit field indicating which parts are selected currently.
protected long	versionNumber A number recording the version number.

Fields inherited from class mesquite.lib.Listened

allListeners, classes, classesNotified, listeners, listenersRemaining, notifications

Fields inherited from interface mesquite.lib.HTMLDescribable

verbose

Constructor Summary

Associable()

Associable(int numParts)

Method Summary

boolean	addParts(int starting, int num)
boolean	anyAssociatedObject(NameReference nRef) Returns true iff there is at least one associate object of type nRef
boolean	anySelected() Returns whether there are any selected parts
void	clearAllAssociatedBits(NameReference nRef)
boolean	contiguousSelection() Returns whether there are selected parts that form a contiguous selection
boolean	contiguousSelectionOld() Returns whether there are selected parts that form a contiguous selection.
void	copyCurrentToPreviousOrder()
void	deassignAllAssociatedLongs(NameReference nRef)
void	deassignAssociated()
void	deassignAssociated(int node)
void	deleteJustAdded()
boolean	deleteParts(int starting, int num)
void	deselectAll() Deselects all parts
void	dispose() Disposes this associable
java.lang.Object	doCommand(java.lang.String commandName, java.lang.String arguments, CommandChecker checker) For Commandable interface.
void	equalizeParts(Associable other, int otherPart, int part)
void	exchangeAssociated(int node1, int node2)
int	firstSelected() Returns index of first selected part
java.lang.String	getAnnotation() Returns the comment (e.g., footnote) of this element
java.lang.String	getAnnotation(int part) Returns whether the part is selected
boolean	getAssociatedBit(NameReference nRef, int index)
Bits	getAssociatedBits(int index)
double	getAssociatedDouble(NameReference nRef, int index)
DoubleArray	getAssociatedDoubles(int index)
long	getAssociatedLong(NameReference nRef, int index)
LongArray	getAssociatedLongs(int index)
java.lang.Object	getAssociatedObject(NameReference nRef, int index)
ObjectArray	getAssociatedObjects(int index)
int	getDefaultPosition(int part)
boolean	getDirty() Returns whether the element is dirty (changed since last file save) or not
boolean	getJustAdded(int part)
int	getNumberAssociatedBits()
int	getNumberAssociatedDoubles()
int	getNumberAssociatedLongs()
int	getNumberAssociatedObjects()
int	getNumberOfParts()
int	getNumberOfSelectableParts() Returns number of parts that can be selected
boolean	getSelected(int part) Returns whether the part is selected
Bits	getSelectedBits() Returns selected directly
Snapshot	getSnapshot(MesquiteFile file)
long	getVersionNumber() Returns version number of Associable.
Bits	getWhichAssociatedBits(NameReference nRef)
DoubleArray	getWhichAssociatedDouble(NameReference nRef)
LongArray	getWhichAssociatedLong(NameReference nRef)
ObjectArray	getWhichAssociatedObject(NameReference nRef)
protected boolean	inBounds(int part) Returns true if part is within bounds.
int	lastSelected() Returns index of last selected part
java.lang.String	listAssociates()
NameReference	makeAssociatedBits(java.lang.String name)
NameReference	makeAssociatedDoubles(java.lang.String name)
NameReference	makeAssociatedLongs(java.lang.String name)
NameReference	makeAssociatedObjects(java.lang.String name)
boolean	moveParts(int starting, int num, int justAfter)
int	numberSelected() Returns number of selected parts
int	numberSelected(boolean onlyCountSelected) returns number of parts that are selected or, if onlyCountSelected is false, all parts
void	readAssociated(java.lang.String assocString, int node, MesquiteInteger pos)
void	recordCurrentOrder()
protected void	recordDefaultOrder()
void	recordPreviousOrder()
void	removeAssociatedBits(NameReference nRef)
void	removeAssociatedDoubles(NameReference nRef)
void	removeAssociatedLongs(NameReference nRef)
void	removeAssociatedObjects(NameReference nRef)
void	resetDefaultOrderToCurrent()
void	resetJustAdded()
void	restoreToPreviousOrder()
void	selectAll() Selects all parts
void	setAnnotation(int part, java.lang.String comment) Sets the comment for a part
void	setAnnotation(java.lang.String e, boolean notify) Sets the comment (e.g., footnote) of this element
void	setAssociatedBit(NameReference nRef, int index, boolean value)
void	setAssociatedDouble(NameReference nRef, int index, double value)
void	setAssociatedLong(NameReference nRef, int index, long value)
void	setAssociatedObject(NameReference nRef, int index, java.lang.Object value)
void	setAssociateds(Associable a)
void	setDefaultPosition(int part, int position)
void	setDirty(boolean d) Sets the element as dirty (changed since last file save) or not
void	setJustAdded(int part, boolean b)
void	setNumberOfParts(int num) Set the number of parts to given number.
void	setSelected(int part, boolean select) Sets whether or not the part is selected
boolean	swapParts(int first, int second)
java.lang.String	toHTMLStringDescription()
void	transferAssociated(int fromNode, int toNode)
java.lang.String	writeAssociated(int node, boolean associatedUseComments)
void	zeroAllAssociatedDoubles(NameReference nRef)
void	zeroAllAssociatedLongs(NameReference nRef)
void	zeroAllAssociatedObjects(NameReference nRef)

Methods inherited from class mesquite.lib.Attachable

anyAttachments, attach, attachIfUniqueName, detach, getAttachment, getAttachment, getAttachments, listAttachments, readAttachments, setAttachments, writeAttachments

Methods inherited from class mesquite.lib.Listened

addListener, addListenerHighPriority, amIListening, decrementNotifySuppress, doAfterNotify, getRemainingListeners, incrementNotifySuppress, listListeners, notifyDisposing, notifyListeners, notifyListeners, removeListener, reportListeners, setDumpNotified

Methods inherited from class java.lang.Object

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

Methods inherited from interface mesquite.lib.Listable

getName

Methods inherited from interface mesquite.lib.Listenable

addListener, addListenerHighPriority, amIListening, decrementNotifySuppress, incrementNotifySuppress, listListeners, notifyListeners, removeListener

Field Detail

numParts

protected int numParts

rememberDefaultOrder

protected boolean rememberDefaultOrder

versionNumber

protected long versionNumber

A number recording the version number. With every change of the object, the version number is incremented. Used now for trees and taxa.

comment

protected java.lang.String comment

selected

protected Bits selected

The bit field indicating which parts are selected currently. This is instantiated only if needed.

comments

protected ObjectArray comments

The object array storing comments (e.g. footnotes) for each of the parts. This is instantiated only if needed.

Constructor Detail

Associable

public Associable(int numParts)

Associable

public Associable()

Method Detail

dispose

public void dispose()

Disposes this associable

Overrides:

dispose in class Attachable

toHTMLStringDescription

public java.lang.String toHTMLStringDescription()

Specified by:

toHTMLStringDescription in interface HTMLDescribable

Overrides:

toHTMLStringDescription in class Attachable

equalizeParts

public void equalizeParts(Associable other,
                          int otherPart,
                          int part)

setJustAdded

public void setJustAdded(int part,
                         boolean b)

getJustAdded

public boolean getJustAdded(int part)

resetJustAdded

public void resetJustAdded()

deleteJustAdded

public void deleteJustAdded()

recordDefaultOrder

protected void recordDefaultOrder()

recordCurrentOrder

public void recordCurrentOrder()

recordPreviousOrder

public void recordPreviousOrder()

copyCurrentToPreviousOrder

public void copyCurrentToPreviousOrder()

getVersionNumber

public long getVersionNumber()

Returns version number of Associable. Version number should be incremented with each change.

getNumberOfParts

public int getNumberOfParts()

getSnapshot

public Snapshot getSnapshot(MesquiteFile file)

doCommand

public java.lang.Object doCommand(java.lang.String commandName,
                                  java.lang.String arguments,
                                  CommandChecker checker)

For Commandable interface. TODO: have setDouble and pass part; have getDouble and pass part. Likewise for long, etc.

Specified by:

doCommand in interface Commandable

setAnnotation

public void setAnnotation(java.lang.String e,
                          boolean notify)

Sets the comment (e.g., footnote) of this element

Specified by:

setAnnotation in interface Annotatable

getAnnotation

public java.lang.String getAnnotation()

Returns the comment (e.g., footnote) of this element

Specified by:

getAnnotation in interface Annotatable

setDirty

public void setDirty(boolean d)

Sets the element as dirty (changed since last file save) or not

getDirty

public boolean getDirty()

Returns whether the element is dirty (changed since last file save) or not

inBounds

protected boolean inBounds(int part)

Returns true if part is within bounds.

listAssociates

public java.lang.String listAssociates()

writeAssociated

public java.lang.String writeAssociated(int node,
                                        boolean associatedUseComments)

readAssociated

public void readAssociated(java.lang.String assocString,
                           int node,
                           MesquiteInteger pos)

setAssociateds

public void setAssociateds(Associable a)

transferAssociated

public void transferAssociated(int fromNode,
                               int toNode)

exchangeAssociated

public void exchangeAssociated(int node1,
                               int node2)

deassignAssociated

public void deassignAssociated(int node)

deassignAssociated

public void deassignAssociated()

setNumberOfParts

public void setNumberOfParts(int num)

Set the number of parts to given number. THIS MUST BE CALLED whenever the number of parts (characters, nodes, etc.) changes.

addParts

public boolean addParts(int starting,
                        int num)

deleteParts

public boolean deleteParts(int starting,
                           int num)

moveParts

public boolean moveParts(int starting,
                         int num,
                         int justAfter)

restoreToPreviousOrder

public void restoreToPreviousOrder()

swapParts

public boolean swapParts(int first,
                         int second)

getDefaultPosition

public int getDefaultPosition(int part)

setDefaultPosition

public void setDefaultPosition(int part,
                               int position)

resetDefaultOrderToCurrent

public void resetDefaultOrderToCurrent()

setAnnotation

public void setAnnotation(int part,
                          java.lang.String comment)

Sets the comment for a part

getAnnotation

public java.lang.String getAnnotation(int part)

Returns whether the part is selected

getNumberOfSelectableParts

public int getNumberOfSelectableParts()

Returns number of parts that can be selected

Specified by:

getNumberOfSelectableParts in interface Selectionable

setSelected

public void setSelected(int part,
                        boolean select)

Sets whether or not the part is selected

Specified by:

setSelected in interface Selectionable

getSelected

public boolean getSelected(int part)

Returns whether the part is selected

Specified by:

getSelected in interface Selectionable

deselectAll

public void deselectAll()

Deselects all parts

Specified by:

deselectAll in interface Selectionable

selectAll

public void selectAll()

Selects all parts

Specified by:

selectAll in interface Selectionable

firstSelected

public int firstSelected()

Returns index of first selected part

lastSelected

public int lastSelected()

Returns index of last selected part

getSelectedBits

public Bits getSelectedBits()

Returns selected directly

contiguousSelection

public boolean contiguousSelection()

Returns whether there are selected parts that form a contiguous selection

contiguousSelectionOld

public boolean contiguousSelectionOld()

Returns whether there are selected parts that form a contiguous selection. VERY SLOW.

anySelected

public boolean anySelected()

Returns whether there are any selected parts

Specified by:

anySelected in interface Selectionable

numberSelected

public int numberSelected()

Returns number of selected parts

Specified by:

numberSelected in interface Selectionable

numberSelected

public int numberSelected(boolean onlyCountSelected)

returns number of parts that are selected or, if onlyCountSelected is false, all parts

getNumberAssociatedBits

public int getNumberAssociatedBits()

getAssociatedBits

public Bits getAssociatedBits(int index)

makeAssociatedBits

public NameReference makeAssociatedBits(java.lang.String name)

removeAssociatedBits

public void removeAssociatedBits(NameReference nRef)

getWhichAssociatedBits

public Bits getWhichAssociatedBits(NameReference nRef)

clearAllAssociatedBits

public void clearAllAssociatedBits(NameReference nRef)

setAssociatedBit

public void setAssociatedBit(NameReference nRef,
                             int index,
                             boolean value)

getAssociatedBit

public boolean getAssociatedBit(NameReference nRef,
                                int index)

getNumberAssociatedLongs

public int getNumberAssociatedLongs()

getAssociatedLongs

public LongArray getAssociatedLongs(int index)

makeAssociatedLongs

public NameReference makeAssociatedLongs(java.lang.String name)

removeAssociatedLongs

public void removeAssociatedLongs(NameReference nRef)

getWhichAssociatedLong

public LongArray getWhichAssociatedLong(NameReference nRef)

deassignAllAssociatedLongs

public void deassignAllAssociatedLongs(NameReference nRef)

zeroAllAssociatedLongs

public void zeroAllAssociatedLongs(NameReference nRef)

setAssociatedLong

public void setAssociatedLong(NameReference nRef,
                              int index,
                              long value)

getAssociatedLong

public long getAssociatedLong(NameReference nRef,
                              int index)

getNumberAssociatedDoubles

public int getNumberAssociatedDoubles()

getAssociatedDoubles

public DoubleArray getAssociatedDoubles(int index)

makeAssociatedDoubles

public NameReference makeAssociatedDoubles(java.lang.String name)

removeAssociatedDoubles

public void removeAssociatedDoubles(NameReference nRef)

getWhichAssociatedDouble

public DoubleArray getWhichAssociatedDouble(NameReference nRef)

zeroAllAssociatedDoubles

public void zeroAllAssociatedDoubles(NameReference nRef)

setAssociatedDouble

public void setAssociatedDouble(NameReference nRef,
                                int index,
                                double value)

getAssociatedDouble

public double getAssociatedDouble(NameReference nRef,
                                  int index)

getNumberAssociatedObjects

public int getNumberAssociatedObjects()

getAssociatedObjects

public ObjectArray getAssociatedObjects(int index)

makeAssociatedObjects

public NameReference makeAssociatedObjects(java.lang.String name)

removeAssociatedObjects

public void removeAssociatedObjects(NameReference nRef)

getWhichAssociatedObject

public ObjectArray getWhichAssociatedObject(NameReference nRef)

zeroAllAssociatedObjects

public void zeroAllAssociatedObjects(NameReference nRef)

setAssociatedObject

public void setAssociatedObject(NameReference nRef,
                                int index,
                                java.lang.Object value)

getAssociatedObject

public java.lang.Object getAssociatedObject(NameReference nRef,
                                            int index)

anyAssociatedObject

public boolean anyAssociatedObject(NameReference nRef)

Returns true iff there is at least one associate object of type nRef