org.biojava.spice.gui.alignmentchooser
Class AlignmentChooser

java.lang.Object
  org.biojava.spice.gui.alignmentchooser.AlignmentChooser

public class AlignmentChooser

extends Object

A class to choose bewteen differen sequence and structure alignments. The structure choosen here will be displayed as the main structure in SPICE.

Author:

Andreas Prlic

Constructor Summary

AlignmentChooser(DasCoordinateSystem queryCs, DasCoordinateSystem subjectCs)

Method Summary

void	addObjectListener(ObjectListener li) a panel to choose a seq-structure alignment
void	clearAlignment()
void	clearSelection()
Chain	getChain()
float	getScale()
void	initPanels()
void	loadAlignments(String code)
void	newAlignment(AlignmentEvent event) convert the biojava alignment class into biojava feature objects
void	newObjectRequested(String accessionCode)
void	newSequence(SequenceEvent e)
void	noAlignmentFound(AlignmentEvent event)
void	noObjectFound(String accessionCode)
void	repaint()
void	selectedSeqPosition(int position)
void	selectedSeqRange(int start, int end)
void	selectionLocked(boolean flag)
void	setChain(Chain c, int number)
void	setDasSources(SpiceDasSource[] sources)
void	setScale(float s)
void	setSize(Dimension d) overwrite resize, to change the scale of the displayed sequence
void	show()
void	triggerNewObjectRequested(String code)

Methods inherited from class java.lang.Object

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

Constructor Detail

AlignmentChooser

public AlignmentChooser(DasCoordinateSystem queryCs,
                        DasCoordinateSystem subjectCs)

Parameters:

queryCs - query coordinate sytstem

subjectCs -

Method Detail

addObjectListener

public void addObjectListener(ObjectListener li)

a panel to choose a seq-structure alignment

Parameters:

li - listener

initPanels

public void initPanels()

show

public void show()

getScale

public float getScale()

setScale

public void setScale(float s)

repaint

public void repaint()

setDasSources

public void setDasSources(SpiceDasSource[] sources)

loadAlignments

public void loadAlignments(String code)

setChain

public void setChain(Chain c,
                     int number)

getChain

public Chain getChain()

noAlignmentFound

public void noAlignmentFound(AlignmentEvent event)

newAlignment

public void newAlignment(AlignmentEvent event)

convert the biojava alignment class into biojava feature objects

triggerNewObjectRequested

public void triggerNewObjectRequested(String code)

setSize

public void setSize(Dimension d)

overwrite resize, to change the scale of the displayed sequence

Parameters:

d -

newObjectRequested

public void newObjectRequested(String accessionCode)

noObjectFound

public void noObjectFound(String accessionCode)

clearAlignment

public void clearAlignment()

clearSelection

public void clearSelection()

newSequence

public void newSequence(SequenceEvent e)

selectedSeqPosition

public void selectedSeqPosition(int position)

selectedSeqRange

public void selectedSeqRange(int start,
                             int end)

selectionLocked

public void selectionLocked(boolean flag)