Class StructureAlignmentJmol
- java.lang.Object
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- org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
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- org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol
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- All Implemented Interfaces:
java.awt.event.ActionListener
,java.awt.event.MouseListener
,java.awt.event.MouseMotionListener
,java.awt.event.WindowListener
,java.util.EventListener
,javax.swing.event.ChangeListener
public class StructureAlignmentJmol extends AbstractAlignmentJmol implements javax.swing.event.ChangeListener
A class that provides a simple GUI for Jmol- Since:
- 1.6
- Author:
- Andreas Prlic
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Field Summary
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Fields inherited from class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
colorPalette, COMMAND_LINE_HELP, DEFAULT_HEIGHT, DEFAULT_SCRIPT, DEFAULT_WIDTH, frame, jmolPanel, nrOpenWindows, status, structure, text
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Constructor Summary
Constructors Constructor Description StructureAlignmentJmol()
StructureAlignmentJmol(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description void
actionPerformed(java.awt.event.ActionEvent e)
void
destroy()
Set all the member variables to null.java.util.List<Matrix>
getDistanceMatrices()
Returns a List of internal Distance Matrices, one for each structure in the alignment.static java.lang.String
getJmolScript4Block(AFPChain afpChain, Atom[] ca1, Atom[] ca2, int blockNr)
static java.lang.String
getJmolString(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
protected void
initCoords()
Display the structures after the variable initialization in the constructor.static void
main(java.lang.String[] args)
void
resetDisplay()
Return to the initial state of the alignment visualization.void
stateChanged(javax.swing.event.ChangeEvent e)
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Methods inherited from class org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol
evalString, getColorPalette, getJmolPanel, getStructure, getTitle, mouseClicked, mouseDragged, mouseEntered, mouseExited, mouseMoved, mousePressed, mouseReleased, setAtoms, setJmolPanel, setStructure, setTitle, windowActivated, windowClosed, windowClosing, windowDeactivated, windowDeiconified, windowIconified, windowOpened
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Method Detail
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main
public static void main(java.lang.String[] args)
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initCoords
protected void initCoords()
Description copied from class:AbstractAlignmentJmol
Display the structures after the variable initialization in the constructor.- Specified by:
initCoords
in classAbstractAlignmentJmol
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destroy
public void destroy()
Description copied from class:AbstractAlignmentJmol
Set all the member variables to null.- Overrides:
destroy
in classAbstractAlignmentJmol
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actionPerformed
public void actionPerformed(java.awt.event.ActionEvent e)
- Specified by:
actionPerformed
in interfacejava.awt.event.ActionListener
- Specified by:
actionPerformed
in classAbstractAlignmentJmol
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getJmolString
public static java.lang.String getJmolString(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
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getJmolScript4Block
public static java.lang.String getJmolScript4Block(AFPChain afpChain, Atom[] ca1, Atom[] ca2, int blockNr)
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resetDisplay
public void resetDisplay()
Description copied from class:AbstractAlignmentJmol
Return to the initial state of the alignment visualization.- Specified by:
resetDisplay
in classAbstractAlignmentJmol
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getDistanceMatrices
public java.util.List<Matrix> getDistanceMatrices()
Description copied from class:AbstractAlignmentJmol
Returns a List of internal Distance Matrices, one for each structure in the alignment. Returns null if no alignment is being displayed.- Specified by:
getDistanceMatrices
in classAbstractAlignmentJmol
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stateChanged
public void stateChanged(javax.swing.event.ChangeEvent e)
- Specified by:
stateChanged
in interfacejavax.swing.event.ChangeListener
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