public class MultipleAlignmentJmol extends AbstractAlignmentJmol
MultipleAlignments.colorPalette, COMMAND_LINE_HELP, DEFAULT_HEIGHT, DEFAULT_SCRIPT, DEFAULT_WIDTH, frame, jmolPanel, nrOpenWindows, status, structure, text| Constructor | Description |
|---|---|
MultipleAlignmentJmol() |
Default constructor creates an empty JmolPanel window, from where
alignments can be made through the align menu.
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MultipleAlignmentJmol(MultipleAlignment msa,
java.util.List<Atom[]> rotatedAtoms) |
The constructor displays the Mutltiple Alignment in a new JmolPanel
Frame.
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| Modifier and Type | Method | Description |
|---|---|---|
void |
actionPerformed(java.awt.event.ActionEvent ae) |
|
void |
destroy() |
Set all the member variables to null.
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java.util.List<Matrix> |
getDistanceMatrices() |
Returns a List of internal Distance Matrices,
one for each structure in the alignment.
|
javax.swing.JFrame |
getFrame() |
|
static java.lang.String |
getJmolString(MultipleAlignment multAln,
java.util.List<Atom[]> transformedAtoms,
ColorBrewer colorPalette,
boolean colorByBlocks) |
Generate a Jmol command String that colors the aligned residues of every
structure.
|
static java.lang.String |
getMultiBlockJmolString(MultipleAlignment multAln,
java.util.List<Atom[]> transformedAtoms,
ColorBrewer colorPalette,
boolean colorByBlocks) |
Colors every Block of the structures with a different color, following
the palette.
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MultipleAlignment |
getMultipleAlignment() |
|
protected void |
initCoords() |
Display the structures after the variable initialization in the
constructor.
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void |
resetDisplay() |
Return to the initial state of the alignment visualization.
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void |
setColorByBlocks(boolean colorByBlocks) |
evalString, getColorPalette, getJmolPanel, getStructure, getTitle, mouseClicked, mouseDragged, mouseEntered, mouseExited, mouseMoved, mousePressed, mouseReleased, setAtoms, setJmolPanel, setStructure, setTitle, windowActivated, windowClosed, windowClosing, windowDeactivated, windowDeiconified, windowIconified, windowOpenedpublic MultipleAlignmentJmol()
public MultipleAlignmentJmol(MultipleAlignment msa, java.util.List<Atom[]> rotatedAtoms)
msa - : contains the aligned residues.rotatedAtoms - : contains the transformed Atom coordinates.protected void initCoords()
AbstractAlignmentJmolinitCoords in class AbstractAlignmentJmolpublic void destroy()
AbstractAlignmentJmoldestroy in class AbstractAlignmentJmolpublic void actionPerformed(java.awt.event.ActionEvent ae)
actionPerformed in class AbstractAlignmentJmolpublic static java.lang.String getJmolString(MultipleAlignment multAln, java.util.List<Atom[]> transformedAtoms, ColorBrewer colorPalette, boolean colorByBlocks)
public static java.lang.String getMultiBlockJmolString(MultipleAlignment multAln, java.util.List<Atom[]> transformedAtoms, ColorBrewer colorPalette, boolean colorByBlocks)
public void resetDisplay()
AbstractAlignmentJmolresetDisplay in class AbstractAlignmentJmolpublic java.util.List<Matrix> getDistanceMatrices()
AbstractAlignmentJmolgetDistanceMatrices in class AbstractAlignmentJmolpublic void setColorByBlocks(boolean colorByBlocks)
public javax.swing.JFrame getFrame()
public MultipleAlignment getMultipleAlignment()