public class MultipleAlignmentJmol extends AbstractAlignmentJmol
MultipleAlignment
s.colorPalette, COMMAND_LINE_HELP, DEFAULT_HEIGHT, DEFAULT_SCRIPT, DEFAULT_WIDTH, frame, jmolPanel, LIGAND_DISPLAY_SCRIPT, nrOpenWindows, status, structure, text
Constructor and Description |
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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 JmolPanel window.
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Modifier and Type | Method and Description |
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void |
actionPerformed(java.awt.event.ActionEvent e) |
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.
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protected void |
initCoords()
Display the structures in its initial coordinates.
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void |
resetDisplay()
Return to the initial state of the alignment visualization.
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evalString, getColorPalette, getJmolPanel, getStructure, getTitle, mouseClicked, mouseDragged, mouseEntered, mouseExited, mouseMoved, mousePressed, mouseReleased, setAtoms, setJmolPanel, setStructure, setTitle, windowActivated, windowClosed, windowClosing, windowDeactivated, windowDeiconified, windowIconified, windowOpened
public MultipleAlignmentJmol()
public MultipleAlignmentJmol(MultipleAlignment msa, java.util.List<Atom[]> rotatedAtoms)
multAln:
- contains the aligned residues.atomArrays:
- contains the atom coordinates to display, already rotated.protected void initCoords()
AbstractAlignmentJmol
initCoords
in class AbstractAlignmentJmol
public void destroy()
AbstractAlignmentJmol
destroy
in class AbstractAlignmentJmol
public void actionPerformed(java.awt.event.ActionEvent e)
actionPerformed
in interface java.awt.event.ActionListener
actionPerformed
in class AbstractAlignmentJmol
public void resetDisplay()
AbstractAlignmentJmol
resetDisplay
in class AbstractAlignmentJmol
public java.util.List<Matrix> getDistanceMatrices()
AbstractAlignmentJmol
getDistanceMatrices
in class AbstractAlignmentJmol