* - add the alignment panel to the list used for aligning these
* structures
* @param leaveColouringToJmol
- * - do not update the colours from any other source. Jmol is handling them
+ * - do not update the colours from any other source. Jmol is
+ * handling them
* @param loadStatus
* @param bounds
* @param viewid
*/
public AppJmol(String[] files, String[] ids, SequenceI[][] seqs,
- AlignmentPanel ap, boolean usetoColour, boolean useToAlign, boolean leaveColouringToJmol,
- String loadStatus, Rectangle bounds, String viewid)
+ AlignmentPanel ap, boolean usetoColour, boolean useToAlign,
+ boolean leaveColouringToJmol, String loadStatus,
+ Rectangle bounds, String viewid)
{
PDBEntry[] pdbentrys = new PDBEntry[files.length];
for (int i = 0; i < pdbentrys.length; i++)
}
// / TODO: check if protocol is needed to be set, and if chains are
// autodiscovered.
- jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(), pdbentrys, seqs, null, null);
+ jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(),
+ pdbentrys, seqs, null, null);
jmb.setLoadingFromArchive(true);
addAlignmentPanel(ap);
{
seqColour.setSelected(jmb.isColourBySequence());
jmolColour.setSelected(!jmb.isColourBySequence());
- if (_colourwith==null)
+ if (_colourwith == null)
{
- _colourwith=new Vector<AlignmentPanel>();
+ _colourwith = new Vector<AlignmentPanel>();
}
- if (_alignwith==null)
+ if (_alignwith == null)
{
- _alignwith=new Vector<AlignmentPanel>();
+ _alignwith = new Vector<AlignmentPanel>();
}
-
+
seqColourBy = new ViewSelectionMenu("Colour by ..", this, _colourwith,
new ItemListener()
{
}
});
}
+
IProgressIndicator progressBar = null;
/**
* add a single PDB structure to a new or existing Jmol view
+ *
* @param pdbentry
* @param seq
* @param chains
progressBar = ap.alignFrame;
// ////////////////////////////////
// Is the pdb file already loaded?
- String alreadyMapped = ap.getStructureSelectionManager().alreadyMappedToFile(
- pdbentry.getId());
+ String alreadyMapped = ap.getStructureSelectionManager()
+ .alreadyMappedToFile(pdbentry.getId());
if (alreadyMapped != null)
{
if (option == JOptionPane.YES_OPTION)
{
// TODO : Fix multiple seq to one chain issue here.
- ap.getStructureSelectionManager().setMapping(seq, chains, alreadyMapped,
- AppletFormatAdapter.FILE);
+ ap.getStructureSelectionManager().setMapping(seq, chains,
+ alreadyMapped, AppletFormatAdapter.FILE);
if (ap.seqPanel.seqCanvas.fr != null)
{
ap.seqPanel.seqCanvas.fr.featuresAdded();
// add it to the set used for colouring
topJmol.useAlignmentPanelForColourbyseq(ap);
topJmol.buildJmolActionMenu();
- ap.getStructureSelectionManager().sequenceColoursChanged(ap);
+ ap.getStructureSelectionManager()
+ .sequenceColoursChanged(ap);
break;
}
}
}
}
// /////////////////////////////////
- openNewJmol(ap, new PDBEntry[] { pdbentry }, new SequenceI[][] { seq });
+ openNewJmol(ap, new PDBEntry[]
+ { pdbentry }, new SequenceI[][]
+ { seq });
}
- private void openNewJmol(AlignmentPanel ap, PDBEntry[] pdbentrys, SequenceI[][] seqs) {
+
+ private void openNewJmol(AlignmentPanel ap, PDBEntry[] pdbentrys,
+ SequenceI[][] seqs)
+ {
progressBar = ap.alignFrame;
- jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(), pdbentrys, seqs, null, null);
+ jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(),
+ pdbentrys, seqs, null, null);
addAlignmentPanel(ap);
useAlignmentPanelForColourbyseq(ap);
- if (pdbentrys.length>1)
+ if (pdbentrys.length > 1)
{
- alignAddedStructures=true;
+ alignAddedStructures = true;
useAlignmentPanelForSuperposition(ap);
}
jmb.setColourBySequence(true);
setSize(400, 400); // probably should be a configurable/dynamic default here
initMenus();
- worker=null;
- {
- addingStructures = false;
- worker = new Thread(this);
- worker.start();
- }
+ worker = null;
+ {
+ addingStructures = false;
+ worker = new Thread(this);
+ worker.start();
+ }
this.addInternalFrameListener(new InternalFrameAdapter()
{
public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
}
/**
- * create a new Jmol containing several structures superimposed using the given alignPanel.
+ * create a new Jmol containing several structures superimposed using the
+ * given alignPanel.
+ *
* @param ap
* @param pe
* @param seqs
}
}
- public void useAlignmentPanelForColourbyseq(AlignmentPanel nap, boolean enableColourBySeq)
+ public void useAlignmentPanelForColourbyseq(AlignmentPanel nap,
+ boolean enableColourBySeq)
{
useAlignmentPanelForColourbyseq(nap);
jmb.setColourBySequence(enableColourBySeq);
seqColour.setSelected(enableColourBySeq);
jmolColour.setSelected(!enableColourBySeq);
}
+
public void useAlignmentPanelForColourbyseq(AlignmentPanel nap)
{
addAlignmentPanel(nap);
jmb.allocateViewer(renderPanel, true, "", null, null, "", scriptWindow,
null);
jmb.newJmolPopup(true, "Jmol", true);
- if (command==null)
+ if (command == null)
{
- command="";
+ command = "";
}
jmb.evalStateCommand(command);
jmb.setFinishedInit(true);
{
// just transfer the file name from the first sequence's first
// PDBEntry
- file = new File(((PDBEntry) pdbseq
- .getSequenceAt(0).getPDBId().elementAt(0)).getFile()).getAbsolutePath();
+ file = new File(((PDBEntry) pdbseq.getSequenceAt(0).getPDBId()
+ .elementAt(0)).getFile()).getAbsolutePath();
jmb.pdbentry[pi].setFile(file);
-
+
files.append(" \"" + Platform.escapeString(file) + "\"");
}
else
final String command = cmd.toString();
cmd = null;
lastnotify = jmb.getLoadNotifiesHandled();
-
+
try
{
jmb.evalStateCommand(command);
Cache.log.error("Couldn't add files to Jmol viewer!", ex);
}
}
-
+
// need to wait around until script has finished
while (addingStructures ? lastnotify >= jmb.getLoadNotifiesHandled()
- : (jmb.isFinishedInit() && jmb.getPdbFile().length!=jmb.pdbentry.length))
+ : (jmb.isFinishedInit() && jmb.getPdbFile().length != jmb.pdbentry.length))
{
try
{
{
for (int pdbe = 0; pdbe < jmb.pdbentry.length; pdbe++)
{
- cap.appendText(jmb.printMapping(
- jmb.pdbentry[pdbe].getFile()));
+ cap.appendText(jmb.printMapping(jmb.pdbentry[pdbe].getFile()));
cap.appendText("\n");
}
} catch (OutOfMemoryError e)
im.writeImage();
}
}
+
public void jmolColour_actionPerformed(ActionEvent actionEvent)
{
- if (jmolColour.isSelected()) {
+ if (jmolColour.isSelected())
+ {
// disable automatic sequence colouring.
jmb.setColourBySequence(false);
}
}
+
public void seqColour_actionPerformed(ActionEvent actionEvent)
{
jmb.setColourBySequence(seqColour.isSelected());
{
if (!jmb.isLoadingFromArchive())
{
- if (_colourwith.size()==0 && ap!=null) {
+ if (_colourwith.size() == 0 && ap != null)
+ {
// Make the currently displayed alignment panel the associated view
_colourwith.add(ap.alignFrame.alignPanel);
}
buriedColour.setSelected(true);
jmb.setJalviewColourScheme(new BuriedColourScheme());
}
-
+
public void purinePyrimidineColour_actionPerformed(ActionEvent actionEvent)
{
setJalviewColourScheme(new PurinePyrimidineColourScheme());
}
-
+
public void userColour_actionPerformed(ActionEvent actionEvent)
{
userColour.setSelected(true);
public boolean isColouredByJmol()
{
return !jmb.isColourBySequence();
- }
-
+ }
}
git://source.jalview.org / jalview.git / blobdiff