X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmol.java;h=cc37b66af6c036bde7b0264af97cf48b563b4fb3;hb=c5efb963ed347a8af8ebc4311cd9e8fb5b66291f;hp=9d68c1bcb047b2a1e3860422b350c48b379fdd2b;hpb=a65993fd311b1a53617c5df3c84abfb78740a900;p=jalview.git
diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index 9d68c1b..cc37b66 100644
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -1,19 +1,20 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
@@ -30,10 +31,11 @@ import jalview.api.SequenceStructureBinding;
import jalview.bin.Cache;
import jalview.datamodel.*;
import jalview.gui.ViewSelectionMenu.ViewSetProvider;
-import jalview.structure.*;
import jalview.datamodel.PDBEntry;
import jalview.io.*;
import jalview.schemes.*;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
public class AppJmol extends GStructureViewer implements Runnable,
SequenceStructureBinding, ViewSetProvider
@@ -79,7 +81,7 @@ public class AppJmol extends GStructureViewer implements Runnable,
this(new String[]
{ file }, new String[]
{ id }, new SequenceI[][]
- { seq }, ap, true, true, loadStatus, bounds, viewid);
+ { seq }, ap, true, true, false, loadStatus, bounds, viewid);
}
ViewSelectionMenu seqColourBy;
@@ -96,13 +98,17 @@ public class AppJmol extends GStructureViewer implements Runnable,
* @param useToAlign
* - 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
* @param loadStatus
* @param bounds
* @param viewid
*/
public AppJmol(String[] files, String[] ids, SequenceI[][] seqs,
AlignmentPanel ap, boolean usetoColour, boolean useToAlign,
- String loadStatus, Rectangle bounds, String viewid)
+ boolean leaveColouringToJmol, String loadStatus,
+ Rectangle bounds, String viewid)
{
PDBEntry[] pdbentrys = new PDBEntry[files.length];
for (int i = 0; i < pdbentrys.length; i++)
@@ -114,7 +120,8 @@ public class AppJmol extends GStructureViewer implements Runnable,
}
// / TODO: check if protocol is needed to be set, and if chains are
// autodiscovered.
- jmb = new AppJmolBinding(this, pdbentrys, seqs, null, null);
+ jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(),
+ pdbentrys, seqs, null, null);
jmb.setLoadingFromArchive(true);
addAlignmentPanel(ap);
@@ -122,15 +129,18 @@ public class AppJmol extends GStructureViewer implements Runnable,
{
useAlignmentPanelForSuperposition(ap);
}
+ if (leaveColouringToJmol || !usetoColour)
+ {
+ jmb.setColourBySequence(false);
+ seqColour.setSelected(false);
+ jmolColour.setSelected(true);
+ }
if (usetoColour)
{
useAlignmentPanelForColourbyseq(ap);
jmb.setColourBySequence(true);
seqColour.setSelected(true);
- } else {
- jmb.setColourBySequence(false);
- seqColour.setSelected(false);
- jmolColour.setSelected(true);
+ jmolColour.setSelected(false);
}
this.setBounds(bounds);
initMenus();
@@ -153,6 +163,15 @@ public class AppJmol extends GStructureViewer implements Runnable,
{
seqColour.setSelected(jmb.isColourBySequence());
jmolColour.setSelected(!jmb.isColourBySequence());
+ if (_colourwith == null)
+ {
+ _colourwith = new Vector();
+ }
+ if (_alignwith == null)
+ {
+ _alignwith = new Vector();
+ }
+
seqColourBy = new ViewSelectionMenu("Colour by ..", this, _colourwith,
new ItemListener()
{
@@ -181,8 +200,7 @@ public class AppJmol extends GStructureViewer implements Runnable,
public void itemStateChanged(ItemEvent e)
{
alignStructs.setEnabled(_alignwith.size() > 0);
- alignStructs.setToolTipText("Align structures using "
- + _alignwith.size() + " linked alignment views");
+ alignStructs.setToolTipText(MessageManager.formatMessage("label.align_structures_using_linked_alignment_views", new String[] {new Integer(_alignwith.size()).toString()}));
}
});
handler.itemStateChanged(null);
@@ -210,55 +228,39 @@ public class AppJmol extends GStructureViewer implements Runnable,
}
});
- colourMenu.addMenuListener(new MenuListener()
- {
-
- @Override
- public void menuSelected(MenuEvent arg0)
- {
-
- handlingGuiEvents=true;
- }
-
- @Override
- public void menuDeselected(MenuEvent arg0)
- {
- handlingGuiEvents=false;
- }
-
- @Override
- public void menuCanceled(MenuEvent arg0)
- {
- handlingGuiEvents=false;
- }
- });
}
IProgressIndicator progressBar = null;
+ /**
+ * add a single PDB structure to a new or existing Jmol view
+ *
+ * @param pdbentry
+ * @param seq
+ * @param chains
+ * @param ap
+ */
public AppJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
- AlignmentPanel ap)
+ final AlignmentPanel ap)
{
progressBar = ap.alignFrame;
// ////////////////////////////////
// Is the pdb file already loaded?
- String alreadyMapped = StructureSelectionManager
- .getStructureSelectionManager().alreadyMappedToFile(
- pdbentry.getId());
+ String alreadyMapped = ap.getStructureSelectionManager()
+ .alreadyMappedToFile(pdbentry.getId());
if (alreadyMapped != null)
{
int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
- pdbentry.getId() + " is already displayed."
- + "\nDo you want to re-use this viewer ?",
- "Map Sequences to Visible Window: " + pdbentry.getId(),
+ MessageManager.formatMessage("label.pdb_entry_is_already_displayed", new String[]{pdbentry.getId()}),
+ MessageManager.formatMessage("label.map_sequences_to_visible_window", new String[]{pdbentry.getId()}),
JOptionPane.YES_NO_OPTION);
if (option == JOptionPane.YES_OPTION)
{
- StructureSelectionManager.getStructureSelectionManager()
- .setMapping(seq, chains, alreadyMapped,
- AppletFormatAdapter.FILE);
+ // TODO : Fix multiple seq to one chain issue here.
+ ap.getStructureSelectionManager().setMapping(seq, chains,
+ alreadyMapped, AppletFormatAdapter.FILE);
if (ap.seqPanel.seqCanvas.fr != null)
{
ap.seqPanel.seqCanvas.fr.featuresAdded();
@@ -273,7 +275,7 @@ public class AppJmol extends GStructureViewer implements Runnable,
{
if (frames[i] instanceof AppJmol)
{
- AppJmol topJmol = ((AppJmol) frames[i]);
+ final AppJmol topJmol = ((AppJmol) frames[i]);
// JBPNOTE: this looks like a binding routine, rather than a gui
// routine
for (int pe = 0; pe < topJmol.jmb.pdbentry.length; pe++)
@@ -282,7 +284,11 @@ public class AppJmol extends GStructureViewer implements Runnable,
{
topJmol.jmb.addSequence(pe, seq);
topJmol.addAlignmentPanel(ap);
+ // add it to the set used for colouring
+ topJmol.useAlignmentPanelForColourbyseq(ap);
topJmol.buildJmolActionMenu();
+ ap.getStructureSelectionManager()
+ .sequenceColoursChanged(ap);
break;
}
}
@@ -304,9 +310,8 @@ public class AppJmol extends GStructureViewer implements Runnable,
AppJmol topJmol = (AppJmol) jm.nextElement();
// TODO: highlight topJmol in view somehow
int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
- "Do you want to add " + pdbentry.getId()
- + " to the view called\n'" + topJmol.getTitle()
- + "'\n", "Align to existing structure view",
+ MessageManager.formatMessage("label.add_pdbentry_to_view", new String[]{pdbentry.getId(),topJmol.getTitle()}),
+ MessageManager.getString("label.align_to_existing_structure_view"),
JOptionPane.YES_NO_OPTION);
if (option == JOptionPane.YES_OPTION)
{
@@ -317,27 +322,33 @@ public class AppJmol extends GStructureViewer implements Runnable,
}
}
// /////////////////////////////////
-
- jmb = new AppJmolBinding(this, new PDBEntry[]
+ openNewJmol(ap, new PDBEntry[]
{ pdbentry }, new SequenceI[][]
- { seq }, null, null);
+ { seq });
+ }
+
+ private void openNewJmol(AlignmentPanel ap, PDBEntry[] pdbentrys,
+ SequenceI[][] seqs)
+ {
+ progressBar = ap.alignFrame;
+ jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(),
+ pdbentrys, seqs, null, null);
addAlignmentPanel(ap);
useAlignmentPanelForColourbyseq(ap);
+ if (pdbentrys.length > 1)
+ {
+ alignAddedStructures = true;
+ useAlignmentPanelForSuperposition(ap);
+ }
jmb.setColourBySequence(true);
setSize(400, 400); // probably should be a configurable/dynamic default here
initMenus();
-
- if (pdbentry.getFile() != null)
- {
- initJmol("load \"" + pdbentry.getFile() + "\"");
- }
- else
+ worker = null;
{
addingStructures = false;
worker = new Thread(this);
worker.start();
}
-
this.addInternalFrameListener(new InternalFrameAdapter()
{
public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
@@ -349,6 +360,19 @@ public class AppJmol extends GStructureViewer implements Runnable,
}
/**
+ * create a new Jmol containing several structures superimposed using the
+ * given alignPanel.
+ *
+ * @param ap
+ * @param pe
+ * @param seqs
+ */
+ public AppJmol(AlignmentPanel ap, PDBEntry[] pe, SequenceI[][] seqs)
+ {
+ openNewJmol(ap, pe, seqs);
+ }
+
+ /**
* list of sequenceSet ids associated with the view
*/
ArrayList _aps = new ArrayList();
@@ -374,13 +398,13 @@ public class AppJmol extends GStructureViewer implements Runnable,
/**
* list of alignment panels to use for superposition
*/
- ArrayList _alignwith = new ArrayList();
+ Vector _alignwith = new Vector();
/**
* list of alignment panels that are used for colouring structures by aligned
* sequences
*/
- ArrayList _colourwith = new ArrayList();
+ Vector _colourwith = new Vector();
/**
* set the primary alignmentPanel reference and add another alignPanel to the
@@ -449,6 +473,15 @@ public class AppJmol extends GStructureViewer implements Runnable,
}
}
+ 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);
@@ -569,9 +602,9 @@ public class AppJmol extends GStructureViewer implements Runnable,
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);
@@ -584,7 +617,7 @@ public class AppJmol extends GStructureViewer implements Runnable,
{
return;
}
- JMenuItem menuItem = new JMenuItem("All");
+ JMenuItem menuItem = new JMenuItem(MessageManager.getString("label.all"));
menuItem.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent evt)
@@ -658,13 +691,6 @@ public class AppJmol extends GStructureViewer implements Runnable,
*/
private boolean _started = false;
- /**
- * state flag indicating if the GUI is active when a particular button event
- * takes place (e.g. when a stateChange occurs on a checkbox - this could be
- * programmatic or due to the user doing something)
- */
- private boolean handlingGuiEvents=false;
-
public void run()
{
_started = true;
@@ -710,9 +736,11 @@ public class AppJmol extends GStructureViewer implements Runnable,
{
// just transfer the file name from the first sequence's first
// PDBEntry
- jmb.pdbentry[pi].setFile(file = ((PDBEntry) pdbseq
- .getSequenceAt(0).getPDBId().elementAt(0)).getFile());
- files.append(" \"" + file + "\"");
+ file = new File(((PDBEntry) pdbseq.getSequenceAt(0).getPDBId()
+ .elementAt(0)).getFile()).getAbsolutePath();
+ jmb.pdbentry[pi].setFile(file);
+
+ files.append(" \"" + Platform.escapeString(file) + "\"");
}
else
{
@@ -735,7 +763,7 @@ public class AppJmol extends GStructureViewer implements Runnable,
}
if (file != null)
{
- files.append(" \"" + file + "\"");
+ files.append(" \"" + Platform.escapeString(file) + "\"");
}
}
}
@@ -752,12 +780,11 @@ public class AppJmol extends GStructureViewer implements Runnable,
{
JOptionPane.showInternalMessageDialog(Desktop.desktop,
- "The following pdb entries could not be retrieved from the PDB:\n"
- + errormsgs.toString()
- + "\nPlease try downloading them manually.",
- "Couldn't load file", JOptionPane.ERROR_MESSAGE);
+ MessageManager.formatMessage("label.pdb_entries_couldnt_be_retrieved", new String[]{errormsgs.toString()}),
+ MessageManager.getString("label.couldnt_load_file"), JOptionPane.ERROR_MESSAGE);
}
+ long lastnotify = jmb.getLoadNotifiesHandled();
if (files.length() > 0)
{
if (!addingStructures)
@@ -783,7 +810,8 @@ public class AppJmol extends GStructureViewer implements Runnable,
cmd.append("\nloadingJalviewdata=null");
final String command = cmd.toString();
cmd = null;
- long lastnotify = jmb.getLoadNotifiesHandled();
+ lastnotify = jmb.getLoadNotifiesHandled();
+
try
{
jmb.evalStateCommand(command);
@@ -797,37 +825,40 @@ public class AppJmol extends GStructureViewer implements Runnable,
{
Cache.log.error("Couldn't add files to Jmol viewer!", ex);
}
- // need to wait around until script has finished
- while (lastnotify >= jmb.getLoadNotifiesHandled())
- ;
+ }
+
+ // need to wait around until script has finished
+ while (addingStructures ? lastnotify >= jmb.getLoadNotifiesHandled()
+ : (jmb.isFinishedInit() && jmb.getPdbFile().length != jmb.pdbentry.length))
+ {
+ try
{
- try
- {
- Thread.sleep(35);
- } catch (Exception e)
- {
- }
- }
- // refresh the sequence colours for the new structure(s)
- for (AlignmentPanel ap : _colourwith)
+ Cache.log.debug("Waiting around for jmb notify.");
+ Thread.sleep(35);
+ } catch (Exception e)
{
- jmb.updateColours(ap);
}
- // do superposition if asked to
- if (alignAddedStructures)
+ }
+ // refresh the sequence colours for the new structure(s)
+ for (AlignmentPanel ap : _colourwith)
+ {
+ jmb.updateColours(ap);
+ }
+ // do superposition if asked to
+ if (alignAddedStructures)
+ {
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
{
- javax.swing.SwingUtilities.invokeLater(new Runnable()
+ public void run()
{
- public void run()
- {
- alignStructs_withAllAlignPanels();
- // jmb.superposeStructures(ap.av.getAlignment(), -1, null);
- }
- });
- alignAddedStructures = false;
- }
- addingStructures = false;
+ alignStructs_withAllAlignPanels();
+ // jmb.superposeStructures(ap.av.getAlignment(), -1, null);
+ }
+ });
+ alignAddedStructures = false;
}
+ addingStructures = false;
+
}
_started = false;
worker = null;
@@ -840,7 +871,7 @@ public class AppJmol extends GStructureViewer implements Runnable,
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle("Save PDB File");
- chooser.setToolTipText("Save");
+ chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(this);
@@ -877,9 +908,7 @@ public class AppJmol extends GStructureViewer implements Runnable,
{
for (int pdbe = 0; pdbe < jmb.pdbentry.length; pdbe++)
{
- cap.appendText(StructureSelectionManager
- .getStructureSelectionManager().printMapping(
- jmb.pdbentry[pdbe].getFile()));
+ cap.appendText(jmb.printMapping(jmb.pdbentry[pdbe].getFile()));
cap.appendText("\n");
}
} catch (OutOfMemoryError e)
@@ -890,7 +919,7 @@ public class AppJmol extends GStructureViewer implements Runnable,
cap.dispose();
return;
}
- jalview.gui.Desktop.addInternalFrame(cap, "PDB - Sequence Mapping",
+ jalview.gui.Desktop.addInternalFrame(cap, MessageManager.getString("label.pdb_sequence_mapping"),
550, 600);
}
@@ -942,27 +971,31 @@ public class AppJmol extends GStructureViewer implements Runnable,
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 (_colourwith == null)
{
- _colourwith = new ArrayList();
+ _colourwith = new Vector();
}
if (jmb.isColourBySequence())
{
- if (!jmb.isLoadingFromArchive() && handlingGuiEvents)
+ if (!jmb.isLoadingFromArchive())
{
- if (ap!=null) {
- // Make the currently displayed alignment panel the associated view
- _colourwith.add(ap.alignFrame.alignPanel);
+ if (_colourwith.size() == 0 && ap != null)
+ {
+ // Make the currently displayed alignment panel the associated view
+ _colourwith.add(ap.alignFrame.alignPanel);
}
}
// Set the colour using the current view for the associated alignframe
@@ -1027,6 +1060,11 @@ public class AppJmol extends GStructureViewer implements Runnable,
jmb.setJalviewColourScheme(new BuriedColourScheme());
}
+ public void purinePyrimidineColour_actionPerformed(ActionEvent actionEvent)
+ {
+ setJalviewColourScheme(new PurinePyrimidineColourScheme());
+ }
+
public void userColour_actionPerformed(ActionEvent actionEvent)
{
userColour.setSelected(true);
@@ -1104,7 +1142,7 @@ public class AppJmol extends GStructureViewer implements Runnable,
g.fillRect(0, 0, currentSize.width, currentSize.height);
g.setColor(Color.white);
g.setFont(new Font("Verdana", Font.BOLD, 14));
- g.drawString("Error loading file...", 20, currentSize.height / 2);
+ g.drawString(MessageManager.getString("label.error_loading_file") + "...", 20, currentSize.height / 2);
StringBuffer sb = new StringBuffer();
int lines = 0;
for (int e = 0; e < jmb.pdbentry.length; e++)
@@ -1129,7 +1167,7 @@ public class AppJmol extends GStructureViewer implements Runnable,
g.fillRect(0, 0, currentSize.width, currentSize.height);
g.setColor(Color.white);
g.setFont(new Font("Verdana", Font.BOLD, 14));
- g.drawString("Retrieving PDB data....", 20, currentSize.height / 2);
+ g.drawString(MessageManager.getString("label.retrieving_pdb_data"), 20, currentSize.height / 2);
}
else
{
@@ -1173,7 +1211,7 @@ public class AppJmol extends GStructureViewer implements Runnable,
{
if (_alignwith == null)
{
- _alignwith = new ArrayList();
+ _alignwith = new Vector();
}
if (_alignwith.size() == 0 && ap != null)
{
@@ -1288,4 +1326,13 @@ public class AppJmol extends GStructureViewer implements Runnable,
return (_colourwith != null) && _colourwith.contains(ap2);
}
+ /**
+ *
+ * @return TRUE if the view is NOT being coloured by sequence associations.
+ */
+ public boolean isColouredByJmol()
+ {
+ return !jmb.isColourBySequence();
+ }
+
}