X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmol.java;h=bab8a2d7fc145b9a577425674a6d5f0c6933746b;hb=58afea88095280d807e5c2ac8b9155de5ba3503c;hp=f71cd3077ee666176e11d98e472016cd44b2d9cb;hpb=6aae80a714d6cf5c2d28d02f74fbbf5296a0b71a;p=jalview.git
diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index f71cd30..bab8a2d 100644
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -1,24 +1,28 @@
/*
- * 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 2.8.2)
+ * 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.
- *
+ * 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 .
+ * 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;
import java.util.*;
import java.awt.*;
+
import javax.swing.*;
import javax.swing.event.*;
@@ -27,16 +31,19 @@ import java.io.*;
import jalview.jbgui.GStructureViewer;
import jalview.api.SequenceStructureBinding;
+import jalview.api.structures.JalviewStructureDisplayI;
import jalview.bin.Cache;
import jalview.datamodel.*;
import jalview.gui.ViewSelectionMenu.ViewSetProvider;
-import jalview.structure.*;
import jalview.datamodel.PDBEntry;
+import jalview.ext.jmol.JalviewJmolBinding;
import jalview.io.*;
import jalview.schemes.*;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
public class AppJmol extends GStructureViewer implements Runnable,
- SequenceStructureBinding, ViewSetProvider
+ ViewSetProvider, JalviewStructureDisplayI
{
AppJmolBinding jmb;
@@ -79,7 +86,7 @@ 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 +103,17 @@ 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 +125,8 @@ 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 +134,18 @@ 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();
@@ -153,16 +168,16 @@ public class AppJmol extends GStructureViewer implements Runnable,
{
seqColour.setSelected(jmb.isColourBySequence());
jmolColour.setSelected(!jmb.isColourBySequence());
- if (_colourwith==null)
+ if (_colourwith == null)
{
- _colourwith=new Vector();
+ _colourwith = new Vector();
}
- if (_alignwith==null)
+ if (_alignwith == null)
{
- _alignwith=new Vector();
+ _alignwith = new Vector();
}
-
- seqColourBy = new ViewSelectionMenu("Colour by ..", this, _colourwith,
+
+ seqColourBy = new ViewSelectionMenu(MessageManager.getString("label.colour_by"), this, _colourwith,
new ItemListener()
{
@@ -182,7 +197,7 @@ public class AppJmol extends GStructureViewer implements Runnable,
});
viewMenu.add(seqColourBy);
final ItemListener handler;
- JMenu alpanels = new ViewSelectionMenu("Superpose with ..", this,
+ JMenu alpanels = new ViewSelectionMenu(MessageManager.getString("label.superpose_with"), this,
_alignwith, handler = new ItemListener()
{
@@ -190,8 +205,11 @@ 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);
@@ -220,31 +238,40 @@ public class AppJmol extends GStructureViewer implements Runnable,
}
});
}
+
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(),
- JOptionPane.YES_NO_OPTION);
+ 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();
@@ -259,7 +286,7 @@ 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++)
@@ -268,7 +295,11 @@ 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;
}
}
@@ -289,11 +320,15 @@ 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",
- JOptionPane.YES_NO_OPTION);
+ int option = JOptionPane
+ .showInternalConfirmDialog(
+ Desktop.desktop,
+ 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)
{
topJmol.useAlignmentPanelForSuperposition(ap);
@@ -303,27 +338,33 @@ 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)
@@ -335,6 +376,19 @@ 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();
@@ -435,6 +489,15 @@ 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);
@@ -555,9 +618,9 @@ 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);
@@ -570,7 +633,8 @@ 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)
@@ -627,7 +691,7 @@ public class AppJmol extends GStructureViewer implements Runnable,
jmb.centerViewer(toshow);
}
- void closeViewer()
+ public void closeViewer()
{
jmb.closeViewer();
ap = null;
@@ -689,9 +753,11 @@ 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
{
@@ -714,7 +780,7 @@ public class AppJmol extends GStructureViewer implements Runnable,
}
if (file != null)
{
- files.append(" \"" + file + "\"");
+ files.append(" \"" + Platform.escapeString(file) + "\"");
}
}
}
@@ -730,13 +796,15 @@ public class AppJmol extends GStructureViewer implements Runnable,
if (errormsgs.length() > 0)
{
- 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);
+ JOptionPane.showInternalMessageDialog(Desktop.desktop, 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)
@@ -762,7 +830,8 @@ 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);
@@ -776,37 +845,41 @@ 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() != null && 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;
@@ -819,7 +892,7 @@ 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);
@@ -856,9 +929,7 @@ 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)
@@ -869,8 +940,9 @@ public class AppJmol extends GStructureViewer implements Runnable,
cap.dispose();
return;
}
- jalview.gui.Desktop.addInternalFrame(cap, "PDB - Sequence Mapping",
- 550, 600);
+ jalview.gui.Desktop.addInternalFrame(cap,
+ MessageManager.getString("label.pdb_sequence_mapping"), 550,
+ 600);
}
/**
@@ -921,13 +993,16 @@ 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());
@@ -939,7 +1014,8 @@ public class AppJmol extends GStructureViewer implements Runnable,
{
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);
}
@@ -1006,6 +1082,11 @@ 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);
@@ -1083,7 +1164,8 @@ 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++)
@@ -1108,7 +1190,8 @@ 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
{
@@ -1267,4 +1350,18 @@ 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();
+ }
+
+ public JalviewJmolBinding getBinding()
+ {
+ return jmb;
+ }
+
}