X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmol.java;h=bf32dff35fd4a4a565a9063570009d3093f87508;hb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;hp=e500240773a4f728a2ba30040dad8ffe03fc8a22;hpb=77ab7d6694e27575261ab58c098eee76e68c2228;p=jalview.git
diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index e500240..bf32dff 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 2.8.1)
+ * 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;
@@ -26,15 +27,15 @@ import java.awt.event.*;
import java.io.*;
import jalview.jbgui.GStructureViewer;
-import jalview.api.AlignmentViewPanel;
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
@@ -98,14 +99,16 @@ public class AppJmol extends GStructureViewer implements Runnable,
* - 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++)
@@ -117,7 +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, ap.getStructureSelectionManager(), pdbentrys, seqs, null, null);
+ jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(),
+ pdbentrys, seqs, null, null);
jmb.setLoadingFromArchive(true);
addAlignmentPanel(ap);
@@ -159,15 +163,15 @@ 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,
new ItemListener()
{
@@ -196,8 +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);
@@ -226,10 +229,12 @@ 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
@@ -241,22 +246,21 @@ public class AppJmol extends GStructureViewer implements Runnable,
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)
{
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)
{
// 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();
@@ -283,7 +287,8 @@ public class AppJmol extends GStructureViewer implements Runnable,
// add it to the set used for colouring
topJmol.useAlignmentPanelForColourbyseq(ap);
topJmol.buildJmolActionMenu();
- ap.getStructureSelectionManager().sequenceColoursChanged(ap);
+ ap.getStructureSelectionManager()
+ .sequenceColoursChanged(ap);
break;
}
}
@@ -305,9 +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)
{
@@ -318,41 +322,33 @@ public class AppJmol extends GStructureViewer implements Runnable,
}
}
// /////////////////////////////////
- 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) {
- boolean promptUser=pdbentrys.length==1;
+
+ 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;
- String filelist="";
-// for (PDBEntry pe: pdbentrys)
-// {
-// if (pe.getFile()==null)
- {
- addingStructures = false;
- worker = new Thread(this);
- worker.start();
-// break;
- }
-// filelist+=" \""+pe.getFile()+"\"";
-
-/* }
- if (worker==null)
+ worker = null;
{
- initJmol("load"+(pdbentrys.length>1 ? " APPEND" : "") + filelist);
+ addingStructures = false;
+ worker = new Thread(this);
+ worker.start();
}
-*/
this.addInternalFrameListener(new InternalFrameAdapter()
{
public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
@@ -364,7 +360,9 @@ public class AppJmol extends GStructureViewer implements Runnable,
}
/**
- * 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
@@ -475,13 +473,15 @@ public class AppJmol extends GStructureViewer implements Runnable,
}
}
- 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);
@@ -602,9 +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);
@@ -617,7 +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)
@@ -736,9 +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
{
@@ -761,7 +763,7 @@ public class AppJmol extends GStructureViewer implements Runnable,
}
if (file != null)
{
- files.append(" \"" + file + "\"");
+ files.append(" \"" + Platform.escapeString(file) + "\"");
}
}
}
@@ -778,10 +780,8 @@ 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();
@@ -811,7 +811,7 @@ public class AppJmol extends GStructureViewer implements Runnable,
final String command = cmd.toString();
cmd = null;
lastnotify = jmb.getLoadNotifiesHandled();
-
+
try
{
jmb.evalStateCommand(command);
@@ -826,10 +826,10 @@ 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 (addingStructures ? lastnotify >= jmb.getLoadNotifiesHandled()
- : (jmb.isFinishedInit() && jmb.getPdbFile().length!=jmb.pdbentry.length))
+ : (jmb.isFinishedInit() && jmb.getPdbFile()!=null && jmb.getPdbFile().length != jmb.pdbentry.length))
{
try
{
@@ -871,7 +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);
@@ -908,8 +908,7 @@ public class AppJmol extends GStructureViewer implements Runnable,
{
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)
@@ -920,7 +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);
}
@@ -972,13 +971,16 @@ 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());
@@ -990,7 +992,8 @@ 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);
}
@@ -1057,6 +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);
@@ -1134,7 +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++)
@@ -1159,7 +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
{
@@ -1325,7 +1333,6 @@ public class AppJmol extends GStructureViewer implements Runnable,
public boolean isColouredByJmol()
{
return !jmb.isColourBySequence();
- }
-
+ }
}