X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmol.java;h=55d5f8c5fb67b7772ad1cc7194db01d26b7419c7;hp=fdf00c0fa867e603d542489166509c336dff9b3c;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hpb=362f2db1b01f3562784864a1d6ac5f7b9be0a18a
diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index fdf00c0..55d5f8c 100644
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -1,43 +1,81 @@
/*
- * 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 2.9)
+ * Copyright (C) 2015 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.*;
-
-import java.awt.event.*;
-import java.io.*;
-
-import jalview.jbgui.GStructureViewer;
-import jalview.api.SequenceStructureBinding;
import jalview.bin.Cache;
-import jalview.datamodel.*;
-import jalview.gui.ViewSelectionMenu.ViewSetProvider;
-import jalview.structure.*;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
import jalview.datamodel.PDBEntry;
-import jalview.io.*;
-import jalview.schemes.*;
-
-public class AppJmol extends GStructureViewer implements Runnable,
- SequenceStructureBinding, ViewSetProvider
-
+import jalview.datamodel.SequenceI;
+import jalview.gui.StructureViewer.ViewerType;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
+import jalview.schemes.BuriedColourScheme;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.HelixColourScheme;
+import jalview.schemes.HydrophobicColourScheme;
+import jalview.schemes.PurinePyrimidineColourScheme;
+import jalview.schemes.StrandColourScheme;
+import jalview.schemes.TaylorColourScheme;
+import jalview.schemes.TurnColourScheme;
+import jalview.schemes.ZappoColourScheme;
+import jalview.structures.models.AAStructureBindingModel;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.Graphics;
+import java.awt.Rectangle;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.PrintWriter;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Vector;
+
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JColorChooser;
+import javax.swing.JInternalFrame;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JSplitPane;
+import javax.swing.event.InternalFrameAdapter;
+import javax.swing.event.InternalFrameEvent;
+import javax.swing.event.MenuEvent;
+import javax.swing.event.MenuListener;
+
+public class AppJmol extends StructureViewerBase
{
AppJmolBinding jmb;
@@ -47,41 +85,6 @@ public class AppJmol extends GStructureViewer implements Runnable,
RenderPanel renderPanel;
- AlignmentPanel ap;
-
- Vector atomsPicked = new Vector();
-
- private boolean addingStructures = false;
-
- /**
- *
- * @param file
- * @param id
- * @param seq
- * @param ap
- * @param loadStatus
- * @param bounds
- * @deprecated defaults to AppJmol(String[] files, ... , viewid);
- */
- public AppJmol(String file, String id, SequenceI[] seq,
- AlignmentPanel ap, String loadStatus, Rectangle bounds)
- {
- this(file, id, seq, ap, loadStatus, bounds, null);
- }
-
- /**
- * @deprecated
- */
- public AppJmol(String file, String id, SequenceI[] seq,
- AlignmentPanel ap, String loadStatus, Rectangle bounds,
- String viewid)
- {
- this(new String[]
- { file }, new String[]
- { id }, new SequenceI[][]
- { seq }, ap, true, true, false, loadStatus, bounds, viewid);
- }
-
ViewSelectionMenu seqColourBy;
/**
@@ -97,26 +100,29 @@ 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++)
{
- PDBEntry pdbentry = new PDBEntry();
- pdbentry.setFile(files[i]);
- pdbentry.setId(ids[i]);
+ // PDBEntry pdbentry = new PDBEntry(files[i], ids[i]);
+ PDBEntry pdbentry = new PDBEntry(ids[i], null, PDBEntry.Type.PDB,
+ files[i]);
pdbentrys[i] = pdbentry;
}
// / 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);
@@ -128,26 +134,27 @@ public class AppJmol extends GStructureViewer implements Runnable,
{
jmb.setColourBySequence(false);
seqColour.setSelected(false);
- jmolColour.setSelected(true);
+ viewerColour.setSelected(true);
}
- if (usetoColour)
+ else if (usetoColour)
{
useAlignmentPanelForColourbyseq(ap);
jmb.setColourBySequence(true);
seqColour.setSelected(true);
- jmolColour.setSelected(false);
+ viewerColour.setSelected(false);
}
this.setBounds(bounds);
initMenus();
- viewId = viewid;
+ setViewId(viewid);
// jalview.gui.Desktop.addInternalFrame(this, "Loading File",
// bounds.width,bounds.height);
this.addInternalFrameListener(new InternalFrameAdapter()
{
+ @Override
public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
{
- closeViewer();
+ closeViewer(false);
}
});
initJmol(loadStatus); // pdbentry, seq, JBPCHECK!
@@ -157,17 +164,18 @@ public class AppJmol extends GStructureViewer implements Runnable,
private void initMenus()
{
seqColour.setSelected(jmb.isColourBySequence());
- jmolColour.setSelected(!jmb.isColourBySequence());
- if (_colourwith==null)
+ viewerColour.setSelected(!jmb.isColourBySequence());
+ 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()
{
@@ -187,7 +195,8 @@ 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()
{
@@ -195,13 +204,16 @@ 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);
- jmolActionMenu.add(alpanels);
- jmolActionMenu.addMenuListener(new MenuListener()
+ viewerActionMenu.add(alpanels);
+ viewerActionMenu.addMenuListener(new MenuListener()
{
@Override
@@ -225,323 +237,124 @@ 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 = jmb.ssm.alreadyMappedToFile(
- pdbentry.getId());
+ String pdbId = pdbentry.getId();
- if (alreadyMapped != null)
+ /*
+ * If the PDB file is already loaded, the user may just choose to add to an
+ * existing viewer (or cancel)
+ */
+ if (addAlreadyLoadedFile(seq, chains, ap, pdbId))
{
- 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);
-
- if (option == JOptionPane.YES_OPTION)
- {
- jmb.ssm.setMapping(seq, chains, alreadyMapped,
- AppletFormatAdapter.FILE);
- if (ap.seqPanel.seqCanvas.fr != null)
- {
- ap.seqPanel.seqCanvas.fr.featuresAdded();
- ap.paintAlignment(true);
- }
-
- // Now this AppJmol is mapped to new sequences. We must add them to
- // the exisiting array
- JInternalFrame[] frames = Desktop.instance.getAllFrames();
-
- for (int i = 0; i < frames.length; i++)
- {
- if (frames[i] instanceof AppJmol)
- {
- 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++)
- {
- if (topJmol.jmb.pdbentry[pe].getFile().equals(alreadyMapped))
- {
- topJmol.jmb.addSequence(pe, seq);
- topJmol.addAlignmentPanel(ap);
- topJmol.buildJmolActionMenu();
- break;
- }
- }
- }
- }
-
- return;
- }
+ return;
}
- // /////////////////////////////////
- // Check if there are other Jmol views involving this alignment
- // and prompt user about adding this molecule to one of them
- Vector existingViews = getJmolsFor(ap);
- if (existingViews.size() > 0)
+
+ /*
+ * Check if there are other Jmol views involving this alignment and prompt
+ * user about adding this molecule to one of them
+ */
+ if (addToExistingViewer(pdbentry, seq, chains, ap, pdbId))
{
- Enumeration jm = existingViews.elements();
- while (jm.hasMoreElements())
- {
- 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);
- if (option == JOptionPane.YES_OPTION)
- {
- topJmol.useAlignmentPanelForSuperposition(ap);
- topJmol.addStructure(pdbentry, seq, chains, true, ap.alignFrame);
- return;
- }
- }
+ return;
}
- // /////////////////////////////////
- jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(), new PDBEntry[]
- { pdbentry }, new SequenceI[][]
- { seq }, null, null);
+ /*
+ * If the options above are declined or do not apply, open a new viewer
+ */
+ openNewJmol(ap, new PDBEntry[] { pdbentry }, new SequenceI[][] { seq });
+ }
+
+ /**
+ * Answers true if this viewer already involves the given PDB ID
+ */
+ @Override
+ protected boolean hasPdbId(String pdbId)
+ {
+ return jmb.hasPdbId(pdbId);
+ }
+
+ 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()
{
+ @Override
public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
{
- closeViewer();
+ closeViewer(false);
}
});
}
/**
- * list of sequenceSet ids associated with the view
- */
- ArrayList _aps = new ArrayList();
-
- public AlignmentPanel[] getAllAlignmentPanels()
- {
- AlignmentPanel[] t, list = new AlignmentPanel[0];
- for (String setid : _aps)
- {
- AlignmentPanel[] panels = PaintRefresher.getAssociatedPanels(setid);
- if (panels != null)
- {
- t = new AlignmentPanel[list.length + panels.length];
- System.arraycopy(list, 0, t, 0, list.length);
- System.arraycopy(panels, 0, t, list.length, panels.length);
- list = t;
- }
- }
-
- return list;
- }
-
- /**
- * list of alignment panels to use for superposition
- */
- Vector _alignwith = new Vector();
-
- /**
- * list of alignment panels that are used for colouring structures by aligned
- * sequences
- */
- Vector _colourwith = new Vector();
-
- /**
- * set the primary alignmentPanel reference and add another alignPanel to the
- * list of ones to use for colouring and aligning
+ * create a new Jmol containing several structures superimposed using the
+ * given alignPanel.
*
- * @param nap
+ * @param ap
+ * @param pe
+ * @param seqs
*/
- public void addAlignmentPanel(AlignmentPanel nap)
+ public AppJmol(AlignmentPanel ap, PDBEntry[] pe, SequenceI[][] seqs)
{
- if (ap == null)
- {
- ap = nap;
- }
- if (!_aps.contains(nap.av.getSequenceSetId()))
- {
- _aps.add(nap.av.getSequenceSetId());
- }
+ openNewJmol(ap, pe, seqs);
}
/**
- * remove any references held to the given alignment panel
- *
- * @param nap
- */
- public void removeAlignmentPanel(AlignmentPanel nap)
- {
- try
- {
- _alignwith.remove(nap);
- _colourwith.remove(nap);
- if (ap == nap)
- {
- ap = null;
- for (AlignmentPanel aps : getAllAlignmentPanels())
- {
- if (aps != nap)
- {
- ap = aps;
- break;
- }
- }
- }
- } catch (Exception ex)
- {
- }
- if (ap != null)
- {
- buildJmolActionMenu();
- }
- }
-
- public void useAlignmentPanelForSuperposition(AlignmentPanel nap)
- {
- addAlignmentPanel(nap);
- if (!_alignwith.contains(nap))
- {
- _alignwith.add(nap);
- }
- }
-
- public void excludeAlignmentPanelForSuperposition(AlignmentPanel nap)
- {
- if (_alignwith.contains(nap))
- {
- _alignwith.remove(nap);
- }
- }
-
- 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);
- if (!_colourwith.contains(nap))
- {
- _colourwith.add(nap);
- }
- }
-
- public void excludeAlignmentPanelForColourbyseq(AlignmentPanel nap)
- {
- if (_colourwith.contains(nap))
- {
- _colourwith.remove(nap);
- }
- }
-
- /**
- * pdb retrieval thread.
- */
- private Thread worker = null;
-
- /**
- * add a new structure (with associated sequences and chains) to this viewer,
- * retrieving it if necessary first.
- *
- * @param pdbentry
- * @param seq
- * @param chains
- * @param alignFrame
- * @param align
- * if true, new structure(s) will be align using associated alignment
+ * Returns a list of any Jmol viewers. The list is restricted to those linked
+ * to the given alignment panel if it is not null.
*/
- private void addStructure(final PDBEntry pdbentry, final SequenceI[] seq,
- final String[] chains, final boolean b,
- final IProgressIndicator alignFrame)
- {
- if (pdbentry.getFile() == null)
- {
- if (worker != null && worker.isAlive())
- {
- // a retrieval is in progress, wait around and add ourselves to the
- // queue.
- new Thread(new Runnable()
- {
- public void run()
- {
- while (worker != null && worker.isAlive() && _started)
- {
- try
- {
- Thread.sleep(100 + ((int) Math.random() * 100));
-
- } catch (Exception e)
- {
- }
-
- }
- // and call ourselves again.
- addStructure(pdbentry, seq, chains, b, alignFrame);
- }
- }).start();
- return;
- }
- }
- // otherwise, start adding the structure.
- jmb.addSequenceAndChain(new PDBEntry[]
- { pdbentry }, new SequenceI[][]
- { seq }, new String[][]
- { chains });
- addingStructures = true;
- _started = false;
- alignAddedStructures = b;
- progressBar = alignFrame; // visual indication happens on caller frame.
- (worker = new Thread(this)).start();
- return;
- }
-
- private Vector getJmolsFor(AlignmentPanel ap2)
+ @Override
+ protected List getViewersFor(AlignmentPanel apanel)
{
- Vector otherJmols = new Vector();
- // Now this AppJmol is mapped to new sequences. We must add them to
- // the exisiting array
+ List result = new ArrayList();
JInternalFrame[] frames = Desktop.instance.getAllFrames();
- for (int i = 0; i < frames.length; i++)
+ for (JInternalFrame frame : frames)
{
- if (frames[i] instanceof AppJmol)
+ if (frame instanceof AppJmol)
{
- AppJmol topJmol = ((AppJmol) frames[i]);
- if (topJmol.isLinkedWith(ap2))
+ if (apanel == null
+ || ((StructureViewerBase) frame).isLinkedWith(apanel))
{
- otherJmols.addElement(topJmol);
+ result.add((StructureViewerBase) frame);
}
}
}
- return otherJmols;
+ return result;
}
void initJmol(String command)
@@ -561,26 +374,27 @@ public class AppJmol extends GStructureViewer implements Runnable,
scriptWindow = new JPanel(bl);
scriptWindow.setVisible(false);
}
- ;
+
jmb.allocateViewer(renderPanel, true, "", null, null, "", scriptWindow,
null);
- jmb.newJmolPopup(true, "Jmol", true);
- if (command==null)
+ // jmb.newJmolPopup("Jmol");
+ if (command == null)
{
- command="";
+ command = "";
}
jmb.evalStateCommand(command);
jmb.setFinishedInit(true);
}
- void setChainMenuItems(Vector chains)
+ void setChainMenuItems(Vector chains)
{
chainMenu.removeAll();
if (chains == null)
{
return;
}
- JMenuItem menuItem = new JMenuItem("All");
+ JMenuItem menuItem = new JMenuItem(
+ MessageManager.getString("label.all"));
menuItem.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent evt)
@@ -589,7 +403,9 @@ public class AppJmol extends GStructureViewer implements Runnable,
for (int i = 0; i < chainMenu.getItemCount(); i++)
{
if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
+ {
((JCheckBoxMenuItem) chainMenu.getItem(i)).setSelected(true);
+ }
}
centerViewer();
allChainsSelected = false;
@@ -598,15 +414,17 @@ public class AppJmol extends GStructureViewer implements Runnable,
chainMenu.add(menuItem);
- for (int c = 0; c < chains.size(); c++)
+ for (String chain : chains)
{
- menuItem = new JCheckBoxMenuItem(chains.elementAt(c).toString(), true);
+ menuItem = new JCheckBoxMenuItem(chain, true);
menuItem.addItemListener(new ItemListener()
{
public void itemStateChanged(ItemEvent evt)
{
if (!allChainsSelected)
+ {
centerViewer();
+ }
}
});
@@ -616,13 +434,9 @@ public class AppJmol extends GStructureViewer implements Runnable,
boolean allChainsSelected = false;
- private boolean alignAddedStructures = false;
-
void centerViewer()
{
- Vector toshow = new Vector();
- String lbl;
- int mlength, p, mnum;
+ Vector toshow = new Vector();
for (int i = 0; i < chainMenu.getItemCount(); i++)
{
if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
@@ -637,10 +451,14 @@ public class AppJmol extends GStructureViewer implements Runnable,
jmb.centerViewer(toshow);
}
- void closeViewer()
+ public void closeViewer(boolean closeExternalViewer)
{
- jmb.closeViewer();
- ap = null;
+ // Jmol does not use an external viewer
+ if (jmb != null)
+ {
+ jmb.closeViewer();
+ }
+ setAlignmentPanel(null);
_aps.clear();
_alignwith.clear();
_colourwith.clear();
@@ -649,11 +467,6 @@ public class AppJmol extends GStructureViewer implements Runnable,
jmb = null;
}
- /**
- * state flag for PDB retrieval thread
- */
- private boolean _started = false;
-
public void run()
{
_started = true;
@@ -666,23 +479,23 @@ public class AppJmol extends GStructureViewer implements Runnable,
// TODO: replace with reference fetching/transfer code (validate PDBentry
// as a DBRef?)
jalview.ws.dbsources.Pdb pdbclient = new jalview.ws.dbsources.Pdb();
- for (int pi = 0; pi < jmb.pdbentry.length; pi++)
+ for (int pi = 0; pi < jmb.getPdbCount(); pi++)
{
- String file = jmb.pdbentry[pi].getFile();
+ String file = jmb.getPdbEntry(pi).getFile();
if (file == null)
{
// retrieve the pdb and store it locally
AlignmentI pdbseq = null;
- pdbid = jmb.pdbentry[pi].getId();
+ pdbid = jmb.getPdbEntry(pi).getId();
long hdl = pdbid.hashCode() - System.currentTimeMillis();
if (progressBar != null)
{
- progressBar.setProgressBar("Fetching PDB " + pdbid, hdl);
+ progressBar.setProgressBar(MessageManager.formatMessage(
+ "status.fetching_pdb", new String[] { pdbid }), hdl);
}
try
{
- pdbseq = pdbclient.getSequenceRecords(pdbid = jmb.pdbentry[pi]
- .getId());
+ pdbseq = pdbclient.getSequenceRecords(pdbid);
} catch (OutOfMemoryError oomerror)
{
new OOMWarning("Retrieving PDB id " + pdbid, oomerror);
@@ -693,15 +506,18 @@ public class AppJmol extends GStructureViewer implements Runnable,
}
if (progressBar != null)
{
- progressBar.setProgressBar("Finished.", hdl);
+ progressBar.setProgressBar(
+ MessageManager.getString("label.state_completed"), hdl);
}
if (pdbseq != null)
{
// 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(pdbseq.getSequenceAt(0).getAllPDBEntries()
+ .elementAt(0).getFile()).getAbsolutePath();
+ jmb.getPdbEntry(pi).setFile(file);
+
+ files.append(" \"" + Platform.escapeString(file) + "\"");
}
else
{
@@ -724,7 +540,7 @@ public class AppJmol extends GStructureViewer implements Runnable,
}
if (file != null)
{
- files.append(" \"" + file + "\"");
+ files.append(" \"" + Platform.escapeString(file) + "\"");
}
}
}
@@ -740,13 +556,14 @@ 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)
@@ -772,7 +589,8 @@ 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);
@@ -786,60 +604,80 @@ 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.getPdbCount()))
+ {
+ 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 (Cache.getDefault("AUTOSUPERIMPOSE", true) && alignAddedStructures)
+ {
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
{
- javax.swing.SwingUtilities.invokeLater(new Runnable()
+ public void run()
{
- public void run()
+ if (jmb.viewer.isScriptExecuting())
+ {
+ javax.swing.SwingUtilities.invokeLater(this);
+ try
+ {
+ Thread.sleep(5);
+ } catch (InterruptedException q)
+ {
+ }
+ ;
+ return;
+ }
+ else
{
alignStructs_withAllAlignPanels();
- // jmb.superposeStructures(ap.av.getAlignment(), -1, null);
}
- });
- alignAddedStructures = false;
- }
- addingStructures = false;
+ }
+ });
+ alignAddedStructures = false;
}
+ addingStructures = false;
+
}
_started = false;
worker = null;
}
+ @Override
public void pdbFile_actionPerformed(ActionEvent actionEvent)
{
JalviewFileChooser chooser = new JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle("Save PDB File");
- chooser.setToolTipText("Save");
+ chooser.setDialogTitle(MessageManager.getString("label.save_pdb_file"));
+ chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(this);
if (value == JalviewFileChooser.APPROVE_OPTION)
{
+ BufferedReader in = null;
try
{
// TODO: cope with multiple PDB files in view
- BufferedReader in = new BufferedReader(new FileReader(
- jmb.getPdbFile()[0]));
+ in = new BufferedReader(new FileReader(jmb.getPdbFile()[0]));
File outFile = chooser.getSelectedFile();
PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
@@ -855,21 +693,29 @@ public class AppJmol extends GStructureViewer implements Runnable,
} catch (Exception ex)
{
ex.printStackTrace();
+ } finally
+ {
+ if (in != null)
+ {
+ try
+ {
+ in.close();
+ } catch (IOException e)
+ {
+ // ignore
+ }
+ }
}
}
}
+ @Override
public void viewMapping_actionPerformed(ActionEvent actionEvent)
{
jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
try
{
- for (int pdbe = 0; pdbe < jmb.pdbentry.length; pdbe++)
- {
- cap.appendText(jmb.printMapping(
- jmb.pdbentry[pdbe].getFile()));
- cap.appendText("\n");
- }
+ cap.appendText(jmb.printMappings());
} catch (OutOfMemoryError e)
{
new OOMWarning(
@@ -878,65 +724,68 @@ 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);
}
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
+ @Override
public void eps_actionPerformed(ActionEvent e)
{
- makePDBImage(jalview.util.ImageMaker.EPS);
+ makePDBImage(jalview.util.ImageMaker.TYPE.EPS);
}
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
+ @Override
public void png_actionPerformed(ActionEvent e)
{
- makePDBImage(jalview.util.ImageMaker.PNG);
+ makePDBImage(jalview.util.ImageMaker.TYPE.PNG);
}
- void makePDBImage(int type)
+ void makePDBImage(jalview.util.ImageMaker.TYPE type)
{
int width = getWidth();
int height = getHeight();
jalview.util.ImageMaker im;
- if (type == jalview.util.ImageMaker.PNG)
+ if (type == jalview.util.ImageMaker.TYPE.PNG)
+ {
+ im = new jalview.util.ImageMaker(this,
+ jalview.util.ImageMaker.TYPE.PNG, "Make PNG image from view",
+ width, height, null, null);
+ }
+ else if (type == jalview.util.ImageMaker.TYPE.EPS)
{
- im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.PNG,
- "Make PNG image from view", width, height, null, null);
+ im = new jalview.util.ImageMaker(this,
+ jalview.util.ImageMaker.TYPE.EPS, "Make EPS file from view",
+ width, height, null, this.getTitle());
}
else
{
- im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.EPS,
- "Make EPS file from view", width, height, null,
- this.getTitle());
+
+ im = new jalview.util.ImageMaker(this,
+ jalview.util.ImageMaker.TYPE.SVG, "Make SVG file from PCA",
+ width, height, null, this.getTitle());
}
if (im.getGraphics() != null)
{
- Rectangle rect = new Rectangle(width, height);
- jmb.viewer.renderScreenImage(im.getGraphics(), rect.getSize(), rect);
+ jmb.viewer.renderScreenImage(im.getGraphics(), width, height);
im.writeImage();
}
}
- public void jmolColour_actionPerformed(ActionEvent actionEvent)
+
+ @Override
+ public void viewerColour_actionPerformed(ActionEvent actionEvent)
{
- if (jmolColour.isSelected()) {
+ if (viewerColour.isSelected())
+ {
// disable automatic sequence colouring.
jmb.setColourBySequence(false);
}
}
+
+ @Override
public void seqColour_actionPerformed(ActionEvent actionEvent)
{
jmb.setColourBySequence(seqColour.isSelected());
@@ -948,90 +797,110 @@ public class AppJmol extends GStructureViewer implements Runnable,
{
if (!jmb.isLoadingFromArchive())
{
- if (_colourwith.size()==0 && ap!=null) {
+ if (_colourwith.size() == 0 && getAlignmentPanel() != null)
+ {
// Make the currently displayed alignment panel the associated view
- _colourwith.add(ap.alignFrame.alignPanel);
+ _colourwith.add(getAlignmentPanel().alignFrame.alignPanel);
}
}
// Set the colour using the current view for the associated alignframe
for (AlignmentPanel ap : _colourwith)
{
- jmb.colourBySequence(ap.av.showSequenceFeatures, ap);
+ jmb.colourBySequence(ap);
}
}
}
+ @Override
public void chainColour_actionPerformed(ActionEvent actionEvent)
{
chainColour.setSelected(true);
jmb.colourByChain();
}
+ @Override
public void chargeColour_actionPerformed(ActionEvent actionEvent)
{
chargeColour.setSelected(true);
jmb.colourByCharge();
}
+ @Override
public void zappoColour_actionPerformed(ActionEvent actionEvent)
{
zappoColour.setSelected(true);
jmb.setJalviewColourScheme(new ZappoColourScheme());
}
+ @Override
public void taylorColour_actionPerformed(ActionEvent actionEvent)
{
taylorColour.setSelected(true);
jmb.setJalviewColourScheme(new TaylorColourScheme());
}
+ @Override
public void hydroColour_actionPerformed(ActionEvent actionEvent)
{
hydroColour.setSelected(true);
jmb.setJalviewColourScheme(new HydrophobicColourScheme());
}
+ @Override
public void helixColour_actionPerformed(ActionEvent actionEvent)
{
helixColour.setSelected(true);
jmb.setJalviewColourScheme(new HelixColourScheme());
}
+ @Override
public void strandColour_actionPerformed(ActionEvent actionEvent)
{
strandColour.setSelected(true);
jmb.setJalviewColourScheme(new StrandColourScheme());
}
+ @Override
public void turnColour_actionPerformed(ActionEvent actionEvent)
{
turnColour.setSelected(true);
jmb.setJalviewColourScheme(new TurnColourScheme());
}
+ @Override
public void buriedColour_actionPerformed(ActionEvent actionEvent)
{
buriedColour.setSelected(true);
jmb.setJalviewColourScheme(new BuriedColourScheme());
}
+ @Override
+ public void purinePyrimidineColour_actionPerformed(ActionEvent actionEvent)
+ {
+ setJalviewColourScheme(new PurinePyrimidineColourScheme());
+ }
+
+ @Override
public void userColour_actionPerformed(ActionEvent actionEvent)
{
userColour.setSelected(true);
new UserDefinedColours(this, null);
}
+ @Override
public void backGround_actionPerformed(ActionEvent actionEvent)
{
- java.awt.Color col = JColorChooser.showDialog(this,
- "Select Background Colour", null);
+ java.awt.Color col = JColorChooser
+ .showDialog(this, MessageManager
+ .getString("label.select_backgroud_colour"), null);
if (col != null)
{
jmb.setBackgroundColour(col);
}
}
- public void jmolHelp_actionPerformed(ActionEvent actionEvent)
+ @Override
+ public void showHelp_actionPerformed(ActionEvent actionEvent)
{
try
{
@@ -1079,31 +948,30 @@ public class AppJmol extends GStructureViewer implements Runnable,
{
final Dimension currentSize = new Dimension();
- final Rectangle rectClip = new Rectangle();
-
+ @Override
public void paintComponent(Graphics g)
{
getSize(currentSize);
- g.getClipBounds(rectClip);
- if (jmb.fileLoadingError != null)
+ if (jmb != null && jmb.fileLoadingError != null)
{
g.setColor(Color.black);
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++)
+ for (int e = 0; e < jmb.getPdbCount(); e++)
{
- sb.append(jmb.pdbentry[e].getId());
- if (e < jmb.pdbentry.length - 1)
+ sb.append(jmb.getPdbEntry(e).getId());
+ if (e < jmb.getPdbCount() - 1)
{
sb.append(",");
}
- if (e == jmb.pdbentry.length - 1 || sb.length() > 20)
+ if (e == jmb.getPdbCount() - 1 || sb.length() > 20)
{
lines++;
g.drawString(sb.toString(), 20, currentSize.height / 2 - lines
@@ -1117,26 +985,17 @@ 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
{
- jmb.viewer.renderScreenImage(g, currentSize, rectClip);
+ jmb.viewer.renderScreenImage(g, currentSize.width,
+ currentSize.height);
}
}
}
- String viewId = null;
-
- public String getViewId()
- {
- if (viewId == null)
- {
- viewId = System.currentTimeMillis() + "." + this.hashCode();
- }
- return viewId;
- }
-
public void updateTitleAndMenus()
{
if (jmb.fileLoadingError != null && jmb.fileLoadingError.length() > 0)
@@ -1147,9 +1006,9 @@ public class AppJmol extends GStructureViewer implements Runnable,
setChainMenuItems(jmb.chainNames);
this.setTitle(jmb.getViewerTitle());
- if (jmb.getPdbFile().length > 1 && jmb.sequence.length > 1)
+ if (jmb.getPdbFile().length > 1 && jmb.getSequence().length > 1)
{
- jmolActionMenu.setVisible(true);
+ viewerActionMenu.setVisible(true);
}
if (!jmb.isLoadingFromArchive())
{
@@ -1157,27 +1016,6 @@ public class AppJmol extends GStructureViewer implements Runnable,
}
}
- protected void buildJmolActionMenu()
- {
- if (_alignwith == null)
- {
- _alignwith = new Vector();
- }
- if (_alignwith.size() == 0 && ap != null)
- {
- _alignwith.add(ap);
- }
- ;
- for (Component c : jmolActionMenu.getMenuComponents())
- {
- if (c != alignStructs)
- {
- jmolActionMenu.remove((JMenuItem) c);
- }
- }
- final ItemListener handler;
- }
-
/*
* (non-Javadoc)
*
@@ -1193,14 +1031,14 @@ public class AppJmol extends GStructureViewer implements Runnable,
private void alignStructs_withAllAlignPanels()
{
- if (ap == null)
+ if (getAlignmentPanel() == null)
{
return;
}
;
if (_alignwith.size() == 0)
{
- _alignwith.add(ap);
+ _alignwith.add(getAlignmentPanel());
}
;
try
@@ -1252,38 +1090,31 @@ public class AppJmol extends GStructureViewer implements Runnable,
return ap;
}
}
- return ap;
+ return getAlignmentPanel();
}
- /**
- *
- * @param ap2
- * @return true if this Jmol instance is linked with the given alignPanel
- */
- public boolean isLinkedWith(AlignmentPanel ap2)
+ @Override
+ public AAStructureBindingModel getBinding()
{
- return _aps.contains(ap2.av.getSequenceSetId());
+ return this.jmb;
}
- public boolean isUsedforaligment(AlignmentPanel ap2)
+ @Override
+ public String getStateInfo()
{
-
- return (_alignwith != null) && _alignwith.contains(ap2);
+ return jmb == null ? null : jmb.viewer.getStateInfo();
}
- public boolean isUsedforcolourby(AlignmentPanel ap2)
+ @Override
+ public ViewerType getViewerType()
{
- return (_colourwith != null) && _colourwith.contains(ap2);
+ return ViewerType.JMOL;
}
- /**
- *
- * @return TRUE if the view is NOT being coloured by sequence associations.
- */
- public boolean isColouredByJmol()
+ @Override
+ protected AAStructureBindingModel getBindingModel()
{
- return !jmb.isColourBySequence();
- }
-
+ return jmb;
+ }
}