/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*/
package jalview.gui;
-import jalview.bin.Cache;
-import jalview.datamodel.Alignment;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceI;
-import jalview.ext.rbvi.chimera.JalviewChimeraBinding;
-import jalview.gui.Jalview2XML.ViewerData;
-import jalview.io.AppletFormatAdapter;
-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 jalview.ws.dbsources.Pdb;
-
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.ItemEvent;
import java.io.PrintWriter;
import java.util.ArrayList;
import java.util.List;
+import java.util.Random;
import java.util.Vector;
import javax.swing.JCheckBoxMenuItem;
import javax.swing.event.MenuEvent;
import javax.swing.event.MenuListener;
+import jalview.bin.Cache;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.ext.rbvi.chimera.JalviewChimeraBinding;
+import jalview.io.AppletFormatAdapter;
+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 jalview.ws.dbsources.Pdb;
+
/**
* GUI elements for handlnig an external chimera display
*
private Thread worker = null;
/*
- * Path to Chimera session file - set in saveSession()
+ * Path to Chimera session file. This is set when an open Jalview/Chimera
+ * session is saved, or on restore from a Jalview project (if it holds the
+ * filename of any saved Chimera sessions).
*/
- private String chimeraSessionFile = "";
+ private String chimeraSessionFile = null;
+
+ private Random random = new Random();
/**
* Initialise menu options.
for (ChimeraViewFrame topView : existingViews)
{
// TODO: highlight topView in view somehow
+ /*
+ * JAL-1742 exclude view with this structure already mapped (don't offer
+ * to align chain B to chain A of the same structure)
+ */
+ if (topView.hasPdbId(pdbentry.getId()))
+ {
+ continue;
+ }
int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
MessageManager.formatMessage("label.add_pdbentry_to_view",
new Object[]
{ seq });
}
+ /**
+ * Create a helper to manage progress bar display
+ */
+ protected void createProgressBar()
+ {
+ if (progressBar == null)
+ {
+ progressBar = new ProgressBar(statusPanel, statusBar);
+ }
+ }
+
+ protected boolean hasPdbId(String pdbId)
+ {
+ return jmb.hasPdbId(pdbId);
+ }
+
private void openNewChimera(AlignmentPanel ap, PDBEntry[] pdbentrys,
SequenceI[][] seqs)
{
- progressBar = ap.alignFrame;
+ createProgressBar();
+
jmb = new JalviewChimeraBindingModel(this,
ap.getStructureSelectionManager(), pdbentrys, seqs, null, null);
addAlignmentPanel(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();
- }
+
+ addingStructures = false;
+ worker = new Thread(this);
+ worker.start();
+
this.addInternalFrameListener(new InternalFrameAdapter()
{
public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
{
- closeViewer();
+ closeViewer(false);
}
});
}
/**
- * Create a new viewer from saved session state data.
+ * Create a new viewer from saved session state data including Chimera session
+ * file.
+ *
+ * @param chimeraSession
*
- * @param viewerData
- * @param af
+ * @param alignPanel
+ * @param pdbArray
+ * @param seqsArray
+ * @param colourByChimera
+ * @param colourBySequence
*/
- public ChimeraViewFrame(ViewerData viewerData, AlignFrame af)
+ public ChimeraViewFrame(String chimeraSession, AlignmentPanel alignPanel,
+ PDBEntry[] pdbArray,
+ SequenceI[][] seqsArray, boolean colourByChimera,
+ boolean colourBySequence)
{
super();
- String chimeraSessionFile = viewerData.stateData;
- openNewChimera(af.alignPanel, new PDBEntry[]
- {}, new SequenceI[][]
- {});
- initChimera("open " + chimeraSessionFile);
- // TODO restore mappings
+ this.chimeraSessionFile = chimeraSession;
+ openNewChimera(alignPanel, pdbArray, seqsArray);
+ if (colourByChimera)
+ {
+ jmb.setColourBySequence(false);
+ seqColour.setSelected(false);
+ viewerColour.setSelected(true);
+ }
+ else if (colourBySequence)
+ {
+ jmb.setColourBySequence(true);
+ seqColour.setSelected(true);
+ viewerColour.setSelected(false);
+ }
}
/**
return result;
}
- void initChimera(String command)
+ /**
+ * Launch Chimera. If we have a chimera session file name, send Chimera the
+ * command to open its saved session file.
+ */
+ void initChimera()
{
jmb.setFinishedInit(false);
- // TODO: consider waiting until the structure/view is fully loaded before
- // displaying
jalview.gui.Desktop.addInternalFrame(this, jmb.getViewerTitle("Chimera", true),
getBounds().width, getBounds().height);
- if (command == null)
+
+ /*
+ * Pass an empty 'command' to launch Chimera
+ */
+ jmb.evalStateCommand("", false);
+
+ if (this.chimeraSessionFile != null)
{
- command = "";
+ boolean opened = jmb.openSession(chimeraSessionFile);
+ if (!opened)
+ {
+ System.err
+ .println("An error occurred opening Chimera session file "
+ + chimeraSessionFile);
+ }
}
- jmb.evalStateCommand(command, false);
jmb.setFinishedInit(true);
+
+ jmb.startChimeraListener();
}
void setChainMenuItems(List<String> chainNames)
* Close down this instance of Jalview's Chimera viewer, giving the user the
* option to close the associated Chimera window (process). They may wish to
* keep it open until they have had an opportunity to save any work.
+ *
+ * @param closeChimera
+ * if true, close any linked Chimera process; if false, prompt first
*/
- public void closeViewer()
+ public void closeViewer(boolean closeChimera)
{
if (jmb.isChimeraRunning())
{
- String prompt = MessageManager
- .formatMessage("label.confirm_close_chimera", new Object[]
- { jmb.getViewerTitle("Chimera", false) });
- prompt = JvSwingUtils.wrapTooltip(true, prompt);
- int confirm = JOptionPane.showConfirmDialog(this, prompt,
- MessageManager.getString("label.close_viewer"),
- JOptionPane.YES_NO_OPTION);
- jmb.closeViewer(confirm == JOptionPane.YES_OPTION);
+ if (!closeChimera)
+ {
+ String prompt = MessageManager.formatMessage(
+ "label.confirm_close_chimera", new Object[]
+ { jmb.getViewerTitle("Chimera", false) });
+ prompt = JvSwingUtils.wrapTooltip(true, prompt);
+ int confirm = JOptionPane.showConfirmDialog(this, prompt,
+ MessageManager.getString("label.close_viewer"),
+ JOptionPane.YES_NO_OPTION);
+ closeChimera = confirm == JOptionPane.YES_OPTION;
+ }
+ jmb.closeViewer(closeChimera);
}
setAlignmentPanel(null);
_aps.clear();
{
try
{
- initChimera("");
+ initChimera();
} catch (Exception ex)
{
Cache.log.error("Couldn't open Chimera viewer!", ex);
try
{
int pos = filePDBpos.get(num).intValue();
+ long startTime = startProgressBar("Chimera "
+ + MessageManager.getString("status.opening_file"));
jmb.openFile(pe);
jmb.addSequence(pos, jmb.getSequence()[pos]);
File fl = new File(pe.getFile());
}
} catch (Throwable e)
{
+ } finally
+ {
+ stopProgressBar("", startTime);
}
// Explicitly map to the filename used by Chimera ;
// TODO: use pe.getId() instead of pe.getFile() ?
Pdb pdbclient = new Pdb();
AlignmentI pdbseq = null;
String pdbid = processingEntry.getId();
- long hdl = pdbid.hashCode() - System.currentTimeMillis();
- if (progressBar != null)
- {
- progressBar.setProgressBar(MessageManager.formatMessage(
- "status.fetching_pdb", new Object[]
- { pdbid }), hdl);
- }
+ long hdl = startProgressBar(MessageManager.formatMessage(
+ "status.fetching_pdb", new Object[]
+ { pdbid }));
try
{
pdbseq = pdbclient.getSequenceRecords(pdbid);
new OOMWarning("Retrieving PDB id " + pdbid, oomerror);
} finally
{
- if (progressBar != null)
- {
- progressBar
- .setProgressBar(
- pdbid
- + " "
- + MessageManager
- .getString("label.state_completed"),
- hdl);
- }
+ String msg = pdbid + " "
+ + MessageManager.getString("label.state_completed");
+ stopProgressBar(msg, hdl);
}
/*
* If PDB data were saved and are not invalid (empty alignment), return the
if (pdbseq != null && pdbseq.getHeight() > 0)
{
// just use the file name from the first sequence's first PDBEntry
- filePath = new File(((PDBEntry) pdbseq.getSequenceAt(0).getPDBId()
- .elementAt(0)).getFile()).getAbsolutePath();
+ filePath = new File(pdbseq.getSequenceAt(0).getPDBId()
+ .elementAt(0).getFile()).getAbsolutePath();
processingEntry.setFile(filePath);
}
return filePath;
}
+ /**
+ * Convenience method to update the progress bar if there is one. Be sure to
+ * call stopProgressBar with the returned handle to remove the message.
+ *
+ * @param msg
+ * @param handle
+ */
+ public long startProgressBar(String msg)
+ {
+ // TODO would rather have startProgress/stopProgress as the
+ // IProgressIndicator interface
+ long tm = random.nextLong();
+ if (progressBar != null)
+ {
+ progressBar.setProgressBar(msg, tm);
+ }
+ return tm;
+ }
+
+ public void stopProgressBar(String msg, long handle)
+ {
+ if (progressBar != null)
+ {
+ progressBar.setProgressBar(msg, handle);
+ }
+ }
+
@Override
public void pdbFile_actionPerformed(ActionEvent actionEvent)
{
// Set the colour using the current view for the associated alignframe
for (AlignmentPanel ap : _colourwith)
{
- jmb.colourBySequence(ap.av.showSequenceFeatures, ap);
+ jmb.colourBySequence(ap.av.isShowSequenceFeatures(), ap);
}
}
}
repaint();
return;
}
- setChainMenuItems(jmb.chainNames);
+ setChainMenuItems(jmb.getChainNames());
this.setTitle(jmb.getViewerTitle("Chimera", true));
if (jmb.getPdbFile().length > 1 && jmb.getSequence().length > 1)
git://source.jalview.org / jalview.git / blobdiff