/*
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
* Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
* 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 .
*/
package jalview.gui;
import java.util.regex.*;
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.*;
import jalview.structure.*;
import jalview.datamodel.PDBEntry;
import jalview.io.*;
import jalview.schemes.*;
import jalview.ws.ebi.EBIFetchClient;
import org.jmol.api.*;
import org.jmol.adapter.smarter.SmarterJmolAdapter;
import org.jmol.popup.*;
import org.jmol.viewer.JmolConstants;
public class AppJmol extends GStructureViewer implements Runnable,
SequenceStructureBinding
{
AppJmolBinding jmb;
ScriptWindow scriptWindow;
JSplitPane splitPane;
RenderPanel renderPanel;
AlignmentPanel ap;
Vector atomsPicked = new Vector();
public AppJmol(String file, String id, SequenceI[] seq,
AlignmentPanel ap, String loadStatus, Rectangle bounds)
{
this(file, id, seq, ap, loadStatus, bounds, null);
}
public AppJmol(String file, String id, SequenceI[] seq,
AlignmentPanel ap, String loadStatus, Rectangle bounds,
String viewid)
{
PDBEntry pdbentry = new PDBEntry();
pdbentry.setFile(file);
pdbentry.setId(id);
// / TODO: check if protocol is needed to be set, and if chains are
// autodiscovered.
jmb = new AppJmolBinding(this, new PDBEntry[]
{ pdbentry }, seq, null, null);
jmb.setLoadingFromArchive(true);
this.ap = ap;
this.setBounds(bounds);
jmb.setColourBySequence(false);
seqColour.setSelected(false);
viewId = viewid;
// jalview.gui.Desktop.addInternalFrame(this, "Loading File",
// bounds.width,bounds.height);
this.addInternalFrameListener(new InternalFrameAdapter()
{
public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
{
closeViewer();
}
});
initJmol(loadStatus); // pdbentry, seq, JBPCHECK!
}
public AppJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
AlignmentPanel ap)
{
// ////////////////////////////////
// Is the pdb file already loaded?
String alreadyMapped = StructureSelectionManager
.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);
if (option == JOptionPane.YES_OPTION)
{
StructureSelectionManager.getStructureSelectionManager()
.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(seq);
break;
}
}
}
}
return;
}
}
// /////////////////////////////////
jmb = new AppJmolBinding(this, new PDBEntry[]
{ pdbentry }, seq, null, null);
this.ap = ap;
setSize(400, 400); // probably should be a configurable/dynamic default here
if (pdbentry.getFile() != null)
{
initJmol("load \"" + pdbentry.getFile() + "\"");
}
else
{
Thread worker = new Thread(this);
worker.start();
}
this.addInternalFrameListener(new InternalFrameAdapter()
{
public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
{
closeViewer();
}
});
}
void initJmol(String command)
{
jmb.setFinishedInit(false);
renderPanel = new RenderPanel();
// TODO: consider waiting until the structure/view is fully loaded before
// displaying
this.getContentPane().add(renderPanel, java.awt.BorderLayout.CENTER);
jalview.gui.Desktop.addInternalFrame(this, jmb.getViewerTitle(),
getBounds().width, getBounds().height);
jmb.allocateViewer(renderPanel, true, "", null, null, "");
jmb.newJmolPopup(true, "Jmol", true);
jmb.evalStateCommand(command);
jmb.setFinishedInit(true);
}
void setChainMenuItems(Vector chains)
{
chainMenu.removeAll();
if (chains==null)
{
return;
}
JMenuItem menuItem = new JMenuItem("All");
menuItem.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent evt)
{
allChainsSelected = true;
for (int i = 0; i < chainMenu.getItemCount(); i++)
{
if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
((JCheckBoxMenuItem) chainMenu.getItem(i)).setSelected(true);
}
centerViewer();
allChainsSelected = false;
}
});
chainMenu.add(menuItem);
for (int c = 0; c < chains.size(); c++)
{
menuItem = new JCheckBoxMenuItem(chains.elementAt(c).toString(), true);
menuItem.addItemListener(new ItemListener()
{
public void itemStateChanged(ItemEvent evt)
{
if (!allChainsSelected)
centerViewer();
}
});
chainMenu.add(menuItem);
}
}
boolean allChainsSelected = false;
void centerViewer()
{
Vector toshow = new Vector();
String lbl;
int mlength, p, mnum;
for (int i = 0; i < chainMenu.getItemCount(); i++)
{
if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
{
JCheckBoxMenuItem item = (JCheckBoxMenuItem) chainMenu.getItem(i);
if (item.isSelected())
{
toshow.addElement(item.getText());
}
}
}
jmb.centerViewer(toshow);
}
void closeViewer()
{
jmb.closeViewer();
// TODO: check for memory leaks where instance isn't finalised because jmb
// holds a reference to the window
jmb = null;
}
public void run()
{
String pdbid = "";
// todo - record which pdbids were successfuly imported.
StringBuffer errormsgs = new StringBuffer(), files = new StringBuffer();
try
{
// 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++)
{
AlignmentI pdbseq;
if ((pdbseq = pdbclient.getSequenceRecords(pdbid = jmb.pdbentry[pi]
.getId())) != null)
{
String file;
// 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 + "\"");
}
else
{
errormsgs.append("'" + pdbid + "' ");
}
}
} catch (OutOfMemoryError oomerror)
{
new OOMWarning("Retrieving PDB id " + pdbid, oomerror);
} catch (Exception ex)
{
ex.printStackTrace();
errormsgs.append("'" + pdbid + "'");
}
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);
}
if (files.length() > 0)
{
try
{
initJmol("load FILES " + files.toString());
} catch (OutOfMemoryError oomerror)
{
new OOMWarning("When trying to open the Jmol viewer!", oomerror);
Cache.log.debug("File locations are " + files);
} catch (Exception ex)
{
Cache.log.error("Couldn't open Jmol viewer!", ex);
}
}
}
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");
int value = chooser.showSaveDialog(this);
if (value == JalviewFileChooser.APPROVE_OPTION)
{
try
{
// TODO: cope with multiple PDB files in view
BufferedReader in = new BufferedReader(new FileReader(jmb.getPdbFile()[0]));
File outFile = chooser.getSelectedFile();
PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
String data;
while ((data = in.readLine()) != null)
{
if (!(data.indexOf("
") > -1 || data.indexOf("
") > -1))
{
out.println(data);
}
}
out.close();
} catch (Exception ex)
{
ex.printStackTrace();
}
}
}
public void viewMapping_actionPerformed(ActionEvent actionEvent)
{
jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
try {for (int pdbe = 0; pdbe20)
{
lines++;
g.drawString(sb.toString(), 20, currentSize.height/2 - lines*g.getFontMetrics().getHeight());
}
}
}
else
if (jmb == null || jmb.viewer == null || !jmb.isFinishedInit())
{
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("Retrieving PDB data....", 20, currentSize.height / 2);
}
else
{
jmb.viewer.renderScreenImage(g, currentSize, rectClip);
}
}
}
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)
{
repaint();
return;
}
setChainMenuItems(jmb.chainNames);
jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment);
this.setTitle(jmb.getViewerTitle());
}
public void setJalviewColourScheme(ColourSchemeI ucs)
{
jmb.setJalviewColourScheme(ucs);
}
}