/*
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
* 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;
import org.openscience.jmol.app.jmolpanel.AppConsole;
public class AppJmol extends GStructureViewer implements Runnable,
SequenceStructureBinding
{
AppJmolBinding jmb;
JPanel scriptWindow;
JSplitPane splitPane;
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, loadStatus, bounds, viewid);
}
/**
*
* @param files
* @param ids
* @param seqs
* @param ap
* @param loadStatus
* @param bounds
* @param viewid
*/
public AppJmol(String[] files, String[] ids, SequenceI[][] seqs,
AlignmentPanel ap, 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]);
pdbentrys[i] = pdbentry;
}
// / TODO: check if protocol is needed to be set, and if chains are
// autodiscovered.
jmb = new AppJmolBinding(this, pdbentrys, seqs, 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!
}
IProgressIndicator progressBar = null;
public AppJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
AlignmentPanel ap)
{
progressBar = ap.alignFrame;
// ////////////////////////////////
// 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(pe, seq);
break;
}
}
}
}
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)
{
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.addStructure(pdbentry, seq, chains, true, ap.alignFrame);
return;
}
}
}
// /////////////////////////////////
jmb = new AppJmolBinding(this, new PDBEntry[]
{ pdbentry }, new SequenceI[][]
{ 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
{
addingStructures = false;
worker = new Thread(this);
worker.start();
}
this.addInternalFrameListener(new InternalFrameAdapter()
{
public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
{
closeViewer();
}
});
}
/**
* 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
*/
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)
{
Vector otherJmols = new Vector();
// 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]);
if (topJmol.ap == ap2)
{
otherJmols.addElement(topJmol);
}
}
}
return otherJmols;
}
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);
if (scriptWindow == null)
{
BorderLayout bl = new BorderLayout();
bl.setHgap(0);
bl.setVgap(0);
scriptWindow = new JPanel(bl);
scriptWindow.setVisible(false);
}
;
jmb.allocateViewer(renderPanel, true, "", null, null, "", scriptWindow,
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;
private boolean alignAddedStructures = 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;
}
/**
* state flag for PDB retrieval thread
*/
private boolean _started = false;
public void run()
{
_started = true;
String pdbid = "";
// todo - record which pdbids were successfuly imported.
StringBuffer errormsgs = new StringBuffer(), files = new StringBuffer();
try
{
String[] curfiles = jmb.getPdbFile(); // files currently in viewer
// 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++)
{
String file = jmb.pdbentry[pi].getFile();
if (file == null)
{
// retrieve the pdb and store it locally
AlignmentI pdbseq = null;
pdbid = jmb.pdbentry[pi].getId();
long hdl = pdbid.hashCode() - System.currentTimeMillis();
if (progressBar != null)
{
progressBar.setProgressBar("Fetching PDB " + pdbid, hdl);
}
try
{
pdbseq = pdbclient.getSequenceRecords(pdbid = jmb.pdbentry[pi]
.getId());
} catch (OutOfMemoryError oomerror)
{
new OOMWarning("Retrieving PDB id " + pdbid, oomerror);
} catch (Exception ex)
{
ex.printStackTrace();
errormsgs.append("'" + pdbid + "'");
}
if (progressBar != null)
{
progressBar.setProgressBar("Finished.", 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 + "\"");
}
else
{
errormsgs.append("'" + pdbid + "' ");
}
}
else
{
if (curfiles != null && curfiles.length > 0)
{
addingStructures = true; // already files loaded.
for (int c = 0; c < curfiles.length; c++)
{
if (curfiles[c].equals(file))
{
file = null;
break;
}
}
}
if (file != null)
{
files.append(" \"" + file + "\"");
}
}
}
} catch (OutOfMemoryError oomerror)
{
new OOMWarning("Retrieving PDB files: " + pdbid, oomerror);
} catch (Exception ex)
{
ex.printStackTrace();
errormsgs.append("When retrieving pdbfiles : current was: '" + 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)
{
if (!addingStructures)
{
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);
}
}
else
{
StringBuffer cmd = new StringBuffer();
cmd.append("loadingJalviewdata=true\nload APPEND ");
cmd.append(files.toString());
cmd.append("\nloadingJalviewdata=null");
final String command = cmd.toString();
cmd = null;
long lastnotify = jmb.getLoadNotifiesHandled();
try
{
jmb.evalStateCommand(command);
} catch (OutOfMemoryError oomerror)
{
new OOMWarning(
"When trying to add structures to the Jmol viewer!",
oomerror);
Cache.log.debug("File locations are " + files);
} catch (Exception ex)
{
Cache.log.error("Couldn't add files to Jmol viewer!", ex);
}
// need to wait around until script has finished
while (lastnotify >= jmb.getLoadNotifiesHandled())
;
{
try
{
Thread.sleep(35);
} catch (Exception e)
{
}
}
// refresh the sequence colours for the new structure(s)
jmb.updateColours(ap);
// do superposition if asked to
if (alignAddedStructures)
{
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
public void run()
{
jmb.superposeStructures(ap.av.getAlignment(), -1, null);
}
});
alignAddedStructures = false;
}
addingStructures = false;
}
}
_started = false;
worker = null;
}
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; pdbe < jmb.pdbentry.length; pdbe++)
{
cap.appendText(StructureSelectionManager
.getStructureSelectionManager().printMapping(
jmb.pdbentry[pdbe].getFile()));
cap.appendText("\n");
}
} catch (OutOfMemoryError e)
{
new OOMWarning(
"composing sequence-structure alignments for display in text box.",
e);
cap.dispose();
return;
}
jalview.gui.Desktop.addInternalFrame(cap, "PDB - Sequence Mapping",
550, 600);
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
public void eps_actionPerformed(ActionEvent e)
{
makePDBImage(jalview.util.ImageMaker.EPS);
}
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
public void png_actionPerformed(ActionEvent e)
{
makePDBImage(jalview.util.ImageMaker.PNG);
}
void makePDBImage(int type)
{
int width = getWidth();
int height = getHeight();
jalview.util.ImageMaker im;
if (type == jalview.util.ImageMaker.PNG)
{
im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.PNG,
"Make PNG image from view", width, height, null, null);
}
else
{
im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.EPS,
"Make EPS file from view", width, height, null,
this.getTitle());
}
if (im.getGraphics() != null)
{
Rectangle rect = new Rectangle(width, height);
jmb.viewer.renderScreenImage(im.getGraphics(), rect.getSize(), rect);
im.writeImage();
}
}
public void seqColour_actionPerformed(ActionEvent actionEvent)
{
jmb.setColourBySequence(seqColour.isSelected());
// Set the colour using the current view for the associated alignframe
jmb.colourBySequence(ap.alignFrame.viewport.showSequenceFeatures,
ap.alignFrame.viewport.alignment);
}
public void chainColour_actionPerformed(ActionEvent actionEvent)
{
chainColour.setSelected(true);
jmb.colourByChain();
}
public void chargeColour_actionPerformed(ActionEvent actionEvent)
{
chargeColour.setSelected(true);
jmb.colourByCharge();
}
public void zappoColour_actionPerformed(ActionEvent actionEvent)
{
zappoColour.setSelected(true);
jmb.setJalviewColourScheme(new ZappoColourScheme());
}
public void taylorColour_actionPerformed(ActionEvent actionEvent)
{
taylorColour.setSelected(true);
jmb.setJalviewColourScheme(new TaylorColourScheme());
}
public void hydroColour_actionPerformed(ActionEvent actionEvent)
{
hydroColour.setSelected(true);
jmb.setJalviewColourScheme(new HydrophobicColourScheme());
}
public void helixColour_actionPerformed(ActionEvent actionEvent)
{
helixColour.setSelected(true);
jmb.setJalviewColourScheme(new HelixColourScheme());
}
public void strandColour_actionPerformed(ActionEvent actionEvent)
{
strandColour.setSelected(true);
jmb.setJalviewColourScheme(new StrandColourScheme());
}
public void turnColour_actionPerformed(ActionEvent actionEvent)
{
turnColour.setSelected(true);
jmb.setJalviewColourScheme(new TurnColourScheme());
}
public void buriedColour_actionPerformed(ActionEvent actionEvent)
{
buriedColour.setSelected(true);
jmb.setJalviewColourScheme(new BuriedColourScheme());
}
public void userColour_actionPerformed(ActionEvent actionEvent)
{
userColour.setSelected(true);
new UserDefinedColours(this, null);
}
public void backGround_actionPerformed(ActionEvent actionEvent)
{
java.awt.Color col = JColorChooser.showDialog(this,
"Select Background Colour", null);
if (col != null)
{
jmb.setBackgroundColour(col);
}
}
public void jmolHelp_actionPerformed(ActionEvent actionEvent)
{
try
{
jalview.util.BrowserLauncher
.openURL("http://jmol.sourceforge.net/docs/JmolUserGuide/");
} catch (Exception ex)
{
}
}
public void showConsole(boolean showConsole)
{
if (showConsole)
{
if (splitPane == null)
{
splitPane = new JSplitPane(JSplitPane.VERTICAL_SPLIT);
splitPane.setTopComponent(renderPanel);
splitPane.setBottomComponent(scriptWindow);
this.getContentPane().add(splitPane, BorderLayout.CENTER);
splitPane.setDividerLocation(getHeight() - 200);
scriptWindow.setVisible(true);
scriptWindow.validate();
splitPane.validate();
}
}
else
{
if (splitPane != null)
{
splitPane.setVisible(false);
}
splitPane = null;
this.getContentPane().add(renderPanel, BorderLayout.CENTER);
}
validate();
}
class RenderPanel extends JPanel
{
final Dimension currentSize = new Dimension();
final Rectangle rectClip = new Rectangle();
public void paintComponent(Graphics g)
{
getSize(currentSize);
g.getClipBounds(rectClip);
if (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);
StringBuffer sb = new StringBuffer();
int lines = 0;
for (int e = 0; e < jmb.pdbentry.length; e++)
{
sb.append(jmb.pdbentry[e].getId());
if (e < jmb.pdbentry.length - 1)
{
sb.append(",");
}
if (e == jmb.pdbentry.length - 1 || sb.length() > 20)
{
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());
if (jmb.getPdbFile().length > 1 && jmb.sequence.length > 1)
{
jmolActionMenu.setVisible(true);
}
}
/*
* (non-Javadoc)
*
* @see
* jalview.jbgui.GStructureViewer#alignStructs_actionPerformed(java.awt.event
* .ActionEvent)
*/
@Override
protected void alignStructs_actionPerformed(ActionEvent actionEvent)
{
try
{
jmb.superposeStructures(ap.av.getAlignment(), -1,
ap.av.getColumnSelection());
} catch (Exception e)
{
Cache.log.info("Couldn't align structures in alignframe "
+ ap.alignFrame.getTitle(), e);
}
}
public void setJalviewColourScheme(ColourSchemeI ucs)
{
jmb.setJalviewColourScheme(ucs);
}
}