();
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);
}
public void closeViewer(boolean closeExternalViewer)
{
// JMol does not use an external viewer
jmb.closeViewer();
setAlignmentPanel(null);
_aps.clear();
_alignwith.clear();
_colourwith.clear();
// 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.getPdbCount(); pi++)
{
String file = jmb.getPdbEntry(pi).getFile();
if (file == null)
{
// retrieve the pdb and store it locally
AlignmentI pdbseq = null;
pdbid = jmb.getPdbEntry(pi).getId();
long hdl = pdbid.hashCode() - System.currentTimeMillis();
if (progressBar != null)
{
progressBar.setProgressBar(MessageManager.formatMessage("status.fetching_pdb", new String[]{pdbid}), hdl);
}
try
{
pdbseq = pdbclient.getSequenceRecords(pdbid);
} catch (OutOfMemoryError oomerror)
{
new OOMWarning("Retrieving PDB id " + pdbid, oomerror);
} catch (Exception ex)
{
ex.printStackTrace();
errormsgs.append("'" + pdbid + "'");
}
if (progressBar != null)
{
progressBar.setProgressBar(MessageManager.getString("label.state_completed"), hdl);
}
if (pdbseq != null)
{
// just transfer the file name from the first sequence's first
// PDBEntry
file = new File(pdbseq.getSequenceAt(0).getPDBId()
.elementAt(0).getFile()).getAbsolutePath();
jmb.getPdbEntry(pi).setFile(file);
files.append(" \"" + Platform.escapeString(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(" \"" + Platform.escapeString(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, 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)
{
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;
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 (addingStructures ? lastnotify >= jmb.getLoadNotifiesHandled()
: (!jmb.isFinishedInit() && jmb.getPdbFile() != null && jmb
.getPdbFile().length != jmb.getPdbCount()))
{
try
{
Cache.log.debug("Waiting around for jmb notify.");
Thread.sleep(35);
} catch (Exception e)
{
}
}
// refresh the sequence colours for the new structure(s)
for (AlignmentPanel ap : _colourwith)
{
jmb.updateColours(ap);
}
// do superposition if asked to
if (alignAddedStructures)
{
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
public void run()
{
alignStructs_withAllAlignPanels();
// jmb.superposeStructures(ap.av.getAlignment(), -1, null);
}
});
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(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
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();
} 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
{
cap.appendText(jmb.printMappings());
} catch (OutOfMemoryError e)
{
new OOMWarning(
"composing sequence-structure alignments for display in text box.",
e);
cap.dispose();
return;
}
jalview.gui.Desktop.addInternalFrame(cap,
MessageManager.getString("label.pdb_sequence_mapping"), 550,
600);
}
@Override
public void eps_actionPerformed(ActionEvent e)
{
makePDBImage(jalview.util.ImageMaker.TYPE.EPS);
}
@Override
public void png_actionPerformed(ActionEvent e)
{
makePDBImage(jalview.util.ImageMaker.TYPE.PNG);
}
void makePDBImage(jalview.util.ImageMaker.TYPE type)
{
int width = getWidth();
int height = getHeight();
jalview.util.ImageMaker im;
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.TYPE.EPS,
"Make EPS file from view", width, height, null,
this.getTitle());
}
else
{
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)
{
jmb.viewer.renderScreenImage(im.getGraphics(), width, height);
im.writeImage();
}
}
@Override
public void viewerColour_actionPerformed(ActionEvent actionEvent)
{
if (viewerColour.isSelected())
{
// disable automatic sequence colouring.
jmb.setColourBySequence(false);
}
}
@Override
public void seqColour_actionPerformed(ActionEvent actionEvent)
{
jmb.setColourBySequence(seqColour.isSelected());
if (_colourwith == null)
{
_colourwith = new Vector();
}
if (jmb.isColourBySequence())
{
if (!jmb.isLoadingFromArchive())
{
if (_colourwith.size() == 0 && getAlignmentPanel() != null)
{
// Make the currently displayed alignment panel the associated view
_colourwith.add(getAlignmentPanel().alignFrame.alignPanel);
}
}
// Set the colour using the current view for the associated alignframe
for (AlignmentPanel ap : _colourwith)
{
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,
MessageManager.getString("label.select_backgroud_colour"), null);
if (col != null)
{
jmb.setBackgroundColour(col);
}
}
@Override
public void showHelp_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();
@Override
public void paintComponent(Graphics g)
{
getSize(currentSize);
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(MessageManager.getString("label.error_loading_file")
+ "...", 20, currentSize.height / 2);
StringBuffer sb = new StringBuffer();
int lines = 0;
for (int e = 0; e < jmb.getPdbCount(); e++)
{
sb.append(jmb.getPdbEntry(e).getId());
if (e < jmb.getPdbCount() - 1)
{
sb.append(",");
}
if (e == jmb.getPdbCount() - 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(MessageManager.getString("label.retrieving_pdb_data"),
20, currentSize.height / 2);
}
else
{
jmb.viewer.renderScreenImage(g, currentSize.width,
currentSize.height);
}
}
}
public void updateTitleAndMenus()
{
if (jmb.fileLoadingError != null && jmb.fileLoadingError.length() > 0)
{
repaint();
return;
}
setChainMenuItems(jmb.chainNames);
this.setTitle(jmb.getViewerTitle());
if (jmb.getPdbFile().length > 1 && jmb.getSequence().length > 1)
{
viewerActionMenu.setVisible(true);
}
if (!jmb.isLoadingFromArchive())
{
seqColour_actionPerformed(null);
}
}
/*
* (non-Javadoc)
*
* @see
* jalview.jbgui.GStructureViewer#alignStructs_actionPerformed(java.awt.event
* .ActionEvent)
*/
@Override
protected void alignStructs_actionPerformed(ActionEvent actionEvent)
{
alignStructs_withAllAlignPanels();
}
private void alignStructs_withAllAlignPanels()
{
if (getAlignmentPanel() == null)
{
return;
}
;
if (_alignwith.size() == 0)
{
_alignwith.add(getAlignmentPanel());
}
;
try
{
AlignmentI[] als = new Alignment[_alignwith.size()];
ColumnSelection[] alc = new ColumnSelection[_alignwith.size()];
int[] alm = new int[_alignwith.size()];
int a = 0;
for (AlignmentPanel ap : _alignwith)
{
als[a] = ap.av.getAlignment();
alm[a] = -1;
alc[a++] = ap.av.getColumnSelection();
}
jmb.superposeStructures(als, alm, alc);
} catch (Exception e)
{
StringBuffer sp = new StringBuffer();
for (AlignmentPanel ap : _alignwith)
{
sp.append("'" + ap.alignFrame.getTitle() + "' ");
}
Cache.log.info("Couldn't align structures with the " + sp.toString()
+ "associated alignment panels.", e);
}
}
public void setJalviewColourScheme(ColourSchemeI ucs)
{
jmb.setJalviewColourScheme(ucs);
}
/**
*
* @param alignment
* @return first alignment panel displaying given alignment, or the default
* alignment panel
*/
public AlignmentPanel getAlignmentPanelFor(AlignmentI alignment)
{
for (AlignmentPanel ap : getAllAlignmentPanels())
{
if (ap.av.getAlignment() == alignment)
{
return ap;
}
}
return getAlignmentPanel();
}
@Override
public AAStructureBindingModel getBinding()
{
return this.jmb;
}
@Override
public String getStateInfo()
{
return jmb == null ? null : jmb.viewer.getStateInfo();
}
@Override
public ViewerType getViewerType()
{
return ViewerType.JMOL;
}
}