/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * 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.
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;
- ScriptWindow scriptWindow;
+ JPanel scriptWindow;
JSplitPane splitPane;
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)
{
- PDBEntry pdbentry = new PDBEntry();
- pdbentry.setFile(file);
- pdbentry.setId(id);
+ 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, new PDBEntry[]
- { pdbentry }, seq, null, null);
+ jmb = new AppJmolBinding(this, pdbentrys, seqs, null, null);
jmb.setLoadingFromArchive(true);
this.ap = ap;
}
+ 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
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);
+ 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)
{
{
if (topJmol.jmb.pdbentry[pe].getFile().equals(alreadyMapped))
{
- topJmol.jmb.addSequence(seq);
+ topJmol.jmb.addSequence(pe, seq);
break;
}
}
}
}
// /////////////////////////////////
+ // 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 }, seq, null, null);
+ { pdbentry }, new SequenceI[][]
+ { seq }, null, null);
this.ap = ap;
setSize(400, 400); // probably should be a configurable/dynamic default here
}
else
{
- Thread worker = new Thread(this);
+ addingStructures = false;
+ worker = new Thread(this);
worker.start();
}
}
+ /**
+ * 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);
this.getContentPane().add(renderPanel, java.awt.BorderLayout.CENTER);
jalview.gui.Desktop.addInternalFrame(this, jmb.getViewerTitle(),
getBounds().width, getBounds().height);
- jmb.allocateViewer(renderPanel, "", null, null, "");
+ 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)
+ if (chains == null)
{
return;
}
boolean allChainsSelected = false;
+ private boolean alignAddedStructures = false;
+
void centerViewer()
{
Vector toshow = new Vector();
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++)
{
- AlignmentI pdbseq;
- if ((pdbseq = pdbclient.getSequenceRecords(pdbid = jmb.pdbentry[pi]
- .getId())) != null)
+ String file = jmb.pdbentry[pi].getFile();
+ if (file == 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 + "\"");
+ // 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
{
- errormsgs.append("'" + pdbid + "' ");
+ 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 id " + pdbid, oomerror);
+ new OOMWarning("Retrieving PDB files: " + pdbid, oomerror);
} catch (Exception ex)
{
ex.printStackTrace();
- errormsgs.append("'" + pdbid + "'");
+ errormsgs.append("When retrieving pdbfiles : current was: '" + pdbid
+ + "'");
}
if (errormsgs.length() > 0)
{
}
if (files.length() > 0)
{
- try
- {
- initJmol("load FILES " + files.toString());
- } catch (OutOfMemoryError oomerror)
+ if (!addingStructures)
{
- new OOMWarning("When trying to open the Jmol viewer!", oomerror);
- Cache.log.debug("File locations are " + files);
- } catch (Exception ex)
+
+ 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
{
- Cache.log.error("Couldn't open Jmol viewer!", ex);
+ 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;
+ 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);
+ }
+ long lastnotify = jmb.getLoadNotifiesHandled();
+ // 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"));
+ JalviewFileChooser chooser = new JalviewFileChooser(
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle("Save PDB File");
{
try
{
- // TODO: cope with multiple PDB files in view
- BufferedReader in = new BufferedReader(new FileReader(jmb.getPdbFile()[0]));
+ // 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));
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)
+ try
{
- new OOMWarning("composing sequence-structure alignments for display in text box.", e);
+ 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;
}
else
{
im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.EPS,
- "Make EPS file from view", width, height, null, this
- .getTitle());
+ "Make EPS file from view", width, height, null,
+ this.getTitle());
}
if (im.getGraphics() != null)
{
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);
+ jmb.colourBySequence(ap.alignFrame.viewport.showSequenceFeatures,
+ ap.alignFrame.viewport.alignment);
}
public void chainColour_actionPerformed(ActionEvent actionEvent)
jmb.setJalviewColourScheme(new BuriedColourScheme());
}
-
public void userColour_actionPerformed(ActionEvent actionEvent)
{
userColour.setSelected(true);
public void showConsole(boolean showConsole)
{
- if (scriptWindow == null)
- scriptWindow = new ScriptWindow(this);
if (showConsole)
{
splitPane.setTopComponent(renderPanel);
splitPane.setBottomComponent(scriptWindow);
this.getContentPane().add(splitPane, BorderLayout.CENTER);
+ splitPane.setDividerLocation(getHeight() - 200);
+ scriptWindow.setVisible(true);
+ scriptWindow.validate();
+ splitPane.validate();
}
- splitPane.setDividerLocation(getHeight() - 200);
- splitPane.validate();
}
else
{
if (splitPane != null)
+ {
splitPane.setVisible(false);
+ }
splitPane = null;
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("Error loading file...", 20, currentSize.height / 2);
StringBuffer sb = new StringBuffer();
- int lines=0;
- for (int e=0;e<jmb.pdbentry.length; e++)
+ int lines = 0;
+ for (int e = 0; e < jmb.pdbentry.length; e++)
{
sb.append(jmb.pdbentry[e].getId());
- if (e<jmb.pdbentry.length-1) {
+ if (e < jmb.pdbentry.length - 1)
+ {
sb.append(",");
}
- if (e==jmb.pdbentry.length-1 || sb.length()>20)
+ if (e == jmb.pdbentry.length - 1 || sb.length() > 20)
{
lines++;
- g.drawString(sb.toString(), 20, currentSize.height/2 - lines*g.getFontMetrics().getHeight());
+ 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
- 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);
}
}
return viewId;
}
+
public void updateTitleAndMenus()
{
if (jmb.fileLoadingError != null && jmb.fileLoadingError.length() > 0)
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);
-
+
}
}
git://source.jalview.org / jalview.git / blobdiff