Vector atomsPicked = new Vector();
+ private boolean addingStructures = false;
+
public AppJmol(String file, String id, SequenceI[] seq,
AlignmentPanel ap, String loadStatus, Rectangle bounds)
{
// / TODO: check if protocol is needed to be set, and if chains are
// autodiscovered.
jmb = new AppJmolBinding(this, new PDBEntry[]
- { pdbentry }, new SequenceI[][] { seq }, null, null);
+ { pdbentry }, new SequenceI[][]
+ { seq }, null, null);
jmb.setLoadingFromArchive(true);
this.ap = ap;
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)
{
// 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)
+ if (existingViews.size() > 0)
{
Enumeration jm = existingViews.elements();
- while (jm.hasMoreElements()) {
+ 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);
+ 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.jmb.addStructure(pdbentry, seq, chains,true);
+ topJmol.addStructure(pdbentry, seq, chains, true);
return;
}
}
// /////////////////////////////////
jmb = new AppJmolBinding(this, new PDBEntry[]
- { pdbentry }, new SequenceI[][]{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 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)
+ {
+ 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);
+ }
+ }).start();
+ return;
+ }
+ }
+ // otherwise, start adding the structure.
+ jmb.addSequenceAndChain(new PDBEntry[]
+ { pdbentry }, new SequenceI[][]
+ { seq }, new String[][]
+ { chains });
+ addingStructures = true;
+ _started = false;
+ (worker = new Thread(this)).start();
+ return;
+ }
+
private Vector getJmolsFor(AlignmentPanel ap2)
{
- Vector otherJmols= new Vector();
+ 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();
if (frames[i] instanceof AppJmol)
{
AppJmol topJmol = ((AppJmol) frames[i]);
- if (topJmol.ap==ap2)
+ if (topJmol.ap == ap2)
{
otherJmols.addElement(topJmol);
}
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();
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;
+ 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 (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)
{
+ 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("load APPEND ");
+ cmd.append(files.toString());
+ cmd.append("\n");
+ final String command = cmd.toString();
+ cmd = null;
try
{
- initJmol("load FILES " + files.toString());
+ jmb.evalStateCommand(command);
} catch (OutOfMemoryError oomerror)
{
- new OOMWarning("When trying to open the Jmol viewer!", 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 open Jmol viewer!", ex);
+ Cache.log.error("Couldn't add files to Jmol viewer!", ex);
}
+ if (alignAddedStructures)
+ {
+ // may need to wait around until script has finished
+ while (jmb.viewer.isScriptExecuting())
+ {
+ try
+ {
+ Thread.sleep(20);
+ } catch (Exception e)
+ {
+ }
+ ;
+ }
+ 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);
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)
}
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);
+ if (jmb.getPdbFile().length > 1 && jmb.sequence.length > 1)
+ {
+ jmolActionMenu.setVisible(true);
}
}
- /* (non-Javadoc)
- * @see jalview.jbgui.GStructureViewer#alignStructs_actionPerformed(java.awt.event.ActionEvent)
+ /*
+ * (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());
+
+ 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);
-
+ Cache.log.info("Couldn't align structures in alignframe "
+ + ap.alignFrame.getTitle(), e);
+
}
}
public void setJalviewColourScheme(ColourSchemeI ucs)
{
jmb.setJalviewColourScheme(ucs);
-
+
}
}
package jalview.gui;
import java.util.BitSet;
-import java.util.Vector;
import jalview.bin.Cache;
import jalview.datamodel.PDBEntry;
import org.jmol.popup.JmolPopup;
-class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
+public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
{
/**
asPopup);
}
- /**
- * add structures and any known sequence associations
- *
- * @returns the pdb entries added to the current set.
- */
- private PDBEntry[] addSequenceAndChain(PDBEntry[] pdbe,
- SequenceI[][] seq, String[][] chns)
- {
- int pe = -1;
- Vector v = new Vector();
- Vector rtn = new Vector();
- for (int i = 0; i < pdbentry.length; i++)
- {
- v.addElement(pdbentry[i]);
- }
- for (int i = 0; i < pdbe.length; i++)
- {
- int r = v.indexOf(pdbe[i]);
- if (r == -1 || r >= pdbentry.length)
- {
- rtn.addElement(new int[]
- { v.size(), i });
- v.addElement(pdbe[i]);
- }
- else
- {
- // just make sure the sequence/chain entries are all up to date
- addSequenceAndChain(r, seq[i], chns[i]);
- }
- }
- pdbe = new PDBEntry[v.size()];
- v.copyInto(pdbe);
- pdbentry = pdbe;
- if (rtn.size() > 0)
- {
- // expand the tied seuqence[] and string[] arrays
- SequenceI[][] sqs = new SequenceI[pdbentry.length][];
- String[][] sch = new String[pdbentry.length][];
- System.arraycopy(sequence, 0, sqs, 0, sequence.length);
- System.arraycopy(chains, 0, sch, 0, this.chains.length);
- sequence = sqs;
- chains = sch;
- pdbe = new PDBEntry[rtn.size()];
- for (int r = 0; r < pdbe.length; r++)
- {
- int[] stri = ((int[]) rtn.elementAt(r));
- // record the pdb file as a new addition
- pdbe[r] = pdbentry[stri[0]];
- // and add the new sequence/chain entries
- addSequenceAndChain(stri[0], seq[stri[1]], chns[stri[1]]);
- }
- }
- else
- {
- pdbe = null;
- }
- return pdbe;
- }
-
- void addSequence(int pe, SequenceI[] seq)
- {
- // add sequences to the pe'th pdbentry's seuqence set.
- addSequenceAndChain(pe, seq, null);
- }
-
- private void addSequenceAndChain(int pe, SequenceI[] seq, String[] tchain)
- {
- if (pe < 0 || pe >= pdbentry.length)
- {
- throw new Error(
- "Implementation error - no corresponding pdbentry (for index "
- + pe + ") to add sequences mappings to");
- }
- final String nullChain = "TheNullChain";
- Vector s = new Vector();
- Vector c = new Vector();
- if (chains == null)
- {
- chains = new String[pdbentry.length][];
- }
- if (sequence[pe] != null)
- {
- for (int i = 0; i < sequence[pe].length; i++)
- {
- s.addElement(sequence[pe][i]);
- if (chains[pe] != null)
- {
- if (i < chains[pe].length)
- {
- c.addElement(chains[pe][i]);
- }
- else
- {
- c.addElement(nullChain);
- }
- }
- else
- {
- if (tchain != null && tchain.length > 0)
- {
- c.addElement(nullChain);
- }
- }
- }
- }
- for (int i = 0; i < seq.length; i++)
- {
- if (!s.contains(seq[i]))
- {
- s.addElement(seq[i]);
- if (tchain != null && i < tchain.length)
- {
- c.addElement(tchain[i] == null ? nullChain : tchain[i]);
- }
- }
- }
- SequenceI[] tmp = new SequenceI[s.size()];
- s.copyInto(tmp);
- sequence[pe] = tmp;
- if (c.size() > 0)
- {
- String[] tch = new String[c.size()];
- c.copyInto(tch);
- for (int i = 0; i < tch.length; i++)
- {
- if (tch[i] == nullChain)
- {
- tch[i] = null;
- }
- }
- chains[pe] = tch;
- }
- else
- {
- chains[pe] = null;
- }
- }
-
public void selectionChanged(BitSet arg0)
{
// TODO Auto-generated method stub
}
- /**
- * add another pdb entry into the view, with associated sequences and chains
- *
- * @param pdbentry
- * @param seq
- * @param chains
- * @param align
- * if true, new structure(s) will be align using associated alignment
- */
- public synchronized void addStructure(PDBEntry pdbentry, SequenceI[] seq,
- String[] chains, final boolean align)
- {
- PDBEntry[] pe = addSequenceAndChain(new PDBEntry[]
- { pdbentry }, new SequenceI[][]
- { seq }, new String[][]
- { chains });
- if (pe != null)
- {
- StringBuffer cmd = new StringBuffer();
- cmd.append("load APPEND");
- for (int p = 0; p < pe.length; p++)
- {
- cmd.append(" \"");
- cmd.append(pe[p].getFile());
- cmd.append("\"");
- }
- cmd.append("\n");
- final String command = cmd.toString();
- cmd = null;
- new Thread(new Runnable()
- {
- public void run()
- {
- evalStateCommand(command);
- if (align)
- {
- // may need to wait around until script has finished
- while (viewer.isScriptExecuting())
- {
- try
- {
- Thread.sleep(20);
- } catch (Exception e)
- {
- }
- ;
- }
- superposeStructures(appJmolWindow.ap.av.getAlignment(), -1, null);
- }
- }
- }).start();
- }
- }
/**
* add the given sequences to the mapping scope for the given pdb file handle
git://source.jalview.org / jalview.git / commitdiff