sequencesForPdb = data.getSeqList();
+ seqs[i] = sequencesForPdb
+ .toArray(new SequenceI[sequencesForPdb.size()]);
+ i++;
+ }
- public AppJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
- AlignmentPanel ap)
- {
- // ////////////////////////////////
- // Is the pdb file already loaded?
- String alreadyMapped = StructureSelectionManager
- .getStructureSelectionManager().alreadyMappedToFile(
- pdbentry.getId());
+ // TODO: check if protocol is needed to be set, and if chains are
+ // autodiscovered.
+ jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(),
+ pdbentrys, seqs, null);
- if (alreadyMapped != null)
+ jmb.setLoadingFromArchive(true);
+ addAlignmentPanel(ap);
+ if (viewerModel.isAlignWithPanel())
{
- int option = JOptionPane
- .showInternalConfirmDialog(
- Desktop.desktop,
- pdbentry.getId()
- + " is already displayed."
- + "\nDo you want to map sequences to the visible structure?",
- "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]);
- if (topJmol.pdbentry.getFile().equals(alreadyMapped))
- {
- topJmol.addSequence(seq);
- break;
- }
- }
- }
-
- return;
- }
+ useAlignmentPanelForSuperposition(ap);
}
- // /////////////////////////////////
-
- this.ap = ap;
- this.pdbentry = pdbentry;
- this.sequence = seq;
- this.setSize(400, 400);
- // jalview.gui.Desktop.addInternalFrame(this, "Jmol
- // View"+(pdbentry.getId()!=null ? "for "+pdbentry.getId()
- // : ""), 400, 400);
-
- if (pdbentry.getFile() != null)
+ initMenus();
+ boolean useToColour = viewerModel.isColourWithAlignPanel();
+ boolean leaveColouringToJmol = viewerModel.isColourByViewer();
+ if (leaveColouringToJmol || !useToColour)
{
- initJmol("load \"" + pdbentry.getFile() + "\"");
+ jmb.setColourBySequence(false);
+ seqColour.setSelected(false);
+ viewerColour.setSelected(true);
}
- else
+ else if (useToColour)
{
- Thread worker = new Thread(this);
- worker.start();
+ useAlignmentPanelForColourbyseq(ap);
+ jmb.setColourBySequence(true);
+ seqColour.setSelected(true);
+ viewerColour.setSelected(false);
}
+ this.setBounds(viewerModel.getX(), viewerModel.getY(),
+ viewerModel.getWidth(), viewerModel.getHeight());
+ setViewId(viewid);
+
this.addInternalFrameListener(new InternalFrameAdapter()
{
- public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
+ @Override
+ public void internalFrameClosing(
+ InternalFrameEvent internalFrameEvent)
{
- closeViewer();
+ closeViewer(false);
}
});
+ StringBuilder cmd = new StringBuilder();
+ cmd.append("load FILES ").append(QUOTE)
+ .append(Platform.escapeBackslashes(sessionFile)).append(QUOTE);
+ initJmol(cmd.toString());
}
- void initJmol(String command)
+ @Override
+ protected void initMenus()
{
- renderPanel = new RenderPanel();
+ super.initMenus();
- this.getContentPane().add(renderPanel, java.awt.BorderLayout.CENTER);
-
- StringBuffer title = new StringBuffer(sequence[0].getName() + ":"
- + pdbentry.getId());
-
- if (pdbentry.getProperty() != null)
- {
- if (pdbentry.getProperty().get("method") != null)
- {
- title.append(" Method: ");
- title.append(pdbentry.getProperty().get("method"));
- }
- if (pdbentry.getProperty().get("chains") != null)
- {
- title.append(" Chain:");
- title.append(pdbentry.getProperty().get("chains"));
- }
- }
-
- this.setTitle(title.toString());
- jalview.gui.Desktop.addInternalFrame(this, title.toString(),
- getBounds().width, getBounds().height);
- // * OK, but safer to assign htmlName, URL bases, comandOptions, and
- // statusListener now.
-
- viewer = org.jmol.api.JmolViewer.allocateViewer(renderPanel,
- new SmarterJmolAdapter(), "", null, null, "", this);
-
- jmolpopup = JmolPopup.newJmolPopup(viewer, true, "Jmol", true);
-
- viewer.evalStringQuiet(command);
+ viewerColour
+ .setText(MessageManager.getString("label.colour_with_jmol"));
+ viewerColour.setToolTipText(MessageManager
+ .getString("label.let_jmol_manage_structure_colours"));
}
- void setChainMenuItems(Vector chains)
+ /**
+ * display a single PDB structure in a new Jmol view
+ *
+ * @param pdbentry
+ * @param seq
+ * @param chains
+ * @param ap
+ */
+ public AppJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
+ final AlignmentPanel ap)
{
- chainMenu.removeAll();
+ setProgressIndicator(ap.alignFrame);
- 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);
- }
+ openNewJmol(ap, alignAddedStructures, new PDBEntry[] { pdbentry },
+ new SequenceI[][]
+ { seq });
}
- boolean allChainsSelected = false;
-
- void centerViewer()
+ private void openNewJmol(AlignmentPanel ap, boolean alignAdded,
+ PDBEntry[] pdbentrys, SequenceI[][] seqs)
{
- jmolHistory(false);
- StringBuffer cmd = new StringBuffer();
- 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())
- { lbl = item.getText();
- mlength = 0;
- do
- {
- p = mlength;
- mlength = lbl.indexOf(":", p);
- } while (p < mlength && mlength < (lbl.length() - 2));
- if (pdbentry.getId().equals(lbl.substring(0,mlength)))
- {
- mnum = 1+getModelNum(pdbentry.getFile());
- if (mnum>0)
- {cmd.append(":" + lbl.substring(mlength + 1) + " /"
- + mnum + " or ");
- }
- }
- }
- }
- }
-
- if (cmd.length() > 0)
- cmd.setLength(cmd.length() - 4);
+ setProgressIndicator(ap.alignFrame);
+ jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(),
+ pdbentrys, seqs, null);
+ addAlignmentPanel(ap);
+ useAlignmentPanelForColourbyseq(ap);
- viewer.evalStringQuiet("select *;restrict " + cmd + ";cartoon;center "
- + cmd);
- jmolHistory(true);
- }
- private int getModelNum(String modelFileName)
- {
- String[] mfn = getPdbFile();
- if (mfn == null)
- {
- return -1;
- }
- for (int i = 0; i < mfn.length; i++)
+ alignAddedStructures = alignAdded;
+ if (pdbentrys.length > 1)
{
- if (mfn[i].equalsIgnoreCase(modelFileName))
- return i;
+ useAlignmentPanelForSuperposition(ap);
}
- return -1;
- }
- void closeViewer()
- {
- viewer.setModeMouse(org.jmol.viewer.JmolConstants.MOUSE_NONE);
- // remove listeners for all structures in viewer
- StructureSelectionManager.getStructureSelectionManager()
- .removeStructureViewerListener(this, getPdbFile());
- // and shut down jmol
- viewer.evalStringQuiet("zap");
- viewer.setJmolStatusListener(null);
- viewer = null;
- }
-
- public void run()
- {
- try
- {
- // TODO: replace with reference fetching/transfer code (validate PDBentry
- // as a DBRef?)
- jalview.ws.dbsources.Pdb pdbclient = new jalview.ws.dbsources.Pdb();
- AlignmentI pdbseq;
- if ((pdbseq = pdbclient.getSequenceRecords(pdbentry.getId())) != null)
- {
- // just transfer the file name from the first seuqence's first PDBEntry
- pdbentry.setFile(((PDBEntry) pdbseq.getSequenceAt(0).getPDBId()
- .elementAt(0)).getFile());
- initJmol("load " + pdbentry.getFile());
- }
- else
- {
- JOptionPane
- .showInternalMessageDialog(
- Desktop.desktop,
- pdbentry.getId()
- + " could not be retrieved. Please try downloading the file manually.",
- "Couldn't load file", JOptionPane.ERROR_MESSAGE);
+ jmb.setColourBySequence(true);
+ setSize(400, 400); // probably should be a configurable/dynamic default here
+ initMenus();
+ addingStructures = false;
+ worker = new Thread(this);
+ worker.start();
- }
- } catch (OutOfMemoryError oomerror)
- {
- new OOMWarning("Retrieving PDB id " + pdbentry.getId() + " from MSD",
- oomerror);
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
-
- 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)
+ this.addInternalFrameListener(new InternalFrameAdapter()
{
- try
- {
- BufferedReader in = new BufferedReader(new FileReader(pdbentry
- .getFile()));
- 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)
+ @Override
+ public void internalFrameClosing(
+ InternalFrameEvent internalFrameEvent)
{
- ex.printStackTrace();
+ closeViewer(false);
}
- }
- }
-
- public void viewMapping_actionPerformed(ActionEvent actionEvent)
- {
- jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
- jalview.gui.Desktop.addInternalFrame(cap, "PDB - Sequence Mapping",
- 550, 600);
- cap.setText(StructureSelectionManager.getStructureSelectionManager()
- .printMapping(pdbentry.getFile()));
- }
+ });
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- public void eps_actionPerformed(ActionEvent e)
- {
- makePDBImage(jalview.util.ImageMaker.EPS);
}
/**
- * DOCUMENT ME!
+ * create a new Jmol containing several structures optionally superimposed
+ * using the given alignPanel.
*
- * @param e
- * DOCUMENT ME!
+ * @param ap
+ * @param alignAdded
+ * - true to superimpose
+ * @param pe
+ * @param seqs
*/
- 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);
- viewer.renderScreenImage(im.getGraphics(), rect.getSize(), rect);
- im.writeImage();
- }
- }
-
- public void seqColour_actionPerformed(ActionEvent actionEvent)
- {
- lastCommand = null;
- colourBySequence = seqColour.isSelected();
- colourBySequence(ap.alignFrame.alignPanel);
- }
-
- public void chainColour_actionPerformed(ActionEvent actionEvent)
- {
- colourBySequence = false;
- seqColour.setSelected(false);
- jmolHistory(false);
- viewer.evalStringQuiet("select *;color chain");
- jmolHistory(true);
- }
-
- public void chargeColour_actionPerformed(ActionEvent actionEvent)
- {
- colourBySequence = false;
- seqColour.setSelected(false);
- jmolHistory(false);
- viewer.evalStringQuiet("select *;color white;select ASP,GLU;color red;"
- + "select LYS,ARG;color blue;select CYS;color yellow");
- jmolHistory(true);
- }
-
- public void zappoColour_actionPerformed(ActionEvent actionEvent)
- {
- setJalviewColourScheme(new ZappoColourScheme());
- }
-
- public void taylorColour_actionPerformed(ActionEvent actionEvent)
- {
- setJalviewColourScheme(new TaylorColourScheme());
- }
-
- public void hydroColour_actionPerformed(ActionEvent actionEvent)
- {
- setJalviewColourScheme(new HydrophobicColourScheme());
- }
-
- public void helixColour_actionPerformed(ActionEvent actionEvent)
- {
- setJalviewColourScheme(new HelixColourScheme());
- }
-
- public void strandColour_actionPerformed(ActionEvent actionEvent)
- {
- setJalviewColourScheme(new StrandColourScheme());
- }
-
- public void turnColour_actionPerformed(ActionEvent actionEvent)
+ public AppJmol(AlignmentPanel ap, boolean alignAdded, PDBEntry[] pe,
+ SequenceI[][] seqs)
{
- setJalviewColourScheme(new TurnColourScheme());
+ openNewJmol(ap, alignAdded, pe, seqs);
}
- public void buriedColour_actionPerformed(ActionEvent actionEvent)
- {
- setJalviewColourScheme(new BuriedColourScheme());
- }
-
- public void setJalviewColourScheme(ColourSchemeI cs)
+ void initJmol(String command)
{
- jmolHistory(false);
- colourBySequence = false;
- seqColour.setSelected(false);
-
- if (cs == null)
- return;
-
- String res;
- int index;
- Color col;
-
- Enumeration en = ResidueProperties.aa3Hash.keys();
- StringBuffer command = new StringBuffer("select *;color white;");
- while (en.hasMoreElements())
+ 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)
{
- res = en.nextElement().toString();
- index = ((Integer) ResidueProperties.aa3Hash.get(res)).intValue();
- if (index > 20)
- continue;
-
- col = cs.findColour(ResidueProperties.aa[index].charAt(0));
-
- command.append("select " + res + ";color[" + col.getRed() + ","
- + col.getGreen() + "," + col.getBlue() + "];");
+ BorderLayout bl = new BorderLayout();
+ bl.setHgap(0);
+ bl.setVgap(0);
+ scriptWindow = new JPanel(bl);
+ scriptWindow.setVisible(false);
}
- viewer.evalStringQuiet(command.toString());
- jmolHistory(true);
- }
-
- public void userColour_actionPerformed(ActionEvent actionEvent)
- {
- 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.allocateViewer(renderPanel, true, "", null, null, "", scriptWindow,
+ null);
+ // jmb.newJmolPopup("Jmol");
+ if (command == null)
{
- jmolHistory(false);
- viewer.evalStringQuiet("background [" + col.getRed() + ","
- + col.getGreen() + "," + col.getBlue() + "];");
- jmolHistory(true);
+ command = "";
}
- }
- private void jmolHistory(boolean enable)
- {
- viewer.setBooleanProperty("history", enable);
+ jmb.executeCommand(new StructureCommand(command), false);
+ jmb.executeCommand(new StructureCommand("set hoverDelay=0.1"), false);
+ jmb.executeCommand(new StructureCommand("set antialiasdisplay on"),
+ false);
+ jmb.setFinishedInit(true);
}
- public void jmolHelp_actionPerformed(ActionEvent actionEvent)
+ @Override
+ public void run()
{
+ _started = true;
try
{
- jalview.util.BrowserLauncher
- .openURL("http://jmol.sourceforge.net/docs/JmolUserGuide/");
- } catch (Exception ex)
+ List files = jmb.fetchPdbFiles(this);
+ if (files.size() > 0)
+ {
+ showFilesInViewer(files);
+ }
+ } finally
{
+ _started = false;
+ worker = null;
}
}
- String[] modelFileNames = null;
- // ////////////////////////////////
- // /StructureListener
- public String[] getPdbFile()
+ /**
+ * Either adds the given files to a structure viewer or opens a new viewer to
+ * show them
+ *
+ * @param files
+ * list of absolute paths to structure files
+ */
+ void showFilesInViewer(List files)
{
- if (modelFileNames == null)
+ long lastnotify = jmb.getLoadNotifiesHandled();
+ StringBuilder fileList = new StringBuilder();
+ for (String s : files)
{
- String mset[] = new String[viewer.getModelCount()];
- for (int i = 0; i < mset.length; i++)
- {
- try {
- String mname = viewer.getModelFileName(i);
- if (mname==null)
- {
- System.err.println("Model "+i+" has no filename!");
- continue;
- }
- File fpath = new File(mname);
- mset[i] = fpath.toString();
- } catch (Exception e)
- {
- System.err.println("Couldn't parse "+viewer.getModelFileName(i)+" as a file!");
- }
- }
- modelFileNames = mset;
+ fileList.append(SPACE).append(QUOTE)
+ .append(Platform.escapeBackslashes(s)).append(QUOTE);
}
- return modelFileNames;
- }
-
- Pattern pattern = Pattern
- .compile("\\[(.*)\\]([0-9]+)(:[a-zA-Z]*)?\\.([a-zA-Z]+).*(/[0-9]*)?");
-
- String lastMessage;
-
- public void mouseOverStructure(int atomIndex, String strInfo)
- {
- // copied from AppJmol - will be refactored to binding eventually
- int pdbResNum;
- int mdlSep = strInfo.indexOf("/");
- int chainSeparator = strInfo.indexOf(":"), chainSeparator1 = -1;
+ String filesString = fileList.toString();
- if (chainSeparator == -1)
+ if (!addingStructures)
{
- chainSeparator = strInfo.indexOf(".");
- if (mdlSep > -1 && mdlSep < chainSeparator)
+ try
+ {
+ initJmol("load FILES " + filesString);
+ } catch (OutOfMemoryError oomerror)
+ {
+ new OOMWarning("When trying to open the Jmol viewer!", oomerror);
+ Console.debug("File locations are " + filesString);
+ } catch (Exception ex)
{
- chainSeparator1 = chainSeparator;
- chainSeparator = mdlSep;
+ Console.error("Couldn't open Jmol viewer!", ex);
+ ex.printStackTrace();
+ return;
}
}
- pdbResNum = Integer.parseInt(strInfo.substring(
- strInfo.indexOf("]") + 1, chainSeparator));
-
- String chainId;
-
- if (strInfo.indexOf(":") > -1)
- chainId = strInfo.substring(strInfo.indexOf(":") + 1, strInfo
- .indexOf("."));
else
{
- chainId = " ";
- }
+ StringBuilder cmd = new StringBuilder();
+ cmd.append("loadingJalviewdata=true\nload APPEND ");
+ cmd.append(filesString);
+ cmd.append("\nloadingJalviewdata=null");
+ final StructureCommand command = new StructureCommand(cmd.toString());
+ lastnotify = jmb.getLoadNotifiesHandled();
- String pdbfilename = pdbentry.getFile();
- if (mdlSep > -1)
- {
- if (chainSeparator1 == -1)
- {
- chainSeparator1 = strInfo.indexOf(".", mdlSep);
- }
- String mdlId = (chainSeparator1 > -1) ? strInfo.substring(mdlSep + 1,
- chainSeparator1) : strInfo.substring(mdlSep + 1);
try
{
- // recover PDB filename for the model hovered over.
- pdbfilename = viewer
- .getModelFileName(new Integer(mdlId).intValue() - 1);
- } catch (Exception e)
+ jmb.executeCommand(command, false);
+ } catch (OutOfMemoryError oomerror)
{
+ new OOMWarning("When trying to add structures to the Jmol viewer!",
+ oomerror);
+ Console.debug("File locations are " + filesString);
+ return;
+ } catch (Exception ex)
+ {
+ Console.error("Couldn't add files to Jmol viewer!", ex);
+ ex.printStackTrace();
+ return;
}
- ;
- }
- if (lastMessage == null || !lastMessage.equals(strInfo))
- ssm.mouseOverStructure(pdbResNum, chainId, pdbfilename);
-
- lastMessage = strInfo;
-/*
- * Old Implementation based on Pattern regex.
- Matcher matcher = pattern.matcher(strInfo);
- matcher.find();
- matcher.group(1);
- int pdbResNum = Integer.parseInt(matcher.group(2));
- String chainId = matcher.group(3);
-
- if (chainId != null)
- chainId = chainId.substring(1, chainId.length());
- else
- {
- chainId = " ";
}
- String mdlId = matcher.group(4);
- String pdbfilename = pdbentry.getFile();
- if (mdlId!=null && mdlId.length()>0)
+ // need to wait around until script has finished
+ int waitMax = JMOL_LOAD_TIMEOUT;
+ int waitFor = 35;
+ int waitTotal = 0;
+ while (addingStructures ? lastnotify >= jmb.getLoadNotifiesHandled()
+ : !(jmb.isFinishedInit() && jmb.getStructureFiles() != null
+ && jmb.getStructureFiles().length == files.size()))
{
- try {
- // recover PDB filename for the model hovered over.
- pdbfilename = viewer.getModelFileName(new Integer(mdlId).intValue()-1);
- } catch (Exception e) {};
- }
- if (lastMessage == null || !lastMessage.equals(strInfo))
- {
- ssm.mouseOverStructure(pdbResNum, chainId, pdbfilename);
- }
- lastMessage = strInfo; */
- }
-
- StringBuffer resetLastRes = new StringBuffer();
-
- StringBuffer eval = new StringBuffer();
-
- public void highlightAtom(int atomIndex, int pdbResNum, String chain,
- String pdbfile)
- {
- int mdlNum = 1+getModelNum(pdbfile);
- if (mdlNum==0)
- {
- return;
- }
+ try
+ {
+ Console.debug("Waiting around for jmb notify.");
+ waitTotal += waitFor;
- jmolHistory(false);
- // if (!pdbfile.equals(pdbentry.getFile()))
- // return;
- if (resetLastRes.length() > 0)
- {
- viewer.evalStringQuiet(resetLastRes.toString());
+ // Thread.sleep() throws an exception in JS
+ Thread.sleep(waitFor);
+ } catch (Exception e)
+ {
+ }
+ if (waitTotal > waitMax)
+ {
+ jalview.bin.Console.errPrintln(
+ "Timed out waiting for Jmol to load files after "
+ + waitTotal + "ms");
+ // jalview.bin.Console.errPrintln("finished: " + jmb.isFinishedInit()
+ // + "; loaded: " + Arrays.toString(jmb.getPdbFile())
+ // + "; files: " + files.toString());
+ jmb.getStructureFiles();
+ break;
+ }
}
- eval.setLength(0);
- eval.append("select " + pdbResNum); // +modelNum
-
- resetLastRes.setLength(0);
- resetLastRes.append("select " + pdbResNum); // +modelNum
-
- if (!chain.equals(" "))
+ // refresh the sequence colours for the new structure(s)
+ for (AlignmentViewPanel ap : _colourwith)
{
- eval.append(":");
- resetLastRes.append(":");
- eval.append(chain);
- resetLastRes.append(chain);
+ jmb.updateColours(ap);
}
- // if (mdlNum != 0)
+ // do superposition if asked to
+ if (alignAddedStructures)
{
- eval.append(" /" + (mdlNum));
- resetLastRes.append(" /" + (mdlNum));
+ alignAddedStructures();
}
- eval.append(";wireframe 100;" + eval.toString() + " and not hetero;");
-
- resetLastRes.append(";wireframe 0;" + resetLastRes.toString()
- + " and not hetero; spacefill 0;");
-
- eval.append("spacefill 200;select none");
-
- viewer.evalStringQuiet(eval.toString());
- jmolHistory(true);
- }
-
- public Color getColour(int atomIndex, int pdbResNum, String chain,
- String pdbfile)
- {
- if (!pdbfile.equals(pdbentry.getFile()))
- return null;
-
- return new Color(viewer.getAtomArgb(atomIndex));
+ addingStructures = false;
}
- public void updateColours(Object source)
- {
- colourBySequence((AlignmentPanel) source);
- }
-
- // End StructureListener
- // //////////////////////////
-
- String lastCommand;
-
- FeatureRenderer fr = null;
-
- public void colourBySequence(AlignmentPanel sourceap)
+ /**
+ * Queues a thread to align structures with Jalview alignments
+ */
+ void alignAddedStructures()
{
- this.ap = sourceap;
-
- if (!colourBySequence || ap.alignFrame.getCurrentView() != ap.av)
- return;
-
- String[] files = getPdbFile();
-
- SequenceRenderer sr = new SequenceRenderer(ap.av);
-
- boolean showFeatures = false;
-
- if (ap.av.showSequenceFeatures)
- {
- showFeatures = true;
- if (fr == null)
- {
- fr = new jalview.gui.FeatureRenderer(ap);
- }
-
- fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer());
- }
-
- StringBuffer command = new StringBuffer();
- for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
{
- StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
-
- if (mapping == null || mapping.length < 1)
- continue;
-
-
- int lastPos = -1;
- for (int sp, s = 0; s < sequence.length; s++)
- {
- for (int m = 0; m < mapping.length; m++)
+ @Override
+ public void run()
{
- if (mapping[m].getSequence() == sequence[s]
- && (sp = ap.av.alignment.findIndex(sequence[s])) > -1)
+ if (jmb.jmolViewer.isScriptExecuting())
{
- SequenceI asp = ap.av.alignment.getSequenceAt(sp);
- for (int r = 0; r < asp.getLength(); r++)
+ SwingUtilities.invokeLater(this);
+ try
+ {
+ Thread.sleep(5);
+ } catch (InterruptedException q)
{
- // No mapping to gaps in sequence.
- if (jalview.util.Comparison.isGap(asp.getCharAt(r)))
- {
- continue;
- }
- int pos = mapping[m].getPDBResNum(asp.findPosition(r));
-
- if (pos < 1 || pos == lastPos)
- continue;
-
- lastPos = pos;
-
- Color col = sr.getResidueBoxColour(asp, r);
-
- if (showFeatures)
- col = fr.findFeatureColour(col, asp, r);
- String newSelcom = (mapping[m].getChain() != " " ? ":"
- + mapping[m].getChain() : "")
- + "/"
- + (pdbfnum + 1)
- + ".1"
- + ";color["
- + col.getRed()
- + ","
- + col.getGreen()
- + ","
- + col.getBlue() + "]";
- if (command.toString().endsWith(newSelcom))
- {
- command = condenseCommand(command, pos);
- continue;
- }
-
- command.append(";select " + pos);
- command.append(newSelcom);
}
- break;
+ return;
+ }
+ else
+ {
+ alignStructsWithAllAlignPanels();
}
}
- }
- }
- jmolHistory(false);
+ });
- if (lastCommand == null || !lastCommand.equals(command.toString()))
- {
- viewer.evalStringQuiet(command.toString());
- }
- jmolHistory(true);
- lastCommand = command.toString();
}
- StringBuffer condenseCommand(StringBuffer command, int pos)
+ public boolean isRepainting()
{
- StringBuffer sb = new StringBuffer(command.substring(0, command
- .lastIndexOf("select") + 7));
-
- command.delete(0, sb.length());
-
- String start;
-
- if (command.indexOf("-") > -1)
- {
- start = command.substring(0, command.indexOf("-"));
- }
- else
+ if (renderPanel!=null && renderPanel.isVisible())
{
- start = command.substring(0, command.indexOf(":"));
+ return renderPanel.repainting;
}
-
- sb.append(start + "-" + pos + command.substring(command.indexOf(":")));
-
- return sb;
- }
-
- // ///////////////////////////////
- // JmolStatusListener
-
- public String eval(String strEval)
- {
- // System.out.println(strEval);
- // "# 'eval' is implemented only for the applet.";
- return null;
- }
-
- public void createImage(String file, String type, int quality)
- {
- System.out.println("JMOL CREATE IMAGE");
+ return false;
}
-
- public void notifyFileLoaded(String fullPathName, String fileName2,
- String modelName, String errorMsg, int modelParts)
+ /**
+ * Outputs the Jmol viewer image as an image file, after prompting the user to
+ * choose a file and (for EPS) choice of Text or Lineart character rendering
+ * (unless a preference for this is set)
+ *
+ * @param type
+ */
+ @Override
+ public void makePDBImage(ImageMaker.TYPE type)
{
- if (errorMsg != null)
+ while (!isRepainting())
{
- fileLoadingError = errorMsg;
- repaint();
- return;
+ try {
+ Thread.sleep(2);
+ } catch (Exception q)
+ {}
}
-
- fileLoadingError = null;
- modelFileNames = null;
-
- String[] modelfilenames = getPdbFile();
- ssm = StructureSelectionManager.getStructureSelectionManager();
- boolean modelsloaded=false;
- for (int modelnum = 0; modelnum < modelfilenames.length; modelnum++)
- {
- String fileName = modelfilenames[modelnum];
-
- if (fileName != null)
+ try
{
- modelsloaded=true;
- // search pdbentries and sequences to find correct pdbentry and sequence[] pair for this filename
- if (pdbentry.getFile().equals(fileName))
- {
- // TODO: do some checking using the modelPts number of parts against our
- // own estimate of the number of chains
- // FILE LOADED OK
- MCview.PDBfile pdbFile = ssm.setMapping(sequence, chains, pdbentry
- .getFile(), AppletFormatAdapter.FILE);
- Vector chains = new Vector();
- for (int i = 0; i < pdbFile.chains.size(); i++)
- {
- chains
- .addElement(new String(pdbFile.id+":"+((MCview.PDBChain) pdbFile.chains.elementAt(i)).id));
- }
- setChainMenuItems(chains);
-
- if (!loadingFromArchive)
- {
- viewer
- .evalStringQuiet("model 0; select backbone;restrict;cartoon;wireframe off;spacefill off");
-
- colourBySequence(ap);
- }
- if (fr != null)
- fr.featuresAdded();
-
- loadingFromArchive = false;
- }
- else {
- // this is a foreign pdb file that jalview doesn't know about - add it to the dataset
- // and try to find a home - either on a matching sequence or as a new sequence.
- String pdbcontent = viewer.getData("/" + (modelnum + 1) + ".1",
- "PDB");
- // parse pdb file into a chain, etc.
- // locate best match for pdb in associated views and add mapping to
- // ssm
- modelsloaded=true;
- }
- }
- }
- if (modelsloaded)
+ makePDBImage(null, type, null,
+ BitmapImageSizing.defaultBitmapImageSizing());
+ } catch (ImageOutputException ioex)
{
- ssm.addStructureViewerListener(this);
- jmolpopup.updateComputedMenus();
+ Console.error("Unexpected error whilst writing " + type.toString(),
+ ioex);
}
}
- public void sendConsoleEcho(String strEcho)
- {
- if (scriptWindow != null)
- scriptWindow.sendConsoleEcho(strEcho);
- }
-
- public void sendConsoleMessage(String strStatus)
- {
- if (scriptWindow != null)
- scriptWindow.sendConsoleMessage(strStatus);
- }
-
- public void notifyScriptTermination(String strStatus, int msWalltime)
- {
- if (scriptWindow != null)
- scriptWindow.notifyScriptTermination(strStatus, msWalltime);
- }
-
- public void handlePopupMenu(int x, int y)
+ public void makePDBImage(File file, ImageMaker.TYPE type, String renderer,
+ BitmapImageSizing userBis) throws ImageOutputException
{
- jmolpopup.show(x, y);
- }
+ int width = getWidth();
+ int height = getHeight();
- public void notifyNewPickingModeMeasurement(int iatom, String strMeasure)
- {
- notifyAtomPicked(iatom, strMeasure, null);
- }
+ BitmapImageSizing bis = ImageMaker.getScaleWidthHeight(width, height,
+ userBis);
+ float usescale = bis.scale();
+ int usewidth = bis.width();
+ int useheight = bis.height();
- public void notifyAtomPicked(int atomIndex, String strInfo, String strData)
- {
- if (strData != null)
+ ImageWriterI writer = new ImageWriterI()
{
- Cache.log.info("Non null pick data string: " + strData
- + " (other info: '" + strInfo + "' pos " + atomIndex + ")");
- }
- /*
- Matcher matcher = pattern.matcher(strInfo);
- matcher.find();
-
- matcher.group(1);
- String resnum = new String(matcher.group(2));
- String chainId = matcher.group(3);
-
- String picked = resnum;
-
-
- if (chainId != null)
- picked += (":" + chainId.substring(1, chainId.length()));
-*/
- int chainSeparator = strInfo.indexOf(":");
- int p=0;
- if (chainSeparator == -1)
- chainSeparator = strInfo.indexOf(".");
-
- String picked = strInfo.substring(strInfo.indexOf("]") + 1,
- chainSeparator);
- String mdlString="";
- if ((p=strInfo.indexOf(":")) > -1)
- picked += strInfo.substring(p + 1, strInfo
- .indexOf("."));
+ @Override
+ public void exportImage(Graphics g) throws Exception
+ {
+ Graphics2D ig2 = (Graphics2D) g;
+ ig2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+ RenderingHints.VALUE_ANTIALIAS_ON);
+ if (type == TYPE.PNG && usescale > 0.0f)
+ {
+ // for a scaled image, this scales down a bigger image to give the
+ // right resolution
+ if (usescale > 0.0f)
+ {
+ ig2.scale(1 / usescale, 1 / usescale);
+ }
+ }
- if ((p=strInfo.indexOf("/"))> -1)
- {
- mdlString += strInfo.substring(p, strInfo.indexOf(" #"));
- }
- picked = "((" + picked + ".CA" + mdlString+")|(" + picked + ".P" + mdlString+"))";
- jmolHistory(false);
- if (!atomsPicked.contains(picked))
- {
- // TODO: re-instate chain ID separator dependent labelling for both applet and application
-// if (chainId != null)
- viewer.evalString("select " + picked + ";label %n %r:%c");
-// else
-// viewer.evalString("select " + picked + ";label %n %r");
- atomsPicked.addElement(picked);
- }
- else
+ jmb.jmolViewer.requestRepaintAndWait("image export");
+ jmb.jmolViewer.renderScreenImage(ig2, usewidth, useheight);
+ }
+ };
+ String view = MessageManager.getString("action.view")
+ .toLowerCase(Locale.ROOT);
+ final ImageExporter exporter = new ImageExporter(writer,
+ getProgressIndicator(), type, getTitle());
+
+ final Throwable[] exceptions = new Throwable[1];
+ exceptions[0] = null;
+ final AppJmol us = this;
+ try
{
- viewer.evalString("select " + picked + ";label off");
- atomsPicked.removeElement(picked);
- }
- jmolHistory(true);
- if (scriptWindow != null)
+ Thread runner = Executors.defaultThreadFactory()
+ .newThread(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ try
+ {
+ exporter.doExport(file, us, width, height, view,
+ renderer, userBis);
+ } catch (Throwable t)
+ {
+ exceptions[0] = t;
+ }
+ }
+ });
+ runner.start();
+ long time = 0;
+ do
+ {
+ Thread.sleep(25);
+ } while (runner.isAlive() && time++ < 4000);
+ if (time >= 4000)
+ {
+ runner.interrupt();
+ throw new ImageOutputException(
+ "Jmol took too long to export. Waited for 100 seconds.");
+ }
+ } catch (Throwable e)
{
- scriptWindow.sendConsoleMessage(strInfo);
- scriptWindow.sendConsoleMessage("\n");
+ throw new ImageOutputException(
+ "Unexpected error when generating image", e);
}
- }
-
- public void notifyAtomHovered(int atomIndex, String strInfo, String data)
- {
- if (data != null)
+ if (exceptions[0] != null)
{
- Cache.log.info("Non null hover data string: " + data
- + " (other info: '" + strInfo + "' pos " + atomIndex + ")");
+ if (exceptions[0] instanceof ImageOutputException)
+ {
+ throw ((ImageOutputException) exceptions[0]);
+ }
+ else
+ {
+ throw new ImageOutputException(
+ "Unexpected error when generating image", exceptions[0]);
+ }
}
- mouseOverStructure(atomIndex, strInfo);
}
@Override
- public void showUrl(String url)
+ public void showHelp_actionPerformed()
{
try
{
- jalview.util.BrowserLauncher.openURL(url);
- } catch (IOException e)
+ BrowserLauncher // BH 2018
+ .openURL("http://wiki.jmol.org");// http://jmol.sourceforge.net/docs/JmolUserGuide/");
+ } catch (Exception ex)
{
- Cache.log.error("Failed to launch Jmol-associated url " + url, e);
- // TODO: 2.6 : warn user if browser was not configured.
+ jalview.bin.Console
+ .errPrintln("Show Jmol help failed with: " + ex.getMessage());
}
}
+ @Override
public void showConsole(boolean showConsole)
{
- if (scriptWindow == null)
- scriptWindow = new ScriptWindow(this);
-
if (showConsole)
{
if (splitPane == null)
@@ -1116,15 +573,19 @@ public class AppJmol extends GStructureViewer implements StructureListener,
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;
@@ -1134,156 +595,81 @@ public class AppJmol extends GStructureViewer implements StructureListener,
validate();
}
- public float[][] functionXY(String functionName, int x, int y)
- {
- return null;
- }
-
- // /End JmolStatusListener
- // /////////////////////////////
-
class RenderPanel extends JPanel
{
final Dimension currentSize = new Dimension();
- final Rectangle rectClip = new Rectangle();
-
+ @Override
public void paintComponent(Graphics g)
{
getSize(currentSize);
- g.getClipBounds(rectClip);
- if (viewer == null)
+ if (jmb != null && jmb.hasFileLoadingError())
{
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);
+ 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 (fileLoadingError != null)
+ else if (jmb == null || jmb.jmolViewer == 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("Error loading file..." + pdbentry.getId(), 20,
- currentSize.height / 2);
+ g.drawString(MessageManager.getString("label.retrieving_pdb_data"),
+ 20, currentSize.height / 2);
}
else
{
- viewer.renderScreenImage(g, currentSize, rectClip);
+ repainting=true;
+ synchronized (jmb)
+ {
+ jmb.jmolViewer.renderScreenImage(g, currentSize.width,
+ currentSize.height);
+
+ }
+ repainting=false;
}
}
- }
-
- String viewId = null;
-
- public String getViewId()
- {
- if (viewId == null)
- {
- viewId = System.currentTimeMillis() + "." + this.hashCode();
- }
- return viewId;
- }
-
- @Override
- public String createImage(String fileName, String type,
- Object textOrBytes, int quality)
- {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- public float[][][] functionXYZ(String functionName, int nx, int ny, int nz)
- {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- public Hashtable getRegistryInfo()
- {
- // TODO Auto-generated method stub
- return null;
+ volatile boolean repainting=false;
}
@Override
- public void notifyCallback(int type, Object[] data)
+ public AAStructureBindingModel getBinding()
{
- try
- {
- switch (type)
- {
- case JmolConstants.CALLBACK_LOADSTRUCT:
- notifyFileLoaded((String) data[1], (String) data[2],
- (String) data[3], (String) data[4], ((Integer) data[5])
- .intValue());
-
- break;
- case JmolConstants.CALLBACK_PICK:
- notifyAtomPicked(((Integer) data[2]).intValue(), (String) data[1],
- (String) data[0]);
- // also highlight in alignment
- case JmolConstants.CALLBACK_HOVER:
- notifyAtomHovered(((Integer) data[2]).intValue(), (String) data[1],
- (String) data[0]);
- break;
- case JmolConstants.CALLBACK_SCRIPT:
- notifyScriptTermination((String) data[2], ((Integer) data[3])
- .intValue());
- break;
- case JmolConstants.CALLBACK_ECHO:
- sendConsoleEcho((String) data[1]);
- break;
- case JmolConstants.CALLBACK_MESSAGE:
- sendConsoleMessage((data == null) ? ((String) null)
- : (String) data[1]);
- break;
- case JmolConstants.CALLBACK_MEASURE:
- case JmolConstants.CALLBACK_CLICK:
- default:
- System.err.println("Unhandled callback " + type + " " + data);
- break;
- }
- } catch (Exception e)
- {
- Cache.log.warn("Squashed Jmol callback handler error: ", e);
- }
+ return this.jmb;
}
@Override
- public boolean notifyEnabled(int callbackPick)
+ public ViewerType getViewerType()
{
- switch (callbackPick)
- {
- case JmolConstants.CALLBACK_ECHO:
- case JmolConstants.CALLBACK_LOADSTRUCT:
- case JmolConstants.CALLBACK_MEASURE:
- case JmolConstants.CALLBACK_MESSAGE:
- case JmolConstants.CALLBACK_PICK:
- case JmolConstants.CALLBACK_SCRIPT:
- case JmolConstants.CALLBACK_HOVER:
- case JmolConstants.CALLBACK_ERROR:
- return true;
- case JmolConstants.CALLBACK_CLICK:
- case JmolConstants.CALLBACK_ANIMFRAME:
- case JmolConstants.CALLBACK_MINIMIZATION:
- case JmolConstants.CALLBACK_RESIZE:
- case JmolConstants.CALLBACK_SYNC:
- }
- return false;
+ return ViewerType.JMOL;
}
@Override
- public void setCallbackFunction(String callbackType,
- String callbackFunction)
+ protected String getViewerName()
{
- Cache.log.debug("Ignoring set-callback request to associate "
- + callbackType + " with function " + callbackFunction);
-
+ return "Jmol";
}
-
}