0)
- cmd.setLength(cmd.length() - 4);
-
- viewer.evalStringQuiet("select *;restrict "
- +cmd+";cartoon;center "+cmd);
+ jmb.centerViewer(toshow);
}
- void closeViewer()
+ public void closeViewer()
{
- viewer.setModeMouse(org.jmol.viewer.JmolConstants.MOUSE_NONE);
- viewer.evalStringQuiet("zap");
- viewer.setJmolStatusListener(null);
- viewer = null;
-
- //We'll need to find out what other
- // listeners need to be shut down in Jmol
- StructureSelectionManager
- .getStructureSelectionManager()
- .removeStructureViewerListener(this, pdbentry.getFile());
+ jmb.closeViewer();
+ ap = 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
{
- EBIFetchClient ebi = new EBIFetchClient();
- String query = "pdb:" + pdbentry.getId();
- pdbentry.setFile(ebi.fetchDataAsFile(query, "default", "raw")
- .getAbsolutePath());
- initJmol("load "+pdbentry.getFile());
- }
- catch (Exception ex)
+ 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(MessageManager.formatMessage("status.fetching_pdb", new String[]{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(MessageManager.getString("label.state_completed"), hdl);
+ }
+ if (pdbseq != null)
+ {
+ // just transfer the file name from the first sequence's first
+ // PDBEntry
+ file = new File(((PDBEntry) pdbseq.getSequenceAt(0).getPDBId()
+ .elementAt(0)).getFile()).getAbsolutePath();
+ jmb.pdbentry[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.pdbentry.length))
+ {
+ 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"));
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle("Save PDB File");
- chooser.setToolTipText("Save");
+ chooser.setDialogTitle(MessageManager.getString("label.save_pdb_file"));
+ chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(this);
@@ -323,635 +949,483 @@ public synchronized void addSequence(SequenceI [] seq)
{
try
{
- BufferedReader in = new BufferedReader(new FileReader(pdbentry.getFile()));
+ // 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)
+ while ((data = in.readLine()) != null)
{
- if (
- ! (data.indexOf("") > -1 || data.indexOf("") > -1)
- )
+ if (!(data.indexOf("") > -1 || data.indexOf("") > -1))
{
out.println(data);
}
}
out.close();
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
ex.printStackTrace();
}
}
}
+ @Override
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())
- );
+ try
+ {
+ for (int pdbe = 0; pdbe < jmb.pdbentry.length; pdbe++)
+ {
+ cap.appendText(jmb.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,
+ MessageManager.getString("label.pdb_sequence_mapping"), 550,
+ 600);
}
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
+ @Override
public void eps_actionPerformed(ActionEvent e)
{
- makePDBImage(jalview.util.ImageMaker.EPS);
+ makePDBImage(jalview.util.ImageMaker.TYPE.EPS);
}
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
+ @Override
public void png_actionPerformed(ActionEvent e)
{
- makePDBImage(jalview.util.ImageMaker.PNG);
+ makePDBImage(jalview.util.ImageMaker.TYPE.PNG);
}
- void makePDBImage(int type)
+ void makePDBImage(jalview.util.ImageMaker.TYPE type)
{
int width = getWidth();
int height = getHeight();
jalview.util.ImageMaker im;
- if (type == jalview.util.ImageMaker.PNG)
+ if (type == jalview.util.ImageMaker.TYPE.PNG)
{
im = new jalview.util.ImageMaker(this,
- jalview.util.ImageMaker.PNG,
- "Make PNG image from view",
- width, height,
- null, null);
+ 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.EPS,
- "Make EPS file from view",
- width, height,
- null, this.getTitle());
+ jalview.util.ImageMaker.TYPE.SVG, "Make SVG file from PCA",
+ width, height, null, this.getTitle());
}
if (im.getGraphics() != null)
{
Rectangle rect = new Rectangle(width, height);
- viewer.renderScreenImage(im.getGraphics(),
- rect.getSize(), rect);
+ jmb.viewer.renderScreenImage(im.getGraphics(), rect.getSize(), rect);
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)
{
- lastCommand = null;
- colourBySequence = seqColour.isSelected();
- colourBySequence(ap.alignFrame.alignPanel);
+ jmb.setColourBySequence(seqColour.isSelected());
+ if (_colourwith == null)
+ {
+ _colourwith = new Vector();
+ }
+ if (jmb.isColourBySequence())
+ {
+ if (!jmb.isLoadingFromArchive())
+ {
+ if (_colourwith.size() == 0 && ap != null)
+ {
+ // Make the currently displayed alignment panel the associated view
+ _colourwith.add(ap.alignFrame.alignPanel);
+ }
+ }
+ // Set the colour using the current view for the associated alignframe
+ for (AlignmentPanel ap : _colourwith)
+ {
+ jmb.colourBySequence(ap.av.showSequenceFeatures, ap);
+ }
+ }
}
+ @Override
public void chainColour_actionPerformed(ActionEvent actionEvent)
{
- colourBySequence = false;
- seqColour.setSelected(false);
- viewer.evalStringQuiet("select *;color chain");
+ chainColour.setSelected(true);
+ jmb.colourByChain();
}
+ @Override
public void chargeColour_actionPerformed(ActionEvent actionEvent)
{
- colourBySequence = false;
- seqColour.setSelected(false);
- viewer.evalStringQuiet("select *;color white;select ASP,GLU;color red;"
- +"select LYS,ARG;color blue;select CYS;color yellow");
+ chargeColour.setSelected(true);
+ jmb.colourByCharge();
}
+ @Override
public void zappoColour_actionPerformed(ActionEvent actionEvent)
{
- setJalviewColourScheme(new ZappoColourScheme());
+ zappoColour.setSelected(true);
+ jmb.setJalviewColourScheme(new ZappoColourScheme());
}
+ @Override
public void taylorColour_actionPerformed(ActionEvent actionEvent)
{
- setJalviewColourScheme(new TaylorColourScheme());
+ taylorColour.setSelected(true);
+ jmb.setJalviewColourScheme(new TaylorColourScheme());
}
+ @Override
public void hydroColour_actionPerformed(ActionEvent actionEvent)
{
- setJalviewColourScheme(new HydrophobicColourScheme());
+ hydroColour.setSelected(true);
+ jmb.setJalviewColourScheme(new HydrophobicColourScheme());
}
+ @Override
public void helixColour_actionPerformed(ActionEvent actionEvent)
{
- setJalviewColourScheme(new HelixColourScheme());
+ helixColour.setSelected(true);
+ jmb.setJalviewColourScheme(new HelixColourScheme());
}
+ @Override
public void strandColour_actionPerformed(ActionEvent actionEvent)
{
- setJalviewColourScheme(new StrandColourScheme());
+ strandColour.setSelected(true);
+ jmb.setJalviewColourScheme(new StrandColourScheme());
}
+ @Override
public void turnColour_actionPerformed(ActionEvent actionEvent)
{
- setJalviewColourScheme(new TurnColourScheme());
+ turnColour.setSelected(true);
+ jmb.setJalviewColourScheme(new TurnColourScheme());
}
+ @Override
public void buriedColour_actionPerformed(ActionEvent actionEvent)
{
- setJalviewColourScheme(new BuriedColourScheme());
+ buriedColour.setSelected(true);
+ jmb.setJalviewColourScheme(new BuriedColourScheme());
}
- public void setJalviewColourScheme(ColourSchemeI cs)
+ @Override
+ public void purinePyrimidineColour_actionPerformed(ActionEvent actionEvent)
{
- 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())
- {
- 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() + "];");
- }
-
- viewer.evalStringQuiet(command.toString());
+ 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,
- "Select Background Colour",
- null);
-
+ MessageManager.getString("label.select_backgroud_colour"), null);
if (col != null)
{
- viewer.evalStringQuiet("background ["
- + col.getRed() + ","
- + col.getGreen() + ","
- + col.getBlue() + "];");
+ jmb.setBackgroundColour(col);
}
}
-
- public void jmolHelp_actionPerformed(ActionEvent actionEvent)
- {
- try{
- jalview.util.BrowserLauncher.openURL(
- "http://jmol.sourceforge.net/docs/JmolUserGuide/");
- }catch(Exception ex){}
- }
-
-
- //////////////////////////////////
- ///StructureListener
- public String getPdbFile()
- {
- return pdbentry.getFile();
- }
-
- Pattern pattern = Pattern.compile(
- "\\[(.*)\\]([0-9]+)(:[a-zA-Z]*)?\\.([a-zA-Z]+)(/[0-9]*)?"
- );
-
- String lastMessage;
- public void mouseOverStructure(int atomIndex, String strInfo)
+ @Override
+ public void showHelp_actionPerformed(ActionEvent actionEvent)
{
- 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
+ try
{
- chainId = " ";
- }
-
- if (lastMessage == null || !lastMessage.equals(strInfo))
+ jalview.util.BrowserLauncher
+ .openURL("http://jmol.sourceforge.net/docs/JmolUserGuide/");
+ } catch (Exception ex)
{
- ssm.mouseOverStructure(pdbResNum, chainId, pdbentry.getFile());
}
- lastMessage = strInfo;
}
- StringBuffer resetLastRes = new StringBuffer();
- StringBuffer eval = new StringBuffer();
-
- public void highlightAtom(int atomIndex, int pdbResNum, String chain, String pdbfile)
+ public void showConsole(boolean showConsole)
{
- if (!pdbfile.equals(pdbentry.getFile()))
- return;
- if (resetLastRes.length() > 0)
+ if (showConsole)
{
- viewer.evalStringQuiet(resetLastRes.toString());
- }
-
- eval.setLength(0);
- eval.append("select " + pdbResNum);
-
- resetLastRes.setLength(0);
- resetLastRes.append("select " + pdbResNum);
+ 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();
+ }
- if (!chain.equals(" "))
- {
- eval.append(":" + chain);
- resetLastRes.append(":" + chain);
}
+ else
+ {
+ if (splitPane != null)
+ {
+ splitPane.setVisible(false);
+ }
- eval.append(";wireframe 100;"+eval.toString()+".CA;");
-
- resetLastRes.append(";wireframe 0;"+resetLastRes.toString()+".CA;spacefill 0;");
-
- eval.append("spacefill 200;select none");
-
- viewer.evalStringQuiet(eval.toString());
- }
-
- public Color getColour(int atomIndex, int pdbResNum, String chain, String pdbfile)
- {
- if (!pdbfile.equals(pdbentry.getFile()))
- return null;
+ splitPane = null;
- return new Color(viewer.getAtomArgb(atomIndex));
- }
+ this.getContentPane().add(renderPanel, BorderLayout.CENTER);
+ }
- public void updateColours(Object source)
- {
- colourBySequence( (AlignmentPanel) source);
+ validate();
}
-
-//End StructureListener
-////////////////////////////
-
- String lastCommand;
- FeatureRenderer fr=null;
- public void colourBySequence(AlignmentPanel sourceap)
+ class RenderPanel extends JPanel
{
- this.ap = sourceap;
-
- if(!colourBySequence || ap.alignFrame.getCurrentView()!=ap.av)
- return;
-
- StructureMapping[] mapping = ssm.getMapping(pdbentry.getFile());
-
- if (mapping.length < 1)
- return;
-
-
- SequenceRenderer sr = new SequenceRenderer(ap.av);
+ final Dimension currentSize = new Dimension();
- boolean showFeatures = false;
+ final Rectangle rectClip = new Rectangle();
- if (ap.av.showSequenceFeatures)
+ public void paintComponent(Graphics g)
{
- showFeatures = true;
- if (fr == null)
- {
- fr = new jalview.gui.FeatureRenderer(ap);
- }
-
- fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer());
- }
-
- StringBuffer command = new StringBuffer();
+ getSize(currentSize);
+ g.getClipBounds(rectClip);
- int lastPos = -1;
- for (int s = 0; s < sequence.length; s++)
- {
- for (int m = 0; m < mapping.length; m++)
+ if (jmb.fileLoadingError != null)
{
- if (mapping[m].getSequence() == sequence[s]
- && ap.av.alignment.findIndex(sequence[s])>-1)
+ 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.pdbentry.length; e++)
{
- for (int r = 0; r < sequence[s].getLength(); r++)
+ sb.append(jmb.pdbentry[e].getId());
+ if (e < jmb.pdbentry.length - 1)
{
- int pos = mapping[m].getPDBResNum(
- sequence[s].findPosition(r));
-
- if (pos < 1 || pos==lastPos)
- continue;
-
- lastPos = pos;
-
- Color col = sr.getResidueBoxColour(sequence[s], r);
-
- if (showFeatures)
- col = fr.findFeatureColour(col, sequence[s], r);
-
- if (command.toString().endsWith(":" + mapping[m].getChain()+
- ";color["
- + col.getRed() + ","
- + col.getGreen() + ","
- + col.getBlue() + "]"))
- {
- command = condenseCommand(command, pos);
- continue;
- }
-
- command.append(";select " + pos);
-
- if (!mapping[m].getChain().equals(" "))
- {
- command.append(":" + mapping[m].getChain());
- }
-
- command.append(";color["
- + col.getRed() + ","
- + col.getGreen() + ","
- + col.getBlue() + "]");
+ sb.append(",");
+ }
+ if (e == jmb.pdbentry.length - 1 || sb.length() > 20)
+ {
+ lines++;
+ g.drawString(sb.toString(), 20, currentSize.height / 2 - lines
+ * g.getFontMetrics().getHeight());
}
- break;
}
}
+ 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, rectClip);
+ }
}
+ }
+
+ String viewId = null;
- if (lastCommand == null || !lastCommand.equals(command.toString()))
+ public String getViewId()
+ {
+ if (viewId == null)
{
- viewer.evalStringQuiet(command.toString());
+ viewId = System.currentTimeMillis() + "." + this.hashCode();
}
- lastCommand = command.toString();
+ return viewId;
}
- StringBuffer condenseCommand(StringBuffer command, int pos)
+ public void updateTitleAndMenus()
{
- StringBuffer sb = new StringBuffer(command.substring(0, command.lastIndexOf("select")+7));
-
- command.delete(0, sb.length());
-
- String start;
+ if (jmb.fileLoadingError != null && jmb.fileLoadingError.length() > 0)
+ {
+ repaint();
+ return;
+ }
+ setChainMenuItems(jmb.chainNames);
- if (command.indexOf("-") > -1)
+ this.setTitle(jmb.getViewerTitle());
+ if (jmb.getPdbFile().length > 1 && jmb.sequence.length > 1)
{
- start = command.substring(0,command.indexOf("-"));
+ viewerActionMenu.setVisible(true);
}
- else
+ if (!jmb.isLoadingFromArchive())
{
- start = command.substring(0, command.indexOf(":"));
+ seqColour_actionPerformed(null);
}
-
- sb.append(start+"-"+pos+command.substring(command.indexOf(":")));
-
- return sb;
}
- /////////////////////////////////
- //JmolStatusListener
-
- public String eval(String strEval)
+ protected void buildJmolActionMenu()
{
- // System.out.println(strEval);
- //"# 'eval' is implemented only for the applet.";
- return null;
+ if (_alignwith == null)
+ {
+ _alignwith = new Vector();
+ }
+ if (_alignwith.size() == 0 && ap != null)
+ {
+ _alignwith.add(ap);
+ }
+ ;
+ for (Component c : viewerActionMenu.getMenuComponents())
+ {
+ if (c != alignStructs)
+ {
+ viewerActionMenu.remove((JMenuItem) c);
+ }
+ }
+ final ItemListener handler;
}
- public void createImage(String file, String type, int quality)
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GStructureViewer#alignStructs_actionPerformed(java.awt.event
+ * .ActionEvent)
+ */
+ @Override
+ protected void alignStructs_actionPerformed(ActionEvent actionEvent)
{
- System.out.println("JMOL CREATE IMAGE");
+ alignStructs_withAllAlignPanels();
}
- public void setCallbackFunction(String callbackType,
- String callbackFunction)
- {}
-
- public void notifyFileLoaded(String fullPathName, String fileName,
- String modelName, Object clientFile,
- String errorMsg)
+ private void alignStructs_withAllAlignPanels()
{
- if(errorMsg!=null)
+ if (ap == null)
{
- fileLoadingError = errorMsg;
- repaint();
return;
}
-
- fileLoadingError = null;
-
- if (fileName != null)
+ ;
+ if (_alignwith.size() == 0)
{
+ _alignwith.add(ap);
+ }
+ ;
+ try
+ {
+ AlignmentI[] als = new Alignment[_alignwith.size()];
+ ColumnSelection[] alc = new ColumnSelection[_alignwith.size()];
+ int[] alm = new int[_alignwith.size()];
+ int a = 0;
- //FILE LOADED OK
- ssm = StructureSelectionManager.getStructureSelectionManager();
- MCview.PDBfile pdbFile = ssm.setMapping(sequence,chains,pdbentry.getFile(), AppletFormatAdapter.FILE);
- ssm.addStructureViewerListener(this);
- Vector chains = new Vector();
- for(int i=0; i