files)
+ {
+ long lastnotify = jmb.getLoadNotifiesHandled();
+ StringBuilder fileList = new StringBuilder();
+ for (String s : files)
+ {
+ fileList.append(SPACE).append(BACKSLASH)
+ .append(Platform.escapeString(s)).append(BACKSLASH);
}
- if (files.length() > 0)
+ String filesString = fileList.toString();
+
+ if (!addingStructures)
{
try
{
- initJmol("load FILES " + files.toString());
+ initJmol("load FILES " + filesString);
} catch (OutOfMemoryError oomerror)
{
new OOMWarning("When trying to open the Jmol viewer!", oomerror);
- Cache.log.debug("File locations are " + files);
+ Cache.log.debug("File locations are " + filesString);
} catch (Exception ex)
{
Cache.log.error("Couldn't open Jmol viewer!", ex);
}
}
- }
-
- 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");
+ else
+ {
+ StringBuilder cmd = new StringBuilder();
+ cmd.append("loadingJalviewdata=true\nload APPEND ");
+ cmd.append(filesString);
+ cmd.append("\nloadingJalviewdata=null");
+ final String command = cmd.toString();
+ lastnotify = jmb.getLoadNotifiesHandled();
- int value = chooser.showSaveDialog(this);
+ 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 " + filesString);
+ } catch (Exception ex)
+ {
+ Cache.log.error("Couldn't add files to Jmol viewer!", ex);
+ }
+ }
- if (value == JalviewFileChooser.APPROVE_OPTION)
+ // 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.getPdbFile() != null && jmb
+ .getPdbFile().length == files.size()))
{
try
{
- // 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)
- {
- if (!(data.indexOf("") > -1 || data.indexOf("") > -1))
- {
- out.println(data);
- }
- }
- out.close();
- } catch (Exception ex)
+ Cache.log.debug("Waiting around for jmb notify.");
+ Thread.sleep(waitFor);
+ waitTotal += waitFor;
+ } catch (Exception e)
{
- ex.printStackTrace();
+ }
+ if (waitTotal > waitMax)
+ {
+ System.err
+ .println("Timed out waiting for Jmol to load files after "
+ + waitTotal + "ms");
+// System.err.println("finished: " + jmb.isFinishedInit()
+// + "; loaded: " + Arrays.toString(jmb.getPdbFile())
+// + "; files: " + files.toString());
+ jmb.getPdbFile();
+ break;
}
}
- }
- public void viewMapping_actionPerformed(ActionEvent actionEvent)
- {
- jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
- jalview.gui.Desktop.addInternalFrame(cap, "PDB - Sequence Mapping",
- 550, 600);
- for (int pdbe = 0; pdbe fetchPdbFiles()
{
- makePDBImage(jalview.util.ImageMaker.PNG);
- }
+ // todo - record which pdbids were successfully imported.
+ StringBuilder errormsgs = new StringBuilder();
- void makePDBImage(int type)
- {
- int width = getWidth();
- int height = getHeight();
-
- jalview.util.ImageMaker im;
-
- if (type == jalview.util.ImageMaker.PNG)
+ List files = new ArrayList();
+ String pdbid = "";
+ try
{
- im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.PNG,
- "Make PNG image from view", width, height, null, null);
- }
- else
+ String[] filesInViewer = jmb.getPdbFile();
+ // TODO: replace with reference fetching/transfer code (validate PDBentry
+ // as a DBRef?)
+ Pdb pdbclient = new Pdb();
+ for (int pi = 0; pi < jmb.getPdbCount(); pi++)
+ {
+ String file = jmb.getPdbEntry(pi).getFile();
+ if (file == null)
+ {
+ // retrieve the pdb and store it locally
+ AlignmentI pdbseq = null;
+ pdbid = jmb.getPdbEntry(pi).getId();
+ long hdl = pdbid.hashCode() - System.currentTimeMillis();
+ if (progressBar != null)
+ {
+ progressBar.setProgressBar(MessageManager.formatMessage(
+ "status.fetching_pdb", new String[] { pdbid }), hdl);
+ }
+ try
+ {
+ pdbseq = pdbclient.getSequenceRecords(pdbid);
+ } catch (OutOfMemoryError oomerror)
+ {
+ new OOMWarning("Retrieving PDB id " + pdbid, oomerror);
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ errormsgs.append("'").append(pdbid).append("'");
+ } finally
+ {
+ if (progressBar != null)
+ {
+ progressBar.setProgressBar(
+ MessageManager.getString("label.state_completed"),
+ hdl);
+ }
+ }
+ if (pdbseq != null)
+ {
+ // just transfer the file name from the first sequence's first
+ // PDBEntry
+ file = new File(pdbseq.getSequenceAt(0).getAllPDBEntries()
+ .elementAt(0).getFile()).getAbsolutePath();
+ jmb.getPdbEntry(pi).setFile(file);
+ files.add(file);
+ }
+ else
+ {
+ errormsgs.append("'").append(pdbid).append("' ");
+ }
+ }
+ else
+ {
+ if (filesInViewer != null && filesInViewer.length > 0)
+ {
+ addingStructures = true; // already files loaded.
+ for (int c = 0; c < filesInViewer.length; c++)
+ {
+ if (filesInViewer[c].equals(file))
+ {
+ file = null;
+ break;
+ }
+ }
+ }
+ if (file != null)
+ {
+ files.add(file);
+ }
+ }
+ }
+ } catch (OutOfMemoryError oomerror)
{
- im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.EPS,
- "Make EPS file from view", width, height, null, this
- .getTitle());
+ new OOMWarning("Retrieving PDB files: " + pdbid, oomerror);
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ errormsgs.append("When retrieving pdbfiles : current was: '")
+ .append(pdbid).append("'");
}
-
- if (im.getGraphics() != null)
+ if (errormsgs.length() > 0)
{
- Rectangle rect = new Rectangle(width, height);
- jmb.viewer.renderScreenImage(im.getGraphics(), rect.getSize(), rect);
- im.writeImage();
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
+ .formatMessage("label.pdb_entries_couldnt_be_retrieved",
+ new String[] { errormsgs.toString() }),
+ MessageManager.getString("label.couldnt_load_file"),
+ JvOptionPane.ERROR_MESSAGE);
}
+ return files;
}
- public void seqColour_actionPerformed(ActionEvent actionEvent)
- {
- 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);
- }
-
- public void chainColour_actionPerformed(ActionEvent actionEvent)
- {
- chainColour.setSelected(true);
- jmb.colourByChain();
- }
-
- public void chargeColour_actionPerformed(ActionEvent actionEvent)
- {
- chargeColour.setSelected(true);
- jmb.colourByCharge();
- }
-
- public void zappoColour_actionPerformed(ActionEvent actionEvent)
- {
- zappoColour.setSelected(true);
- jmb.setJalviewColourScheme(new ZappoColourScheme());
- }
-
- public void taylorColour_actionPerformed(ActionEvent actionEvent)
- {
- taylorColour.setSelected(true);
- jmb.setJalviewColourScheme(new TaylorColourScheme());
- }
-
- public void hydroColour_actionPerformed(ActionEvent actionEvent)
- {
- hydroColour.setSelected(true);
- jmb.setJalviewColourScheme(new HydrophobicColourScheme());
- }
-
- public void helixColour_actionPerformed(ActionEvent actionEvent)
+ @Override
+ public void eps_actionPerformed(ActionEvent e)
{
- helixColour.setSelected(true);
- jmb.setJalviewColourScheme(new HelixColourScheme());
+ makePDBImage(jalview.util.ImageMaker.TYPE.EPS);
}
- public void strandColour_actionPerformed(ActionEvent actionEvent)
+ @Override
+ public void png_actionPerformed(ActionEvent e)
{
- strandColour.setSelected(true);
- jmb.setJalviewColourScheme(new StrandColourScheme());
+ makePDBImage(jalview.util.ImageMaker.TYPE.PNG);
}
- public void turnColour_actionPerformed(ActionEvent actionEvent)
+ void makePDBImage(jalview.util.ImageMaker.TYPE type)
{
- turnColour.setSelected(true);
- jmb.setJalviewColourScheme(new TurnColourScheme());
- }
+ int width = getWidth();
+ int height = getHeight();
- public void buriedColour_actionPerformed(ActionEvent actionEvent)
- {
- buriedColour.setSelected(true);
- jmb.setJalviewColourScheme(new BuriedColourScheme());
- }
+ jalview.util.ImageMaker im;
+ if (type == jalview.util.ImageMaker.TYPE.PNG)
+ {
+ im = new jalview.util.ImageMaker(this,
+ jalview.util.ImageMaker.TYPE.PNG, "Make PNG image from view",
+ width, height, null, null, null, 0, false);
+ }
+ 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(), null, 0, false);
+ }
+ else
+ {
- public void userColour_actionPerformed(ActionEvent actionEvent)
- {
- userColour.setSelected(true);
- new UserDefinedColours(this, null);
- }
+ im = new jalview.util.ImageMaker(this,
+ jalview.util.ImageMaker.TYPE.SVG, "Make SVG file from PCA",
+ width, height, null, this.getTitle(), null, 0, false);
+ }
- public void backGround_actionPerformed(ActionEvent actionEvent)
- {
- java.awt.Color col = JColorChooser.showDialog(this,
- "Select Background Colour", null);
- if (col != null)
+ if (im.getGraphics() != null)
{
- jmb.setBackgroundColour(col);
+ jmb.viewer.renderScreenImage(im.getGraphics(), width, height);
+ im.writeImage();
}
}
- public void jmolHelp_actionPerformed(ActionEvent actionEvent)
+ @Override
+ public void showHelp_actionPerformed(ActionEvent actionEvent)
{
try
{
- jalview.util.BrowserLauncher
+ BrowserLauncher
.openURL("http://jmol.sourceforge.net/docs/JmolUserGuide/");
} catch (Exception ex)
{
@@ -513,8 +646,6 @@ public class AppJmol extends GStructureViewer implements Runnable,
public void showConsole(boolean showConsole)
{
- if (scriptWindow == null)
- scriptWindow = new ScriptWindow(this);
if (showConsole)
{
@@ -524,15 +655,19 @@ public class AppJmol extends GStructureViewer implements Runnable,
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;
@@ -546,80 +681,75 @@ public class AppJmol extends GStructureViewer implements Runnable,
{
final Dimension currentSize = new Dimension();
- final Rectangle rectClip = new Rectangle();
-
+ @Override
public void paintComponent(Graphics g)
{
getSize(currentSize);
- g.getClipBounds(rectClip);
- if (jmb.fileLoadingError != 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("Error loading file...", 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;e20)
+ if (e == jmb.getPdbCount() - 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(MessageManager.getString("label.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);
+ jmb.viewer.renderScreenImage(g, currentSize.width,
+ currentSize.height);
}
}
}
- String viewId = null;
-
- public String getViewId()
+ @Override
+ public AAStructureBindingModel getBinding()
{
- if (viewId == null)
- {
- viewId = System.currentTimeMillis() + "." + this.hashCode();
- }
- return viewId;
+ return this.jmb;
}
- public void updateTitleAndMenus()
- {
- if (jmb.fileLoadingError != null && jmb.fileLoadingError.length() > 0)
- {
- repaint();
- return;
- }
- setChainMenuItems(jmb.chainNames);
- jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment);
- this.setTitle(jmb.getViewerTitle());
+ @Override
+ public String getStateInfo()
+ {
+ return jmb == null ? null : jmb.viewer.getStateInfo();
}
- public void setJalviewColourScheme(ColourSchemeI ucs)
+ @Override
+ public ViewerType getViewerType()
{
- jmb.setJalviewColourScheme(ucs);
-
+ return ViewerType.JMOL;
}
+ @Override
+ protected String getViewerName()
+ {
+ return "Jmol";
+ }
}