package jalview.gui;
import jalview.bin.Cache;
-import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
-import jalview.datamodel.ColumnSelection;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.gui.StructureViewer.ViewerType;
-import jalview.io.AppletFormatAdapter;
-import jalview.io.JalviewFileChooser;
-import jalview.io.JalviewFileView;
-import jalview.schemes.BuriedColourScheme;
-import jalview.schemes.ColourSchemeI;
-import jalview.schemes.HelixColourScheme;
-import jalview.schemes.HydrophobicColourScheme;
-import jalview.schemes.PurinePyrimidineColourScheme;
-import jalview.schemes.StrandColourScheme;
-import jalview.schemes.TaylorColourScheme;
-import jalview.schemes.TurnColourScheme;
-import jalview.schemes.ZappoColourScheme;
import jalview.structures.models.AAStructureBindingModel;
+import jalview.util.BrowserLauncher;
import jalview.util.MessageManager;
import jalview.util.Platform;
+import jalview.ws.dbsources.Pdb;
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Graphics;
import java.awt.Rectangle;
import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.ItemEvent;
-import java.awt.event.ItemListener;
-import java.io.BufferedReader;
import java.io.File;
-import java.io.FileOutputStream;
-import java.io.FileReader;
-import java.io.IOException;
-import java.io.PrintWriter;
+import java.util.ArrayList;
+import java.util.List;
import java.util.Vector;
import javax.swing.JCheckBoxMenuItem;
-import javax.swing.JColorChooser;
import javax.swing.JInternalFrame;
import javax.swing.JMenu;
-import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JSplitPane;
+import javax.swing.SwingUtilities;
import javax.swing.event.InternalFrameAdapter;
import javax.swing.event.InternalFrameEvent;
-import javax.swing.event.MenuEvent;
-import javax.swing.event.MenuListener;
public class AppJmol extends StructureViewerBase
{
+ // ms to wait for Jmol to load files
+ private static final int JMOL_LOAD_TIMEOUT = 20000;
+
+ private static final String SPACE = " ";
+
+ private static final String BACKSLASH = "\"";
+
AppJmolBinding jmb;
JPanel scriptWindow;
RenderPanel renderPanel;
- private boolean addingStructures = false;
-
- ViewSelectionMenu seqColourBy;
-
/**
*
* @param files
// / TODO: check if protocol is needed to be set, and if chains are
// autodiscovered.
jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(),
- pdbentrys, seqs, null, null);
+ pdbentrys, seqs, null);
jmb.setLoadingFromArchive(true);
addAlignmentPanel(ap);
{
useAlignmentPanelForSuperposition(ap);
}
+ initMenus();
if (leaveColouringToJmol || !usetoColour)
{
jmb.setColourBySequence(false);
viewerColour.setSelected(false);
}
this.setBounds(bounds);
- initMenus();
setViewId(viewid);
// jalview.gui.Desktop.addInternalFrame(this, "Loading File",
// bounds.width,bounds.height);
}
});
initJmol(loadStatus); // pdbentry, seq, JBPCHECK!
-
}
- private void initMenus()
+ @Override
+ protected void initMenus()
{
- seqColour.setSelected(jmb.isColourBySequence());
- viewerColour.setSelected(!jmb.isColourBySequence());
- if (_colourwith == null)
- {
- _colourwith = new Vector<AlignmentPanel>();
- }
- if (_alignwith == null)
- {
- _alignwith = new Vector<AlignmentPanel>();
- }
-
- seqColourBy = new ViewSelectionMenu(MessageManager.getString("label.colour_by"), this, _colourwith,
- new ItemListener()
- {
-
- @Override
- public void itemStateChanged(ItemEvent e)
- {
- if (!seqColour.isSelected())
- {
- seqColour.doClick();
- }
- else
- {
- // update the jmol display now.
- seqColour_actionPerformed(null);
- }
- }
- });
- viewMenu.add(seqColourBy);
- final ItemListener handler;
- JMenu alpanels = new ViewSelectionMenu(MessageManager.getString("label.superpose_with"), this,
- _alignwith, handler = new ItemListener()
- {
-
- @Override
- public void itemStateChanged(ItemEvent e)
- {
- alignStructs.setEnabled(_alignwith.size() > 0);
- alignStructs.setToolTipText(MessageManager
- .formatMessage(
- "label.align_structures_using_linked_alignment_views",
- new String[]
- { new Integer(_alignwith.size()).toString() }));
- }
- });
- handler.itemStateChanged(null);
- viewerActionMenu.add(alpanels);
- viewerActionMenu.addMenuListener(new MenuListener()
- {
-
- @Override
- public void menuSelected(MenuEvent e)
- {
- handler.itemStateChanged(null);
- }
+ super.initMenus();
- @Override
- public void menuDeselected(MenuEvent e)
- {
- // TODO Auto-generated method stub
+ viewerActionMenu = new JMenu(MessageManager.getString("label.jmol"));
- }
-
- @Override
- public void menuCanceled(MenuEvent e)
- {
- // TODO Auto-generated method stub
-
- }
- });
+ viewerColour
+ .setText(MessageManager.getString("label.colour_with_jmol"));
+ viewerColour.setToolTipText(MessageManager
+ .getString("label.let_jmol_manage_structure_colours"));
}
IProgressIndicator progressBar = null;
final AlignmentPanel ap)
{
progressBar = ap.alignFrame;
- // ////////////////////////////////
- // Is the pdb file already loaded?
- String alreadyMapped = ap.getStructureSelectionManager()
- .alreadyMappedToFile(pdbentry.getId());
+ String pdbId = pdbentry.getId();
- if (alreadyMapped != null)
+ /*
+ * If the PDB file is already loaded, the user may just choose to add to an
+ * existing viewer (or cancel)
+ */
+ if (addAlreadyLoadedFile(seq, chains, ap, pdbId))
{
- int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
- MessageManager.formatMessage(
- "label.pdb_entry_is_already_displayed", new String[]
- { pdbentry.getId() }), MessageManager.formatMessage(
- "label.map_sequences_to_visible_window", new String[]
- { pdbentry.getId() }),
- JOptionPane.YES_NO_CANCEL_OPTION);
-
- if (option == JOptionPane.CANCEL_OPTION)
- {
- return;
- }
- if (option == JOptionPane.YES_OPTION)
- {
- // TODO : Fix multiple seq to one chain issue here.
- ap.getStructureSelectionManager().setMapping(seq, chains,
- alreadyMapped, AppletFormatAdapter.FILE);
- if (ap.getSeqPanel().seqCanvas.fr != null)
- {
- ap.getSeqPanel().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)
- {
- final AppJmol topJmol = ((AppJmol) frames[i]);
- // JBPNOTE: this looks like a binding routine, rather than a gui
- // routine
- for (int pe = 0; pe < topJmol.jmb.getPdbCount(); pe++)
- {
- if (topJmol.jmb.getPdbEntry(pe).getFile()
- .equals(alreadyMapped))
- {
- topJmol.jmb.addSequence(pe, seq);
- topJmol.addAlignmentPanel(ap);
- // add it to the set used for colouring
- topJmol.useAlignmentPanelForColourbyseq(ap);
- topJmol.buildActionMenu();
- ap.getStructureSelectionManager()
- .sequenceColoursChanged(ap);
- break;
- }
- }
- }
- }
-
- return;
- }
+ return;
}
/*
* Check if there are other Jmol views involving this alignment and prompt
* user about adding this molecule to one of them
*/
- for (AppJmol topJmol : getJmolsFor(ap))
+ if (addToExistingViewer(pdbentry, seq, chains, ap, pdbId))
{
- // TODO: highlight topJmol in view somehow
- int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
- MessageManager.formatMessage("label.add_pdbentry_to_view",
- new String[]
- { pdbentry.getId(), topJmol.getTitle() }),
- MessageManager
- .getString("label.align_to_existing_structure_view"),
- JOptionPane.YES_NO_CANCEL_OPTION);
- if (option == JOptionPane.CANCEL_OPTION)
- {
- return;
- }
- if (option == JOptionPane.YES_OPTION)
- {
- topJmol.useAlignmentPanelForSuperposition(ap);
- topJmol.addStructure(pdbentry, seq, chains, true, ap.alignFrame);
- return;
- }
+ return;
}
- // /////////////////////////////////
- openNewJmol(ap, new PDBEntry[]
- { pdbentry }, new SequenceI[][]
- { seq });
+
+ /*
+ * If the options above are declined or do not apply, open a new viewer
+ */
+ openNewJmol(ap, new PDBEntry[] { pdbentry }, new SequenceI[][] { seq });
}
private void openNewJmol(AlignmentPanel ap, PDBEntry[] pdbentrys,
{
progressBar = ap.alignFrame;
jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(),
- pdbentrys, seqs, null, null);
+ pdbentrys, seqs, null);
addAlignmentPanel(ap);
useAlignmentPanelForColourbyseq(ap);
+
if (pdbentrys.length > 1)
{
alignAddedStructures = true;
jmb.setColourBySequence(true);
setSize(400, 400); // probably should be a configurable/dynamic default here
initMenus();
- worker = null;
- {
- addingStructures = false;
- worker = new Thread(this);
- worker.start();
- }
+ addingStructures = false;
+ worker = new Thread(this);
+ worker.start();
+
this.addInternalFrameListener(new InternalFrameAdapter()
{
@Override
}
/**
- * pdb retrieval thread.
+ * Returns a list of any Jmol viewers. The list is restricted to those linked
+ * to the given alignment panel if it is not null.
*/
- private Thread worker = null;
-
- /**
- * add a new structure (with associated sequences and chains) to this viewer,
- * retrieving it if necessary first.
- *
- * @param pdbentry
- * @param seq
- * @param chains
- * @param alignFrame
- * @param align
- * if true, new structure(s) will be align using associated alignment
- */
- private void addStructure(final PDBEntry pdbentry, final SequenceI[] seq,
- final String[] chains, final boolean b,
- final IProgressIndicator alignFrame)
- {
- if (pdbentry.getFile() == null)
- {
- if (worker != null && worker.isAlive())
- {
- // a retrieval is in progress, wait around and add ourselves to the
- // queue.
- new Thread(new Runnable()
- {
- public void run()
- {
- while (worker != null && worker.isAlive() && _started)
- {
- try
- {
- Thread.sleep(100 + ((int) Math.random() * 100));
-
- } catch (Exception e)
- {
- }
-
- }
- // and call ourselves again.
- addStructure(pdbentry, seq, chains, b, alignFrame);
- }
- }).start();
- return;
- }
- }
- // otherwise, start adding the structure.
- jmb.addSequenceAndChain(new PDBEntry[]
- { pdbentry }, new SequenceI[][]
- { seq }, new String[][]
- { chains });
- addingStructures = true;
- _started = false;
- alignAddedStructures = b;
- progressBar = alignFrame; // visual indication happens on caller frame.
- (worker = new Thread(this)).start();
- return;
- }
-
- private Vector<AppJmol> getJmolsFor(AlignmentPanel apanel)
+ @Override
+ protected List<StructureViewerBase> getViewersFor(AlignmentPanel apanel)
{
- Vector<AppJmol> result = new Vector<AppJmol>();
+ List<StructureViewerBase> result = new ArrayList<StructureViewerBase>();
JInternalFrame[] frames = Desktop.instance.getAllFrames();
for (JInternalFrame frame : frames)
{
if (frame instanceof AppJmol)
{
- if (((AppJmol) frame).isLinkedWith(apanel))
+ if (apanel == null
+ || ((StructureViewerBase) frame).isLinkedWith(apanel))
{
- result.addElement((AppJmol) frame);
+ result.add((StructureViewerBase) frame);
}
}
}
scriptWindow.setVisible(false);
}
- jmb.allocateViewer(renderPanel, true, "", null, null, "", scriptWindow,
- null);
+ jmb.allocateViewer(renderPanel, true, "", null, null, "",
+ scriptWindow, null);
// jmb.newJmolPopup("Jmol");
if (command == null)
{
command = "";
}
jmb.evalStateCommand(command);
+ jmb.evalStateCommand("set hoverDelay=0.1");
jmb.setFinishedInit(true);
}
- void setChainMenuItems(Vector<String> chains)
- {
- chainMenu.removeAll();
- if (chains == null)
- {
- return;
- }
- JMenuItem menuItem = new JMenuItem(
- MessageManager.getString("label.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 (String chain : chains)
- {
- menuItem = new JCheckBoxMenuItem(chain, true);
- menuItem.addItemListener(new ItemListener()
- {
- public void itemStateChanged(ItemEvent evt)
- {
- if (!allChainsSelected)
- {
- centerViewer();
- }
- }
- });
-
- chainMenu.add(menuItem);
- }
- }
boolean allChainsSelected = false;
- private boolean alignAddedStructures = false;
-
- void centerViewer()
+ @Override
+ void showSelectedChains()
{
Vector<String> toshow = new Vector<String>();
for (int i = 0; i < chainMenu.getItemCount(); i++)
jmb.centerViewer(toshow);
}
+ @Override
public void closeViewer(boolean closeExternalViewer)
{
- // JMol does not use an external viewer
- jmb.closeViewer();
+ // Jmol does not use an external viewer
+ if (jmb != null)
+ {
+ jmb.closeViewer();
+ }
setAlignmentPanel(null);
_aps.clear();
_alignwith.clear();
jmb = null;
}
+ @Override
+ public void run()
+ {
+ _started = true;
+ try
+ {
+ List<String> files = fetchPdbFiles();
+ if (files.size() > 0)
+ {
+ showFilesInViewer(files);
+ }
+ } finally
+ {
+ _started = false;
+ worker = null;
+ }
+ }
+
/**
- * state flag for PDB retrieval thread
+ * 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
*/
- private boolean _started = false;
+ void showFilesInViewer(List<String> files)
+ {
+ long lastnotify = jmb.getLoadNotifiesHandled();
+ StringBuilder fileList = new StringBuilder();
+ for (String s : files)
+ {
+ fileList.append(SPACE).append(BACKSLASH)
+ .append(Platform.escapeString(s)).append(BACKSLASH);
+ }
+ String filesString = fileList.toString();
- public void run()
+ if (!addingStructures)
+ {
+ try
+ {
+ initJmol("load FILES " + filesString);
+ } catch (OutOfMemoryError oomerror)
+ {
+ new OOMWarning("When trying to open the Jmol viewer!", oomerror);
+ Cache.log.debug("File locations are " + filesString);
+ } catch (Exception ex)
+ {
+ Cache.log.error("Couldn't open Jmol viewer!", ex);
+ }
+ }
+ 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();
+
+ 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);
+ }
+ }
+
+ // 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
+ {
+ Cache.log.debug("Waiting around for jmb notify.");
+ Thread.sleep(waitFor);
+ waitTotal += waitFor;
+ } catch (Exception e)
+ {
+ }
+ 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;
+ }
+ }
+
+ // refresh the sequence colours for the new structure(s)
+ for (AlignmentPanel ap : _colourwith)
+ {
+ jmb.updateColours(ap);
+ }
+ // do superposition if asked to
+ if (Cache.getDefault("AUTOSUPERIMPOSE", true) && alignAddedStructures)
+ {
+ alignAddedStructures();
+ }
+ addingStructures = false;
+ }
+
+ /**
+ * Queues a thread to align structures with Jalview alignments
+ */
+ void alignAddedStructures()
{
- _started = true;
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ if (jmb.viewer.isScriptExecuting())
+ {
+ SwingUtilities.invokeLater(this);
+ try
+ {
+ Thread.sleep(5);
+ } catch (InterruptedException q)
+ {
+ }
+ return;
+ }
+ else
+ {
+ alignStructs_withAllAlignPanels();
+ }
+ }
+ });
+ alignAddedStructures = false;
+ }
+
+ /**
+ * Retrieves and saves as file any modelled PDB entries for which we do not
+ * already have a file saved. Returns a list of absolute paths to structure
+ * files which were either retrieved, or already stored but not modelled in
+ * the structure viewer (i.e. files to add to the viewer display).
+ *
+ * @return
+ */
+ List<String> fetchPdbFiles()
+ {
+ // todo - record which pdbids were successfully imported.
+ StringBuilder errormsgs = new StringBuilder();
+
+ List<String> files = new ArrayList<String>();
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
+ String[] filesInViewer = jmb.getPdbFile();
// TODO: replace with reference fetching/transfer code (validate PDBentry
// as a DBRef?)
- jalview.ws.dbsources.Pdb pdbclient = new jalview.ws.dbsources.Pdb();
+ Pdb pdbclient = new Pdb();
for (int pi = 0; pi < jmb.getPdbCount(); pi++)
{
String file = jmb.getPdbEntry(pi).getFile();
long hdl = pdbid.hashCode() - System.currentTimeMillis();
if (progressBar != null)
{
- progressBar.setProgressBar(MessageManager.formatMessage("status.fetching_pdb", new String[]{pdbid}), hdl);
+ progressBar.setProgressBar(MessageManager.formatMessage(
+ "status.fetching_pdb", new String[] { pdbid }), hdl);
}
try
{
} catch (Exception ex)
{
ex.printStackTrace();
- errormsgs.append("'" + pdbid + "'");
- }
- if (progressBar != null)
+ errormsgs.append("'").append(pdbid).append("'");
+ } finally
{
- progressBar.setProgressBar(MessageManager.getString("label.state_completed"), hdl);
+ 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).getPDBId()
+ file = new File(pdbseq.getSequenceAt(0).getAllPDBEntries()
.elementAt(0).getFile()).getAbsolutePath();
jmb.getPdbEntry(pi).setFile(file);
-
- files.append(" \"" + Platform.escapeString(file) + "\"");
+ files.add(file);
}
else
{
- errormsgs.append("'" + pdbid + "' ");
+ errormsgs.append("'").append(pdbid).append("' ");
}
}
else
{
- if (curfiles != null && curfiles.length > 0)
+ if (filesInViewer != null && filesInViewer.length > 0)
{
addingStructures = true; // already files loaded.
- for (int c = 0; c < curfiles.length; c++)
+ for (int c = 0; c < filesInViewer.length; c++)
{
- if (curfiles[c].equals(file))
+ if (filesInViewer[c].equals(file))
{
file = null;
break;
}
if (file != null)
{
- files.append(" \"" + Platform.escapeString(file) + "\"");
+ files.add(file);
}
}
}
} catch (Exception ex)
{
ex.printStackTrace();
- errormsgs.append("When retrieving pdbfiles : current was: '" + pdbid
- + "'");
+ errormsgs.append("When retrieving pdbfiles : current was: '")
+ .append(pdbid).append("'");
}
if (errormsgs.length() > 0)
{
-
- JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
+ JvOptionPane.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.getPdbCount()))
- {
- 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;
-
+ new String[] { errormsgs.toString() }),
+ MessageManager.getString("label.couldnt_load_file"),
+ JvOptionPane.ERROR_MESSAGE);
}
- _started = false;
- worker = null;
- }
-
- @Override
- public void pdbFile_actionPerformed(ActionEvent actionEvent)
- {
- JalviewFileChooser chooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
-
- chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(MessageManager.getString("label.save_pdb_file"));
- chooser.setToolTipText(MessageManager.getString("action.save"));
-
- int value = chooser.showSaveDialog(this);
-
- if (value == JalviewFileChooser.APPROVE_OPTION)
- {
- BufferedReader in = null;
- try
- {
- // TODO: cope with multiple PDB files in view
- 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("<PRE>") > -1 || data.indexOf("</PRE>") > -1))
- {
- out.println(data);
- }
- }
- out.close();
- } catch (Exception ex)
- {
- ex.printStackTrace();
- } finally
- {
- if (in != null)
- {
- try
- {
- in.close();
- } catch (IOException e)
- {
- // ignore
- }
- }
- }
- }
- }
-
- @Override
- public void viewMapping_actionPerformed(ActionEvent actionEvent)
- {
- jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
- try
- {
- cap.appendText(jmb.printMappings());
- } 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);
+ return files;
}
@Override
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);
+ 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());
+ jalview.util.ImageMaker.TYPE.EPS, "Make EPS file from view",
+ width, height, null, this.getTitle(), null, 0, false);
}
else
{
im = new jalview.util.ImageMaker(this,
jalview.util.ImageMaker.TYPE.SVG, "Make SVG file from PCA",
- width, height, null, this.getTitle());
+ width, height, null, this.getTitle(), null, 0, false);
}
if (im.getGraphics() != null)
}
@Override
- public void viewerColour_actionPerformed(ActionEvent actionEvent)
- {
- if (viewerColour.isSelected())
- {
- // disable automatic sequence colouring.
- jmb.setColourBySequence(false);
- }
- }
-
- @Override
- public void seqColour_actionPerformed(ActionEvent actionEvent)
- {
- jmb.setColourBySequence(seqColour.isSelected());
- if (_colourwith == null)
- {
- _colourwith = new Vector<AlignmentPanel>();
- }
- if (jmb.isColourBySequence())
- {
- if (!jmb.isLoadingFromArchive())
- {
- if (_colourwith.size() == 0 && getAlignmentPanel() != null)
- {
- // Make the currently displayed alignment panel the associated view
- _colourwith.add(getAlignmentPanel().alignFrame.alignPanel);
- }
- }
- // Set the colour using the current view for the associated alignframe
- for (AlignmentPanel ap : _colourwith)
- {
- jmb.colourBySequence(ap);
- }
- }
- }
-
- @Override
- public void chainColour_actionPerformed(ActionEvent actionEvent)
- {
- chainColour.setSelected(true);
- jmb.colourByChain();
- }
-
- @Override
- public void chargeColour_actionPerformed(ActionEvent actionEvent)
- {
- chargeColour.setSelected(true);
- jmb.colourByCharge();
- }
-
- @Override
- public void zappoColour_actionPerformed(ActionEvent actionEvent)
- {
- zappoColour.setSelected(true);
- jmb.setJalviewColourScheme(new ZappoColourScheme());
- }
-
- @Override
- public void taylorColour_actionPerformed(ActionEvent actionEvent)
- {
- taylorColour.setSelected(true);
- jmb.setJalviewColourScheme(new TaylorColourScheme());
- }
-
- @Override
- public void hydroColour_actionPerformed(ActionEvent actionEvent)
- {
- hydroColour.setSelected(true);
- jmb.setJalviewColourScheme(new HydrophobicColourScheme());
- }
-
- @Override
- public void helixColour_actionPerformed(ActionEvent actionEvent)
- {
- helixColour.setSelected(true);
- jmb.setJalviewColourScheme(new HelixColourScheme());
- }
-
- @Override
- public void strandColour_actionPerformed(ActionEvent actionEvent)
- {
- strandColour.setSelected(true);
- jmb.setJalviewColourScheme(new StrandColourScheme());
- }
-
- @Override
- public void turnColour_actionPerformed(ActionEvent actionEvent)
- {
- turnColour.setSelected(true);
- jmb.setJalviewColourScheme(new TurnColourScheme());
- }
-
- @Override
- public void buriedColour_actionPerformed(ActionEvent actionEvent)
- {
- buriedColour.setSelected(true);
- jmb.setJalviewColourScheme(new BuriedColourScheme());
- }
-
- @Override
- public void purinePyrimidineColour_actionPerformed(ActionEvent actionEvent)
- {
- 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,
- MessageManager.getString("label.select_backgroud_colour"), null);
- if (col != null)
- {
- jmb.setBackgroundColour(col);
- }
- }
-
- @Override
public void showHelp_actionPerformed(ActionEvent actionEvent)
{
try
{
- jalview.util.BrowserLauncher
+ BrowserLauncher
.openURL("http://jmol.sourceforge.net/docs/JmolUserGuide/");
} catch (Exception ex)
{
{
getSize(currentSize);
- if (jmb != null && jmb.fileLoadingError != null)
+ if (jmb != null && jmb.hasFileLoadingError())
{
g.setColor(Color.black);
g.fillRect(0, 0, currentSize.width, currentSize.height);
}
}
- public void updateTitleAndMenus()
- {
- if (jmb.fileLoadingError != null && jmb.fileLoadingError.length() > 0)
- {
- repaint();
- return;
- }
- setChainMenuItems(jmb.chainNames);
-
- this.setTitle(jmb.getViewerTitle());
- if (jmb.getPdbFile().length > 1 && jmb.getSequence().length > 1)
- {
- viewerActionMenu.setVisible(true);
- }
- if (!jmb.isLoadingFromArchive())
- {
- seqColour_actionPerformed(null);
- }
- }
-
- /*
- * (non-Javadoc)
- *
- * @see
- * jalview.jbgui.GStructureViewer#alignStructs_actionPerformed(java.awt.event
- * .ActionEvent)
- */
- @Override
- protected void alignStructs_actionPerformed(ActionEvent actionEvent)
- {
- alignStructs_withAllAlignPanels();
- }
-
- private void alignStructs_withAllAlignPanels()
- {
- if (getAlignmentPanel() == null)
- {
- return;
- }
- ;
- if (_alignwith.size() == 0)
- {
- _alignwith.add(getAlignmentPanel());
- }
- ;
- try
- {
- AlignmentI[] als = new Alignment[_alignwith.size()];
- ColumnSelection[] alc = new ColumnSelection[_alignwith.size()];
- int[] alm = new int[_alignwith.size()];
- int a = 0;
-
- for (AlignmentPanel ap : _alignwith)
- {
- als[a] = ap.av.getAlignment();
- alm[a] = -1;
- alc[a++] = ap.av.getColumnSelection();
- }
- jmb.superposeStructures(als, alm, alc);
- } catch (Exception e)
- {
- StringBuffer sp = new StringBuffer();
- for (AlignmentPanel ap : _alignwith)
- {
- sp.append("'" + ap.alignFrame.getTitle() + "' ");
- }
- Cache.log.info("Couldn't align structures with the " + sp.toString()
- + "associated alignment panels.", e);
-
- }
-
- }
-
- public void setJalviewColourScheme(ColourSchemeI ucs)
- {
- jmb.setJalviewColourScheme(ucs);
-
- }
-
- /**
- *
- * @param alignment
- * @return first alignment panel displaying given alignment, or the default
- * alignment panel
- */
- public AlignmentPanel getAlignmentPanelFor(AlignmentI alignment)
- {
- for (AlignmentPanel ap : getAllAlignmentPanels())
- {
- if (ap.av.getAlignment() == alignment)
- {
- return ap;
- }
- }
- return getAlignmentPanel();
- }
-
@Override
public AAStructureBindingModel getBinding()
{
return ViewerType.JMOL;
}
+ @Override
+ protected String getViewerName()
+ {
+ return "Jmol";
+ }
}
git://source.jalview.org / jalview.git / blobdiff