import java.awt.event.ItemListener;
import java.io.BufferedReader;
import java.io.File;
+import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.FileReader;
import java.io.IOException;
+import java.io.InputStream;
import java.io.PrintWriter;
import java.util.ArrayList;
import java.util.List;
+import java.util.Map;
import java.util.Random;
+import java.util.Set;
import java.util.Vector;
import javax.swing.JCheckBoxMenuItem;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.ext.rbvi.chimera.JalviewChimeraBinding;
+import jalview.gui.StructureViewer.ViewerType;
import jalview.io.AppletFormatAdapter;
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
import jalview.ws.dbsources.Pdb;
/**
- * GUI elements for handlnig an external chimera display
+ * GUI elements for handling an external chimera display
*
* @author jprocter
*
}
});
viewMenu.add(seqColourBy);
+ viewMenu.add(fitToWindow);
+
final ItemListener handler;
JMenu alpanels = new ViewSelectionMenu(
MessageManager.getString("label.superpose_with"), this,
String[] chains, final AlignmentPanel ap)
{
super();
- progressBar = ap.alignFrame;
- // ////////////////////////////////
- // Is the pdb file already loaded?
+
+ /*
+ * is the pdb file already loaded?
+ */
+ String pdbId = pdbentry.getId();
String alreadyMapped = ap.getStructureSelectionManager()
- .alreadyMappedToFile(pdbentry.getId());
+ .alreadyMappedToFile(pdbId);
if (alreadyMapped != null)
{
- int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
- MessageManager.formatMessage(
- "label.pdb_entry_is_already_displayed", new Object[]
- { pdbentry.getId() }), MessageManager.formatMessage(
- "label.map_sequences_to_visible_window", new Object[]
- { pdbentry.getId() }),
- JOptionPane.YES_NO_CANCEL_OPTION);
-
+ int option = chooseAddSequencesToViewer(pdbId);
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 ChimeraViewFrame is mapped to new sequences. We must add
- // them to the existing array
- JInternalFrame[] frames = Desktop.instance.getAllFrames();
-
- for (JInternalFrame frame : frames)
- {
- if (frame instanceof ChimeraViewFrame)
- {
- final ChimeraViewFrame topView = ((ChimeraViewFrame) frame);
- // JBPNOTE: this looks like a binding routine, rather than a gui
- // routine
- for (int pe = 0; pe < topView.jmb.getPdbCount(); pe++)
- {
- if (topView.jmb.getPdbEntry(pe).getFile()
- .equals(
- alreadyMapped))
- {
- topView.jmb.addSequence(pe, seq);
- topView.addAlignmentPanel(ap);
- // add it to the set used for colouring
- topView.useAlignmentPanelForColourbyseq(ap);
- topView.buildActionMenu();
- ap.getStructureSelectionManager()
- .sequenceColoursChanged(ap);
- break;
- }
- }
- }
- }
-
+ addSequenceMappingsToStructure(seq, chains, ap, alreadyMapped);
return;
}
}
- // /////////////////////////////////
- // Check if there are other Chimera views involving this alignment
- // and prompt user about adding this molecule to one of them
+
+ /*
+ * Check if there are other Chimera views involving this alignment and give
+ * user the option to add and align this molecule to one of them
+ */
List<ChimeraViewFrame> existingViews = getChimeraWindowsFor(ap);
- for (ChimeraViewFrame topView : existingViews)
+ for (ChimeraViewFrame view : existingViews)
{
- // TODO: highlight topView in view somehow
+ // TODO: highlight view somehow
/*
* JAL-1742 exclude view with this structure already mapped (don't offer
* to align chain B to chain A of the same structure)
*/
- if (topView.hasPdbId(pdbentry.getId()))
+ if (view.hasPdbId(pdbId))
{
continue;
}
- int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
- MessageManager.formatMessage("label.add_pdbentry_to_view",
- new Object[]
- { pdbentry.getId(), topView.getTitle() }),
- MessageManager
- .getString("label.align_to_existing_structure_view"),
- JOptionPane.YES_NO_CANCEL_OPTION);
+ int option = chooseAlignStructureToViewer(pdbId, view);
if (option == JOptionPane.CANCEL_OPTION)
{
return;
}
if (option == JOptionPane.YES_OPTION)
{
- topView.useAlignmentPanelForSuperposition(ap);
- topView.addStructure(pdbentry, seq, chains, true, ap.alignFrame);
+ view.useAlignmentPanelForSuperposition(ap);
+ view.addStructure(pdbentry, seq, chains, true, ap.alignFrame);
return;
}
}
- // /////////////////////////////////
+
+ /*
+ * If the options above are declined or do not apply, open a new viewer
+ */
openNewChimera(ap, new PDBEntry[]
{ pdbentry }, new SequenceI[][]
{ seq });
}
/**
+ * Presents a dialog with the option to add an align a structure to an
+ * existing Chimera view
+ *
+ * @param pdbId
+ * @param view
+ * @return YES, NO or CANCEL JOptionPane code
+ */
+ protected int chooseAlignStructureToViewer(String pdbId,
+ ChimeraViewFrame view)
+ {
+ int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
+ MessageManager.formatMessage("label.add_pdbentry_to_view",
+ new Object[]
+ { pdbId, view.getTitle() }), MessageManager
+ .getString("label.align_to_existing_structure_view"),
+ JOptionPane.YES_NO_CANCEL_OPTION);
+ return option;
+ }
+
+ /**
+ * Presents a dialog with the option to add sequences to a viewer which
+ * already has their structure open
+ *
+ * @param pdbId
+ * @return YES, NO or CANCEL JOptionPane code
+ */
+ protected int chooseAddSequencesToViewer(String pdbId)
+ {
+ int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
+ MessageManager.formatMessage(
+ "label.pdb_entry_is_already_displayed", new Object[]
+ { pdbId }), MessageManager.formatMessage(
+ "label.map_sequences_to_visible_window", new Object[]
+ { pdbId }), JOptionPane.YES_NO_CANCEL_OPTION);
+ return option;
+ }
+
+ /**
+ * Adds mappings for the given sequences to an already opened PDB structure,
+ * and updates any viewers that have the PDB file
+ *
+ * @param seq
+ * @param chains
+ * @param ap
+ * @param pdbFilename
+ */
+ protected void addSequenceMappingsToStructure(SequenceI[] seq,
+ String[] chains, final AlignmentPanel ap, String pdbFilename)
+ {
+ // TODO : Fix multiple seq to one chain issue here.
+ /*
+ * create the mappings
+ */
+ ap.getStructureSelectionManager().setMapping(seq, chains, pdbFilename,
+ AppletFormatAdapter.FILE);
+
+ /*
+ * alert the FeatureRenderer to show new (PDB RESNUM) features
+ */
+ if (ap.getSeqPanel().seqCanvas.fr != null)
+ {
+ ap.getSeqPanel().seqCanvas.fr.featuresAdded();
+ ap.paintAlignment(true);
+ }
+
+ /*
+ * add the sequences to any other Chimera viewers for this pdb file
+ */
+ // JBPNOTE: this looks like a binding routine, rather than a gui routine
+ for (JInternalFrame frame : Desktop.instance.getAllFrames())
+ {
+ if (frame instanceof ChimeraViewFrame)
+ {
+ ChimeraViewFrame chimeraView = ((ChimeraViewFrame) frame);
+ for (int pe = 0; pe < chimeraView.jmb.getPdbCount(); pe++)
+ {
+ if (chimeraView.jmb.getPdbEntry(pe).getFile().equals(pdbFilename))
+ {
+ chimeraView.jmb.addSequence(pe, seq);
+ chimeraView.addAlignmentPanel(ap);
+ /*
+ * add it to the set of alignments used for colouring structure by
+ * sequence
+ */
+ chimeraView.useAlignmentPanelForColourbyseq(ap);
+ chimeraView.buildActionMenu();
+ ap.getStructureSelectionManager().sequenceColoursChanged(ap);
+ break;
+ }
+ }
+ }
+ }
+ }
+
+ /**
* Create a helper to manage progress bar display
*/
protected void createProgressBar()
SequenceI[][] seqs)
{
createProgressBar();
-
String[][] chains = extractChains(seqs);
jmb = new JalviewChimeraBindingModel(this,
ap.getStructureSelectionManager(), pdbentrys, seqs, chains,
}
/**
- * create a new viewer containing several structures superimposed using the
- * given alignPanel.
- *
- * @param ap
- * @param pe
- * @param seqs
- */
- public ChimeraViewFrame(AlignmentPanel ap, PDBEntry[] pe,
- SequenceI[][] seqs)
- {
- super();
- openNewChimera(ap, pe, seqs);
- }
-
- /**
* Create a new viewer from saved session state data including Chimera session
- * file.
- *
- * @param chimeraSession
+ * file
*
+ * @param chimeraSessionFile
* @param alignPanel
* @param pdbArray
* @param seqsArray
* @param colourByChimera
* @param colourBySequence
+ * @param newViewId
*/
- public ChimeraViewFrame(String chimeraSession, AlignmentPanel alignPanel,
+ public ChimeraViewFrame(String chimeraSessionFile,
+ AlignmentPanel alignPanel,
PDBEntry[] pdbArray,
SequenceI[][] seqsArray, boolean colourByChimera,
- boolean colourBySequence)
+ boolean colourBySequence, String newViewId)
{
super();
- this.chimeraSessionFile = chimeraSession;
+ setViewId(newViewId);
+ this.chimeraSessionFile = chimeraSessionFile;
openNewChimera(alignPanel, pdbArray, seqsArray);
if (colourByChimera)
{
}
/**
+ * create a new viewer containing several structures superimposed using the
+ * given alignPanel.
+ *
+ * @param pe
+ * @param seqs
+ * @param ap
+ */
+ public ChimeraViewFrame(PDBEntry[] pe, SequenceI[][] seqs,
+ AlignmentPanel ap)
+ {
+ super();
+ openNewChimera(ap, pe, seqs);
+ }
+
+ public ChimeraViewFrame(Map<PDBEntry, List<SequenceI>> toView,
+ AlignmentPanel alignPanel)
+ {
+ super();
+
+ /*
+ * Convert the map of sequences per pdb entry into the tied arrays expected
+ * by openNewChimera
+ *
+ * TODO pass the Map down to openNewChimera and its callees instead
+ */
+ final Set<PDBEntry> pdbEntries = toView.keySet();
+ PDBEntry[] pdbs = pdbEntries.toArray(new PDBEntry[pdbEntries.size()]);
+ SequenceI[][] seqsForPdbs = new SequenceI[pdbEntries.size()][];
+ for (int i = 0; i < pdbs.length; i++)
+ {
+ final List<SequenceI> seqsForPdb = toView.get(pdbs[i]);
+ seqsForPdbs[i] = seqsForPdb.toArray(new SequenceI[seqsForPdb.size()]);
+ }
+
+ openNewChimera(alignPanel, pdbs, seqsForPdbs);
+ }
+
+ /**
* add a new structure (with associated sequences and chains) to this viewer,
* retrieving it if necessary first.
*
addingStructures = true;
_started = false;
alignAddedStructures = b;
- progressBar = alignFrame; // visual indication happens on caller frame.
+ // progressBar = alignFrame; // visual indication happens on caller frame.
(worker = new Thread(this)).start();
return;
}
jalview.gui.Desktop.addInternalFrame(this, jmb.getViewerTitle("Chimera", true),
getBounds().width, getBounds().height);
- /*
- * Pass an empty 'command' to launch Chimera
- */
- jmb.evalStateCommand("", false);
+ if (!jmb.launchChimera())
+ {
+ JOptionPane
+ .showMessageDialog(
+ Desktop.desktop,
+ MessageManager.getString("label.chimera_failed"),
+ MessageManager.getString("label.error_loading_file"),
+ JOptionPane.ERROR_MESSAGE);
+ this.dispose();
+ return;
+ }
if (this.chimeraSessionFile != null)
{
jmb.startChimeraListener();
}
+ /**
+ * If the list is not empty, add menu items for 'All' and each individual
+ * chain to the "View | Show Chain" sub-menu. Multiple selections are allowed.
+ *
+ * @param chainNames
+ */
void setChainMenuItems(List<String> chainNames)
{
chainMenu.removeAll();
- if (chainNames == null)
+ if (chainNames == null || chainNames.isEmpty())
{
return;
}
((JCheckBoxMenuItem) chainMenu.getItem(i)).setSelected(true);
}
}
- centerViewer();
+ showSelectedChains();
allChainsSelected = false;
}
});
{
if (!allChainsSelected)
{
- centerViewer();
+ showSelectedChains();
}
}
});
}
}
- void centerViewer()
+ /**
+ * Show only the selected chain(s) in the viewer
+ */
+ void showSelectedChains()
{
List<String> toshow = new ArrayList<String>();
for (int i = 0; i < chainMenu.getItemCount(); i++)
}
}
}
- jmb.centerViewer(toshow);
+ jmb.showChains(toshow);
}
/**
stopProgressBar("", startTime);
}
// Explicitly map to the filename used by Chimera ;
- // TODO: use pe.getId() instead of pe.getFile() ?
- jmb.getSsm().setMapping(jmb.getSequence()[pos], null,
+ jmb.getSsm().setMapping(jmb.getSequence()[pos],
+ jmb.getChains()[pos],
pe.getFile(),
protocol);
} catch (OutOfMemoryError oomerror)
Pdb pdbclient = new Pdb();
AlignmentI pdbseq = null;
String pdbid = processingEntry.getId();
- long hdl = startProgressBar(MessageManager.formatMessage(
- "status.fetching_pdb", new Object[]
- { pdbid }));
+ long handle = System.currentTimeMillis()
+ + Thread.currentThread().hashCode();
+
+ /*
+ * Write 'fetching PDB' progress on AlignFrame as we are not yet visible
+ */
+ String msg = MessageManager.formatMessage("status.fetching_pdb",
+ new Object[]
+ { pdbid });
+ getAlignmentPanel().alignFrame.setProgressBar(msg, handle);
+ // long hdl = startProgressBar(MessageManager.formatMessage(
+ // "status.fetching_pdb", new Object[]
+ // { pdbid }));
try
{
pdbseq = pdbclient.getSequenceRecords(pdbid);
new OOMWarning("Retrieving PDB id " + pdbid, oomerror);
} finally
{
- String msg = pdbid + " "
+ msg = pdbid + " "
+ MessageManager.getString("label.state_completed");
- stopProgressBar(msg, hdl);
+ getAlignmentPanel().alignFrame.setProgressBar(msg, handle);
+ // stopProgressBar(msg, hdl);
}
/*
* If PDB data were saved and are not invalid (empty alignment), return the
return tm;
}
+ /**
+ * End the progress bar with the specified handle, leaving a message (if not
+ * null) on the status bar
+ *
+ * @param msg
+ * @param handle
+ */
public void stopProgressBar(String msg, long handle)
{
if (progressBar != null)
{
return;
}
- ;
+
if (_alignwith.size() == 0)
{
_alignwith.add(getAlignmentPanel());
}
- ;
+
try
{
AlignmentI[] als = new Alignment[_alignwith.size()];
}
Cache.log.info("Couldn't align structures with the " + sp.toString()
+ "associated alignment panels.", e);
-
}
-
}
public void setJalviewColourScheme(ColourSchemeI ucs)
}
/**
- * Ask Chimera to save its session to the designated file path. Returns true
- * if successful, else false.
+ * Ask Chimera to save its session to the designated file path, or to a
+ * temporary file if the path is null. Returns the file path if successful,
+ * else null.
*
* @param filepath
* @see getStateInfo
*/
- public boolean saveSession(String filepath)
+ protected String saveSession(String filepath)
{
- boolean result = jmb.saveSession(filepath);
- if (result)
+ String pathUsed = filepath;
+ try
+ {
+ if (pathUsed == null)
+ {
+ File tempFile = File.createTempFile("chimera", ".py");
+ tempFile.deleteOnExit();
+ pathUsed = tempFile.getPath();
+ }
+ boolean result = jmb.saveSession(pathUsed);
+ if (result)
+ {
+ this.chimeraSessionFile = pathUsed;
+ return pathUsed;
+ }
+ } catch (IOException e)
{
- this.chimeraSessionFile = filepath;
}
- return result;
+ return null;
}
/**
- * Returns the file path of the Chimera session file the last time it was
- * saved. If it was never saved, returns an empty string. There is no
- * guarantee that the Chimera session has not changed since it was saved.
+ * Returns a string representing the state of the Chimera session. This is
+ * done by requesting Chimera to save its session to a temporary file, then
+ * reading the file contents. Returns an empty string on any error.
*/
@Override
public String getStateInfo()
{
- return this.chimeraSessionFile;
+ String sessionFile = saveSession(null);
+ if (sessionFile == null)
+ {
+ return "";
+ }
+ InputStream is = null;
+ try
+ {
+ File f = new File(sessionFile);
+ byte[] bytes = new byte[(int) f.length()];
+ is = new FileInputStream(sessionFile);
+ is.read(bytes);
+ return new String(bytes);
+ } catch (IOException e)
+ {
+ return "";
+ } finally
+ {
+ if (is != null)
+ {
+ try
+ {
+ is.close();
+ } catch (IOException e)
+ {
+ // ignoreß
+ }
+ }
+ }
+ // return this.chimeraSessionFile == null ? "" : chimeraSessionFile;
}
@Override
{
jmb.focusView();
}
+
+ @Override
+ public ViewerType getViewerType()
+ {
+ return ViewerType.CHIMERA;
+ }
}
git://source.jalview.org / jalview.git / blobdiff