/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
*/
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.ext.rbvi.chimera.JalviewChimeraBinding;
+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.MessageManager;
+import jalview.util.Platform;
+import jalview.ws.dbsources.Pdb;
+
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.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 javax.swing.event.MenuEvent;
import javax.swing.event.MenuListener;
-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.ext.rbvi.chimera.JalviewChimeraBinding;
-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.MessageManager;
-import jalview.util.Platform;
-import jalview.ws.dbsources.Pdb;
-
/**
* GUI elements for handling an external chimera display
*
private boolean allChainsSelected = false;
- private boolean alignAddedStructures = false;
-
- /*
- * state flag for PDB retrieval thread
- */
- private boolean _started = false;
-
- private boolean addingStructures = false;
-
private IProgressIndicator progressBar = null;
/*
- * pdb retrieval thread.
- */
- private Thread worker = null;
-
- /*
* Path to Chimera session file. This is set when an open Jalview/Chimera
* session is saved, or on restore from a Jalview project (if it holds the
* filename of any saved Chimera sessions).
alignStructs.setToolTipText(MessageManager
.formatMessage(
"label.align_structures_using_linked_alignment_views",
- new Object[]
- { new Integer(_alignwith.size()).toString() }));
+ new Object[] { new Integer(_alignwith
+ .size()).toString() }));
}
});
handler.itemStateChanged(null);
String[] chains, final AlignmentPanel ap)
{
super();
-
- /*
- * is the pdb file already loaded?
- */
String pdbId = pdbentry.getId();
- String alreadyMapped = ap.getStructureSelectionManager()
- .alreadyMappedToFile(pdbId);
-
- if (alreadyMapped != null)
- {
- int option = chooseAddSequencesToViewer(pdbId);
- if (option == JOptionPane.CANCEL_OPTION)
- {
- return;
- }
- if (option == JOptionPane.YES_OPTION)
- {
- addSequenceMappingsToStructure(seq, chains, ap, alreadyMapped);
- return;
- }
- }
/*
- * 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
+ * If the PDB file is already loaded, the user may just choose to add to an
+ * existing viewer (or cancel)
*/
- List<ChimeraViewFrame> existingViews = getChimeraWindowsFor(ap);
- for (ChimeraViewFrame view : existingViews)
+ if (addAlreadyLoadedFile(seq, chains, ap, pdbId))
{
- // 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 (view.hasPdbId(pdbId))
- {
- continue;
- }
- int option = chooseAlignStructureToViewer(pdbId, view);
- if (option == JOptionPane.CANCEL_OPTION)
- {
- return;
- }
- if (option == JOptionPane.YES_OPTION)
- {
- view.useAlignmentPanelForSuperposition(ap);
- view.addStructure(pdbentry, seq, chains, true, ap.alignFrame);
- return;
- }
+ 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
+ * 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 (or cancel)
*/
- if (ap.getSeqPanel().seqCanvas.fr != null)
+ if (addToExistingViewer(pdbentry, seq, chains, ap, pdbId))
{
- ap.getSeqPanel().seqCanvas.fr.featuresAdded();
- ap.paintAlignment(true);
+ return;
}
/*
- * add the sequences to any other Chimera viewers for this pdb file
+ * If the options above are declined or do not apply, show the structure in
+ * a new viewer
*/
- // 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;
- }
- }
- }
- }
+ openNewChimera(ap, new PDBEntry[] { pdbentry },
+ new SequenceI[][] { seq });
}
/**
}
}
+ /**
+ * Answers true if this viewer already involves the given PDB ID
+ */
+ @Override
protected boolean hasPdbId(String pdbId)
{
return jmb.hasPdbId(pdbId);
String chain = null;
if (seq.getDatasetSequence() != null)
{
- Vector<PDBEntry> pdbrefs = seq.getDatasetSequence().getPDBId();
+ Vector<PDBEntry> pdbrefs = seq.getDatasetSequence()
+ .getAllPDBEntries();
if (pdbrefs != null && pdbrefs.size() > 0)
{
chain = pdbrefs.get(0).getChainCode();
/**
* 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,
- PDBEntry[] pdbArray,
+ 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)
{
}
/**
- * 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
+ * Returns a list of any Chimera viewers in the desktop. The list is
+ * restricted to those linked to the given alignment panel if it is not null.
*/
- 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 List<ChimeraViewFrame> getChimeraWindowsFor(AlignmentPanel apanel)
+ @Override
+ protected List<StructureViewerBase> getViewersFor(AlignmentPanel ap)
{
- List<ChimeraViewFrame> result = new ArrayList<ChimeraViewFrame>();
+ List<StructureViewerBase> result = new ArrayList<StructureViewerBase>();
JInternalFrame[] frames = Desktop.instance.getAllFrames();
for (JInternalFrame frame : frames)
{
if (frame instanceof ChimeraViewFrame)
{
- if (((StructureViewerBase) frame).isLinkedWith(apanel))
+ if (ap == null || ((StructureViewerBase) frame).isLinkedWith(ap))
{
- result.add((ChimeraViewFrame) frame);
+ result.add((StructureViewerBase) frame);
}
}
}
void initChimera()
{
jmb.setFinishedInit(false);
- jalview.gui.Desktop.addInternalFrame(this, jmb.getViewerTitle("Chimera", true),
- getBounds().width, getBounds().height);
+ jalview.gui.Desktop.addInternalFrame(this,
+ jmb.getViewerTitle("Chimera", true), getBounds().width,
+ getBounds().height);
if (!jmb.launchChimera())
{
- JOptionPane
- .showMessageDialog(
- Desktop.desktop,
+ JOptionPane.showMessageDialog(Desktop.desktop,
MessageManager.getString("label.chimera_failed"),
MessageManager.getString("label.error_loading_file"),
JOptionPane.ERROR_MESSAGE);
*/
public void closeViewer(boolean closeChimera)
{
- if (jmb.isChimeraRunning())
+ if (jmb != null && jmb.isChimeraRunning())
{
if (!closeChimera)
{
String prompt = MessageManager.formatMessage(
- "label.confirm_close_chimera", new Object[]
- { jmb.getViewerTitle("Chimera", false) });
+ "label.confirm_close_chimera",
+ new Object[] { jmb.getViewerTitle("Chimera", false) });
prompt = JvSwingUtils.wrapTooltip(true, prompt);
int confirm = JOptionPane.showConfirmDialog(this, prompt,
MessageManager.getString("label.close_viewer"),
JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
.formatMessage("label.pdb_entries_couldnt_be_retrieved",
- new Object[]
- { errormsgs.toString() }), MessageManager
- .getString("label.couldnt_load_file"),
+ new Object[] { errormsgs.toString() }),
+ MessageManager.getString("label.couldnt_load_file"),
JOptionPane.ERROR_MESSAGE);
}
}
// Explicitly map to the filename used by Chimera ;
jmb.getSsm().setMapping(jmb.getSequence()[pos],
- jmb.getChains()[pos],
- pe.getFile(),
- protocol);
+ jmb.getChains()[pos], pe.getFile(), protocol);
} catch (OutOfMemoryError oomerror)
{
new OOMWarning(
jmb.updateColours(ap);
}
// do superposition if asked to
- if (alignAddedStructures)
+ if (Cache.getDefault("AUTOSUPERIMPOSE", true) && alignAddedStructures)
{
new Thread(new Runnable()
{
* Write 'fetching PDB' progress on AlignFrame as we are not yet visible
*/
String msg = MessageManager.formatMessage("status.fetching_pdb",
- new Object[]
- { pdbid });
+ new Object[] { pdbid });
getAlignmentPanel().alignFrame.setProgressBar(msg, handle);
// long hdl = startProgressBar(MessageManager.formatMessage(
// "status.fetching_pdb", new Object[]
new OOMWarning("Retrieving PDB id " + pdbid, oomerror);
} finally
{
- msg = pdbid + " "
- + MessageManager.getString("label.state_completed");
+ msg = pdbid + " " + MessageManager.getString("label.state_completed");
getAlignmentPanel().alignFrame.setProgressBar(msg, handle);
// stopProgressBar(msg, hdl);
}
if (pdbseq != null && pdbseq.getHeight() > 0)
{
// just use the file name from the first sequence's first PDBEntry
- filePath = new File(pdbseq.getSequenceAt(0).getPDBId()
+ filePath = new File(pdbseq.getSequenceAt(0).getAllPDBEntries()
.elementAt(0).getFile()).getAbsolutePath();
processingEntry.setFile(filePath);
}
}
/**
- * 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 == null ? "" : 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)
+ {
+ // ignore
+ }
+ }
+ }
}
@Override
{
jmb.focusView();
}
+
+ @Override
+ public ViewerType getViewerType()
+ {
+ return ViewerType.CHIMERA;
+ }
+
+ @Override
+ protected AAStructureBindingModel getBindingModel()
+ {
+ return jmb;
+ }
}
git://source.jalview.org / jalview.git / blobdiff