/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*/
package jalview.gui;
-import jalview.api.SequenceStructureBinding;
-import jalview.api.structures.JalviewStructureDisplayI;
-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.ViewSelectionMenu.ViewSetProvider;
-import jalview.io.AppletFormatAdapter;
-import jalview.io.JalviewFileChooser;
-import jalview.io.JalviewFileView;
-import jalview.jbgui.GStructureViewer;
-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.util.MessageManager;
-import jalview.util.Platform;
-import jalview.ws.dbsources.Pdb;
-
-import java.awt.Component;
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 java.util.Map;
+import java.util.Random;
+import java.util.Set;
import java.util.Vector;
import javax.swing.JCheckBoxMenuItem;
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.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;
+
/**
- * GUI elements for handlnig an external chimera display
+ * GUI elements for handling an external chimera display
*
* @author jprocter
*
*/
-public class ChimeraViewFrame extends GStructureViewer implements Runnable,
- ViewSetProvider, JalviewStructureDisplayI
-
+public class ChimeraViewFrame extends StructureViewerBase
{
- private JalviewChimeraBindingModel jmb;
-
- /*
- * list of sequenceSet ids associated with the view
- */
- private ArrayList<String> _aps = new ArrayList<String>();
-
- /*
- * list of alignment panels to use for superposition
- */
- private Vector<AlignmentPanel> _alignwith = new Vector<AlignmentPanel>();
-
- /*
- * list of alignment panels that are used for colouring structures by aligned
- * sequences
- */
- private Vector<AlignmentPanel> _colourwith = new Vector<AlignmentPanel>();
+ private JalviewChimeraBinding jmb;
private boolean allChainsSelected = false;
private boolean alignAddedStructures = false;
- AlignmentPanel ap;
-
/*
* state flag for PDB retrieval thread
*/
private IProgressIndicator progressBar = null;
- private String viewId = 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).
+ */
+ private String chimeraSessionFile = null;
+
+ private Random random = new Random();
+
/**
* Initialise menu options.
*/
_alignwith = new Vector<AlignmentPanel>();
}
- // no colour by chain command in Chimera?
- chainColour.setVisible(false);
-
// save As not yet implemented
savemenu.setVisible(false);
}
});
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.seqPanel.seqCanvas.fr != null)
- {
- ap.seqPanel.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.pdbentry.length; pe++)
- {
- if (topView.jmb.pdbentry[pe].getFile().equals(alreadyMapped))
- {
- topView.jmb.addSequence(pe, seq);
- topView.addAlignmentPanel(ap);
- // add it to the set used for colouring
- topView.useAlignmentPanelForColourbyseq(ap);
- topView.buildChimeraActionMenu();
- 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
- 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);
+ // 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)
{
- 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()
+ {
+ if (progressBar == null)
+ {
+ progressBar = new ProgressBar(statusPanel, statusBar);
+ }
+ }
+
+ protected boolean hasPdbId(String pdbId)
+ {
+ return jmb.hasPdbId(pdbId);
+ }
+
private void openNewChimera(AlignmentPanel ap, PDBEntry[] pdbentrys,
SequenceI[][] seqs)
{
- progressBar = ap.alignFrame;
+ createProgressBar();
+ String[][] chains = extractChains(seqs);
jmb = new JalviewChimeraBindingModel(this,
- ap.getStructureSelectionManager(), pdbentrys, seqs, null, null);
+ ap.getStructureSelectionManager(), pdbentrys, seqs, chains,
+ null);
addAlignmentPanel(ap);
useAlignmentPanelForColourbyseq(ap);
if (pdbentrys.length > 1)
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()
{
public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
{
- closeViewer();
+ closeViewer(false);
}
});
}
/**
- * create a new viewer containing several structures superimposed using the
- * given alignPanel.
+ * Retrieve chains for sequences by inspecting their PDB refs. The hope is
+ * that the first will be to the sequence's own chain. Really need a more
+ * managed way of doing this.
*
- * @param ap
- * @param pe
* @param seqs
+ * @return
*/
- public ChimeraViewFrame(AlignmentPanel ap, PDBEntry[] pe,
- SequenceI[][] seqs)
+ protected String[][] extractChains(SequenceI[][] seqs)
{
- super();
- openNewChimera(ap, pe, seqs);
- }
-
- public AlignmentPanel[] getAllAlignmentPanels()
- {
- AlignmentPanel[] t, list = new AlignmentPanel[0];
- for (String setid : _aps)
+ String[][] chains = new String[seqs.length][];
+ for (int i = 0; i < seqs.length; i++)
{
- AlignmentPanel[] panels = PaintRefresher.getAssociatedPanels(setid);
- if (panels != null)
+ chains[i] = new String[seqs[i].length];
+ int seqno = 0;
+ for (SequenceI seq : seqs[i])
{
- t = new AlignmentPanel[list.length + panels.length];
- System.arraycopy(list, 0, t, 0, list.length);
- System.arraycopy(panels, 0, t, list.length, panels.length);
- list = t;
+ String chain = null;
+ if (seq.getDatasetSequence() != null)
+ {
+ Vector<PDBEntry> pdbrefs = seq.getDatasetSequence().getPDBId();
+ if (pdbrefs != null && pdbrefs.size() > 0)
+ {
+ chain = pdbrefs.get(0).getChainCode();
+ }
+ }
+ chains[i][seqno++] = chain;
}
}
-
- return list;
+ return chains;
}
/**
- * set the primary alignmentPanel reference and add another alignPanel to the
- * list of ones to use for colouring and aligning
+ * Create a new viewer from saved session state data including Chimera session
+ * file
*
- * @param nap
+ * @param chimeraSessionFile
+ * @param alignPanel
+ * @param pdbArray
+ * @param seqsArray
+ * @param colourByChimera
+ * @param colourBySequence
+ * @param newViewId
*/
- public void addAlignmentPanel(AlignmentPanel nap)
+ public ChimeraViewFrame(String chimeraSessionFile,
+ AlignmentPanel alignPanel,
+ PDBEntry[] pdbArray,
+ SequenceI[][] seqsArray, boolean colourByChimera,
+ boolean colourBySequence, String newViewId)
{
- if (ap == null)
+ super();
+ setViewId(newViewId);
+ this.chimeraSessionFile = chimeraSessionFile;
+ openNewChimera(alignPanel, pdbArray, seqsArray);
+ if (colourByChimera)
{
- ap = nap;
+ jmb.setColourBySequence(false);
+ seqColour.setSelected(false);
+ viewerColour.setSelected(true);
}
- if (!_aps.contains(nap.av.getSequenceSetId()))
+ else if (colourBySequence)
{
- _aps.add(nap.av.getSequenceSetId());
+ jmb.setColourBySequence(true);
+ seqColour.setSelected(true);
+ viewerColour.setSelected(false);
}
}
/**
- * remove any references held to the given alignment panel
+ * create a new viewer containing several structures superimposed using the
+ * given alignPanel.
*
- * @param nap
+ * @param pe
+ * @param seqs
+ * @param ap
*/
- public void removeAlignmentPanel(AlignmentPanel nap)
- {
- try
- {
- _alignwith.remove(nap);
- _colourwith.remove(nap);
- if (ap == nap)
- {
- ap = null;
- for (AlignmentPanel aps : getAllAlignmentPanels())
- {
- if (aps != nap)
- {
- ap = aps;
- break;
- }
- }
- }
- } catch (Exception ex)
- {
- }
- if (ap != null)
- {
- buildChimeraActionMenu();
- }
- }
-
- public void useAlignmentPanelForSuperposition(AlignmentPanel nap)
- {
- addAlignmentPanel(nap);
- if (!_alignwith.contains(nap))
- {
- _alignwith.add(nap);
- }
- }
-
- public void excludeAlignmentPanelForSuperposition(AlignmentPanel nap)
+ public ChimeraViewFrame(PDBEntry[] pe, SequenceI[][] seqs,
+ AlignmentPanel ap)
{
- if (_alignwith.contains(nap))
- {
- _alignwith.remove(nap);
- }
+ super();
+ openNewChimera(ap, pe, seqs);
}
- public void useAlignmentPanelForColourbyseq(AlignmentPanel nap,
- boolean enableColourBySeq)
+ public ChimeraViewFrame(Map<PDBEntry, List<SequenceI>> toView,
+ AlignmentPanel alignPanel)
{
- useAlignmentPanelForColourbyseq(nap);
- jmb.setColourBySequence(enableColourBySeq);
- seqColour.setSelected(enableColourBySeq);
- viewerColour.setSelected(!enableColourBySeq);
- }
+ super();
- public void useAlignmentPanelForColourbyseq(AlignmentPanel nap)
- {
- addAlignmentPanel(nap);
- if (!_colourwith.contains(nap))
+ /*
+ * 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++)
{
- _colourwith.add(nap);
+ final List<SequenceI> seqsForPdb = toView.get(pdbs[i]);
+ seqsForPdbs[i] = seqsForPdb.toArray(new SequenceI[seqsForPdb.size()]);
}
- }
- public void excludeAlignmentPanelForColourbyseq(AlignmentPanel nap)
- {
- if (_colourwith.contains(nap))
- {
- _colourwith.remove(nap);
- }
+ openNewChimera(alignPanel, pdbs, seqsForPdbs);
}
/**
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;
}
{
if (frame instanceof ChimeraViewFrame)
{
- if (((ChimeraViewFrame) frame).isLinkedWith(apanel))
+ if (((StructureViewerBase) frame).isLinkedWith(apanel))
{
result.add((ChimeraViewFrame) frame);
}
return result;
}
- void initChimera(String command)
+ /**
+ * Launch Chimera. If we have a chimera session file name, send Chimera the
+ * command to open its saved session file.
+ */
+ void initChimera()
{
jmb.setFinishedInit(false);
- // TODO: consider waiting until the structure/view is fully loaded before
- // displaying
- jalview.gui.Desktop.addInternalFrame(this, jmb.getViewerTitle(true),
+ jalview.gui.Desktop.addInternalFrame(this, jmb.getViewerTitle("Chimera", true),
getBounds().width, getBounds().height);
- if (command == null)
+
+ 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)
{
- command = "";
+ boolean opened = jmb.openSession(chimeraSessionFile);
+ if (!opened)
+ {
+ System.err
+ .println("An error occurred opening Chimera session file "
+ + chimeraSessionFile);
+ }
}
- jmb.evalStateCommand(command, false);
jmb.setFinishedInit(true);
+
+ 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);
}
/**
* Close down this instance of Jalview's Chimera viewer, giving the user the
* option to close the associated Chimera window (process). They may wish to
* keep it open until they have had an opportunity to save any work.
+ *
+ * @param closeChimera
+ * if true, close any linked Chimera process; if false, prompt first
*/
- public void closeViewer()
+ public void closeViewer(boolean closeChimera)
{
if (jmb.isChimeraRunning())
{
- String prompt = MessageManager
- .formatMessage("label.confirm_close_chimera", new Object[]
- { jmb.getViewerTitle(false) });
- prompt = JvSwingUtils.wrapTooltip(true, prompt);
- int confirm = JOptionPane.showConfirmDialog(this, prompt,
- MessageManager.getString("label.close_viewer"),
- JOptionPane.YES_NO_OPTION);
- jmb.closeViewer(confirm == JOptionPane.YES_OPTION);
+ if (!closeChimera)
+ {
+ String prompt = MessageManager.formatMessage(
+ "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.YES_NO_OPTION);
+ closeChimera = confirm == JOptionPane.YES_OPTION;
+ }
+ jmb.closeViewer(closeChimera);
}
- ap = null;
+ setAlignmentPanel(null);
_aps.clear();
_alignwith.clear();
_colourwith.clear();
String[] curfiles = jmb.getPdbFile(); // files currently in viewer
// TODO: replace with reference fetching/transfer code (validate PDBentry
// as a DBRef?)
- for (int pi = 0; pi < jmb.pdbentry.length; pi++)
+ for (int pi = 0; pi < jmb.getPdbCount(); pi++)
{
String file = null;
- thePdbEntry = jmb.pdbentry[pi];
+ thePdbEntry = jmb.getPdbEntry(pi);
if (thePdbEntry.getFile() == null)
{
/*
{
try
{
- initChimera("");
+ initChimera();
} catch (Exception ex)
{
Cache.log.error("Couldn't open Chimera viewer!", ex);
try
{
int pos = filePDBpos.get(num).intValue();
+ long startTime = startProgressBar("Chimera "
+ + MessageManager.getString("status.opening_file"));
jmb.openFile(pe);
- jmb.addSequence(pos, jmb.sequence[pos]);
+ jmb.addSequence(pos, jmb.getSequence()[pos]);
File fl = new File(pe.getFile());
String protocol = AppletFormatAdapter.URL;
try
}
} catch (Throwable e)
{
+ } finally
+ {
+ stopProgressBar("", startTime);
}
// Explicitly map to the filename used by Chimera ;
- // TODO: use pe.getId() instead of pe.getFile() ?
- jmb.ssm.setMapping(jmb.sequence[pos], null, pe.getFile(),
+ 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 = pdbid.hashCode() - System.currentTimeMillis();
- if (progressBar != null)
- {
- progressBar.setProgressBar(MessageManager.formatMessage(
- "status.fetching_pdb", new Object[]
- { pdbid }), hdl);
- }
+ 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
{
- if (progressBar != null)
- {
- progressBar.setProgressBar(
- MessageManager.getString("label.state_completed"), hdl);
- }
+ msg = pdbid + " "
+ + MessageManager.getString("label.state_completed");
+ getAlignmentPanel().alignFrame.setProgressBar(msg, handle);
+ // stopProgressBar(msg, hdl);
}
/*
* If PDB data were saved and are not invalid (empty alignment), return the
if (pdbseq != null && pdbseq.getHeight() > 0)
{
// just use the file name from the first sequence's first PDBEntry
- filePath = new File(((PDBEntry) pdbseq.getSequenceAt(0).getPDBId()
- .elementAt(0)).getFile()).getAbsolutePath();
+ filePath = new File(pdbseq.getSequenceAt(0).getPDBId()
+ .elementAt(0).getFile()).getAbsolutePath();
processingEntry.setFile(filePath);
}
return filePath;
}
+ /**
+ * Convenience method to update the progress bar if there is one. Be sure to
+ * call stopProgressBar with the returned handle to remove the message.
+ *
+ * @param msg
+ * @param handle
+ */
+ public long startProgressBar(String msg)
+ {
+ // TODO would rather have startProgress/stopProgress as the
+ // IProgressIndicator interface
+ long tm = random.nextLong();
+ if (progressBar != null)
+ {
+ progressBar.setProgressBar(msg, tm);
+ }
+ 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)
+ {
+ progressBar.setProgressBar(msg, handle);
+ }
+ }
+
@Override
public void pdbFile_actionPerformed(ActionEvent actionEvent)
{
jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
try
{
- for (int pdbe = 0; pdbe < jmb.pdbentry.length; pdbe++)
- {
- cap.appendText(jmb.printMapping(jmb.pdbentry[pdbe].getFile()));
- cap.appendText("\n");
- }
+ cap.appendText(jmb.printMappings());
} catch (OutOfMemoryError e)
{
new OOMWarning(
{
if (!jmb.isLoadingFromArchive())
{
- if (_colourwith.size() == 0 && ap != null)
+ if (_colourwith.size() == 0 && getAlignmentPanel() != null)
{
// Make the currently displayed alignment panel the associated view
- _colourwith.add(ap.alignFrame.alignPanel);
+ _colourwith.add(getAlignmentPanel().alignFrame.alignPanel);
}
}
// Set the colour using the current view for the associated alignframe
for (AlignmentPanel ap : _colourwith)
{
- jmb.colourBySequence(ap.av.showSequenceFeatures, ap);
+ jmb.colourBySequence(ap.av.isShowSequenceFeatures(), ap);
}
}
}
}
}
- public String getViewId()
- {
- if (viewId == null)
- {
- viewId = System.currentTimeMillis() + "." + this.hashCode();
- }
- return viewId;
- }
-
public void updateTitleAndMenus()
{
if (jmb.fileLoadingError != null && jmb.fileLoadingError.length() > 0)
repaint();
return;
}
- setChainMenuItems(jmb.chainNames);
+ setChainMenuItems(jmb.getChainNames());
- this.setTitle(jmb.getViewerTitle(true));
- if (jmb.getPdbFile().length > 1 && jmb.sequence.length > 1)
+ this.setTitle(jmb.getViewerTitle("Chimera", true));
+ if (jmb.getPdbFile().length > 1 && jmb.getSequence().length > 1)
{
viewerActionMenu.setVisible(true);
}
}
}
- protected void buildChimeraActionMenu()
- {
- if (_alignwith == null)
- {
- _alignwith = new Vector<AlignmentPanel>();
- }
- if (_alignwith.size() == 0 && ap != null)
- {
- _alignwith.add(ap);
- }
- ;
- for (Component c : viewerActionMenu.getMenuComponents())
- {
- if (c != alignStructs)
- {
- viewerActionMenu.remove((JMenuItem) c);
- }
- }
- }
-
/*
* (non-Javadoc)
*
private void alignStructs_withAllAlignPanels()
{
- if (ap == null)
+ if (getAlignmentPanel() == null)
{
return;
}
- ;
+
if (_alignwith.size() == 0)
{
- _alignwith.add(ap);
+ _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)
return ap;
}
}
- return ap;
- }
-
- /**
- *
- * @param ap2
- * @return true if this Chimera instance is linked with the given alignPanel
- */
- public boolean isLinkedWith(AlignmentPanel ap2)
- {
- return _aps.contains(ap2.av.getSequenceSetId());
+ return getAlignmentPanel();
}
- public boolean isUsedforaligment(AlignmentPanel ap2)
+ @Override
+ public AAStructureBindingModel getBinding()
{
-
- return (_alignwith != null) && _alignwith.contains(ap2);
+ return jmb;
}
- public boolean isUsedforcolourby(AlignmentPanel ap2)
+ /**
+ * 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
+ */
+ protected String saveSession(String filepath)
{
- return (_colourwith != null) && _colourwith.contains(ap2);
+ 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)
+ {
+ }
+ return null;
}
/**
- *
- * @return TRUE if the view is NOT being coloured by sequence associations.
+ * 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.
*/
- public boolean isColouredByChimera()
+ @Override
+ public String getStateInfo()
{
- return !jmb.isColourBySequence();
+ 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;
}
- public SequenceStructureBinding getBinding()
+ @Override
+ protected void fitToWindow_actionPerformed()
{
- return jmb;
+ jmb.focusView();
}
+ @Override
+ public ViewerType getViewerType()
+ {
+ return ViewerType.CHIMERA;
+ }
}