/*
- * 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 2.9)
+ * Copyright (C) 2015 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.ext.rbvi.chimera.JalviewChimeraBinding;
+import jalview.gui.StructureViewer.ViewerType;
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.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.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.Enumeration;
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.MenuListener;
/**
- * 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
{
- JalviewChimeraBindingModel jmb;
+ private JalviewChimeraBinding jmb;
- AlignmentPanel ap;
+ private boolean allChainsSelected = false;
- Vector atomsPicked = new Vector();
+ private IProgressIndicator progressBar = null;
- private boolean addingStructures = false;
+ /*
+ * 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;
- ViewSelectionMenu seqColourBy;
+ private Random random = new Random();
/**
- *
- * @param files
- * @param ids
- * @param seqs
- * @param ap
- * @param usetoColour
- * - add the alignment panel to the list used for colouring these
- * structures
- * @param useToAlign
- * - add the alignment panel to the list used for aligning these
- * structures
- * @param leaveColouringToJmol
- * - do not update the colours from any other source. Jmol is
- * handling them
- * @param loadStatus
- * @param bounds
- * @param viewid
- *
- * public ChimeraViewFrame(String[] files, String[] ids,
- * SequenceI[][] seqs, AlignmentPanel ap, boolean usetoColour,
- * boolean useToAlign, boolean leaveColouringToJmol, String
- * loadStatus, Rectangle bounds, String viewid) { PDBEntry[]
- * pdbentrys = new PDBEntry[files.length]; for (int i = 0; i <
- * pdbentrys.length; i++) { PDBEntry pdbentry = new PDBEntry();
- * pdbentry.setFile(files[i]); pdbentry.setId(ids[i]); pdbentrys[i] =
- * pdbentry; } // / TODO: check if protocol is needed to be set, and
- * if chains are // autodiscovered. jmb = new
- * JalviewChimeraBindingModel(this,
- * ap.getStructureSelectionManager(), pdbentrys, seqs, null, null);
- *
- * jmb.setLoadingFromArchive(true); addAlignmentPanel(ap); if
- * (useToAlign) { useAlignmentPanelForSuperposition(ap); } if
- * (leaveColouringToJmol || !usetoColour) {
- * jmb.setColourBySequence(false); seqColour.setSelected(false);
- * jmolColour.setSelected(true); } if (usetoColour) {
- * useAlignmentPanelForColourbyseq(ap);
- * jmb.setColourBySequence(true); seqColour.setSelected(true);
- * jmolColour.setSelected(false); } this.setBounds(bounds);
- * initMenus(); viewId = viewid; //
- * jalview.gui.Desktop.addInternalFrame(this, "Loading File", //
- * bounds.width,bounds.height);
- *
- * this.addInternalFrameListener(new InternalFrameAdapter() { public
- * void internalFrameClosing(InternalFrameEvent internalFrameEvent) {
- * closeViewer(); } }); initJmol(loadStatus); // pdbentry, seq,
- * JBPCHECK!
- *
- * }
+ * Initialise menu options.
*/
private void initMenus()
{
+ viewerActionMenu.setText(MessageManager.getString("label.chimera"));
+ viewerColour.setText(MessageManager
+ .getString("label.colour_with_chimera"));
+ viewerColour.setToolTipText(MessageManager
+ .getString("label.let_chimera_manage_structure_colours"));
+ helpItem.setText(MessageManager.getString("label.chimera_help"));
seqColour.setSelected(jmb.isColourBySequence());
- jmolColour.setSelected(!jmb.isColourBySequence());
+ viewerColour.setSelected(!jmb.isColourBySequence());
if (_colourwith == null)
{
_colourwith = new Vector<AlignmentPanel>();
_alignwith = new Vector<AlignmentPanel>();
}
- seqColourBy = new ViewSelectionMenu("Colour by ..", this, _colourwith,
+ // save As not yet implemented
+ savemenu.setVisible(false);
+
+ ViewSelectionMenu seqColourBy = new ViewSelectionMenu(
+ MessageManager.getString("label.colour_by"), this, _colourwith,
new ItemListener()
{
-
@Override
public void itemStateChanged(ItemEvent e)
{
}
else
{
- // update the jmol display now.
+ // update the Chimera display now.
seqColour_actionPerformed(null);
}
}
});
viewMenu.add(seqColourBy);
+ viewMenu.add(fitToWindow);
+
final ItemListener handler;
- JMenu alpanels = new ViewSelectionMenu("Superpose with ..", this,
+ JMenu alpanels = new ViewSelectionMenu(
+ MessageManager.getString("label.superpose_with"), this,
_alignwith, handler = new ItemListener()
{
-
@Override
public void itemStateChanged(ItemEvent e)
{
alignStructs.setToolTipText(MessageManager
.formatMessage(
"label.align_structures_using_linked_alignment_views",
- new String[]
- { new Integer(_alignwith.size()).toString() }));
+ new Object[] { new Integer(_alignwith
+ .size()).toString() }));
}
});
handler.itemStateChanged(null);
- jmolActionMenu.add(alpanels);
- jmolActionMenu.addMenuListener(new MenuListener()
+ viewerActionMenu.add(alpanels);
+ viewerActionMenu.addMenuListener(new MenuListener()
{
@Override
public void menuDeselected(MenuEvent e)
{
// TODO Auto-generated method stub
-
}
@Override
public void menuCanceled(MenuEvent e)
{
// TODO Auto-generated method stub
-
}
});
}
- IProgressIndicator progressBar = null;
-
/**
- * add a single PDB structure to a new or existing Jmol view
+ * add a single PDB structure to a new or existing Chimera view
*
* @param pdbentry
* @param seq
public ChimeraViewFrame(PDBEntry pdbentry, SequenceI[] seq,
String[] chains, final AlignmentPanel ap)
{
- progressBar = ap.alignFrame;
- // ////////////////////////////////
- // Is the pdb file already loaded?
- String alreadyMapped = ap.getStructureSelectionManager()
- .alreadyMappedToFile(pdbentry.getId());
-
- if (alreadyMapped != null)
+ super();
+ String pdbId = pdbentry.getId();
+
+ /*
+ * 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_OPTION);
-
- 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);
- }
+ return;
+ }
- // Now this AppJmol is mapped to new sequences. We must add them to
- // the exisiting array
- JInternalFrame[] frames = Desktop.instance.getAllFrames();
+ /*
+ * 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 (addToExistingViewer(pdbentry, seq, chains, ap, pdbId))
+ {
+ return;
+ }
- for (int i = 0; i < frames.length; i++)
- {
- if (frames[i] instanceof ChimeraViewFrame)
- {
- final ChimeraViewFrame topJmol = ((ChimeraViewFrame) frames[i]);
- // JBPNOTE: this looks like a binding routine, rather than a gui
- // routine
- for (int pe = 0; pe < topJmol.jmb.pdbentry.length; pe++)
- {
- if (topJmol.jmb.pdbentry[pe].getFile().equals(alreadyMapped))
- {
- topJmol.jmb.addSequence(pe, seq);
- topJmol.addAlignmentPanel(ap);
- // add it to the set used for colouring
- topJmol.useAlignmentPanelForColourbyseq(ap);
- topJmol.buildChimeraActionMenu();
- ap.getStructureSelectionManager()
- .sequenceColoursChanged(ap);
- break;
- }
- }
- }
- }
+ /*
+ * If the options above are declined or do not apply, show the structure in
+ * a new viewer
+ */
+ openNewChimera(ap, new PDBEntry[] { pdbentry },
+ new SequenceI[][] { seq });
+ }
- return;
- }
- }
- // /////////////////////////////////
- // Check if there are other Jmol views involving this alignment
- // and prompt user about adding this molecule to one of them
- Vector existingViews = getJmolsFor(ap);
- if (existingViews.size() > 0)
+ /**
+ * Create a helper to manage progress bar display
+ */
+ protected void createProgressBar()
+ {
+ if (progressBar == null)
{
- Enumeration jm = existingViews.elements();
- while (jm.hasMoreElements())
- {
- ChimeraViewFrame topJmol = (ChimeraViewFrame) jm.nextElement();
- // 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_OPTION);
- if (option == JOptionPane.YES_OPTION)
- {
- topJmol.useAlignmentPanelForSuperposition(ap);
- topJmol.addStructure(pdbentry, seq, chains, true, ap.alignFrame);
- return;
- }
- }
+ progressBar = new ProgressBar(statusPanel, statusBar);
}
- // /////////////////////////////////
- openNewJmol(ap, new PDBEntry[]
- { pdbentry }, new SequenceI[][]
- { seq });
}
- private void openNewJmol(AlignmentPanel ap, PDBEntry[] pdbentrys,
+ /**
+ * Answers true if this viewer already involves the given PDB ID
+ */
+ @Override
+ 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 Jmol 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)
{
- openNewJmol(ap, pe, seqs);
- }
-
- /**
- * list of sequenceSet ids associated with the view
- */
- ArrayList<String> _aps = new ArrayList();
-
- 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()
+ .getAllPDBEntries();
+ if (pdbrefs != null && pdbrefs.size() > 0)
+ {
+ chain = pdbrefs.get(0).getChainCode();
+ }
+ }
+ chains[i][seqno++] = chain;
}
}
-
- return list;
+ return chains;
}
/**
- * list of alignment panels to use for superposition
- */
- Vector<AlignmentPanel> _alignwith = new Vector<AlignmentPanel>();
-
- /**
- * list of alignment panels that are used for colouring structures by aligned
- * sequences
- */
- Vector<AlignmentPanel> _colourwith = new Vector<AlignmentPanel>();
-
- /**
- * 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)
+ public ChimeraViewFrame(PDBEntry[] pe, SequenceI[][] seqs,
+ AlignmentPanel ap)
{
- 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);
- }
+ super();
+ openNewChimera(ap, pe, seqs);
}
- public void excludeAlignmentPanelForSuperposition(AlignmentPanel nap)
+ public ChimeraViewFrame(Map<PDBEntry, List<SequenceI>> toView,
+ AlignmentPanel alignPanel)
{
- if (_alignwith.contains(nap))
+ 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++)
{
- _alignwith.remove(nap);
+ final List<SequenceI> seqsForPdb = toView.get(pdbs[i]);
+ seqsForPdbs[i] = seqsForPdb.toArray(new SequenceI[seqsForPdb.size()]);
}
- }
- public void useAlignmentPanelForColourbyseq(AlignmentPanel nap,
- boolean enableColourBySeq)
- {
- useAlignmentPanelForColourbyseq(nap);
- jmb.setColourBySequence(enableColourBySeq);
- seqColour.setSelected(enableColourBySeq);
- jmolColour.setSelected(!enableColourBySeq);
- }
-
- public void useAlignmentPanelForColourbyseq(AlignmentPanel nap)
- {
- addAlignmentPanel(nap);
- if (!_colourwith.contains(nap))
- {
- _colourwith.add(nap);
- }
- }
-
- public void excludeAlignmentPanelForColourbyseq(AlignmentPanel nap)
- {
- if (_colourwith.contains(nap))
- {
- _colourwith.remove(nap);
- }
+ openNewChimera(alignPanel, pdbs, seqsForPdbs);
}
/**
- * pdb retrieval thread.
+ * 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 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 getJmolsFor(AlignmentPanel ap2)
+ @Override
+ protected List<StructureViewerBase> getViewersFor(AlignmentPanel ap)
{
- Vector otherJmols = new Vector();
- // Now this AppJmol is mapped to new sequences. We must add them to
- // the exisiting array
+ List<StructureViewerBase> result = new ArrayList<StructureViewerBase>();
JInternalFrame[] frames = Desktop.instance.getAllFrames();
- for (int i = 0; i < frames.length; i++)
+ for (JInternalFrame frame : frames)
{
- if (frames[i] instanceof ChimeraViewFrame)
+ if (frame instanceof ChimeraViewFrame)
{
- ChimeraViewFrame topJmol = ((ChimeraViewFrame) frames[i]);
- if (topJmol.isLinkedWith(ap2))
+ if (ap == null || ((StructureViewerBase) frame).isLinkedWith(ap))
{
- otherJmols.addElement(topJmol);
+ result.add((StructureViewerBase) frame);
}
}
}
- return otherJmols;
+ 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(),
- getBounds().width, getBounds().height);
- if (command == null)
+ jalview.gui.Desktop.addInternalFrame(this,
+ jmb.getViewerTitle("Chimera", true), getBounds().width,
+ getBounds().height);
+
+ 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);
jmb.setFinishedInit(true);
+
+ jmb.startChimeraListener();
}
- void setChainMenuItems(Vector chains)
+ /**
+ * 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 (chains == null)
+ if (chainNames == null || chainNames.isEmpty())
{
return;
}
for (int i = 0; i < chainMenu.getItemCount(); i++)
{
if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
+ {
((JCheckBoxMenuItem) chainMenu.getItem(i)).setSelected(true);
+ }
}
- centerViewer();
+ showSelectedChains();
allChainsSelected = false;
}
});
chainMenu.add(menuItem);
- for (int c = 0; c < chains.size(); c++)
+ for (String chainName : chainNames)
{
- menuItem = new JCheckBoxMenuItem(chains.elementAt(c).toString(), true);
+ menuItem = new JCheckBoxMenuItem(chainName, true);
menuItem.addItemListener(new ItemListener()
{
public void itemStateChanged(ItemEvent evt)
{
if (!allChainsSelected)
- centerViewer();
+ {
+ showSelectedChains();
+ }
}
});
}
}
- boolean allChainsSelected = false;
-
- private boolean alignAddedStructures = false;
-
- void centerViewer()
+ /**
+ * Show only the selected chain(s) in the viewer
+ */
+ void showSelectedChains()
{
- Vector toshow = new Vector();
- String lbl;
- int mlength, p, mnum;
+ List<String> toshow = new ArrayList<String>();
for (int i = 0; i < chainMenu.getItemCount(); i++)
{
if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
JCheckBoxMenuItem item = (JCheckBoxMenuItem) chainMenu.getItem(i);
if (item.isSelected())
{
- toshow.addElement(item.getText());
+ toshow.add(item.getText());
}
}
}
- jmb.centerViewer(toshow);
+ jmb.showChains(toshow);
}
- public void closeViewer()
+ /**
+ * 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(boolean closeChimera)
{
- jmb.closeViewer();
- ap = null;
+ if (jmb != null && jmb.isChimeraRunning())
+ {
+ 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);
+ }
+ setAlignmentPanel(null);
_aps.clear();
_alignwith.clear();
_colourwith.clear();
}
/**
- * state flag for PDB retrieval thread
+ * Open any newly added PDB structures in Chimera, having first fetched data
+ * from PDB (if not already saved).
*/
- private boolean _started = false;
-
public void run()
{
_started = true;
- String pdbid = "";
- // todo - record which pdbids were successfuly imported.
- StringBuffer errormsgs = new StringBuffer(), files = new StringBuffer();
- List<String> fileToLoad=new ArrayList<String>();
+ // todo - record which pdbids were successfully imported.
+ StringBuilder errormsgs = new StringBuilder(128);
+ StringBuilder files = new StringBuilder(128);
List<PDBEntry> filePDB = new ArrayList<PDBEntry>();
- List<Integer> filePDBpos =new ArrayList<Integer>();
+ List<Integer> filePDBpos = new ArrayList<Integer>();
+ PDBEntry thePdbEntry = null;
try
{
String[] curfiles = jmb.getPdbFile(); // files currently in viewer
// TODO: replace with reference fetching/transfer code (validate PDBentry
// as a DBRef?)
- jalview.ws.dbsources.Pdb pdbclient = new jalview.ws.dbsources.Pdb();
- for (int pi = 0; pi < jmb.pdbentry.length; pi++)
+ for (int pi = 0; pi < jmb.getPdbCount(); pi++)
{
- String file = new File(jmb.pdbentry[pi].getFile())
- .getAbsoluteFile().getPath();
- if (file == null)
+ String file = null;
+ thePdbEntry = jmb.getPdbEntry(pi);
+ if (thePdbEntry.getFile() == null)
{
- // retrieve the pdb and store it locally
- AlignmentI pdbseq = null;
- pdbid = jmb.pdbentry[pi].getId();
- long hdl = pdbid.hashCode() - System.currentTimeMillis();
- if (progressBar != null)
+ /*
+ * Retrieve PDB data, save to file, attach to PDBEntry
+ */
+ file = fetchPdbFile(thePdbEntry);
+ if (file == null)
{
- progressBar.setProgressBar("Fetching PDB " + pdbid, hdl);
- }
- try
- {
- pdbseq = pdbclient.getSequenceRecords(pdbid = jmb.pdbentry[pi]
- .getId());
- } catch (OutOfMemoryError oomerror)
- {
- new OOMWarning("Retrieving PDB id " + pdbid, oomerror);
- } catch (Exception ex)
- {
- ex.printStackTrace();
- errormsgs.append("'" + pdbid + "'");
- }
- if (progressBar != null)
- {
- progressBar.setProgressBar("Finished.", hdl);
- }
- if (pdbseq != null)
- {
- // just transfer the file name from the first sequence's first
- // PDBEntry
- file = new File(((PDBEntry) pdbseq.getSequenceAt(0).getPDBId()
- .elementAt(0)).getFile()).getAbsolutePath();
- jmb.pdbentry[pi].setFile(file);
-
- files.append(" \"" + Platform.escapeString(file) + "\"");
- }
- else
- {
- errormsgs.append("'" + pdbid + "' ");
+ errormsgs.append("'" + thePdbEntry.getId() + "' ");
}
}
else
{
+ /*
+ * Got file already - ignore if already loaded in Chimera.
+ */
+ file = new File(thePdbEntry.getFile()).getAbsoluteFile()
+ .getPath();
if (curfiles != null && curfiles.length > 0)
{
addingStructures = true; // already files loaded.
}
}
}
-
- if (file != null)
- {
- fileToLoad.add(file);
- filePDB.add(jmb.pdbentry[pi]);
- filePDBpos.add(Integer.valueOf(pi));
- files.append(" \"" + Platform.escapeString(file) + "\"");
- }
+ }
+ if (file != null)
+ {
+ filePDB.add(thePdbEntry);
+ filePDBpos.add(Integer.valueOf(pi));
+ files.append(" \"" + Platform.escapeString(file) + "\"");
}
}
} catch (OutOfMemoryError oomerror)
{
- new OOMWarning("Retrieving PDB files: " + pdbid, oomerror);
+ new OOMWarning("Retrieving PDB files: " + thePdbEntry.getId(),
+ oomerror);
} catch (Exception ex)
{
ex.printStackTrace();
- errormsgs.append("When retrieving pdbfiles : current was: '" + pdbid
- + "'");
+ errormsgs.append("When retrieving pdbfiles for '"
+ + thePdbEntry.getId() + "'");
}
if (errormsgs.length() > 0)
{
JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
.formatMessage("label.pdb_entries_couldnt_be_retrieved",
- new String[]
- { errormsgs.toString() }), MessageManager
- .getString("label.couldnt_load_file"),
+ new Object[] { errormsgs.toString() }),
+ MessageManager.getString("label.couldnt_load_file"),
JOptionPane.ERROR_MESSAGE);
-
}
- long lastnotify = jmb.getLoadNotifiesHandled();
+
if (files.length() > 0)
{
if (!addingStructures)
{
try
{
- initChimera("");
+ initChimera();
} catch (Exception ex)
{
Cache.log.error("Couldn't open Chimera viewer!", ex);
}
- }
- int num=-1;
+ }
+ int num = -1;
for (PDBEntry pe : filePDB)
{
num++;
{
try
{
- int pos=filePDBpos.get(num).intValue();
+ int pos = filePDBpos.get(num).intValue();
+ long startTime = startProgressBar("Chimera "
+ + MessageManager.getString("status.opening_file"));
jmb.openFile(pe);
- jmb.addSequence(pos, jmb.sequence[pos]);
- File fl=new File(pe.getFile());
+ jmb.addSequence(pos, jmb.getSequence()[pos]);
+ File fl = new File(pe.getFile());
String protocol = AppletFormatAdapter.URL;
try
{
if (fl.exists())
- {
- protocol = AppletFormatAdapter.FILE;
- }
- } catch (Exception e)
- {
- } catch (Error e)
{
+ protocol = AppletFormatAdapter.FILE;
}
- // Explicitly map to the filename used by Jmol ;
- jmb.ssm.setMapping(jmb.sequence[pos], null, pe.getFile(),
- protocol);
- // pdbentry[pe].getFile(), protocol);
+ } catch (Throwable e)
+ {
+ } finally
+ {
+ stopProgressBar("", startTime);
+ }
+ // Explicitly map to the filename used by Chimera ;
+ jmb.getSsm().setMapping(jmb.getSequence()[pos],
+ jmb.getChains()[pos], pe.getFile(), protocol);
} catch (OutOfMemoryError oomerror)
{
new OOMWarning(
}
}
}
- // jmb.getPdbFile();
jmb.setFinishedInit(true);
jmb.setLoadingFromArchive(false);
-
+
// refresh the sequence colours for the new structure(s)
for (AlignmentPanel ap : _colourwith)
{
jmb.updateColours(ap);
}
// do superposition if asked to
- if (alignAddedStructures)
+ if (Cache.getDefault("AUTOSUPERIMPOSE", true) && alignAddedStructures)
{
- javax.swing.SwingUtilities.invokeLater(new Runnable()
+ new Thread(new Runnable()
{
public void run()
{
alignStructs_withAllAlignPanels();
}
- });
+ }).start();
alignAddedStructures = false;
}
addingStructures = false;
worker = null;
}
+ /**
+ * Fetch PDB data and save to a local file. Returns the full path to the file,
+ * or null if fetch fails.
+ *
+ * @param processingEntry
+ * @return
+ * @throws Exception
+ */
+ private String fetchPdbFile(PDBEntry processingEntry) throws Exception
+ {
+ String filePath = null;
+ Pdb pdbclient = new Pdb();
+ AlignmentI pdbseq = null;
+ String pdbid = processingEntry.getId();
+ 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);
+ } catch (OutOfMemoryError oomerror)
+ {
+ new OOMWarning("Retrieving PDB id " + pdbid, oomerror);
+ } finally
+ {
+ 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
+ * file path.
+ */
+ if (pdbseq != null && pdbseq.getHeight() > 0)
+ {
+ // just use the file name from the first sequence's first PDBEntry
+ filePath = new File(pdbseq.getSequenceAt(0).getAllPDBEntries()
+ .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)
{
JalviewFileChooser chooser = new JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle("Save PDB File");
+ 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
- BufferedReader in = new BufferedReader(new FileReader(
- jmb.getPdbFile()[0]));
+ in = new BufferedReader(new FileReader(jmb.getPdbFile()[0]));
File outFile = chooser.getSelectedFile();
PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
} catch (Exception ex)
{
ex.printStackTrace();
+ } finally
+ {
+ if (in != null)
+ {
+ try
+ {
+ in.close();
+ } catch (IOException e)
+ {
+ e.printStackTrace();
+ }
+ }
}
}
}
+ @Override
public void viewMapping_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(
600);
}
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
+ @Override
public void eps_actionPerformed(ActionEvent e)
{
- throw new Error("EPS Generation not yet implemented.");
+ throw new Error(
+ MessageManager
+ .getString("error.eps_generation_not_implemented"));
}
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
+ @Override
public void png_actionPerformed(ActionEvent e)
{
- throw new Error("PNG Generation not yet implemented.");
+ throw new Error(
+ MessageManager
+ .getString("error.png_generation_not_implemented"));
}
- public void jmolColour_actionPerformed(ActionEvent actionEvent)
+ @Override
+ public void viewerColour_actionPerformed(ActionEvent actionEvent)
{
- if (jmolColour.isSelected())
+ if (viewerColour.isSelected())
{
// disable automatic sequence colouring.
jmb.setColourBySequence(false);
}
}
+ @Override
public void seqColour_actionPerformed(ActionEvent actionEvent)
{
jmb.setColourBySequence(seqColour.isSelected());
{
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);
}
}
}
+ @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,
- "Select Background Colour", null);
+ java.awt.Color col = JColorChooser
+ .showDialog(this, MessageManager
+ .getString("label.select_backgroud_colour"), null);
if (col != null)
{
jmb.setBackgroundColour(col);
}
}
- public void jmolHelp_actionPerformed(ActionEvent actionEvent)
+ @Override
+ public void showHelp_actionPerformed(ActionEvent actionEvent)
{
try
{
}
}
- String viewId = null;
-
- 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());
- if (jmb.getPdbFile().length > 1 && jmb.sequence.length > 1)
+ this.setTitle(jmb.getViewerTitle("Chimera", true));
+ if (jmb.getPdbFile().length > 1 && jmb.getSequence().length > 1)
{
- jmolActionMenu.setVisible(true);
+ viewerActionMenu.setVisible(true);
}
if (!jmb.isLoadingFromArchive())
{
}
}
- protected void buildChimeraActionMenu()
- {
- if (_alignwith == null)
- {
- _alignwith = new Vector<AlignmentPanel>();
- }
- if (_alignwith.size() == 0 && ap != null)
- {
- _alignwith.add(ap);
- }
- ;
- for (Component c : jmolActionMenu.getMenuComponents())
- {
- if (c != alignStructs)
- {
- jmolActionMenu.remove((JMenuItem) c);
- }
- }
- final ItemListener handler;
- }
-
/*
* (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;
+ return getAlignmentPanel();
+ }
+
+ @Override
+ public AAStructureBindingModel getBinding()
+ {
+ return jmb;
}
/**
+ * 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 ap2
- * @return true if this Jmol instance is linked with the given alignPanel
+ * @param filepath
+ * @see getStateInfo
*/
- public boolean isLinkedWith(AlignmentPanel ap2)
+ protected String saveSession(String filepath)
{
- return _aps.contains(ap2.av.getSequenceSetId());
+ 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;
}
- public boolean isUsedforaligment(AlignmentPanel ap2)
+ /**
+ * 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 (_alignwith != null) && _alignwith.contains(ap2);
+ 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
+ }
+ }
+ }
}
- public boolean isUsedforcolourby(AlignmentPanel ap2)
+ @Override
+ protected void fitToWindow_actionPerformed()
{
- return (_colourwith != null) && _colourwith.contains(ap2);
+ jmb.focusView();
}
- /**
- *
- * @return TRUE if the view is NOT being coloured by sequence associations.
- */
- public boolean isColouredByJmol()
+ @Override
+ public ViewerType getViewerType()
{
- return !jmb.isColourBySequence();
+ return ViewerType.CHIMERA;
}
- public SequenceStructureBinding getBinding()
+ @Override
+ protected AAStructureBindingModel getBindingModel()
{
return jmb;
}
-
}
git://source.jalview.org / jalview.git / blobdiff