X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FChimeraViewFrame.java;h=2339636d13a8c8698b04a4a823c6cc4495a8e44f;hb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;hp=a89af2c56c2992d0cd16add3f333c48da63e2121;hpb=a7ea1ba47dae32481aa6390a29cef6c7c5a403c4;p=jalview.git diff --git a/src/jalview/gui/ChimeraViewFrame.java b/src/jalview/gui/ChimeraViewFrame.java index a89af2c..2339636 100644 --- a/src/jalview/gui/ChimeraViewFrame.java +++ b/src/jalview/gui/ChimeraViewFrame.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) - * Copyright (C) $$Year-Rel$$ The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1) + * Copyright (C) 2015 The Jalview Authors * * This file is part of Jalview. * @@ -20,19 +20,48 @@ */ 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 java.util.Map; import java.util.Random; +import java.util.Set; import java.util.Vector; import javax.swing.JCheckBoxMenuItem; @@ -46,32 +75,8 @@ import javax.swing.event.InternalFrameEvent; 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 handlnig an external chimera display + * GUI elements for handling an external chimera display * * @author jprocter * @@ -82,23 +87,9 @@ public class ChimeraViewFrame extends StructureViewerBase 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). @@ -151,6 +142,8 @@ public class ChimeraViewFrame extends StructureViewerBase } }); viewMenu.add(seqColourBy); + viewMenu.add(fitToWindow); + final ItemListener handler; JMenu alpanels = new ViewSelectionMenu( MessageManager.getString("label.superpose_with"), this, @@ -163,8 +156,8 @@ public class ChimeraViewFrame extends StructureViewerBase 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); @@ -204,107 +197,32 @@ public class ChimeraViewFrame extends StructureViewerBase String[] chains, final AlignmentPanel ap) { super(); - progressBar = ap.alignFrame; - // //////////////////////////////// - // Is the pdb file already loaded? - String alreadyMapped = ap.getStructureSelectionManager() - .alreadyMappedToFile(pdbentry.getId()); + String pdbId = pdbentry.getId(); - if (alreadyMapped != null) + /* + * If the PDB file is already loaded, the user may just choose to add to an + * existing viewer (or cancel) + */ + if (addAlreadyLoadedFile(seq, chains, ap, pdbId)) { - int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop, - MessageManager.formatMessage( - "label.pdb_entry_is_already_displayed", new Object[] - { pdbentry.getId() }), MessageManager.formatMessage( - "label.map_sequences_to_visible_window", new Object[] - { pdbentry.getId() }), - JOptionPane.YES_NO_CANCEL_OPTION); - - if (option == JOptionPane.CANCEL_OPTION) - { - return; - } - if (option == JOptionPane.YES_OPTION) - { - // TODO : Fix multiple seq to one chain issue here. - ap.getStructureSelectionManager().setMapping(seq, chains, - alreadyMapped, AppletFormatAdapter.FILE); - if (ap.getSeqPanel().seqCanvas.fr != null) - { - ap.getSeqPanel().seqCanvas.fr.featuresAdded(); - ap.paintAlignment(true); - } - - // Now this 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; - } - } - } - } - - return; - } + return; } - // ///////////////////////////////// - // Check if there are other Chimera views involving this alignment - // and prompt user about adding this molecule to one of them - List existingViews = getChimeraWindowsFor(ap); - for (ChimeraViewFrame topView : existingViews) + + /* + * 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)) { - // TODO: highlight topView in 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())) - { - 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); - if (option == JOptionPane.CANCEL_OPTION) - { - return; - } - if (option == JOptionPane.YES_OPTION) - { - topView.useAlignmentPanelForSuperposition(ap); - topView.addStructure(pdbentry, seq, chains, true, ap.alignFrame); - return; - } + return; } - // ///////////////////////////////// - openNewChimera(ap, new PDBEntry[] - { pdbentry }, new SequenceI[][] - { seq }); + + /* + * 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 }); } /** @@ -318,6 +236,10 @@ public class ChimeraViewFrame extends StructureViewerBase } } + /** + * Answers true if this viewer already involves the given PDB ID + */ + @Override protected boolean hasPdbId(String pdbId) { return jmb.hasPdbId(pdbId); @@ -327,7 +249,6 @@ public class ChimeraViewFrame extends StructureViewerBase SequenceI[][] seqs) { createProgressBar(); - String[][] chains = extractChains(seqs); jmb = new JalviewChimeraBindingModel(this, ap.getStructureSelectionManager(), pdbentrys, seqs, chains, @@ -377,7 +298,8 @@ public class ChimeraViewFrame extends StructureViewerBase String chain = null; if (seq.getDatasetSequence() != null) { - Vector pdbrefs = seq.getDatasetSequence().getPDBId(); + Vector pdbrefs = seq.getDatasetSequence() + .getAllPDBEntries(); if (pdbrefs != null && pdbrefs.size() > 0) { chain = pdbrefs.get(0).getChainCode(); @@ -390,39 +312,25 @@ public class ChimeraViewFrame extends StructureViewerBase } /** - * 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, - 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) { @@ -439,73 +347,60 @@ public class ChimeraViewFrame extends StructureViewerBase } /** - * add a new structure (with associated sequences and chains) to this viewer, - * retrieving it if necessary first. + * create a new viewer containing several structures superimposed using the + * given alignPanel. * - * @param pdbentry - * @param seq - * @param chains - * @param alignFrame - * @param align - * if true, new structure(s) will be align using associated alignment + * @param pe + * @param seqs + * @param ap */ - private void addStructure(final PDBEntry pdbentry, final SequenceI[] seq, - final String[] chains, final boolean b, - final IProgressIndicator alignFrame) + public ChimeraViewFrame(PDBEntry[] pe, SequenceI[][] seqs, + AlignmentPanel ap) { - 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)); + super(); + openNewChimera(ap, pe, seqs); + } - } catch (Exception e) - { - } + public ChimeraViewFrame(Map> toView, + AlignmentPanel alignPanel) + { + super(); - } - // and call ourselves again. - addStructure(pdbentry, seq, chains, b, alignFrame); - } - }).start(); - return; - } + /* + * 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 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 seqsForPdb = toView.get(pdbs[i]); + seqsForPdbs[i] = seqsForPdb.toArray(new SequenceI[seqsForPdb.size()]); } - // 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; + + openNewChimera(alignPanel, pdbs, seqsForPdbs); } - private List getChimeraWindowsFor(AlignmentPanel apanel) + /** + * 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. + */ + @Override + protected List getViewersFor(AlignmentPanel ap) { - List result = new ArrayList(); + List result = new ArrayList(); 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); } } } @@ -519,13 +414,19 @@ public class ChimeraViewFrame extends StructureViewerBase 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); - /* - * 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) { @@ -542,10 +443,16 @@ public class ChimeraViewFrame extends StructureViewerBase 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 chainNames) { chainMenu.removeAll(); - if (chainNames == null) + if (chainNames == null || chainNames.isEmpty()) { return; } @@ -563,7 +470,7 @@ public class ChimeraViewFrame extends StructureViewerBase ((JCheckBoxMenuItem) chainMenu.getItem(i)).setSelected(true); } } - centerViewer(); + showSelectedChains(); allChainsSelected = false; } }); @@ -579,7 +486,7 @@ public class ChimeraViewFrame extends StructureViewerBase { if (!allChainsSelected) { - centerViewer(); + showSelectedChains(); } } }); @@ -588,7 +495,10 @@ public class ChimeraViewFrame extends StructureViewerBase } } - void centerViewer() + /** + * Show only the selected chain(s) in the viewer + */ + void showSelectedChains() { List toshow = new ArrayList(); for (int i = 0; i < chainMenu.getItemCount(); i++) @@ -602,7 +512,7 @@ public class ChimeraViewFrame extends StructureViewerBase } } } - jmb.centerViewer(toshow); + jmb.showChains(toshow); } /** @@ -615,13 +525,13 @@ public class ChimeraViewFrame extends StructureViewerBase */ 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"), @@ -714,9 +624,8 @@ public class ChimeraViewFrame extends StructureViewerBase 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); } @@ -760,10 +669,8 @@ public class ChimeraViewFrame extends StructureViewerBase 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, - pe.getFile(), - protocol); + jmb.getSsm().setMapping(jmb.getSequence()[pos], + jmb.getChains()[pos], pe.getFile(), protocol); } catch (OutOfMemoryError oomerror) { new OOMWarning( @@ -788,7 +695,7 @@ public class ChimeraViewFrame extends StructureViewerBase jmb.updateColours(ap); } // do superposition if asked to - if (alignAddedStructures) + if (Cache.getDefault("AUTOSUPERIMPOSE", true) && alignAddedStructures) { new Thread(new Runnable() { @@ -819,9 +726,18 @@ public class ChimeraViewFrame extends StructureViewerBase 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); @@ -830,9 +746,9 @@ public class ChimeraViewFrame extends StructureViewerBase new OOMWarning("Retrieving PDB id " + pdbid, oomerror); } finally { - String msg = pdbid + " " - + MessageManager.getString("label.state_completed"); - stopProgressBar(msg, 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 @@ -841,7 +757,7 @@ public class ChimeraViewFrame extends StructureViewerBase 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); } @@ -867,6 +783,13 @@ public class ChimeraViewFrame extends StructureViewerBase 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) @@ -1136,12 +1059,12 @@ public class ChimeraViewFrame extends StructureViewerBase { return; } - ; + if (_alignwith.size() == 0) { _alignwith.add(getAlignmentPanel()); } - ; + try { AlignmentI[] als = new Alignment[_alignwith.size()]; @@ -1165,9 +1088,7 @@ public class ChimeraViewFrame extends StructureViewerBase } Cache.log.info("Couldn't align structures with the " + sp.toString() + "associated alignment panels.", e); - } - } public void setJalviewColourScheme(ColourSchemeI ucs) @@ -1201,31 +1122,73 @@ public class ChimeraViewFrame extends StructureViewerBase } /** - * 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) + { + // ignore + } + } + } } @Override @@ -1233,4 +1196,16 @@ public class ChimeraViewFrame extends StructureViewerBase { jmb.focusView(); } + + @Override + public ViewerType getViewerType() + { + return ViewerType.CHIMERA; + } + + @Override + protected AAStructureBindingModel getBindingModel() + { + return jmb; + } }