X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructures%2Fmodels%2FAAStructureBindingModel.java;h=8436b48eef8a8811416955a1b257feaf77cb6dcf;hb=bc97c1d6107222987fc31af58ba390c5425dcdda;hp=594984733efec9d80eb54adbbf9d7e53e4edadee;hpb=ca4ed63aacf92872319f2bf64225c2742c338184;p=jalview.git diff --git a/src/jalview/structures/models/AAStructureBindingModel.java b/src/jalview/structures/models/AAStructureBindingModel.java index 5949847..8436b48 100644 --- a/src/jalview/structures/models/AAStructureBindingModel.java +++ b/src/jalview/structures/models/AAStructureBindingModel.java @@ -29,6 +29,7 @@ import java.util.BitSet; import java.util.HashMap; import java.util.LinkedHashMap; import java.util.List; +import java.util.Locale; import java.util.Map; import javax.swing.SwingUtilities; @@ -39,14 +40,16 @@ import jalview.api.FeatureRenderer; import jalview.api.SequenceRenderer; import jalview.api.StructureSelectionManagerProvider; import jalview.api.structures.JalviewStructureDisplayI; -import jalview.bin.Cache; +import jalview.bin.Console; import jalview.datamodel.AlignmentI; +import jalview.datamodel.ColumnSelection; import jalview.datamodel.HiddenColumns; import jalview.datamodel.MappedFeatures; import jalview.datamodel.PDBEntry; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; import jalview.ext.rbvi.chimera.JalviewChimeraBinding; +import jalview.gui.AlignmentPanel; import jalview.gui.Desktop; import jalview.gui.StructureViewer.ViewerType; import jalview.io.DataSourceType; @@ -58,6 +61,7 @@ import jalview.structure.AtomSpec; import jalview.structure.AtomSpecModel; import jalview.structure.StructureCommandI; import jalview.structure.StructureCommandsI; +import jalview.structure.StructureCommandsI.AtomSpecType; import jalview.structure.StructureListener; import jalview.structure.StructureMapping; import jalview.structure.StructureSelectionManager; @@ -66,9 +70,9 @@ import jalview.util.MessageManager; /** * - * A base class to hold common function for protein structure model binding. - * Initial version created by refactoring JMol and Chimera binding models, but - * other structure viewers could in principle be accommodated in future. + * A base class to hold common function for 3D structure model binding. Initial + * version created by refactoring JMol and Chimera binding models, but other + * structure viewers could in principle be accommodated in future. * * @author gmcarstairs * @@ -83,20 +87,23 @@ public abstract class AAStructureBindingModel public static class SuperposeData { public String filename; - + public String pdbId; - + public String chain = ""; - + + /** + * is the mapped sequence not protein ? + */ public boolean isRna; - + /* * The pdb residue number (if any) mapped to columns of the alignment */ public int[] pdbResNo; // or use SparseIntArray? - + public String modelId; - + /** * Constructor * @@ -164,6 +171,9 @@ public abstract class AAStructureBindingModel protected boolean colourBySequence = true; + /** + * true if all sequences appear to be nucleotide + */ private boolean nucleotide; private boolean finishedInit = false; @@ -175,6 +185,8 @@ public abstract class AAStructureBindingModel public String fileLoadingError; + protected Thread externalViewerMonitor; + /** * Constructor * @@ -260,6 +272,7 @@ public abstract class AAStructureBindingModel chains = newchains; return chainmaps > 0; } + public StructureSelectionManager getSsm() { return ssm; @@ -657,7 +670,8 @@ public abstract class AAStructureBindingModel * @return */ protected int findSuperposableResidues(AlignmentI alignment, - BitSet matched, AAStructureBindingModel.SuperposeData[] structures) + BitSet matched, + AAStructureBindingModel.SuperposeData[] structures) { int refStructure = -1; String[] files = getStructureFiles(); @@ -708,7 +722,7 @@ public abstract class AAStructureBindingModel structures[pdbfnum].chain = chain; } structures[pdbfnum].pdbId = mapping.getPdbId(); - structures[pdbfnum].isRna = theSequence.getRNA() != null; + structures[pdbfnum].isRna = !theSequence.isProtein(); /* * move on to next pdb file (ignore sequences for other chains @@ -857,21 +871,39 @@ public abstract class AAStructureBindingModel { AlignmentI alignment = view.getAlignment(); HiddenColumns hiddenCols = alignment.getHiddenColumns(); - /* * 'matched' bit i will be set for visible alignment columns i where * all sequences have a residue with a mapping to their PDB structure */ - BitSet matched = new BitSet(); final int width = alignment.getWidth(); - for (int m = 0; m < width; m++) + BitSet matched = new BitSet(); + ColumnSelection cs = view.getAlignViewport().getColumnSelection(); + // restrict to active column selection, if there is one + if (cs != null && cs.hasSelectedColumns() + && cs.getSelected().size() >= 4) { - if (hiddenCols == null || hiddenCols.isVisible(m)) + for (int s : cs.getSelected()) { - matched.set(m); + if (hiddenCols == null) + { + matched.set(s); + } + else + { + matched.set(hiddenCols.visibleToAbsoluteColumn(s)); + } + } + } + else + { + for (int m = 0; m < width; m++) + { + if (hiddenCols == null || hiddenCols.isVisible(m)) + { + matched.set(m); + } } } - AAStructureBindingModel.SuperposeData[] structures = new AAStructureBindingModel.SuperposeData[files.length]; for (int f = 0; f < files.length; f++) { @@ -883,8 +915,8 @@ public abstract class AAStructureBindingModel * Calculate the superposable alignment columns ('matched'), and the * corresponding structure residue positions (structures.pdbResNo) */ - int refStructure = findSuperposableResidues(alignment, - matched, structures); + int refStructure = findSuperposableResidues(alignment, matched, + structures); /* * require at least 4 positions to be able to execute superposition @@ -892,8 +924,8 @@ public abstract class AAStructureBindingModel int nmatched = matched.cardinality(); if (nmatched < MIN_POS_TO_SUPERPOSE) { - String msg = MessageManager.formatMessage("label.insufficient_residues", - nmatched); + String msg = MessageManager + .formatMessage("label.insufficient_residues", nmatched); error += view.getViewName() + ": " + msg + "; "; continue; } @@ -911,6 +943,11 @@ public abstract class AAStructureBindingModel // todo better way to ensure synchronous than setting getReply true!! executeCommands(commandGenerator.showBackbone(), true, null); + AtomSpecType backbone = structures[refStructure].isRna + ? AtomSpecType.PHOSPHATE + : AtomSpecType.ALPHA; + List models = new ArrayList(); + models.add(refAtoms); /* * superpose each (other) structure to the reference in turn */ @@ -920,24 +957,29 @@ public abstract class AAStructureBindingModel { AtomSpecModel atomSpec = getAtomSpec(structures[i], matched); List commands = commandGenerator - .superposeStructures(refAtoms, atomSpec); + .superposeStructures(refAtoms, atomSpec, backbone); List replies = executeCommands(commands, true, null); for (String reply : replies) { // return this error (Chimera only) to the user - if (reply.toLowerCase().contains("unequal numbers of atoms")) + if (reply.toLowerCase(Locale.ROOT) + .contains("unequal numbers of atoms")) { error += "; " + reply; } } + models.add(atomSpec); } } + List finalView = commandGenerator + .centerViewOn(models); + executeCommands(finalView, false, "Centered on Superposition"); } - return error; } - private AtomSpecModel getAtomSpec(AAStructureBindingModel.SuperposeData superposeData, + private AtomSpecModel getAtomSpec( + AAStructureBindingModel.SuperposeData superposeData, BitSet matched) { AtomSpecModel model = new AtomSpecModel(); @@ -974,8 +1016,8 @@ public abstract class AAStructureBindingModel // TODO: JAL-628 colour chains distinctly across all visible models - executeCommand(commandGenerator.colourByChain(), false, - COLOURING_STRUCTURES); + executeCommand(false, COLOURING_STRUCTURES, + commandGenerator.colourByChain()); } /** @@ -1006,7 +1048,7 @@ public abstract class AAStructureBindingModel { return; } - + /* * build a map of {Residue3LetterCode, Color} */ @@ -1033,69 +1075,7 @@ public abstract class AAStructureBindingModel public void setBackgroundColour(Color col) { StructureCommandI cmd = commandGenerator.setBackgroundColour(col); - executeCommand(cmd, false, null); - } - - /** - * Sends one command to the structure viewer. If {@code getReply} is true, the - * command is sent synchronously, otherwise in a deferred thread. - *

- * If a progress message is supplied, this is displayed before command - * execution, and removed afterwards. - * - * @param cmd - * @param getReply - * @param msg - * @return - */ - private List executeCommand(StructureCommandI cmd, - boolean getReply, String msg) - { - if (getReply) - { - /* - * synchronous (same thread) execution so reply can be returned - */ - final JalviewStructureDisplayI theViewer = getViewer(); - final long handle = msg == null ? 0 : theViewer.startProgressBar(msg); - try - { - return executeCommand(cmd, getReply); - } finally - { - if (msg != null) - { - theViewer.stopProgressBar(null, handle); - } - } - } - else - { - /* - * asynchronous (new thread) execution if no reply needed - */ - final JalviewStructureDisplayI theViewer = getViewer(); - final long handle = msg == null ? 0 : theViewer.startProgressBar(msg); - - SwingUtilities.invokeLater(new Runnable() - { - @Override - public void run() - { - try - { - executeCommand(cmd, false); - } finally - { - if (msg != null) - { - theViewer.stopProgressBar(null, handle); - } - } - } - }); - return null; - } + executeCommand(false, null, cmd); } /** @@ -1109,59 +1089,99 @@ public abstract class AAStructureBindingModel boolean getReply); /** - * A helper method that converts list of commands to a vararg array + * Executes one or more structure viewer commands * * @param commands * @param getReply * @param msg */ - protected List executeCommands( - List commands, + protected List executeCommands(List commands, boolean getReply, String msg) { - return executeCommands(getReply, msg, + return executeCommand(getReply, msg, commands.toArray(new StructureCommandI[commands.size()])); } /** - * Executes one or more structure viewer commands. If a progress message is - * provided, it is shown first, and removed after all commands have been run. + * Executes one or more structure viewer commands, optionally returning the + * reply, and optionally showing a status message while the command is being + * executed. + *

+ * If a reply is wanted, the execution is done synchronously (waits), + * otherwise it is done in a separate thread (doesn't wait). WARNING: if you + * are sending commands that need to execute before later calls to + * executeCommand (e.g. mouseovers, which clean up after previous ones) then + * set getReply true to ensure that commands are not executed out of order. * * @param getReply * @param msg - * @param commands + * @param cmds * @return */ - protected List executeCommands(boolean getReply, String msg, - StructureCommandI[] commands) + protected List executeCommand(boolean getReply, String msg, + StructureCommandI... cmds) { - // todo: tidy this up - - /* - * show progress message if specified - */ - final JalviewStructureDisplayI theViewer = getViewer(); + JalviewStructureDisplayI theViewer = getViewer(); final long handle = msg == null ? 0 : theViewer.startProgressBar(msg); - List response = getReply ? new ArrayList<>() : null; - try + if (getReply) { - for (StructureCommandI cmd : commands) + /* + * execute and wait for reply + */ + List response = new ArrayList<>(); + try { - List replies = executeCommand(cmd, getReply, null); - if (getReply && replies != null) + for (StructureCommandI cmd : cmds) { - response.addAll(replies); + List replies = executeCommand(cmd, true); + if (replies != null) + { + response.addAll(replies); + } + } + return response; + } finally + { + if (msg != null) + { + theViewer.stopProgressBar(null, handle); } } - return response; - } finally + } + + /* + * fire and forget + */ + String threadName = msg == null ? "StructureCommand" : msg; + new Thread(new Runnable() { - if (msg != null) + @Override + public void run() { - theViewer.stopProgressBar(null, handle); + try + { + for (StructureCommandI cmd : cmds) + { + executeCommand(cmd, false); + } + } finally + { + if (msg != null) + { + SwingUtilities.invokeLater(new Runnable() + { + @Override + public void run() + { + theViewer.stopProgressBar(null, handle); + } + }); + } + } } - } + }, threadName).start(); + return null; } /** @@ -1179,7 +1199,7 @@ public abstract class AAStructureBindingModel List colourBySequenceCommands = commandGenerator .colourBySequence(colourMap); - executeCommands(colourBySequenceCommands, false, null); + executeCommands(colourBySequenceCommands, false, COLOURING_STRUCTURES); } /** @@ -1187,7 +1207,7 @@ public abstract class AAStructureBindingModel */ public void focusView() { - executeCommand(commandGenerator.focusView(), false, null); + executeCommand(false, null, commandGenerator.focusView()); } /** @@ -1235,8 +1255,7 @@ public abstract class AAStructureBindingModel } /** - * Returns the FeatureRenderer for the given alignment view, or null if - * feature display is turned off in the view. + * Returns the FeatureRenderer for the given alignment view * * @param avp * @return @@ -1249,9 +1268,7 @@ public abstract class AAStructureBindingModel { return null; } - return ap.getAlignViewport().isShowSequenceFeatures() - ? ap.getFeatureRenderer() - : null; + return ap.getFeatureRenderer(); } protected void setStructureCommands(StructureCommandsI cmd) @@ -1286,6 +1303,12 @@ public abstract class AAStructureBindingModel @Override public void updateColours(Object source) { + if (getViewer() == null) + { + // can happen if a viewer was not instantiated or cleaned up and is still + // registered - mostly during tests + return; + } AlignmentViewPanel ap = (AlignmentViewPanel) source; // ignore events from panels not used to colour this view if (!getViewer().isUsedForColourBy(ap)) @@ -1306,40 +1329,6 @@ public abstract class AAStructureBindingModel protected abstract ViewerType getViewerType(); /** - * Send a structure viewer command asynchronously in a new thread. If the - * progress message is not null, display this message while the command is - * executing. - * - * @param command - * @param progressMsg - */ - protected void sendAsynchronousCommand(StructureCommandI command, - String progressMsg) - { - final JalviewStructureDisplayI theViewer = getViewer(); - final long handle = progressMsg == null ? 0 - : theViewer.startProgressBar(progressMsg); - SwingUtilities.invokeLater(new Runnable() - { - @Override - public void run() - { - try - { - executeCommand(command, false, null); - } finally - { - if (progressMsg != null) - { - theViewer.stopProgressBar(null, handle); - } - } - } - }); - - } - - /** * Builds a data structure which records mapped structure residues for each * colour. From this we can easily generate the viewer commands for colour by * sequence. Constructs and returns a map of {@code Color} to @@ -1372,17 +1361,17 @@ public abstract class AAStructureBindingModel AlignmentI al = viewport.getAlignment(); Map colourMap = new LinkedHashMap<>(); Color lastColour = null; - + for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) { final String modelId = getModelIdForFile(files[pdbfnum]); StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]); - + if (mapping == null || mapping.length < 1) { continue; } - + int startPos = -1, lastPos = -1; String lastChain = ""; for (int s = 0; s < sequence[pdbfnum].length; s++) @@ -1402,14 +1391,14 @@ public abstract class AAStructureBindingModel continue; } int pos = mapping[m].getPDBResNum(asp.findPosition(r)); - + if (pos < 1 || pos == lastPos) { continue; } - + Color colour = sr.getResidueColour(seq, r, finder); - + /* * darker colour for hidden regions */ @@ -1417,9 +1406,9 @@ public abstract class AAStructureBindingModel { colour = Color.GRAY; } - + final String chain = mapping[m].getChain(); - + /* * Just keep incrementing the end position for this colour range * _unless_ colour, PDB model or chain has changed, or there is a @@ -1432,8 +1421,8 @@ public abstract class AAStructureBindingModel { if (startPos != -1) { - addAtomSpecRange(colourMap, lastColour, modelId, - startPos, lastPos, lastChain); + addAtomSpecRange(colourMap, lastColour, modelId, startPos, + lastPos, lastChain); } startPos = pos; } @@ -1485,8 +1474,9 @@ public abstract class AAStructureBindingModel } /** - * Helper method to add one contiguous range to the AtomSpec model for the given - * value (creating the model if necessary). As used by Jalview, {@code value} is + * Helper method to add one contiguous range to the AtomSpec model for the + * given value (creating the model if necessary). As used by Jalview, + * {@code value} is *

    *
  • a colour, when building a 'colour structure by sequence' command
    • *
  • a feature value, when building a 'set Chimera attributes from features' @@ -1501,8 +1491,8 @@ public abstract class AAStructureBindingModel * @param chain */ public static final void addAtomSpecRange(Map map, - Object value, - String model, int startPos, int endPos, String chain) + Object value, String model, int startPos, int endPos, + String chain) { /* * Get/initialize map of data for the colour @@ -1513,7 +1503,7 @@ public abstract class AAStructureBindingModel atomSpec = new AtomSpecModel(); map.put(value, atomSpec); } - + atomSpec.addRange(model, startPos, endPos, chain); } @@ -1546,8 +1536,8 @@ public abstract class AAStructureBindingModel saveSession(f); } catch (IOException e) { - Cache.log.error(String.format("Error saving %s session: %s", - prefix, e.toString())); + Console.error(String.format("Error saving %s session: %s", prefix, + e.toString())); } return f; @@ -1560,8 +1550,7 @@ public abstract class AAStructureBindingModel */ protected void saveSession(File f) { - StructureCommandI cmd = commandGenerator - .saveSession(f.getPath()); + StructureCommandI cmd = commandGenerator.saveSession(f.getPath()); if (cmd != null) { executeCommand(cmd, false); @@ -1583,7 +1572,7 @@ public abstract class AAStructureBindingModel /** * Closes Jalview's structure viewer panel and releases associated resources. * If it is managing an external viewer program, and {@code forceClose} is - * true, also shuts down that program. + * true, also asks that program to close. * * @param forceClose */ @@ -1592,8 +1581,25 @@ public abstract class AAStructureBindingModel getSsm().removeStructureViewerListener(this, this.getStructureFiles()); releaseUIResources(); - // add external viewer shutdown in overrides - // todo - or can maybe pull up to here + /* + * end the thread that closes this panel if the external viewer closes + */ + if (externalViewerMonitor != null) + { + externalViewerMonitor.interrupt(); + externalViewerMonitor = null; + } + + stopListening(); + + if (forceClose) + { + StructureCommandI cmd = getCommandGenerator().closeViewer(); + if (cmd != null) + { + executeCommand(cmd, false); + } + } } /** @@ -1631,10 +1637,10 @@ public abstract class AAStructureBindingModel { return theMap; } - + AlignViewportI viewport = viewPanel.getAlignViewport(); List visibleFeatures = fr.getDisplayedFeatureTypes(); - + /* * if alignment is showing features from complement, we also transfer * these features to the corresponding mapped structure residues @@ -1656,7 +1662,7 @@ public abstract class AAStructureBindingModel { return theMap; } - + AlignmentI alignment = viewPanel.getAlignment(); SequenceI[][] seqs = getSequence(); @@ -1664,12 +1670,12 @@ public abstract class AAStructureBindingModel { String modelId = getModelIdForFile(files[pdbfnum]); StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]); - + if (mapping == null || mapping.length < 1) { continue; } - + for (int seqNo = 0; seqNo < seqs[pdbfnum].length; seqNo++) { for (int m = 0; m < mapping.length; m++) @@ -1720,8 +1726,8 @@ public abstract class AAStructureBindingModel } /** - * Scans visible features in mapped positions of the CDS/peptide complement, and - * adds any found to the map of attribute values/structure positions + * Scans visible features in mapped positions of the CDS/peptide complement, + * and adds any found to the map of attribute values/structure positions * * @param complementRenderer * @param structureMapping @@ -1750,7 +1756,7 @@ public abstract class AAStructureBindingModel for (SequenceFeature sf : mf.features) { String type = sf.getType(); - + /* * Don't copy features which originated from Chimera */ @@ -1759,14 +1765,14 @@ public abstract class AAStructureBindingModel { continue; } - + /* * record feature 'value' (score/description/type) as at the * corresponding structure position */ List mappedRanges = structureMapping .getPDBResNumRanges(seqPos, seqPos); - + if (!mappedRanges.isEmpty()) { String value = sf.getDescription(); @@ -1816,7 +1822,7 @@ public abstract class AAStructureBindingModel for (SequenceFeature sf : sfs) { String type = sf.getType(); - + /* * Don't copy features which originated from Chimera */ @@ -1825,10 +1831,10 @@ public abstract class AAStructureBindingModel { continue; } - + List mappedRanges = mapping.getPDBResNumRanges(sf.getBegin(), sf.getEnd()); - + if (!mappedRanges.isEmpty()) { String value = sf.getDescription(); @@ -1868,4 +1874,115 @@ public abstract class AAStructureBindingModel String[] files = getStructureFiles(); return files == null ? 0 : files.length; } + + /** + * Starts a thread that waits for the external viewer program process to + * finish, so that we can then close the associated resources. This avoids + * leaving orphaned viewer panels in Jalview if the user closes the external + * viewer. + * + * @param p + */ + protected void startExternalViewerMonitor(Process p) + { + externalViewerMonitor = new Thread(new Runnable() + { + + @Override + public void run() + { + try + { + p.waitFor(); + JalviewStructureDisplayI display = getViewer(); + if (display != null) + { + display.closeViewer(false); + } + } catch (InterruptedException e) + { + // exit thread if Chimera Viewer is closed in Jalview + } + } + }); + externalViewerMonitor.start(); + } + + /** + * If supported by the external structure viewer, sends it commands to notify + * model or selection changes to the specified URL (where Jalview has started + * a listener) + * + * @param uri + */ + protected void startListening(String uri) + { + List commands = getCommandGenerator() + .startNotifications(uri); + if (commands != null) + { + executeCommands(commands, false, null); + } + } + + /** + * If supported by the external structure viewer, sends it commands to stop + * notifying model or selection changes + */ + protected void stopListening() + { + List commands = getCommandGenerator() + .stopNotifications(); + if (commands != null) + { + executeCommands(commands, false, null); + } + } + + /** + * If supported by the structure viewer, queries it for all residue attributes + * with the given attribute name, and creates features on corresponding + * residues of the alignment. Returns the number of features added. + * + * @param attName + * @param alignmentPanel + * @return + */ + public int copyStructureAttributesToFeatures(String attName, + AlignmentPanel alignmentPanel) + { + StructureCommandI cmd = getCommandGenerator() + .getResidueAttributes(attName); + if (cmd == null) + { + return 0; + } + List residueAttributes = executeCommand(cmd, true); + + int featuresAdded = createFeaturesForAttributes(attName, + residueAttributes); + if (featuresAdded > 0) + { + alignmentPanel.getFeatureRenderer().featuresAdded(); + } + return featuresAdded; + } + + /** + * Parses {@code residueAttributes} and creates sequence features on any + * mapped alignment residues. Returns the number of features created. + *

    + * {@code residueAttributes} is the reply from the structure viewer to a + * command to list any residue attributes for the given attribute name. Syntax + * and parsing of this is viewer-specific. + * + * @param attName + * @param residueAttributes + * @return + */ + protected int createFeaturesForAttributes(String attName, + List residueAttributes) + { + return 0; + } }