X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructures%2Fmodels%2FAAStructureBindingModel.java;h=1afa15e7673a9a992a60d268311aef9e7d533b84;hb=4ee3a368d2de9eaa050137f7d45cfac0c432ef53;hp=7899c40633f96ae5fc6294cddf2b7cbc9ae4140b;hpb=1dd1e3cd8272449af3fe4dfa3f69239ca4ae471b;p=jalview.git diff --git a/src/jalview/structures/models/AAStructureBindingModel.java b/src/jalview/structures/models/AAStructureBindingModel.java index 7899c40..1afa15e 100644 --- a/src/jalview/structures/models/AAStructureBindingModel.java +++ b/src/jalview/structures/models/AAStructureBindingModel.java @@ -42,8 +42,13 @@ import jalview.api.structures.JalviewStructureDisplayI; import jalview.bin.Cache; import jalview.datamodel.AlignmentI; 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; import jalview.io.StructureFile; @@ -52,6 +57,7 @@ import jalview.schemes.ColourSchemeI; import jalview.schemes.ResidueProperties; import jalview.structure.AtomSpec; import jalview.structure.AtomSpecModel; +import jalview.structure.StructureCommand; import jalview.structure.StructureCommandI; import jalview.structure.StructureCommandsI; import jalview.structure.StructureListener; @@ -79,20 +85,20 @@ public abstract class AAStructureBindingModel public static class SuperposeData { public String filename; - + public String pdbId; - + public String chain = ""; - + 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 * @@ -171,6 +177,8 @@ public abstract class AAStructureBindingModel public String fileLoadingError; + protected Thread externalViewerMonitor; + /** * Constructor * @@ -256,6 +264,7 @@ public abstract class AAStructureBindingModel chains = newchains; return chainmaps > 0; } + public StructureSelectionManager getSsm() { return ssm; @@ -653,7 +662,8 @@ 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(); @@ -879,8 +889,8 @@ 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 @@ -888,8 +898,8 @@ 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; } @@ -933,7 +943,8 @@ public abstract class AAStructureBindingModel return error; } - private AtomSpecModel getAtomSpec(AAStructureBindingModel.SuperposeData superposeData, + private AtomSpecModel getAtomSpec( + AAStructureBindingModel.SuperposeData superposeData, BitSet matched) { AtomSpecModel model = new AtomSpecModel(); @@ -1002,7 +1013,7 @@ public abstract class AAStructureBindingModel { return; } - + /* * build a map of {Residue3LetterCode, Color} */ @@ -1047,16 +1058,16 @@ public abstract class AAStructureBindingModel private List executeCommand(StructureCommandI cmd, boolean getReply, String msg) { + final JalviewStructureDisplayI theViewer = getViewer(); + final long handle = msg == null ? 0 : theViewer.startProgressBar(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); + return executeCommand(cmd, true); } finally { if (msg != null) @@ -1070,9 +1081,6 @@ public abstract class AAStructureBindingModel /* * 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 @@ -1105,84 +1113,43 @@ 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 */ - private List executeCommands(List commands, + protected List executeCommands(List commands, boolean getReply, String msg) { - return executeCommands(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. - * - * @param getReply - * @param msg - * @param commands - * @return - */ - protected List executeCommands(boolean getReply, String msg, - StructureCommandI[] commands) - { - // todo: tidy this up - - /* - * show progress message if specified - */ - final JalviewStructureDisplayI theViewer = getViewer(); - final long handle = msg == null ? 0 : theViewer.startProgressBar(msg); - List response = getReply ? new ArrayList<>() : null; - try - { - for (StructureCommandI cmd : commands) - { - List replies = executeCommand(cmd, getReply, null); - if (getReply && replies != null) - { - response.addAll(replies); - } - } - return response; - } finally + for (StructureCommandI cmd : commands) { - if (msg != null) + List replies = executeCommand(cmd, getReply, msg); + if (replies != null) { - theViewer.stopProgressBar(null, handle); + response.addAll(replies); } } + return response; } /** - * colour any structures associated with sequences in the given alignment - * using the getFeatureRenderer() and getSequenceRenderer() renderers but only - * if colourBySequence is enabled. + * Colours any structures associated with sequences in the given alignment as + * coloured in the alignment view, provided colourBySequence is enabled */ public void colourBySequence(AlignmentViewPanel alignmentv) { - if (!colourBySequence || !isLoadingFinished()) - { - return; - } - if (getSsm() == null) + if (!colourBySequence || !isLoadingFinished() || getSsm() == null) { return; } - String[] files = getStructureFiles(); - - SequenceRenderer sr = getSequenceRenderer(alignmentv); - Map colourMap = buildColoursMap(ssm, files, - sequence, sr, alignmentv); + Map colourMap = buildColoursMap(ssm, sequence, + alignmentv); List colourBySequenceCommands = commandGenerator .colourBySequence(colourMap); - executeCommands(colourBySequenceCommands, false, null); + executeCommands(colourBySequenceCommands, false, COLOURING_STRUCTURES); } /** @@ -1248,6 +1215,10 @@ public abstract class AAStructureBindingModel { AlignmentViewPanel ap = (avp == null) ? getViewer().getAlignmentPanel() : avp; + if (ap == null) + { + return null; + } return ap.getAlignViewport().isShowSequenceFeatures() ? ap.getFeatureRenderer() : null; @@ -1354,16 +1325,16 @@ public abstract class AAStructureBindingModel * models and chains) * * @param ssm - * @param files * @param sequence - * @param sr * @param viewPanel * @return */ protected Map buildColoursMap( - StructureSelectionManager ssm, String[] files, - SequenceI[][] sequence, SequenceRenderer sr, AlignmentViewPanel viewPanel) + StructureSelectionManager ssm, SequenceI[][] sequence, + AlignmentViewPanel viewPanel) { + String[] files = getStructureFiles(); + SequenceRenderer sr = getSequenceRenderer(viewPanel); FeatureRenderer fr = viewPanel.getFeatureRenderer(); FeatureColourFinder finder = new FeatureColourFinder(fr); AlignViewportI viewport = viewPanel.getAlignViewport(); @@ -1371,18 +1342,17 @@ public abstract class AAStructureBindingModel AlignmentI al = viewport.getAlignment(); Map colourMap = new LinkedHashMap<>(); Color lastColour = null; - + for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) { - // todo indirect this resolution / allow override 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 +1372,14 @@ 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 +1387,9 @@ 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 +1402,8 @@ 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 +1455,9 @@ 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 +1472,8 @@ 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 +1484,7 @@ public abstract class AAStructureBindingModel atomSpec = new AtomSpecModel(); map.put(value, atomSpec); } - + atomSpec.addRange(model, startPos, endPos, chain); } @@ -1546,8 +1517,8 @@ public abstract class AAStructureBindingModel saveSession(f); } catch (IOException e) { - Cache.log.error(String.format("Error saving %s session: %s", - prefix, e.toString())); + Cache.log.error(String.format("Error saving %s session: %s", prefix, + e.toString())); } return f; @@ -1560,11 +1531,439 @@ 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); } } + + /** + * Returns true if the viewer is an external structure viewer for which the + * process is still alive, else false (for Jmol, or an external viewer which + * the user has independently closed) + * + * @return + */ + public boolean isViewerRunning() + { + return false; + } + + /** + * Closes Jalview's structure viewer panel and releases associated resources. + * If it is managing an external viewer program, and {@code forceClose} is + * true, also asks that program to close. + * + * @param forceClose + */ + public void closeViewer(boolean forceClose) + { + getSsm().removeStructureViewerListener(this, this.getStructureFiles()); + releaseUIResources(); + + /* + * 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); + } + } + } + + /** + * Returns the URL of a help page for the structure viewer, or null if none is + * known + * + * @return + */ + public String getHelpURL() + { + return null; + } + + /** + * 
    +   * Helper method to build a map of 
+   *   { featureType, { feature value, AtomSpecModel } }
+   *
    + * + * @param viewPanel + * @return + */ + protected Map> buildFeaturesMap( + AlignmentViewPanel viewPanel) + { + Map> theMap = new LinkedHashMap<>(); + String[] files = getStructureFiles(); + if (files == null) + { + return theMap; + } + + FeatureRenderer fr = viewPanel.getFeatureRenderer(); + if (fr == null) + { + 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 + */ + boolean showLinkedFeatures = viewport.isShowComplementFeatures(); + List complementFeatures = new ArrayList<>(); + FeatureRenderer complementRenderer = null; + if (showLinkedFeatures) + { + AlignViewportI comp = fr.getViewport().getCodingComplement(); + if (comp != null) + { + complementRenderer = Desktop.getAlignFrameFor(comp) + .getFeatureRenderer(); + complementFeatures = complementRenderer.getDisplayedFeatureTypes(); + } + } + if (visibleFeatures.isEmpty() && complementFeatures.isEmpty()) + { + return theMap; + } + + AlignmentI alignment = viewPanel.getAlignment(); + SequenceI[][] seqs = getSequence(); + + for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) + { + 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++) + { + final SequenceI seq = seqs[pdbfnum][seqNo]; + int sp = alignment.findIndex(seq); + StructureMapping structureMapping = mapping[m]; + if (structureMapping.getSequence() == seq && sp > -1) + { + /* + * found a sequence with a mapping to a structure; + * now scan its features + */ + if (!visibleFeatures.isEmpty()) + { + scanSequenceFeatures(visibleFeatures, structureMapping, seq, + theMap, modelId); + } + if (showLinkedFeatures) + { + scanComplementFeatures(complementRenderer, structureMapping, + seq, theMap, modelId); + } + } + } + } + } + return theMap; + } + + /** + * Ask the structure viewer to open a session file. Returns true if + * successful, else false (or not supported). + * + * @param filepath + * @return + */ + public boolean openSession(String filepath) + { + StructureCommandI cmd = getCommandGenerator().openSession(filepath); + if (cmd == null) + { + return false; + } + executeCommand(cmd, true); + // todo: test for failure - how? + return true; + } + + /** + * 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 + * @param seq + * @param theMap + * @param modelNumber + */ + protected static void scanComplementFeatures( + FeatureRenderer complementRenderer, + StructureMapping structureMapping, SequenceI seq, + Map> theMap, + String modelNumber) + { + /* + * for each sequence residue mapped to a structure position... + */ + for (int seqPos : structureMapping.getMapping().keySet()) + { + /* + * find visible complementary features at mapped position(s) + */ + MappedFeatures mf = complementRenderer + .findComplementFeaturesAtResidue(seq, seqPos); + if (mf != null) + { + for (SequenceFeature sf : mf.features) + { + String type = sf.getType(); + + /* + * Don't copy features which originated from Chimera + */ + if (JalviewChimeraBinding.CHIMERA_FEATURE_GROUP + .equals(sf.getFeatureGroup())) + { + 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(); + if (value == null || value.length() == 0) + { + value = type; + } + float score = sf.getScore(); + if (score != 0f && !Float.isNaN(score)) + { + value = Float.toString(score); + } + Map featureValues = theMap.get(type); + if (featureValues == null) + { + featureValues = new HashMap<>(); + theMap.put(type, featureValues); + } + for (int[] range : mappedRanges) + { + addAtomSpecRange(featureValues, value, modelNumber, range[0], + range[1], structureMapping.getChain()); + } + } + } + } + } + } + + /** + * Inspect features on the sequence; for each feature that is visible, + * determine its mapped ranges in the structure (if any) according to the + * given mapping, and add them to the map. + * + * @param visibleFeatures + * @param mapping + * @param seq + * @param theMap + * @param modelId + */ + protected static void scanSequenceFeatures(List visibleFeatures, + StructureMapping mapping, SequenceI seq, + Map> theMap, String modelId) + { + List sfs = seq.getFeatures().getPositionalFeatures( + visibleFeatures.toArray(new String[visibleFeatures.size()])); + for (SequenceFeature sf : sfs) + { + String type = sf.getType(); + + /* + * Don't copy features which originated from Chimera + */ + if (JalviewChimeraBinding.CHIMERA_FEATURE_GROUP + .equals(sf.getFeatureGroup())) + { + continue; + } + + List mappedRanges = mapping.getPDBResNumRanges(sf.getBegin(), + sf.getEnd()); + + if (!mappedRanges.isEmpty()) + { + String value = sf.getDescription(); + if (value == null || value.length() == 0) + { + value = type; + } + float score = sf.getScore(); + if (score != 0f && !Float.isNaN(score)) + { + value = Float.toString(score); + } + Map featureValues = theMap.get(type); + if (featureValues == null) + { + featureValues = new HashMap<>(); + theMap.put(type, featureValues); + } + for (int[] range : mappedRanges) + { + addAtomSpecRange(featureValues, value, modelId, range[0], + range[1], mapping.getChain()); + } + } + } + } + + /** + * Returns the number of structure files in the structure viewer and mapped to + * Jalview. This may be zero if the files are still in the process of loading + * in the viewer. + * + * @return + */ + public int getMappedStructureCount() + { + 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; + } }