X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Frbvi%2Fchimera%2FJalviewChimeraBinding.java;h=6fa06d256365dd2210338957aecfc9e7d52b26a1;hb=defb4c1d5b4edbd8fbd490f25c15ef1f1de6fe37;hp=1ff046612c8c364410ed28ee8d821caf5dce8ba0;hpb=5965127c38ff1a35d10d806c4b4537cdc1e39579;p=jalview.git diff --git a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java index 1ff0466..6fa06d2 100644 --- a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java +++ b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java @@ -20,22 +20,25 @@ */ package jalview.ext.rbvi.chimera; +import jalview.api.AlignViewportI; import jalview.api.AlignmentViewPanel; -import jalview.api.FeatureRenderer; import jalview.api.SequenceRenderer; +import jalview.api.structures.JalviewStructureDisplayI; import jalview.bin.Cache; import jalview.datamodel.AlignmentI; -import jalview.datamodel.ColumnSelection; +import jalview.datamodel.HiddenColumns; import jalview.datamodel.PDBEntry; import jalview.datamodel.SearchResultMatchI; -import jalview.datamodel.SearchResults; +import jalview.datamodel.SearchResultsI; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; +import jalview.datamodel.VisibleContigsIterator; import jalview.httpserver.AbstractRequestHandler; import jalview.io.DataSourceType; import jalview.schemes.ColourSchemeI; import jalview.schemes.ResidueProperties; import jalview.structure.AtomSpec; +import jalview.structure.StructureMapping; import jalview.structure.StructureMappingcommandSet; import jalview.structure.StructureSelectionManager; import jalview.structures.models.AAStructureBindingModel; @@ -48,6 +51,7 @@ import java.io.IOException; import java.io.PrintWriter; import java.net.BindException; import java.util.ArrayList; +import java.util.BitSet; import java.util.Collections; import java.util.Hashtable; import java.util.LinkedHashMap; @@ -75,10 +79,10 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel private static final String ALPHACARBON = "CA"; - private List chainNames = new ArrayList(); + private List chainNames = new ArrayList<>(); + + private Hashtable chainFile = new Hashtable<>(); - private Hashtable chainFile = new Hashtable(); - /* * Object through which we talk to Chimera */ @@ -102,12 +106,10 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel */ private boolean loadingFinished = true; - public String fileLoadingError; - /* * Map of ChimeraModel objects keyed by PDB full local file name */ - private Map> chimeraMaps = new LinkedHashMap>(); + private Map> chimeraMaps = new LinkedHashMap<>(); String lastHighlightCommand; @@ -118,6 +120,8 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel */ private long loadNotifiesHandled = 0; + private Thread chimeraMonitor; + /** * Open a PDB structure file in Chimera and set up mappings from Jalview. * @@ -132,7 +136,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel String file = pe.getFile(); try { - List modelsToMap = new ArrayList(); + List modelsToMap = new ArrayList<>(); List oldList = viewer.getModelList(); boolean alreadyOpen = false; @@ -171,13 +175,6 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel if (getSsm() != null) { getSsm().addStructureViewerListener(this); - // ssm.addSelectionListener(this); - FeatureRenderer fr = getFeatureRenderer(null); - if (fr != null) - { - fr.featuresAdded(); - } - refreshGUI(); } return true; } catch (Exception q) @@ -198,11 +195,42 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel * @param protocol */ public JalviewChimeraBinding(StructureSelectionManager ssm, - PDBEntry[] pdbentry, SequenceI[][] sequenceIs, DataSourceType protocol) + PDBEntry[] pdbentry, SequenceI[][] sequenceIs, + DataSourceType protocol) { super(ssm, pdbentry, sequenceIs, protocol); - viewer = new ChimeraManager( - new ext.edu.ucsf.rbvi.strucviz2.StructureManager(true)); + viewer = new ChimeraManager(new StructureManager(true)); + } + + /** + * Starts a thread that waits for the Chimera process to finish, so that we + * can then close the associated resources. This avoids leaving orphaned + * Chimera viewer panels in Jalview if the user closes Chimera. + */ + protected void startChimeraProcessMonitor() + { + final Process p = viewer.getChimeraProcess(); + chimeraMonitor = 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 + } + } + }); + chimeraMonitor.start(); } /** @@ -217,24 +245,12 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel viewer.startListening(chimeraListener.getUri()); } catch (BindException e) { - System.err.println("Failed to start Chimera listener: " - + e.getMessage()); + System.err.println( + "Failed to start Chimera listener: " + e.getMessage()); } } /** - * Construct a title string for the viewer window based on the data Jalview - * knows about - * - * @param verbose - * @return - */ - public String getViewerTitle(boolean verbose) - { - return getViewerTitle("Chimera", verbose); - } - - /** * Tells Chimera to display only the specified chains * * @param toshow @@ -251,8 +267,8 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel for (String chain : toshow) { int modelNumber = getModelNoForChain(chain); - String showChainCmd = modelNumber == -1 ? "" : modelNumber + ":." - + chain.split(":")[1]; + String showChainCmd = modelNumber == -1 ? "" + : modelNumber + ":." + chain.split(":")[1]; if (!first) { cmd.append(","); @@ -277,7 +293,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel */ public void closeViewer(boolean closeChimera) { - getSsm().removeStructureViewerListener(this, this.getPdbFile()); + getSsm().removeStructureViewerListener(this, this.getStructureFiles()); if (closeChimera) { viewer.exitChimera(); @@ -289,9 +305,14 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel } viewer = null; + if (chimeraMonitor != null) + { + chimeraMonitor.interrupt(); + } releaseUIResources(); } + @Override public void colourByChain() { colourBySequence = false; @@ -307,6 +328,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel *
  • all others - white
    • * */ + @Override public void colourByCharge() { colourBySequence = false; @@ -315,28 +337,18 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel } /** - * Construct and send a command to align structures against a reference - * structure, based on one or more sequence alignments - * - * @param _alignment - * an array of alignments to process - * @param _refStructure - * an array of corresponding reference structures (index into pdb - * file array); if a negative value is passed, the first PDB file - * mapped to an alignment sequence is used as the reference for - * superposition - * @param _hiddenCols - * an array of corresponding hidden columns for each alignment + * {@inheritDoc} */ - public void superposeStructures(AlignmentI[] _alignment, - int[] _refStructure, ColumnSelection[] _hiddenCols) + @Override + public String superposeStructures(AlignmentI[] _alignment, + int[] _refStructure, HiddenColumns[] _hiddenCols) { StringBuilder allComs = new StringBuilder(128); - String[] files = getPdbFile(); + String[] files = getStructureFiles(); if (!waitForFileLoad(files)) { - return; + return null; } refreshPdbEntries(); @@ -345,7 +357,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel { int refStructure = _refStructure[a]; AlignmentI alignment = _alignment[a]; - ColumnSelection hiddenCols = _hiddenCols[a]; + HiddenColumns hiddenCols = _hiddenCols[a]; if (refStructure >= files.length) { @@ -355,13 +367,16 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel } /* - * 'matched' array will hold 'true' for visible alignment columns where + * 'matched' bit i will be set for visible alignment columns i where * all sequences have a residue with a mapping to the PDB structure */ - boolean matched[] = new boolean[alignment.getWidth()]; - for (int m = 0; m < matched.length; m++) + BitSet matched = new BitSet(); + for (int m = 0; m < alignment.getWidth(); m++) { - matched[m] = (hiddenCols != null) ? hiddenCols.isVisible(m) : true; + if (hiddenCols == null || hiddenCols.isVisible(m)) + { + matched.set(m); + } } SuperposeData[] structures = new SuperposeData[files.length]; @@ -385,17 +400,11 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel refStructure = candidateRefStructure; } - int nmatched = 0; - for (boolean b : matched) - { - if (b) - { - nmatched++; - } - } + int nmatched = matched.cardinality(); if (nmatched < 4) { - // TODO: bail out here because superposition illdefined? + return MessageManager.formatMessage("label.insufficient_residues", + nmatched); } /* @@ -408,41 +417,41 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel int lpos = -1; boolean run = false; StringBuilder molsel = new StringBuilder(); - for (int r = 0; r < matched.length; r++) + + int nextColumnMatch = matched.nextSetBit(0); + while (nextColumnMatch != -1) { - if (matched[r]) + int pdbResNum = structures[pdbfnum].pdbResNo[nextColumnMatch]; + if (lpos != pdbResNum - 1) { - int pdbResNum = structures[pdbfnum].pdbResNo[r]; - if (lpos != pdbResNum - 1) + /* + * discontiguous - append last residue now + */ + if (lpos != -1) { - /* - * discontiguous - append last residue now - */ - if (lpos != -1) - { - molsel.append(String.valueOf(lpos)); - molsel.append(chainCd); - molsel.append(","); - } - run = false; + molsel.append(String.valueOf(lpos)); + molsel.append(chainCd); + molsel.append(","); } - else + run = false; + } + else + { + /* + * extending a contiguous run + */ + if (!run) { /* - * extending a contiguous run + * start the range selection */ - if (!run) - { - /* - * start the range selection - */ - molsel.append(String.valueOf(lpos)); - molsel.append("-"); - } - run = true; + molsel.append(String.valueOf(lpos)); + molsel.append("-"); } - lpos = pdbResNum; + run = true; } + lpos = pdbResNum; + nextColumnMatch = matched.nextSetBit(nextColumnMatch + 1); } /* @@ -510,14 +519,16 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel if (debug) { System.out.println("Select regions:\n" + selectioncom.toString()); - System.out.println("Superimpose command(s):\n" - + command.toString()); + System.out.println( + "Superimpose command(s):\n" + command.toString()); } - allComs.append("~display all; chain @CA|P; ribbon ") - .append(selectioncom.toString()) + allComs/*.append("~display all; chain @CA|P; ribbon ") + .append(selectioncom.toString())*/ .append(";" + command.toString()); } } + + String error = null; if (selectioncom.length() > 0) { // TODO: visually distinguish regions that were superposed @@ -529,11 +540,30 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel { System.out.println("Select regions:\n" + selectioncom.toString()); } - allComs.append("; ~display all; chain @CA|P; ribbon ") - .append(selectioncom.toString()).append("; focus"); - sendChimeraCommand(allComs.toString(), false); + allComs.append("; ~display "); // all"); + if (!isShowAlignmentOnly()) + { + allComs.append("; ribbon; chain @CA|P"); + } + else + { + allComs.append("; ~ribbon"); + } + allComs.append("; ribbon ").append(selectioncom.toString()) + .append("; focus"); + List chimeraReplies = sendChimeraCommand(allComs.toString(), + true); + for (String reply : chimeraReplies) + { + String lowerCase = reply.toLowerCase(); + if (lowerCase.contains("unequal numbers of atoms") + || lowerCase.contains("at least")) + { + error = reply; + } + } } - + return error; } /** @@ -562,30 +592,36 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel * to the Chimera command 'list models type molecule', see * ChimeraManager.getModelList(). */ - List maps = chimeraMaps.get(getPdbFile()[pdbfnum]); + List maps = chimeraMaps.get(getStructureFiles()[pdbfnum]); boolean hasSubModels = maps != null && maps.size() > 1; return "#" + String.valueOf(pdbfnum) + (hasSubModels ? ".1" : ""); } /** * Launch Chimera, unless an instance linked to this object is already - * running. Returns true if chimera is successfully launched, or already + * running. Returns true if Chimera is successfully launched, or already * running, else false. * * @return */ public boolean launchChimera() { - if (!viewer.isChimeraLaunched()) - { - return viewer.launchChimera(StructureManager.getChimeraPaths()); - } if (viewer.isChimeraLaunched()) { return true; } - log("Failed to launch Chimera!"); - return false; + + boolean launched = viewer + .launchChimera(StructureManager.getChimeraPaths()); + if (launched) + { + startChimeraProcessMonitor(); + } + else + { + log("Failed to launch Chimera!"); + } + return launched; } /** @@ -649,39 +685,35 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel String progressMsg); /** - * colour any structures associated with sequences in the given alignment - * using the getFeatureRenderer() and getSequenceRenderer() renderers but only - * if colourBySequence is enabled. + * Sends a set of colour commands to the structure viewer + * + * @param colourBySequenceCommands */ - public void colourBySequence(boolean showFeatures, - jalview.api.AlignmentViewPanel alignmentv) + @Override + protected void colourBySequence( + StructureMappingcommandSet[] colourBySequenceCommands) { - if (!colourBySequence || !loadingFinished) - { - return; - } - if (getSsm() == null) - { - return; - } - String[] files = getPdbFile(); - - SequenceRenderer sr = getSequenceRenderer(alignmentv); - - FeatureRenderer fr = null; - if (showFeatures) + for (StructureMappingcommandSet cpdbbyseq : colourBySequenceCommands) { - fr = getFeatureRenderer(alignmentv); + for (String command : cpdbbyseq.commands) + { + sendAsynchronousCommand(command, COLOURING_CHIMERA); + } } - AlignmentI alignment = alignmentv.getAlignment(); + } - StructureMappingcommandSet colourBySequenceCommands = ChimeraCommands - .getColourBySequenceCommand(getSsm(), files, getSequence(), sr, - fr, alignment); - for (String command : colourBySequenceCommands.commands) - { - sendAsynchronousCommand(command, COLOURING_CHIMERA); - } + /** + * @param files + * @param sr + * @param viewPanel + * @return + */ + @Override + protected StructureMappingcommandSet[] getColourBySequenceCommands( + String[] files, SequenceRenderer sr, AlignmentViewPanel viewPanel) + { + return ChimeraCommands.getColourBySequenceCommand(getSsm(), files, + getSequence(), sr, viewPanel); } /** @@ -711,49 +743,34 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel // ////////////////////////// /** - * returns the current featureRenderer that should be used to colour the - * structures - * - * @param alignment - * - * @return - */ - public abstract FeatureRenderer getFeatureRenderer( - AlignmentViewPanel alignment); - - /** * instruct the Jalview binding to update the pdbentries vector if necessary * prior to matching the viewer's contents to the list of structure files * Jalview knows about. */ public abstract void refreshPdbEntries(); + /** + * map between index of model filename returned from getPdbFile and the first + * index of models from this file in the viewer. Note - this is not trimmed - + * use getPdbFile to get number of unique models. + */ + private int _modelFileNameMap[]; + // //////////////////////////////// // /StructureListener @Override - public synchronized String[] getPdbFile() + public synchronized String[] getStructureFiles() { if (viewer == null) { return new String[0]; } - return chimeraMaps.keySet().toArray( - modelFileNames = new String[chimeraMaps.size()]); + return chimeraMaps.keySet() + .toArray(modelFileNames = new String[chimeraMaps.size()]); } /** - * returns the current sequenceRenderer that should be used to colour the - * structures - * - * @param alignment - * - * @return - */ - public abstract SequenceRenderer getSequenceRenderer( - AlignmentViewPanel alignment); - - /** * Construct and send a command to highlight zero, one or more atoms. We do * this by sending an "rlabel" command to show the residue label at that * position. @@ -834,7 +851,8 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel * Parse model number, residue and chain for each selected position, * formatted as #0:123.A or #1.2:87.B (#model.submodel:residue.chain) */ - List atomSpecs = convertStructureResiduesToAlignment(selection); + List atomSpecs = convertStructureResiduesToAlignment( + selection); /* * Broadcast the selection (which may be empty, if the user just cleared all @@ -853,7 +871,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel protected List convertStructureResiduesToAlignment( List structureSelection) { - List atomSpecs = new ArrayList(); + List atomSpecs = new ArrayList<>(); for (String atomSpec : structureSelection) { try @@ -910,6 +928,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel return loadNotifiesHandled; } + @Override public void setJalviewColourScheme(ColourSchemeI cs) { colourBySequence = false; @@ -926,12 +945,15 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel List residueSet = ResidueProperties.getResidues(isNucleotide(), false); - for (String res : residueSet) + for (String resName : residueSet) { - Color col = cs.findColour(res.charAt(0)); + char res = resName.length() == 3 + ? ResidueProperties.getSingleCharacterCode(resName) + : resName.charAt(0); + Color col = cs.findColour(res, 0, null, null, 0f); command.append("color " + col.getRed() / normalise + "," - + col.getGreen() / normalise + "," + col.getBlue() - / normalise + " ::" + res + ";"); + + col.getGreen() / normalise + "," + col.getBlue() / normalise + + " ::" + resName + ";"); } sendAsynchronousCommand(command.toString(), COLOURING_CHIMERA); @@ -977,18 +999,19 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel /** * Send the Chimera 'background solid " command. * - * @see https + * @see https * ://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/background * .html * @param col */ + @Override public void setBackgroundColour(Color col) { viewerCommandHistory(false); double normalise = 255D; final String command = "background solid " + col.getRed() / normalise - + "," + col.getGreen() / normalise + "," + col.getBlue() - / normalise + ";"; + + "," + col.getGreen() / normalise + "," + + col.getBlue() / normalise + ";"; viewer.sendChimeraCommand(command, false); viewerCommandHistory(true); } @@ -1086,30 +1109,22 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel * features visible in Jalview * * @param avp + * @return */ - public void sendFeaturesToViewer(AlignmentViewPanel avp) + public int sendFeaturesToViewer(AlignmentViewPanel avp) { // TODO refactor as required to pull up to an interface AlignmentI alignment = avp.getAlignment(); - FeatureRenderer fr = getFeatureRenderer(avp); - /* - * fr is null if feature display is turned off - */ - if (fr == null) - { - return; - } - - String[] files = getPdbFile(); + String[] files = getStructureFiles(); if (files == null) { - return; + return 0; } StructureMappingcommandSet commandSet = ChimeraCommands .getSetAttributeCommandsForFeatures(getSsm(), files, - getSequence(), fr, alignment); + getSequence(), avp); String[] commands = commandSet.commands; if (commands.length > 10) { @@ -1122,6 +1137,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel sendAsynchronousCommand(command, null); } } + return commands.length; } /** @@ -1148,9 +1164,8 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel sendAsynchronousCommand("open cmd:" + path, null); } catch (IOException e) { - System.err - .println("Sending commands to Chimera via file failed with " - + e.getMessage()); + System.err.println("Sending commands to Chimera via file failed with " + + e.getMessage()); } } @@ -1254,7 +1269,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel /* * locate the mapped position in the alignment (if any) */ - SearchResults sr = getSsm() + SearchResultsI sr = getSsm() .findAlignmentPositionsForStructurePositions(atoms); /* @@ -1288,7 +1303,6 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel return CHIMERA_FEATURE_GROUP; } - public Hashtable getChainFile() { return chainFile; @@ -1308,4 +1322,102 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel } return -1; } + + @Override + public void showStructures(AlignViewportI av) + { + StringBuilder cmd = new StringBuilder(128); + cmd.append("~display; ~ribbon;"); + if (isShowAlignmentOnly()) + { + String atomSpec = getMappedResidues(av); + cmd.append("ribbon ").append(atomSpec); + } + else + { + cmd.append("chain @CA|P; ribbon"); + } + cmd.append("; focus"); + sendChimeraCommand(cmd.toString(), false); + } + + /** + * Builds a Chimera atomSpec of residues mapped from sequences, of the format + * (#model:residues.chain) + * + * 
    +   * #0:2-94.A | #1:1-93.C | #2:1-93.A
+   *
    + * + * Only residues visible in the alignment are included, that is, hidden columns + * and sequences are excluded. + * + * @param av + * @return + */ + private String getMappedResidues(AlignViewportI av) + { + AlignmentI alignment = av.getAlignment(); + final int width = alignment.getWidth(); + + String[] files = getStructureFiles(); + + StringBuilder atomSpec = new StringBuilder(256); + + for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) + { + StructureMapping[] mappings = getSsm().getMapping(files[pdbfnum]); + + /* + * Find the first mapped sequence (if any) for this PDB entry which is in + * the alignment + */ + final int seqCountForPdbFile = getSequence()[pdbfnum].length; + for (int s = 0; s < seqCountForPdbFile; s++) + { + for (StructureMapping mapping : mappings) + { + final SequenceI theSequence = getSequence()[pdbfnum][s]; + if (mapping.getSequence() == theSequence + && alignment.findIndex(theSequence) > -1) + { + String chainCd = mapping.getChain(); + + // TODO only process sequence ranges within visible columns + VisibleContigsIterator visible = alignment.getHiddenColumns() + .getVisContigsIterator(0, width, true); + while (visible.hasNext()) + { + int[] visibleRegion = visible.next(); + int seqStartPos = theSequence.findPosition(visibleRegion[0]); + int seqEndPos = theSequence.findPosition(visibleRegion[1]); + List residueRanges = mapping + .getPDBResNumRanges(seqStartPos, seqEndPos); + if (!residueRanges.isEmpty()) + { + if (atomSpec.length() > 0) + { + atomSpec.append("| "); + } + atomSpec.append(getModelSpec(pdbfnum)).append(":"); + boolean first = true; + for (int[] range : residueRanges) + { + if (!first) + { + atomSpec.append(","); + } + first = false; + atomSpec.append(range[0]).append("-").append(range[1]); + atomSpec.append(".").append(chainCd); + } + } + } + } + } + } + } + + return atomSpec.toString(); + } }