X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Frbvi%2Fchimera%2FJalviewChimeraBinding.java;h=415fc1b2a631d6319350f076bf2a1c8f4c7d73fc;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=3c455c28105ec913f5d7db050b5f5449877e2ff9;hpb=a7ea1ba47dae32481aa6390a29cef6c7c5a403c4;p=jalview.git diff --git a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java index 3c455c2..415fc1b 100644 --- a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java +++ b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.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) + * Copyright (C) 2015 The Jalview Authors * * This file is part of Jalview. * @@ -20,18 +20,6 @@ */ package jalview.ext.rbvi.chimera; -import java.awt.Color; -import java.net.BindException; -import java.util.ArrayList; -import java.util.LinkedHashMap; -import java.util.List; -import java.util.Map; - -import ext.edu.ucsf.rbvi.strucviz2.ChimeraManager; -import ext.edu.ucsf.rbvi.strucviz2.ChimeraModel; -import ext.edu.ucsf.rbvi.strucviz2.StructureManager; -import ext.edu.ucsf.rbvi.strucviz2.StructureManager.ModelType; - import jalview.api.AlignmentViewPanel; import jalview.api.FeatureRenderer; import jalview.api.SequenceRenderer; @@ -44,26 +32,37 @@ import jalview.httpserver.AbstractRequestHandler; 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; -import jalview.util.Comparison; import jalview.util.MessageManager; +import java.awt.Color; +import java.net.BindException; +import java.util.ArrayList; +import java.util.LinkedHashMap; +import java.util.List; +import java.util.Map; + +import ext.edu.ucsf.rbvi.strucviz2.ChimeraManager; +import ext.edu.ucsf.rbvi.strucviz2.ChimeraModel; +import ext.edu.ucsf.rbvi.strucviz2.StructureManager; +import ext.edu.ucsf.rbvi.strucviz2.StructureManager.ModelType; + public abstract class JalviewChimeraBinding extends AAStructureBindingModel { // Chimera clause to exclude alternate locations in atom selection private static final String NO_ALTLOCS = "&~@.B-Z&~@.2-9"; + private static final String COLOURING_CHIMERA = MessageManager + .getString("status.colouring_chimera"); + private static final boolean debug = false; private static final String PHOSPHORUS = "P"; private static final String ALPHACARBON = "CA"; - private StructureManager csm; - /* * Object through which we talk to Chimera */ @@ -87,17 +86,6 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel */ private boolean loadingFinished = true; - /* - * state flag used to check if the Chimera viewer's paint method can be called - */ - private boolean finishedInit = false; - - private List atomsPicked = new ArrayList(); - - private List chainNames; - - private Map chainFile; - public String fileLoadingError; /* @@ -217,7 +205,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel { super(ssm, pdbentry, sequenceIs, chains, protocol); viewer = new ChimeraManager( - csm = new ext.edu.ucsf.rbvi.strucviz2.StructureManager(true)); + new ext.edu.ucsf.rbvi.strucviz2.StructureManager(true)); } /** @@ -238,20 +226,6 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel } /** - * Constructor - * - * @param ssm - * @param theViewer - */ - public JalviewChimeraBinding(StructureSelectionManager ssm, - ChimeraManager theViewer) - { - super(ssm, null); - viewer = theViewer; - csm = viewer.getStructureManager(); - } - - /** * Construct a title string for the viewer window based on the data Jalview * knows about * @@ -264,34 +238,37 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel } /** - * prepare the view for a given set of models/chains. chainList contains - * strings of the form 'pdbfilename:Chaincode' + * Tells Chimera to display only the specified chains * * @param toshow - * list of chains to make visible */ - public void centerViewer(List toshow) + public void showChains(List toshow) { + /* + * Construct a chimera command like + * + * ~display #*;~ribbon #*;ribbon :.A,:.B + */ StringBuilder cmd = new StringBuilder(64); - int mlength, p; - for (String lbl : toshow) + boolean first = true; + for (String chain : toshow) { - mlength = 0; - do + if (!first) { - p = mlength; - mlength = lbl.indexOf(":", p); - } while (p < mlength && mlength < (lbl.length() - 2)); - // TODO: lookup each pdb id and recover proper model number for it. - cmd.append("#" + getModelNum(chainFile.get(lbl)) + "." - + lbl.substring(mlength + 1) + " or "); - } - if (cmd.length() > 0) - { - cmd.setLength(cmd.length() - 4); + cmd.append(","); + } + cmd.append(":.").append(chain); + first = false; } - String cmdstring = cmd.toString(); - evalStateCommand("~display #*; ~ribbon #*; ribbon " + cmdstring, false); + + /* + * could append ";focus" to this command to resize the display to fill the + * window, but it looks more helpful not to (easier to relate chains to the + * whole) + */ + final String command = "~display #*; ~ribbon #*; ribbon " + + cmd.toString(); + sendChimeraCommand(command, false); } /** @@ -319,287 +296,182 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel public void colourByChain() { colourBySequence = false; - evalStateCommand("rainbow chain", false); - } - - public void colourByCharge() - { - colourBySequence = false; - evalStateCommand( - "color white;color red ::ASP;color red ::GLU;color blue ::LYS;color blue ::ARG;color yellow ::CYS", - false); - } - - /** - * superpose the structures associated with sequences in the alignment - * according to their corresponding positions. - */ - public void superposeStructures(AlignmentI alignment) - { - superposeStructures(alignment, -1, null); + sendAsynchronousCommand("rainbow chain", COLOURING_CHIMERA); } /** - * superpose the structures associated with sequences in the alignment - * according to their corresponding positions. ded) - * - * @param refStructure - * - select which pdb file to use as reference (default is -1 - the - * first structure in the alignment) + * Constructs and sends a Chimera command to colour by charge + *
    + *
  • Aspartic acid and Glutamic acid (negative charge) red
    • + *
  • Lysine and Arginine (positive charge) blue
    • + *
  • Cysteine - yellow
    • + *
  • all others - white
    • + *
*/ - public void superposeStructures(AlignmentI alignment, int refStructure) + public void colourByCharge() { - superposeStructures(alignment, refStructure, null); + colourBySequence = false; + String command = "color white;color red ::ASP;color red ::GLU;color blue ::LYS;color blue ::ARG;color yellow ::CYS"; + sendAsynchronousCommand(command, COLOURING_CHIMERA); } /** - * superpose the structures associated with sequences in the alignment - * according to their corresponding positions. ded) + * Construct and send a command to align structures against a reference + * structure, based on one or more sequence alignments * - * @param refStructure - * - select which pdb file to use as reference (default is -1 - the - * first structure in the alignment) - * @param hiddenCols - * TODO + * @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 */ - public void superposeStructures(AlignmentI alignment, int refStructure, - ColumnSelection hiddenCols) - { - superposeStructures(new AlignmentI[] - { alignment }, new int[] - { refStructure }, new ColumnSelection[] - { hiddenCols }); - } - public void superposeStructures(AlignmentI[] _alignment, int[] _refStructure, ColumnSelection[] _hiddenCols) { - assert (_alignment.length == _refStructure.length && _alignment.length != _hiddenCols.length); - StringBuilder allComs = new StringBuilder(128); // Chimera superposition cmd + StringBuilder allComs = new StringBuilder(128); String[] files = getPdbFile(); - // check to see if we are still waiting for Chimera files - long starttime = System.currentTimeMillis(); - boolean waiting = true; - do - { - waiting = false; - for (String file : files) - { - try - { - // HACK - in Jalview 2.8 this call may not be threadsafe so we catch - // every possible exception - StructureMapping[] sm = getSsm().getMapping(file); - if (sm == null || sm.length == 0) - { - waiting = true; - } - } catch (Exception x) - { - waiting = true; - } catch (Error q) - { - waiting = true; - } - } - // we wait around for a reasonable time before we give up - } while (waiting - && System.currentTimeMillis() < (10000 + 1000 * files.length + starttime)); - if (waiting) + + if (!waitForFileLoad(files)) { - System.err - .println("RUNTIME PROBLEM: Chimera seems to be taking a long time to process all the structures."); return; } + refreshPdbEntries(); - StringBuffer selectioncom = new StringBuffer(); + StringBuilder selectioncom = new StringBuilder(256); for (int a = 0; a < _alignment.length; a++) { int refStructure = _refStructure[a]; AlignmentI alignment = _alignment[a]; ColumnSelection hiddenCols = _hiddenCols[a]; - if (a > 0 - && selectioncom.length() > 0 - && !selectioncom.substring(selectioncom.length() - 1).equals( - " ")) - { - selectioncom.append(" "); - } - // process this alignment + if (refStructure >= files.length) { - System.err.println("Invalid reference structure value " + System.err.println("Ignoring invalid reference structure value " + refStructure); refStructure = -1; } - if (refStructure < -1) - { - refStructure = -1; - } + /* + * 'matched' array will hold 'true' for visible alignment columns 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++) { - matched[m] = (hiddenCols != null) ? hiddenCols.isVisible(m) : true; } - int commonrpositions[][] = new int[files.length][alignment.getWidth()]; - String isel[] = new String[files.length]; - String[] targetC = new String[files.length]; - String[] chainNames = new String[files.length]; - String[] atomSpec = new String[files.length]; - for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) + SuperposeData[] structures = new SuperposeData[files.length]; + for (int f = 0; f < files.length; f++) { - StructureMapping[] mapping = getSsm().getMapping(files[pdbfnum]); - // RACE CONDITION - getMapping only returns Jmol loaded filenames once - // Jmol callback has completed. - if (mapping == null || mapping.length < 1) - { - throw new Error(MessageManager.getString("error.implementation_error_chimera_getting_data")); - } - int lastPos = -1; - final int seqCountForPdbFile = getSequence()[pdbfnum].length; - for (int s = 0; s < seqCountForPdbFile; s++) + structures[f] = new SuperposeData(alignment.getWidth()); + } + + /* + * Calculate the superposable alignment columns ('matched'), and the + * corresponding structure residue positions (structures.pdbResNo) + */ + int candidateRefStructure = findSuperposableResidues(alignment, + matched, structures); + if (refStructure < 0) + { + /* + * If no reference structure was specified, pick the first one that has + * a mapping in the alignment + */ + refStructure = candidateRefStructure; + } + + int nmatched = 0; + for (boolean b : matched) + { + if (b) { - for (int sp, m = 0; m < mapping.length; m++) - { - final SequenceI theSequence = getSequence()[pdbfnum][s]; - if (mapping[m].getSequence() == theSequence - && (sp = alignment.findIndex(theSequence)) > -1) - { - if (refStructure == -1) - { - refStructure = pdbfnum; - } - SequenceI asp = alignment.getSequenceAt(sp); - for (int r = 0; r < matched.length; r++) - { - if (!matched[r]) - { - continue; - } - matched[r] = false; // assume this is not a good site - if (r >= asp.getLength()) - { - continue; - } - - if (Comparison.isGap(asp.getCharAt(r))) - { - // no mapping to gaps in sequence - continue; - } - int t = asp.findPosition(r); // sequence position - int apos = mapping[m].getAtomNum(t); - int pos = mapping[m].getPDBResNum(t); - - if (pos < 1 || pos == lastPos) - { - // can't align unmapped sequence - continue; - } - matched[r] = true; // this is a good ite - lastPos = pos; - // just record this residue position - commonrpositions[pdbfnum][r] = pos; - } - // create model selection suffix - isel[pdbfnum] = "#" + pdbfnum; - if (mapping[m].getChain() == null - || mapping[m].getChain().trim().length() == 0) - { - targetC[pdbfnum] = ""; - } - else - { - targetC[pdbfnum] = "." + mapping[m].getChain(); - } - chainNames[pdbfnum] = mapping[m].getPdbId() - + targetC[pdbfnum]; - atomSpec[pdbfnum] = asp.getRNA() != null ? PHOSPHORUS : ALPHACARBON; - // move on to next pdb file - s = seqCountForPdbFile; - break; - } - } + nmatched++; } } + if (nmatched < 4) + { + // TODO: bail out here because superposition illdefined? + } - // TODO: consider bailing if nmatched less than 4 because superposition - // not - // well defined. - // TODO: refactor superposable position search (above) from jmol selection - // construction (below) - + /* + * Generate select statements to select regions to superimpose structures + */ String[] selcom = new String[files.length]; - int nmatched = 0; - String sep = ""; - // generate select statements to select regions to superimpose structures + for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) { - for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) + String chainCd = "." + structures[pdbfnum].chain; + int lpos = -1; + boolean run = false; + StringBuilder molsel = new StringBuilder(); + for (int r = 0; r < matched.length; r++) { - String chainCd = targetC[pdbfnum]; - int lpos = -1; - boolean run = false; - StringBuffer molsel = new StringBuffer(); - for (int r = 0; r < matched.length; r++) + if (matched[r]) { - if (matched[r]) + int pdbResNum = structures[pdbfnum].pdbResNo[r]; + if (lpos != pdbResNum - 1) { - if (pdbfnum == 0) + /* + * discontiguous - append last residue now + */ + if (lpos != -1) { - nmatched++; + molsel.append(String.valueOf(lpos)); + molsel.append(chainCd); + molsel.append(","); } - if (lpos != commonrpositions[pdbfnum][r] - 1) - { - // discontinuity - if (lpos != -1) - { - molsel.append((run ? "" : ":") + lpos); - molsel.append(chainCd); - molsel.append(","); - } - } - else - { - // continuous run - and lpos >-1 - if (!run) - { - // at the beginning, so add dash - molsel.append(":" + lpos); - molsel.append("-"); - } - run = true; - } - lpos = commonrpositions[pdbfnum][r]; - // molsel.append(lpos); + run = false; } - } - // add final selection phrase - if (lpos != -1) - { - molsel.append((run ? "" : ":") + lpos); - molsel.append(chainCd); - // molsel.append(""); - } - if (molsel.length() > 1) - { - selcom[pdbfnum] = molsel.toString(); - selectioncom.append("#" + pdbfnum); - selectioncom.append(selcom[pdbfnum]); - selectioncom.append(" "); - if (pdbfnum < files.length - 1) + else { - selectioncom.append("| "); + /* + * extending a contiguous run + */ + if (!run) + { + /* + * start the range selection + */ + molsel.append(String.valueOf(lpos)); + molsel.append("-"); + } + run = true; } + lpos = pdbResNum; } - else + } + + /* + * and terminate final selection + */ + if (lpos != -1) + { + molsel.append(String.valueOf(lpos)); + molsel.append(chainCd); + } + if (molsel.length() > 1) + { + selcom[pdbfnum] = molsel.toString(); + selectioncom.append("#").append(String.valueOf(pdbfnum)) + .append(":"); + selectioncom.append(selcom[pdbfnum]); + selectioncom.append(" "); + if (pdbfnum < files.length - 1) { - selcom[pdbfnum] = null; + selectioncom.append("| "); } } + else + { + selcom[pdbfnum] = null; + } } + StringBuilder command = new StringBuilder(256); for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) { @@ -615,22 +487,23 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel /* * Form Chimera match command, from the 'new' structure to the - * 'reference' structure e.g. (residues 1-91, chain B/A, alphacarbons): + * 'reference' structure e.g. (50 residues, chain B/A, alphacarbons): * - * match #1:1-91.B@CA #0:1-91.A@CA + * match #1:1-30.B,81-100.B@CA #0:21-40.A,61-90.A@CA * * @see * https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html */ - command.append("match #" + pdbfnum /* +".1" */); - // TODO: handle sub-models + command.append("match ").append(getModelSpec(pdbfnum)).append(":"); command.append(selcom[pdbfnum]); - command.append("@" + atomSpec[pdbfnum]); - // JAL-1757 exclude alternative CA locations + command.append("@").append( + structures[pdbfnum].isRna ? PHOSPHORUS : ALPHACARBON); + // JAL-1757 exclude alternate CA locations command.append(NO_ALTLOCS); - command.append(" #" + refStructure /* +".1" */); + command.append(" ").append(getModelSpec(refStructure)).append(":"); command.append(selcom[refStructure]); - command.append("@" + atomSpec[refStructure]); + command.append("@").append( + structures[refStructure].isRna ? PHOSPHORUS : ALPHACARBON); command.append(NO_ALTLOCS); } if (selectioncom.length() > 0) @@ -641,13 +514,14 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel System.out.println("Superimpose command(s):\n" + command.toString()); } - allComs.append("~display all; chain @CA|P; ribbon " - + selectioncom.toString() + ";"+command.toString()); - // selcom.append("; ribbons; "); + allComs.append("~display all; chain @CA|P; ribbon ") + .append(selectioncom.toString()) + .append(";" + command.toString()); } } if (selectioncom.length() > 0) - {// finally, mark all regions that were superposed. + { + // TODO: visually distinguish regions that were superposed if (selectioncom.substring(selectioncom.length() - 1).equals("|")) { selectioncom.setLength(selectioncom.length() - 1); @@ -656,24 +530,63 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel { System.out.println("Select regions:\n" + selectioncom.toString()); } - allComs.append("; ~display all; chain @CA|P; ribbon " - + selectioncom.toString() + "; focus"); - // evalStateCommand("select *; backbone; select "+selcom.toString()+"; cartoons; center "+selcom.toString()); - evalStateCommand(allComs.toString(), true /* false */); + allComs.append("; ~display all; chain @CA|P; ribbon ") + .append(selectioncom.toString()).append("; focus"); + sendChimeraCommand(allComs.toString(), false); } - + } - private void checkLaunched() + /** + * Helper method to construct model spec in Chimera format: + *
    + *
  • #0 (#1 etc) for a PDB file with no sub-models
    • + *
  • #0.1 (#1.1 etc) for a PDB file with sub-models
    • + *
      + * Note for now we only ever choose the first of multiple models. This + * corresponds to the hard-coded Jmol equivalent (compare {1.1}). Refactor in + * future if there is a need to select specific sub-models. + * + * @param pdbfnum + * @return + */ + protected String getModelSpec(int pdbfnum) { - if (!viewer.isChimeraLaunched()) + if (pdbfnum < 0 || pdbfnum >= getPdbCount()) { - viewer.launchChimera(StructureManager.getChimeraPaths()); + return ""; } + + /* + * For now, the test for having sub-models is whether multiple Chimera + * models are mapped for the PDB file; the models are returned as a response + * to the Chimera command 'list models type molecule', see + * ChimeraManager.getModelList(). + */ + List maps = chimeraMaps.get(getPdbFile()[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, else false. + * + * @return + */ + public boolean launchChimera() + { if (!viewer.isChimeraLaunched()) { - log("Failed to launch Chimera!"); + return viewer.launchChimera(StructureManager.getChimeraPaths()); } + if (viewer.isChimeraLaunched()) + { + return true; + } + log("Failed to launch Chimera!"); + return false; } /** @@ -688,21 +601,24 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel } /** - * Send a command to Chimera, launching it first if necessary, and optionally - * log any responses. + * Send a command to Chimera, and optionally log any responses. * * @param command * @param logResponse */ - public void evalStateCommand(final String command, boolean logResponse) + public void sendChimeraCommand(final String command, boolean logResponse) { + if (viewer == null) + { + // ? thread running after viewer shut down + return; + } viewerCommandHistory(false); - checkLaunched(); if (lastCommand == null || !lastCommand.equals(command)) { // trim command or it may never find a match in the replyLog!! lastReply = viewer.sendChimeraCommand(command.trim(), logResponse); - if (debug && logResponse) + if (logResponse && debug) { log("Response from command ('" + command + "') was:\n" + lastReply); } @@ -712,6 +628,16 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel } /** + * Send a Chimera 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 abstract void sendAsynchronousCommand(String command, + String progressMsg); + + /** * colour any structures associated with sequences in the given alignment * using the getFeatureRenderer() and getSequenceRenderer() renderers but only * if colourBySequence is enabled. @@ -743,7 +669,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel { for (String command : cpdbbyseq.commands) { - executeWhenReady(command); + sendAsynchronousCommand(command, COLOURING_CHIMERA); } } } @@ -769,7 +695,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel protected void executeWhenReady(String command) { waitForChimera(); - evalStateCommand(command, false); + sendChimeraCommand(command, false); waitForChimera(); } @@ -777,15 +703,15 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel { while (viewer != null && viewer.isBusy()) { - try { + try + { Thread.sleep(15); } catch (InterruptedException q) - {} + { + } } } - - // End StructureListener // ////////////////////////// @@ -813,7 +739,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel /** * instruct the Jalview binding to update the pdbentries vector if necessary - * prior to matching the jmol view's contents to the list of structure files + * prior to matching the viewer's contents to the list of structure files * Jalview knows about. */ public abstract void refreshPdbEntries(); @@ -844,6 +770,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel // //////////////////////////////// // /StructureListener + @Override public synchronized String[] getPdbFile() { if (viewer == null) @@ -888,46 +815,63 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel AlignmentViewPanel alignment); /** - * Construct and send a command to highlight an atom. + * Construct and send a command to highlight zero, one or more atoms. * * 
          * Done by generating a command like (to 'highlight' position 44)
-   *   ~show #0:43.C;show #0:44.C
-   * Note this removes the highlight from the previous position.
+   *   show #0:44.C
    *
      */ - public void highlightAtom(int atomIndex, int pdbResNum, String chain, - String pdbfile) + @Override + public void highlightAtoms(List atoms) { - List cms = chimeraMaps.get(pdbfile); - if (cms != null) + if (atoms == null) { - StringBuilder sb = new StringBuilder(); - sb.append(" #" + cms.get(0).getModelNumber()); - sb.append(":" + pdbResNum); - if (!chain.equals(" ")) + return; + } + StringBuilder atomSpecs = new StringBuilder(); + boolean first = true; + for (AtomSpec atom : atoms) + { + int pdbResNum = atom.getPdbResNum(); + String chain = atom.getChain(); + String pdbfile = atom.getPdbFile(); + List cms = chimeraMaps.get(pdbfile); + if (cms != null && !cms.isEmpty()) { - sb.append("." + chain); + /* + * Formatting as #0:34.A,#1:33.A doesn't work as desired, so instead we + * concatenate multiple 'show' commands + */ + atomSpecs.append(first ? "" : ";show "); + first = false; + atomSpecs.append("#" + cms.get(0).getModelNumber()); + atomSpecs.append(":" + pdbResNum); + if (!chain.equals(" ")) + { + atomSpecs.append("." + chain); + } } - String atomSpec = sb.toString(); + } + String atomSpec = atomSpecs.toString(); - StringBuilder command = new StringBuilder(32); - if (lastMousedOverAtomSpec != null) - { - command.append("~show " + lastMousedOverAtomSpec + ";"); - } - viewerCommandHistory(false); + /* + * Avoid repeated commands for the same residue + */ + if (atomSpec.equals(lastMousedOverAtomSpec)) + { + return; + } + + StringBuilder command = new StringBuilder(32); + viewerCommandHistory(false); + if (atomSpec.length() > 0) + { command.append("show ").append(atomSpec); - String cmd = command.toString(); - if (cmd.length() > 0) - { - viewer.stopListening(chimeraListener.getUri()); - viewer.sendChimeraCommand(cmd, false); - viewer.startListening(chimeraListener.getUri()); - } - viewerCommandHistory(true); - this.lastMousedOverAtomSpec = atomSpec; + viewer.sendChimeraCommand(command.toString(), false); } + viewerCommandHistory(true); + this.lastMousedOverAtomSpec = atomSpec; } /** @@ -952,26 +896,28 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel { continue; // malformed } - + int hashPos = atomSpec.indexOf("#"); String modelSubmodel = atomSpec.substring(hashPos + 1, colonPos); int dotPos = modelSubmodel.indexOf("."); int modelId = 0; - try { + try + { modelId = Integer.valueOf(dotPos == -1 ? modelSubmodel : modelSubmodel.substring(0, dotPos)); - } catch (NumberFormatException e) { + } catch (NumberFormatException e) + { // ignore, default to model 0 } - + String residueChain = atomSpec.substring(colonPos + 1); dotPos = residueChain.indexOf("."); int pdbResNum = Integer.parseInt(dotPos == -1 ? residueChain : residueChain.substring(0, dotPos)); - + String chainId = dotPos == -1 ? "" : residueChain .substring(dotPos + 1); - + /* * Work out the pdbfilename from the model number */ @@ -1037,7 +983,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel / normalise + " ::" + res + ";"); } - evalStateCommand(command.toString(),false); + sendAsynchronousCommand(command.toString(), COLOURING_CHIMERA); viewerCommandHistory(true); } @@ -1077,7 +1023,7 @@ 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 @@ -1086,8 +1032,8 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel { viewerCommandHistory(false); double normalise = 255D; - final String command = "background solid " + col.getRed() / normalise + "," - + col.getGreen() / normalise + "," + col.getBlue() + final String command = "background solid " + col.getRed() / normalise + + "," + col.getGreen() / normalise + "," + col.getBlue() / normalise + ";"; viewer.sendChimeraCommand(command, false); viewerCommandHistory(true); @@ -1128,24 +1074,45 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel */ public boolean openSession(String filepath) { - evalStateCommand("open " + filepath, true); + sendChimeraCommand("open " + filepath, true); // todo: test for failure - how? return true; } - public boolean isFinishedInit() - { - return finishedInit; - } - - public void setFinishedInit(boolean finishedInit) + /** + * Returns a list of chains mapped in this viewer. Note this list is not + * currently scoped per structure. + * + * @return + */ + public List getChainNames() { - this.finishedInit = finishedInit; + List names = new ArrayList(); + String[][] allNames = getChains(); + if (allNames != null) + { + for (String[] chainsForPdb : allNames) + { + if (chainsForPdb != null) + { + for (String chain : chainsForPdb) + { + if (chain != null && !names.contains(chain)) + { + names.add(chain); + } + } + } + } + } + return names; } - public List getChainNames() + /** + * Send a 'focus' command to Chimera to recentre the visible display + */ + public void focusView() { - return chainNames; + sendChimeraCommand("focus", false); } - }