X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Frbvi%2Fchimera%2FJalviewChimeraBinding.java;h=6fa06d256365dd2210338957aecfc9e7d52b26a1;hb=defb4c1d5b4edbd8fbd490f25c15ef1f1de6fe37;hp=cb2a9ca3b225f67189c446dfacc2b9388877bd84;hpb=c66902a9536b10a5477b58aaf7c2d75772890a5d;p=jalview.git diff --git a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java index cb2a9ca..6fa06d2 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 2.8.2) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -20,29 +20,40 @@ */ 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.SearchResultsI; +import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; -import jalview.io.AppletFormatAdapter; +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; -import jalview.util.Comparison; import jalview.util.MessageManager; import java.awt.Color; -import java.awt.event.ComponentEvent; import java.io.File; +import java.io.FileOutputStream; +import java.io.IOException; +import java.io.PrintWriter; +import java.net.BindException; import java.util.ArrayList; -import java.util.Enumeration; -import java.util.HashMap; +import java.util.BitSet; +import java.util.Collections; +import java.util.Hashtable; import java.util.LinkedHashMap; import java.util.List; import java.util.Map; @@ -54,6 +65,13 @@ import ext.edu.ucsf.rbvi.strucviz2.StructureManager.ModelType; public abstract class JalviewChimeraBinding extends AAStructureBindingModel { + public static final String CHIMERA_FEATURE_GROUP = "Chimera"; + + // 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; @@ -61,127 +79,104 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel private static final String ALPHACARBON = "CA"; - private StructureManager csm; + private List chainNames = new ArrayList<>(); + private Hashtable chainFile = new Hashtable<>(); + + /* + * Object through which we talk to Chimera + */ private ChimeraManager viewer; - /** + /* + * Object which listens to Chimera notifications + */ + private AbstractRequestHandler chimeraListener; + + /* * set if chimera state is being restored from some source - instructs binding * not to apply default display style when structure set is updated for first * time. */ private boolean loadingFromArchive = false; - /** - * second flag to indicate if the Chimera viewer should ignore sequence - * colouring events from the structure manager because the GUI is still - * setting up + /* + * flag to indicate if the Chimera viewer should ignore sequence colouring + * events from the structure manager because the GUI is still setting up */ private boolean loadingFinished = true; - /** - * state flag used to check if the Chimera viewer's paint method can be called + /* + * Map of ChimeraModel objects keyed by PDB full local file name */ - private boolean finishedInit = false; - - public boolean isFinishedInit() - { - return finishedInit; - } + private Map> chimeraMaps = new LinkedHashMap<>(); - public void setFinishedInit(boolean finishedInit) - { - this.finishedInit = finishedInit; - } + String lastHighlightCommand; - boolean allChainsSelected = false; - - /** - * when true, try to search the associated datamodel for sequences that are - * associated with any unknown structures in the Chimera view. + /* + * incremented every time a load notification is successfully handled - + * lightweight mechanism for other threads to detect when they can start + * referring to new structures. */ - private boolean associateNewStructs = false; - - List atomsPicked = new ArrayList(); - - public List chainNames; - - private Map chainFile; - - StringBuffer eval = new StringBuffer(); - - public String fileLoadingError; - - private Map> chimmaps = new LinkedHashMap>(); + private long loadNotifiesHandled = 0; - private List mdlToFile = new ArrayList(); + private Thread chimeraMonitor; /** - * the default or current model displayed if the model cannot be identified - * from the selection message + * Open a PDB structure file in Chimera and set up mappings from Jalview. + * + * We check if the PDB model id is already loaded in Chimera, if so don't + * reopen it. This is the case if Chimera has opened a saved session file. + * + * @param pe + * @return */ - int frameNo = 0; - - String lastCommand; - - String lastMessage; - - boolean loadedInline; - public boolean openFile(PDBEntry pe) { String file = pe.getFile(); try { + List modelsToMap = new ArrayList<>(); List oldList = viewer.getModelList(); - viewer.openModel(file, pe.getId(), ModelType.PDB_MODEL); - List newList = viewer.getModelList(); - if (oldList.size() < newList.size()) + boolean alreadyOpen = false; + + /* + * If Chimera already has this model, don't reopen it, but do remap it. + */ + for (ChimeraModel open : oldList) { - while (oldList.size() > 0) + if (open.getModelName().equals(pe.getId())) { - oldList.remove(0); - newList.remove(0); + alreadyOpen = true; + modelsToMap.add(open); } - chimmaps.put(file, newList); + } + + /* + * If Chimera doesn't yet have this model, ask it to open it, and retrieve + * the model name(s) added by Chimera. + */ + if (!alreadyOpen) + { + viewer.openModel(file, pe.getId(), ModelType.PDB_MODEL); + List newList = viewer.getModelList(); + // JAL-1728 newList.removeAll(oldList) does not work for (ChimeraModel cm : newList) { - while (mdlToFile.size() < 1 + cm.getModelNumber()) + if (cm.getModelName().equals(pe.getId())) { - mdlToFile.add(new String("")); + modelsToMap.add(cm); } - mdlToFile.set(cm.getModelNumber(), file); } + } - File fl = new File(file); - String protocol = AppletFormatAdapter.URL; - try - { - if (fl.exists()) - { - protocol = AppletFormatAdapter.FILE; - } - } catch (Exception e) - { - } catch (Error e) - { - } - // Explicitly map to the filename used by Chimera ; - // pdbentry[pe].getFile(), protocol); + chimeraMaps.put(file, modelsToMap); - if (getSsm() != null) - { - getSsm().addStructureViewerListener(this); - // ssm.addSelectionListener(this); - FeatureRenderer fr = getFeatureRenderer(null); - if (fr != null) - { - fr.featuresAdded(); - } - refreshGUI(); - } - return true; + if (getSsm() != null) + { + getSsm().addStructureViewerListener(this); } + return true; } catch (Exception q) { log("Exception when trying to open model " + file + "\n" @@ -192,391 +187,299 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel } /** - * current set of model filenames loaded - */ - String[] modelFileNames = null; - - - StringBuffer resetLastRes = new StringBuffer(); - - private List lastReply; - - /** * Constructor * * @param ssm * @param pdbentry * @param sequenceIs - * @param chains * @param protocol */ public JalviewChimeraBinding(StructureSelectionManager ssm, - PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains, - String protocol) + PDBEntry[] pdbentry, SequenceI[][] sequenceIs, + DataSourceType protocol) { - super(ssm, pdbentry, sequenceIs, chains, protocol); - viewer = new ChimeraManager( - csm = new ext.edu.ucsf.rbvi.strucviz2.StructureManager(true)); + super(ssm, pdbentry, sequenceIs, protocol); + viewer = new ChimeraManager(new StructureManager(true)); } /** - * Constructor - * - * @param ssm - * @param theViewer + * 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. */ - public JalviewChimeraBinding(StructureSelectionManager ssm, - ChimeraManager theViewer) + protected void startChimeraProcessMonitor() { - super(ssm, null); - viewer = theViewer; - csm = viewer.getStructureManager(); + 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(); } /** - * Construct a title string for the viewer window based on the data Jalview - * knows about - * - * @param verbose - * @return + * Start a dedicated HttpServer to listen for Chimera notifications, and tell + * it to start listening */ - public String getViewerTitle(boolean verbose) + public void startChimeraListener() { - return getViewerTitle("Chimera", verbose); + try + { + chimeraListener = new ChimeraListener(this); + viewer.startListening(chimeraListener.getUri()); + } catch (BindException e) + { + System.err.println( + "Failed to start Chimera listener: " + e.getMessage()); + } } /** - * 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 + int modelNumber = getModelNoForChain(chain); + String showChainCmd = modelNumber == -1 ? "" + : modelNumber + ":." + chain.split(":")[1]; + 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(showChainCmd); + first = false; } - String cmdstring = cmd.toString(); - evalStateCommand("~display #*; ~ribbon #*; ribbon " + cmdstring - + ";focus " + 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); } /** - * Close down the Jalview viewer, and (optionally) the associated Chimera - * window. + * Close down the Jalview viewer and listener, and (optionally) the associated + * Chimera window. */ public void closeViewer(boolean closeChimera) { - getSsm().removeStructureViewerListener(this, this.getPdbFile()); + getSsm().removeStructureViewerListener(this, this.getStructureFiles()); if (closeChimera) { viewer.exitChimera(); } - lastCommand = null; + if (this.chimeraListener != null) + { + chimeraListener.shutdown(); + chimeraListener = null; + } viewer = null; + + if (chimeraMonitor != null) + { + chimeraMonitor.interrupt(); + } releaseUIResources(); } + @Override 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) + @Override + 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) - * - * @param refStructure - * - select which pdb file to use as reference (default is -1 - the - * first structure in the alignment) - * @param hiddenCols - * TODO + * {@inheritDoc} */ - public void superposeStructures(AlignmentI alignment, int refStructure, - ColumnSelection hiddenCols) + @Override + public String superposeStructures(AlignmentI[] _alignment, + int[] _refStructure, HiddenColumns[] _hiddenCols) { - superposeStructures(new AlignmentI[] - { alignment }, new int[] - { refStructure }, new ColumnSelection[] - { hiddenCols }); - } + StringBuilder allComs = new StringBuilder(128); + String[] files = getStructureFiles(); - 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 - 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; + return null; } + 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 + HiddenColumns hiddenCols = _hiddenCols[a]; + 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) + + /* + * 'matched' bit i will be set for visible alignment columns i where + * all sequences have a residue with a mapping to the PDB structure + */ + BitSet matched = new BitSet(); + for (int m = 0; m < alignment.getWidth(); m++) { - refStructure = -1; + if (hiddenCols == null || hiddenCols.isVisible(m)) + { + matched.set(m); + } } - boolean matched[] = new boolean[alignment.getWidth()]; - for (int m = 0; m < matched.length; m++) + SuperposeData[] structures = new SuperposeData[files.length]; + for (int f = 0; f < files.length; f++) { - - matched[m] = (hiddenCols != null) ? hiddenCols.isVisible(m) : true; + structures[f] = new SuperposeData(alignment.getWidth()); } - 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++) + /* + * Calculate the superposable alignment columns ('matched'), and the + * corresponding structure residue positions (structures.pdbResNo) + */ + int candidateRefStructure = findSuperposableResidues(alignment, + matched, structures); + if (refStructure < 0) { - 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++) - { - 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; - } - } - } + /* + * If no reference structure was specified, pick the first one that has + * a mapping in the alignment + */ + refStructure = candidateRefStructure; } - // TODO: consider bailing if nmatched less than 4 because superposition - // not - // well defined. - // TODO: refactor superposable position search (above) from jmol selection - // construction (below) + int nmatched = matched.cardinality(); + if (nmatched < 4) + { + return MessageManager.formatMessage("label.insufficient_residues", + nmatched); + } + /* + * 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(); + + int nextColumnMatch = matched.nextSetBit(0); + while (nextColumnMatch != -1) { - String chainCd = targetC[pdbfnum]; - int lpos = -1; - boolean run = false; - StringBuffer molsel = new StringBuffer(); - for (int r = 0; r < matched.length; r++) + int pdbResNum = structures[pdbfnum].pdbResNo[nextColumnMatch]; + if (lpos != pdbResNum - 1) { - if (matched[r]) + /* + * discontiguous - append last residue now + */ + if (lpos != -1) { - if (pdbfnum == 0) - { - nmatched++; - } - 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); + molsel.append(String.valueOf(lpos)); + molsel.append(chainCd); + molsel.append(","); } + run = false; } - // add final selection phrase - if (lpos != -1) - { - molsel.append((run ? "" : ":") + lpos); - molsel.append(chainCd); - // molsel.append(""); - } - if (molsel.length() > 1) + else { - selcom[pdbfnum] = molsel.toString(); - selectioncom.append("#" + pdbfnum); - selectioncom.append(selcom[pdbfnum]); - selectioncom.append(" "); - if (pdbfnum < files.length - 1) + /* + * extending a contiguous run + */ + if (!run) { - selectioncom.append("| "); + /* + * start the range selection + */ + molsel.append(String.valueOf(lpos)); + molsel.append("-"); } + run = true; } - else + lpos = pdbResNum; + nextColumnMatch = matched.nextSetBit(nextColumnMatch + 1); + } + + /* + * 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++) { @@ -592,36 +495,43 @@ 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]); - command.append(" #" + refStructure /* +".1" */); + command.append("@").append( + structures[pdbfnum].isRna ? PHOSPHORUS : ALPHACARBON); + // JAL-1757 exclude alternate CA locations + command.append(NO_ALTLOCS); + 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) { 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 " - + selectioncom.toString() + ";"+command.toString()); - // selcom.append("; ribbons; "); + allComs/*.append("~display all; chain @CA|P; ribbon ") + .append(selectioncom.toString())*/ + .append(";" + command.toString()); } } + + String error = null; 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); @@ -630,24 +540,88 @@ 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"); + 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; + } + + /** + * 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 (pdbfnum < 0 || pdbfnum >= getPdbCount()) + { + 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(getStructureFiles()[pdbfnum]); + boolean hasSubModels = maps != null && maps.size() > 1; + return "#" + String.valueOf(pdbfnum) + (hasSubModels ? ".1" : ""); } - private void checkLaunched() + /** + * 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()) + if (viewer.isChimeraLaunched()) + { + return true; + } + + boolean launched = viewer + .launchChimera(StructureManager.getChimeraPaths()); + if (launched) { - viewer.launchChimera(csm.getChimeraPaths()); + startChimeraProcessMonitor(); } - if (!viewer.isChimeraLaunched()) + else { log("Failed to launch Chimera!"); } + return launched; } /** @@ -662,76 +636,68 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel } /** - * Send a command to Chimera, and optionally log any responses. + * Send a command to Chimera, and optionally log and return any responses. + *

      + * Does nothing, and returns null, if the command is the same as the last one + * sent [why?]. * * @param command - * @param logResponse + * @param getResponse */ - public void evalStateCommand(final String command, boolean logResponse) + public List sendChimeraCommand(final String command, + boolean getResponse) { + if (viewer == null) + { + // ? thread running after viewer shut down + return null; + } + List reply = null; viewerCommandHistory(false); - checkLaunched(); - if (lastCommand == null || !lastCommand.equals(command)) + if (true /*lastCommand == null || !lastCommand.equals(command)*/) { -// Thread t = new Thread(new Runnable() -// { -// @Override -// public void run() -// { // trim command or it may never find a match in the replyLog!! - lastReply = viewer.sendChimeraCommand(command.trim(), logResponse); - if (debug && logResponse) - { - log("Response from command ('" + command + "') was:\n" - + lastReply); - } -// } -// }); - // TODO - use j7/8 thread management -// try -// { -// t.join(); -// } catch (InterruptedException foo) -// { -// } -// ; + List lastReply = viewer.sendChimeraCommand(command.trim(), + getResponse); + if (getResponse) + { + reply = lastReply; + if (debug) + { + log("Response from command ('" + command + "') was:\n" + + lastReply); + } + } } viewerCommandHistory(true); - lastCommand = command; + + return reply; } /** - * colour any structures associated with sequences in the given alignment - * using the getFeatureRenderer() and getSequenceRenderer() renderers but only - * if colourBySequence is enabled. + * 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); + + /** + * 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) - { - fr = getFeatureRenderer(alignmentv); - } - AlignmentI alignment = alignmentv.getAlignment(); - - for (jalview.structure.StructureMappingcommandSet cpdbbyseq : getColourBySequenceCommands(files, sr, fr, alignment)) + for (StructureMappingcommandSet cpdbbyseq : colourBySequenceCommands) { for (String command : cpdbbyseq.commands) { - executeWhenReady(command); + sendAsynchronousCommand(command, COLOURING_CHIMERA); } } } @@ -739,18 +705,15 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel /** * @param files * @param sr - * @param fr - * @param alignment + * @param viewPanel * @return */ + @Override protected StructureMappingcommandSet[] getColourBySequenceCommands( - String[] files, SequenceRenderer sr, FeatureRenderer fr, - AlignmentI alignment) + String[] files, SequenceRenderer sr, AlignmentViewPanel viewPanel) { - return ChimeraCommands - .getColourBySequenceCommand(getSsm(), files, getSequence(), sr, - fr, - alignment); + return ChimeraCommands.getColourBySequenceCommand(getSsm(), files, + getSequence(), sr, viewPanel); } /** @@ -759,7 +722,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel protected void executeWhenReady(String command) { waitForChimera(); - evalStateCommand(command, false); + sendChimeraCommand(command, false); waitForChimera(); } @@ -767,64 +730,25 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel { while (viewer != null && viewer.isBusy()) { - try { + try + { Thread.sleep(15); } catch (InterruptedException q) - {} + { + } } } - - // End StructureListener // ////////////////////////// - public Color getColour(int atomIndex, int pdbResNum, String chain, - String pdbfile) - { - if (getModelNum(pdbfile) < 0) - { - return null; - } - log("get model / residue colour attribute unimplemented"); - return null; - } - /** - * 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 jmol view's contents to the list of structure files - * Jalview knows about. + * 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(); - private int getModelNum(String modelFileName) - { - String[] mfn = getPdbFile(); - if (mfn == null) - { - return -1; - } - for (int i = 0; i < mfn.length; i++) - { - if (mfn[i].equalsIgnoreCase(modelFileName)) - { - return i; - } - } - return -1; - } - /** * 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 - @@ -834,337 +758,177 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel // //////////////////////////////// // /StructureListener - public synchronized String[] getPdbFile() + @Override + public synchronized String[] getStructureFiles() { if (viewer == null) { return new String[0]; } - // if (modelFileNames == null) - // { - // Collection chimodels = viewer.getChimeraModels(); - // _modelFileNameMap = new int[chimodels.size()]; - // int j = 0; - // for (ChimeraModel chimodel : chimodels) - // { - // String mdlName = chimodel.getModelName(); - // } - // modelFileNames = new String[j]; - // // System.arraycopy(mset, 0, modelFileNames, 0, j); - // } - - return chimmaps.keySet().toArray( - modelFileNames = new String[chimmaps.size()]); - } - /** - * map from string to applet - */ - public Map getRegistryInfo() - { - // TODO Auto-generated method stub - return null; + return chimeraMaps.keySet() + .toArray(modelFileNames = new String[chimeraMaps.size()]); } /** - * returns the current sequenceRenderer that should be used to colour the - * structures - * - * @param alignment - * - * @return + * 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. */ - public abstract SequenceRenderer getSequenceRenderer( - AlignmentViewPanel alignment); - - // jmol/ssm only - public void highlightAtom(int atomIndex, int pdbResNum, String chain, - String pdbfile) - { - List cms = chimmaps.get(pdbfile); - if (cms != null) - { - int mdlNum = cms.get(0).getModelNumber(); - - viewerCommandHistory(false); - // viewer.stopListening(); - if (resetLastRes.length() > 0) - { - eval.setLength(0); - eval.append(resetLastRes.toString() + ";"); - } - - eval.append("display "); // +modelNum - - resetLastRes.setLength(0); - resetLastRes.append("~display "); - { - eval.append(" #" + (mdlNum)); - resetLastRes.append(" #" + (mdlNum)); - } - // complete select string - - eval.append(":" + pdbResNum); - resetLastRes.append(":" + pdbResNum); - if (!chain.equals(" ")) - { - eval.append("." + chain); - resetLastRes.append("." + chain); - } - - viewer.sendChimeraCommand(eval.toString(), false); - viewerCommandHistory(true); - // viewer.startListening(); - } - } - - private void log(String message) - { - System.err.println("## Chimera log: " + message); - } - - private void viewerCommandHistory(boolean enable) - { - // log("(Not yet implemented) History " - // + ((debug || enable) ? "on" : "off")); - } - - public void loadInline(String string) - { - loadedInline = true; - // TODO: re JAL-623 - // viewer.loadInline(strModel, isAppend); - // could do this: - // construct fake fullPathName and fileName so we can identify the file - // later. - // Then, construct pass a reader for the string to Jmol. - // ((org.jmol.Viewer.Viewer) viewer).loadModelFromFile(fullPathName, - // fileName, null, reader, false, null, null, 0); - // viewer.openStringInline(string); - log("cannot load inline in Chimera, yet"); - } - - public void mouseOverStructure(int atomIndex, String strInfo) + @Override + public void highlightAtoms(List atoms) { - // function to parse a mouseOver event from Chimera - // - int pdbResNum; - int alocsep = strInfo.indexOf("^"); - int mdlSep = strInfo.indexOf("/"); - int chainSeparator = strInfo.indexOf(":"), chainSeparator1 = -1; - - if (chainSeparator == -1) + if (atoms == null || atoms.size() == 0) { - chainSeparator = strInfo.indexOf("."); - if (mdlSep > -1 && mdlSep < chainSeparator) - { - chainSeparator1 = chainSeparator; - chainSeparator = mdlSep; - } + return; } - // handle insertion codes - if (alocsep != -1) - { - pdbResNum = Integer.parseInt(strInfo.substring( - strInfo.indexOf("]") + 1, alocsep)); - } - else - { - pdbResNum = Integer.parseInt(strInfo.substring( - strInfo.indexOf("]") + 1, chainSeparator)); - } - String chainId; + StringBuilder cmd = new StringBuilder(128); + boolean first = true; + boolean found = false; - if (strInfo.indexOf(":") > -1) + for (AtomSpec atom : atoms) { - chainId = strInfo.substring(strInfo.indexOf(":") + 1, - strInfo.indexOf(".")); - } - else - { - chainId = " "; - } - - String pdbfilename = modelFileNames[frameNo]; // default is first or current - // model - if (mdlSep > -1) - { - if (chainSeparator1 == -1) - { - chainSeparator1 = strInfo.indexOf(".", mdlSep); - } - String mdlId = (chainSeparator1 > -1) ? strInfo.substring(mdlSep + 1, - chainSeparator1) : strInfo.substring(mdlSep + 1); - try + int pdbResNum = atom.getPdbResNum(); + String chain = atom.getChain(); + String pdbfile = atom.getPdbFile(); + List cms = chimeraMaps.get(pdbfile); + if (cms != null && !cms.isEmpty()) { - // recover PDB filename for the model hovered over. - int _mp = _modelFileNameMap.length - 1, mnumber = new Integer(mdlId) - .intValue() - 1; - while (mnumber < _modelFileNameMap[_mp]) + if (first) { - _mp--; + cmd.append("rlabel #").append(cms.get(0).getModelNumber()) + .append(":"); } - pdbfilename = modelFileNames[_mp]; - if (pdbfilename == null) + else { - // pdbfilename = new File(viewer.getModelFileName(mnumber)) - // .getAbsolutePath(); + cmd.append(","); } - - } catch (Exception e) - { + first = false; + cmd.append(pdbResNum); + if (!chain.equals(" ")) + { + cmd.append(".").append(chain); + } + found = true; } - ; - } - if (lastMessage == null || !lastMessage.equals(strInfo)) - { - getSsm().mouseOverStructure(pdbResNum, chainId, pdbfilename); } + String command = cmd.toString(); - lastMessage = strInfo; - } - - public void notifyAtomPicked(int atomIndex, String strInfo, String strData) - { - /** - * this implements the toggle label behaviour copied from the original - * structure viewer, MCView + /* + * avoid repeated commands for the same residue */ - if (strData != null) - { - System.err.println("Ignoring additional pick data string " + strData); - } - // rewrite these selections for chimera (DNA, RNA and protein) - int chainSeparator = strInfo.indexOf(":"); - int p = 0; - if (chainSeparator == -1) - { - chainSeparator = strInfo.indexOf("."); - } - - String picked = strInfo.substring(strInfo.indexOf("]") + 1, - chainSeparator); - String mdlString = ""; - if ((p = strInfo.indexOf(":")) > -1) - { - picked += strInfo.substring(p + 1, strInfo.indexOf(".")); - } - - if ((p = strInfo.indexOf("/")) > -1) + if (command.equals(lastHighlightCommand)) { - mdlString += strInfo.substring(p, strInfo.indexOf(" #")); + return; } - picked = "((" + picked + ".CA" + mdlString + ")|(" + picked + ".P" - + mdlString + "))"; - viewerCommandHistory(false); - if (!atomsPicked.contains(picked)) + /* + * unshow the label for the previous residue + */ + if (lastHighlightCommand != null) { - viewer.select(picked); - atomsPicked.add(picked); + viewer.sendChimeraCommand("~" + lastHighlightCommand, false); } - else + if (found) { - viewer.select("not " + picked); - atomsPicked.remove(picked); + viewer.sendChimeraCommand(command, false); } - viewerCommandHistory(true); - // TODO: in application this happens - // - // if (scriptWindow != null) - // { - // scriptWindow.sendConsoleMessage(strInfo); - // scriptWindow.sendConsoleMessage("\n"); - // } - + this.lastHighlightCommand = command; } - // incremented every time a load notification is successfully handled - - // lightweight mechanism for other threads to detect when they can start - // referring to new structures. - private long loadNotifiesHandled = 0; - - public long getLoadNotifiesHandled() + /** + * Query Chimera for its current selection, and highlight it on the alignment + */ + public void highlightChimeraSelection() { - return loadNotifiesHandled; + /* + * Ask Chimera for its current selection + */ + List selection = viewer.getSelectedResidueSpecs(); + + /* + * 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); + + /* + * Broadcast the selection (which may be empty, if the user just cleared all + * selections) + */ + getSsm().mouseOverStructure(atomSpecs); } - public void notifyFileLoaded(String fullPathName, String fileName2, - String modelName, String errorMsg, int modelParts) + /** + * Converts a list of Chimera atomspecs to a list of AtomSpec representing the + * corresponding residues (if any) in Jalview + * + * @param structureSelection + * @return + */ + protected List convertStructureResiduesToAlignment( + List structureSelection) { - if (errorMsg != null) - { - fileLoadingError = errorMsg; - refreshGUI(); - return; - } - // TODO: deal sensibly with models loaded inLine: - // modelName will be null, as will fullPathName. - - // the rest of this routine ignores the arguments, and simply interrogates - // the Jmol view to find out what structures it contains, and adds them to - // the structure selection manager. - fileLoadingError = null; - String[] oldmodels = modelFileNames; - modelFileNames = null; - chainNames = new ArrayList(); - chainFile = new HashMap(); - boolean notifyLoaded = false; - String[] modelfilenames = getPdbFile(); - // first check if we've lost any structures - if (oldmodels != null && oldmodels.length > 0) + List atomSpecs = new ArrayList<>(); + for (String atomSpec : structureSelection) { - int oldm = 0; - for (int i = 0; i < oldmodels.length; i++) + try { - for (int n = 0; n < modelfilenames.length; n++) - { - if (modelfilenames[n] == oldmodels[i]) - { - oldmodels[i] = null; - break; - } - } - if (oldmodels[i] != null) - { - oldm++; - } - } - if (oldm > 0) + AtomSpec spec = AtomSpec.fromChimeraAtomspec(atomSpec); + String pdbfilename = getPdbFileForModel(spec.getModelNumber()); + spec.setPdbFile(pdbfilename); + atomSpecs.add(spec); + } catch (IllegalArgumentException e) { - String[] oldmfn = new String[oldm]; - oldm = 0; - for (int i = 0; i < oldmodels.length; i++) - { - if (oldmodels[i] != null) - { - oldmfn[oldm++] = oldmodels[i]; - } - } - // deregister the Jmol instance for these structures - we'll add - // ourselves again at the end for the current structure set. - getSsm().removeStructureViewerListener(this, oldmfn); + System.err.println("Failed to parse atomspec: " + atomSpec); } } + return atomSpecs; + } - // register ourselves as a listener and notify the gui that it needs to - // update itself. - getSsm().addStructureViewerListener(this); - - if (notifyLoaded) + /** + * @param modelId + * @return + */ + protected String getPdbFileForModel(int modelId) + { + /* + * Work out the pdbfilename from the model number + */ + String pdbfilename = modelFileNames[0]; + findfileloop: for (String pdbfile : this.chimeraMaps.keySet()) { - FeatureRenderer fr = getFeatureRenderer(null); - if (fr != null) + for (ChimeraModel cm : chimeraMaps.get(pdbfile)) { - fr.featuresAdded(); + if (cm.getModelNumber() == modelId) + { + pdbfilename = pdbfile; + break findfileloop; + } } - refreshGUI(); - loadNotifiesHandled++; } - setLoadingFromArchive(false); + return pdbfilename; } + private void log(String message) + { + System.err.println("## Chimera log: " + message); + } + + private void viewerCommandHistory(boolean enable) + { + // log("(Not yet implemented) History " + // + ((debug || enable) ? "on" : "off")); + } + + public long getLoadNotifiesHandled() + { + return loadNotifiesHandled; + } + + @Override public void setJalviewColourScheme(ColourSchemeI cs) { colourBySequence = false; @@ -1174,32 +938,25 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel return; } - String res; - int index; - Color col; // Chimera expects RBG values in the range 0-1 final double normalise = 255D; viewerCommandHistory(false); - // TODO: Switch between nucleotide or aa selection expressions - Enumeration en = ResidueProperties.aa3Hash.keys(); StringBuilder command = new StringBuilder(128); - command.append("color white;"); - while (en.hasMoreElements()) - { - res = en.nextElement().toString(); - index = ((Integer) ResidueProperties.aa3Hash.get(res)).intValue(); - if (index > 20) - { - continue; - } - col = cs.findColour(ResidueProperties.aa[index].charAt(0)); + List residueSet = ResidueProperties.getResidues(isNucleotide(), + false); + for (String resName : residueSet) + { + 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 + ";"); } - evalStateCommand(command.toString(),false); + sendAsynchronousCommand(command.toString(), COLOURING_CHIMERA); viewerCommandHistory(true); } @@ -1210,6 +967,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel */ public abstract void refreshGUI(); + @Override public void setLoadingFromArchive(boolean loadingFromArchive) { this.loadingFromArchive = loadingFromArchive; @@ -1220,6 +978,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel * @return true if Chimeral is still restoring state or loading is still going * on (see setFinsihedLoadingFromArchive) */ + @Override public boolean isLoadingFromArchive() { return loadingFromArchive && !loadingFinished; @@ -1231,6 +990,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel * * @param finishedLoading */ + @Override public void setFinishedLoadingFromArchive(boolean finishedLoading) { loadingFinished = finishedLoading; @@ -1244,29 +1004,19 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel * .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 + ";"; + final String command = "background solid " + col.getRed() / normalise + + "," + col.getGreen() / normalise + "," + + col.getBlue() / normalise + ";"; viewer.sendChimeraCommand(command, false); viewerCommandHistory(true); } /** - * - * @param pdbfile - * @return text report of alignment between pdbfile and any associated - * alignment sequences - */ - public String printMapping(String pdbfile) - { - return getSsm().printMapping(pdbfile); - } - - /** * Ask Chimera to save its session to the given file. Returns true if * successful, else false. * @@ -1279,9 +1029,395 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel { List reply = viewer.sendChimeraCommand("save " + filepath, true); - System.out.println(reply); + if (reply.contains("Session written")) + { + return true; + } + else + { + Cache.log + .error("Error saving Chimera session: " + reply.toString()); + } } return false; } + /** + * Ask Chimera to open a session file. Returns true if successful, else false. + * The filename must have a .py extension for this command to work. + * + * @param filepath + * @return + */ + public boolean openSession(String filepath) + { + sendChimeraCommand("open " + filepath, true); + // todo: test for failure - how? + return true; + } + + /** + * Returns a list of chains mapped in this viewer. Note this list is not + * currently scoped per structure. + * + * @return + */ + @Override + public List getChainNames() + { + return chainNames; + } + + /** + * Send a 'focus' command to Chimera to recentre the visible display + */ + public void focusView() + { + sendChimeraCommand("focus", false); + } + + /** + * Send a 'show' command for all atoms in the currently selected columns + * + * TODO: pull up to abstract structure viewer interface + * + * @param vp + */ + public void highlightSelection(AlignmentViewPanel vp) + { + List cols = vp.getAlignViewport().getColumnSelection() + .getSelected(); + AlignmentI alignment = vp.getAlignment(); + StructureSelectionManager sm = getSsm(); + for (SequenceI seq : alignment.getSequences()) + { + /* + * convert selected columns into sequence positions + */ + int[] positions = new int[cols.size()]; + int i = 0; + for (Integer col : cols) + { + positions[i++] = seq.findPosition(col); + } + sm.highlightStructure(this, seq, positions); + } + } + + /** + * Constructs and send commands to Chimera to set attributes on residues for + * features visible in Jalview + * + * @param avp + * @return + */ + public int sendFeaturesToViewer(AlignmentViewPanel avp) + { + // TODO refactor as required to pull up to an interface + AlignmentI alignment = avp.getAlignment(); + + String[] files = getStructureFiles(); + if (files == null) + { + return 0; + } + + StructureMappingcommandSet commandSet = ChimeraCommands + .getSetAttributeCommandsForFeatures(getSsm(), files, + getSequence(), avp); + String[] commands = commandSet.commands; + if (commands.length > 10) + { + sendCommandsByFile(commands); + } + else + { + for (String command : commands) + { + sendAsynchronousCommand(command, null); + } + } + return commands.length; + } + + /** + * Write commands to a temporary file, and send a command to Chimera to open + * the file as a commands script. For use when sending a large number of + * separate commands would overload the REST interface mechanism. + * + * @param commands + */ + protected void sendCommandsByFile(String[] commands) + { + try + { + File tmp = File.createTempFile("chim", ".com"); + tmp.deleteOnExit(); + PrintWriter out = new PrintWriter(new FileOutputStream(tmp)); + for (String command : commands) + { + out.println(command); + } + out.flush(); + out.close(); + String path = tmp.getAbsolutePath(); + sendAsynchronousCommand("open cmd:" + path, null); + } catch (IOException e) + { + System.err.println("Sending commands to Chimera via file failed with " + + e.getMessage()); + } + } + + /** + * Get Chimera residues which have the named attribute, find the mapped + * positions in the Jalview sequence(s), and set as sequence features + * + * @param attName + * @param alignmentPanel + */ + public void copyStructureAttributesToFeatures(String attName, + AlignmentViewPanel alignmentPanel) + { + // todo pull up to AAStructureBindingModel (and interface?) + + /* + * ask Chimera to list residues with the attribute, reporting its value + */ + // this alternative command + // list residues spec ':*/attName' attr attName + // doesn't report 'None' values (which is good), but + // fails for 'average.bfactor' (which is bad): + + String cmd = "list residues attr '" + attName + "'"; + List residues = sendChimeraCommand(cmd, true); + + boolean featureAdded = createFeaturesForAttributes(attName, residues); + if (featureAdded) + { + alignmentPanel.getFeatureRenderer().featuresAdded(); + } + } + + /** + * Create features in Jalview for the given attribute name and structure + * residues. + * + * 

      +   * The residue list should be 0, 1 or more reply lines of the format: 
+   *     residue id #0:5.A isHelix -155.000836316 index 5 
+   * or 
+   *     residue id #0:6.A isHelix None
+   *
      + * + * @param attName + * @param residues + * @return + */ + protected boolean createFeaturesForAttributes(String attName, + List residues) + { + boolean featureAdded = false; + String featureGroup = getViewerFeatureGroup(); + + for (String residue : residues) + { + AtomSpec spec = null; + String[] tokens = residue.split(" "); + if (tokens.length < 5) + { + continue; + } + String atomSpec = tokens[2]; + String attValue = tokens[4]; + + /* + * ignore 'None' (e.g. for phi) or 'False' (e.g. for isHelix) + */ + if ("None".equalsIgnoreCase(attValue) + || "False".equalsIgnoreCase(attValue)) + { + continue; + } + + try + { + spec = AtomSpec.fromChimeraAtomspec(atomSpec); + } catch (IllegalArgumentException e) + { + System.err.println("Problem parsing atomspec " + atomSpec); + continue; + } + + String chainId = spec.getChain(); + String description = attValue; + float score = Float.NaN; + try + { + score = Float.valueOf(attValue); + description = chainId; + } catch (NumberFormatException e) + { + // was not a float value + } + + String pdbFile = getPdbFileForModel(spec.getModelNumber()); + spec.setPdbFile(pdbFile); + + List atoms = Collections.singletonList(spec); + + /* + * locate the mapped position in the alignment (if any) + */ + SearchResultsI sr = getSsm() + .findAlignmentPositionsForStructurePositions(atoms); + + /* + * expect one matched alignment position, or none + * (if the structure position is not mapped) + */ + for (SearchResultMatchI m : sr.getResults()) + { + SequenceI seq = m.getSequence(); + int start = m.getStart(); + int end = m.getEnd(); + SequenceFeature sf = new SequenceFeature(attName, description, + start, end, score, featureGroup); + // todo: should SequenceFeature have an explicit property for chain? + // note: repeating the action shouldn't duplicate features + featureAdded |= seq.addSequenceFeature(sf); + } + } + return featureAdded; + } + + /** + * Answers the feature group name to apply to features created in Jalview from + * Chimera attributes + * + * @return + */ + protected String getViewerFeatureGroup() + { + // todo pull up to interface + return CHIMERA_FEATURE_GROUP; + } + + public Hashtable getChainFile() + { + return chainFile; + } + + public List getChimeraModelByChain(String chain) + { + return chimeraMaps.get(chainFile.get(chain)); + } + + public int getModelNoForChain(String chain) + { + List foundModels = getChimeraModelByChain(chain); + if (foundModels != null && !foundModels.isEmpty()) + { + return foundModels.get(0).getModelNumber(); + } + 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(); + } }