X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Frbvi%2Fchimera%2FJalviewChimeraBinding.java;h=00446f2ab334d297adb824bfed7a4370a55dee21;hb=3d0101179759ef157b088ea135423cd909512d9f;hp=95ece8a47e2a28fa147a3ef1a46555c53d8c3c4a;hpb=ee91b5df4a306e551e7b75861f86b32fac504d5c;p=jalview.git diff --git a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java index 95ece8a..00446f2 100644 --- a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java +++ b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java @@ -20,49 +20,65 @@ */ 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; +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.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.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.BitSet; +import java.util.Collections; +import java.util.Hashtable; +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 { + 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; private static final String PHOSPHORUS = "P"; 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 @@ -88,41 +104,11 @@ 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; - - /* * Map of ChimeraModel objects keyed by PDB full local file name */ private Map> chimeraMaps = new LinkedHashMap>(); - /* - * the default or current model displayed if the model cannot be identified - * from the selection message - */ - private int frameNo = 0; - - private String lastCommand; - - private boolean loadedInline; - - /** - * current set of model filenames loaded - */ - String[] modelFileNames = null; - - String lastMousedOverAtomSpec; - - private List lastReply; + String lastHighlightCommand; /* * incremented every time a load notification is successfully handled - @@ -131,6 +117,8 @@ 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. * @@ -184,13 +172,6 @@ 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) @@ -208,16 +189,45 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel * @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)); + } + + /** + * 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(); } /** @@ -232,66 +242,46 @@ 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()); } } /** - * 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 - * - * @param verbose - * @return - */ - public String getViewerTitle(boolean verbose) - { - return getViewerTitle("Chimera", verbose); - } - - /** - * 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, 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); } /** @@ -300,7 +290,7 @@ 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(); @@ -310,296 +300,183 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel chimeraListener.shutdown(); chimeraListener = null; } - lastCommand = 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); + sendAsynchronousCommand("rainbow chain", COLOURING_CHIMERA); } /** - * superpose the structures associated with sequences in the alignment - * according to their corresponding positions. + * 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) - { - superposeStructures(alignment, -1, null); - } - - /** - * 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) - */ - 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 + if (!waitForFileLoad(files)) { - 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) - { - 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++) { @@ -615,22 +492,23 @@ 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) @@ -638,16 +516,19 @@ 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 " - + 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); @@ -656,24 +537,77 @@ 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"); + List chimeraReplies = sendChimeraCommand(allComs.toString(), + true); + for (String reply : chimeraReplies) + { + if (reply.toLowerCase().contains("unequal numbers of atoms")) + { + error = reply; + } + } } - + return error; } - 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 ""; } - if (!viewer.isChimeraLaunched()) + + /* + * 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" : ""); + } + + /** + * 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()) + { + return true; + } + + boolean launched = viewer + .launchChimera(StructureManager.getChimeraPaths()); + if (launched) + { + startChimeraProcessMonitor(); + } + else { log("Failed to launch Chimera!"); } + return launched; } /** @@ -688,62 +622,68 @@ 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 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)*/) { // trim command or it may never find a match in the replyLog!! - lastReply = viewer.sendChimeraCommand(command.trim(), logResponse); - if (debug && logResponse) + List lastReply = viewer.sendChimeraCommand(command.trim(), + getResponse); + if (getResponse) { - log("Response from command ('" + command + "') was:\n" + lastReply); + 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 */ - public void colourBySequence(boolean showFeatures, - jalview.api.AlignmentViewPanel alignmentv) - { - if (!colourBySequence || !loadingFinished) - { - return; - } - if (getSsm() == null) - { - return; - } - String[] files = getPdbFile(); - - SequenceRenderer sr = getSequenceRenderer(alignmentv); + protected abstract void sendAsynchronousCommand(String command, + String progressMsg); - FeatureRenderer fr = null; - if (showFeatures) - { - fr = getFeatureRenderer(alignmentv); - } - AlignmentI alignment = alignmentv.getAlignment(); - - for (jalview.structure.StructureMappingcommandSet cpdbbyseq : getColourBySequenceCommands( - files, sr, fr, alignment)) + /** + * Sends a set of colour commands to the structure viewer + * + * @param colourBySequenceCommands + */ + @Override + protected void colourBySequence( + StructureMappingcommandSet[] colourBySequenceCommands) + { + for (StructureMappingcommandSet cpdbbyseq : colourBySequenceCommands) { for (String command : cpdbbyseq.commands) { - executeWhenReady(command); + sendAsynchronousCommand(command, COLOURING_CHIMERA); } } } @@ -751,16 +691,15 @@ 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); + getSequence(), sr, viewPanel); } /** @@ -769,7 +708,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel protected void executeWhenReady(String command) { waitForChimera(); - evalStateCommand(command, false); + sendChimeraCommand(command, false); waitForChimera(); } @@ -777,64 +716,25 @@ 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 + * 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 - @@ -844,90 +744,83 @@ 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 chimeraMaps.keySet().toArray( - modelFileNames = new String[chimeraMaps.size()]); + + return chimeraMaps.keySet() + .toArray(modelFileNames = new String[chimeraMaps.size()]); } /** - * map from string to applet + * 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 Map getRegistryInfo() + @Override + public void highlightAtoms(List atoms) { - // TODO Auto-generated method stub - return null; - } + if (atoms == null || atoms.size() == 0) + { + return; + } - /** - * returns the current sequenceRenderer that should be used to colour the - * structures - * - * @param alignment - * - * @return - */ - public abstract SequenceRenderer getSequenceRenderer( - AlignmentViewPanel alignment); + StringBuilder cmd = new StringBuilder(128); + boolean first = true; + boolean found = false; - /** - * Construct and send a command to highlight an atom. - * - * 

      -   * 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.
-   *
      - */ - public void highlightAtom(int atomIndex, int pdbResNum, String chain, - String pdbfile) - { - List cms = chimeraMaps.get(pdbfile); - if (cms != null) + for (AtomSpec atom : atoms) { - StringBuilder sb = new StringBuilder(); - sb.append(" #" + cms.get(0).getModelNumber()); - sb.append(":" + pdbResNum); - if (!chain.equals(" ")) + 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); + if (first) + { + cmd.append("rlabel #").append(cms.get(0).getModelNumber()) + .append(":"); + } + else + { + cmd.append(","); + } + first = false; + cmd.append(pdbResNum); + if (!chain.equals(" ")) + { + cmd.append(".").append(chain); + } + found = true; } - String atomSpec = sb.toString(); + } + String command = cmd.toString(); - StringBuilder command = new StringBuilder(32); - if (lastMousedOverAtomSpec != null) - { - command.append("~show " + lastMousedOverAtomSpec + ";"); - } - viewerCommandHistory(false); - 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; + /* + * avoid repeated commands for the same residue + */ + if (command.equals(lastHighlightCommand)) + { + return; + } + + /* + * unshow the label for the previous residue + */ + if (lastHighlightCommand != null) + { + viewer.sendChimeraCommand("~" + lastHighlightCommand, false); + } + if (found) + { + viewer.sendChimeraCommand(command, false); } + this.lastHighlightCommand = command; } /** @@ -944,57 +837,65 @@ 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); + + /* + * Broadcast the selection (which may be empty, if the user just cleared all + * selections) + */ + getSsm().mouseOverStructure(atomSpecs); + } + + /** + * 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) + { List atomSpecs = new ArrayList(); - for (String atomSpec : selection) + for (String atomSpec : structureSelection) { - int colonPos = atomSpec.indexOf(":"); - if (colonPos == -1) + try { - continue; // malformed - } - - int hashPos = atomSpec.indexOf("#"); - String modelSubmodel = atomSpec.substring(hashPos + 1, colonPos); - int dotPos = modelSubmodel.indexOf("."); - int modelId = 0; - try { - modelId = Integer.valueOf(dotPos == -1 ? modelSubmodel - : modelSubmodel.substring(0, dotPos)); - } 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 - */ - String pdbfilename = modelFileNames[frameNo]; - findfileloop: for (String pdbfile : this.chimeraMaps.keySet()) + AtomSpec spec = AtomSpec.fromChimeraAtomspec(atomSpec); + String pdbfilename = getPdbFileForModel(spec.getModelNumber()); + spec.setPdbFile(pdbfilename); + atomSpecs.add(spec); + } catch (IllegalArgumentException e) { - for (ChimeraModel cm : chimeraMaps.get(pdbfile)) - { - if (cm.getModelNumber() == modelId) - { - pdbfilename = pdbfile; - break findfileloop; - } - } + System.err.println("Failed to parse atomspec: " + atomSpec); } - atomSpecs.add(new AtomSpec(pdbfilename, chainId, pdbResNum, 0)); } + return atomSpecs; + } + /** + * @param modelId + * @return + */ + protected String getPdbFileForModel(int modelId) + { /* - * Broadcast the selection (which may be empty, if the user just cleared all - * selections) + * Work out the pdbfilename from the model number */ - getSsm().mouseOverStructure(atomSpecs); + String pdbfilename = modelFileNames[0]; + findfileloop: for (String pdbfile : this.chimeraMaps.keySet()) + { + for (ChimeraModel cm : chimeraMaps.get(pdbfile)) + { + if (cm.getModelNumber() == modelId) + { + pdbfilename = pdbfile; + break findfileloop; + } + } + } + return pdbfilename; } private void log(String message) @@ -1013,6 +914,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel return loadNotifiesHandled; } + @Override public void setJalviewColourScheme(ColourSchemeI cs) { colourBySequence = false; @@ -1029,15 +931,18 @@ 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 + ";"); } - evalStateCommand(command.toString(),false); + sendAsynchronousCommand(command.toString(), COLOURING_CHIMERA); viewerCommandHistory(true); } @@ -1048,6 +953,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel */ public abstract void refreshGUI(); + @Override public void setLoadingFromArchive(boolean loadingFromArchive) { this.loadingFromArchive = loadingFromArchive; @@ -1058,6 +964,7 @@ 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; @@ -1069,6 +976,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel * * @param finishedLoading */ + @Override public void setFinishedLoadingFromArchive(boolean finishedLoading) { loadingFinished = finishedLoading; @@ -1082,29 +990,19 @@ 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. * @@ -1139,24 +1037,275 @@ 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() + /** + * Returns a list of chains mapped in this viewer. Note this list is not + * currently scoped per structure. + * + * @return + */ + @Override + public List getChainNames() { - return finishedInit; + return chainNames; } - public void setFinishedInit(boolean finishedInit) + /** + * Send a 'focus' command to Chimera to recentre the visible display + */ + public void focusView() { - this.finishedInit = finishedInit; + sendChimeraCommand("focus", false); } - public List getChainNames() + /** + * 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) { - return chainNames; + 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; + } }