X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Frbvi%2Fchimera%2FJalviewChimeraBinding.java;h=00446f2ab334d297adb824bfed7a4370a55dee21;hb=3d0101179759ef157b088ea135423cd909512d9f;hp=a74b3ab598b9be65ad7b7201b1956080c70463db;hpb=b557f2f2a0bef9d5d4a10cfd0731562e423531db;p=jalview.git diff --git a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java index a74b3ab..00446f2 100644 --- a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java +++ b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java @@ -21,15 +21,18 @@ package jalview.ext.rbvi.chimera; 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; @@ -45,8 +48,9 @@ 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.HashMap; +import java.util.Hashtable; import java.util.LinkedHashMap; import java.util.List; import java.util.Map; @@ -58,6 +62,8 @@ 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"; @@ -70,6 +76,10 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel private static final String ALPHACARBON = "CA"; + private List chainNames = new ArrayList(); + + private Hashtable chainFile = new Hashtable(); + /* * Object through which we talk to Chimera */ @@ -93,8 +103,6 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel */ private boolean loadingFinished = true; - public String fileLoadingError; - /* * Map of ChimeraModel objects keyed by PDB full local file name */ @@ -109,6 +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. * @@ -162,13 +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) @@ -186,16 +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( - 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(); } /** @@ -210,24 +242,12 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel viewer.startListening(chimeraListener.getUri()); } catch (BindException e) { - System.err.println("Failed to start Chimera listener: " - + e.getMessage()); + System.err.println( + "Failed to start Chimera listener: " + e.getMessage()); } } /** - * Construct a title string for the viewer window based on the data Jalview - * knows about - * - * @param verbose - * @return - */ - public String getViewerTitle(boolean verbose) - { - return getViewerTitle("Chimera", verbose); - } - - /** * Tells Chimera to display only the specified chains * * @param toshow @@ -243,11 +263,14 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel boolean first = true; for (String chain : toshow) { + int modelNumber = getModelNoForChain(chain); + String showChainCmd = modelNumber == -1 ? "" + : modelNumber + ":." + chain.split(":")[1]; if (!first) { cmd.append(","); } - cmd.append(":.").append(chain); + cmd.append(showChainCmd); first = false; } @@ -256,7 +279,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel * window, but it looks more helpful not to (easier to relate chains to the * whole) */ - final String command = "~display #*; ~ribbon #*; ribbon " + final String command = "~display #*; ~ribbon #*; ribbon :" + cmd.toString(); sendChimeraCommand(command, false); } @@ -267,7 +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(); @@ -279,9 +302,14 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel } viewer = null; + if (chimeraMonitor != null) + { + chimeraMonitor.interrupt(); + } releaseUIResources(); } + @Override public void colourByChain() { colourBySequence = false; @@ -297,6 +325,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel *
  • all others - white
    • * */ + @Override public void colourByCharge() { colourBySequence = false; @@ -305,28 +334,18 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel } /** - * Construct and send a command to align structures against a reference - * structure, based on one or more sequence alignments - * - * @param _alignment - * an array of alignments to process - * @param _refStructure - * an array of corresponding reference structures (index into pdb - * file array); if a negative value is passed, the first PDB file - * mapped to an alignment sequence is used as the reference for - * superposition - * @param _hiddenCols - * an array of corresponding hidden columns for each alignment + * {@inheritDoc} */ - public void superposeStructures(AlignmentI[] _alignment, - int[] _refStructure, ColumnSelection[] _hiddenCols) + @Override + public String superposeStructures(AlignmentI[] _alignment, + int[] _refStructure, HiddenColumns[] _hiddenCols) { StringBuilder allComs = new StringBuilder(128); - String[] files = getPdbFile(); + String[] files = getStructureFiles(); if (!waitForFileLoad(files)) { - return; + return null; } refreshPdbEntries(); @@ -335,7 +354,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel { int refStructure = _refStructure[a]; AlignmentI alignment = _alignment[a]; - ColumnSelection hiddenCols = _hiddenCols[a]; + HiddenColumns hiddenCols = _hiddenCols[a]; if (refStructure >= files.length) { @@ -345,13 +364,16 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel } /* - * 'matched' array will hold 'true' for visible alignment columns where + * 'matched' bit i will be set for visible alignment columns i where * all sequences have a residue with a mapping to the PDB structure */ - boolean matched[] = new boolean[alignment.getWidth()]; - for (int m = 0; m < matched.length; m++) + BitSet matched = new BitSet(); + for (int m = 0; m < alignment.getWidth(); m++) { - matched[m] = (hiddenCols != null) ? hiddenCols.isVisible(m) : true; + if (hiddenCols == null || hiddenCols.isVisible(m)) + { + matched.set(m); + } } SuperposeData[] structures = new SuperposeData[files.length]; @@ -375,17 +397,11 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel refStructure = candidateRefStructure; } - int nmatched = 0; - for (boolean b : matched) - { - if (b) - { - nmatched++; - } - } + int nmatched = matched.cardinality(); if (nmatched < 4) { - // TODO: bail out here because superposition illdefined? + return MessageManager.formatMessage("label.insufficient_residues", + nmatched); } /* @@ -398,41 +414,41 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel int lpos = -1; boolean run = false; StringBuilder molsel = new StringBuilder(); - for (int r = 0; r < matched.length; r++) + + int nextColumnMatch = matched.nextSetBit(0); + while (nextColumnMatch != -1) { - if (matched[r]) + int pdbResNum = structures[pdbfnum].pdbResNo[nextColumnMatch]; + if (lpos != pdbResNum - 1) { - int pdbResNum = structures[pdbfnum].pdbResNo[r]; - if (lpos != pdbResNum - 1) + /* + * discontiguous - append last residue now + */ + if (lpos != -1) { - /* - * discontiguous - append last residue now - */ - if (lpos != -1) - { - molsel.append(String.valueOf(lpos)); - molsel.append(chainCd); - molsel.append(","); - } - run = false; + molsel.append(String.valueOf(lpos)); + molsel.append(chainCd); + molsel.append(","); } - else + run = false; + } + else + { + /* + * extending a contiguous run + */ + if (!run) { /* - * extending a contiguous run + * start the range selection */ - if (!run) - { - /* - * start the range selection - */ - molsel.append(String.valueOf(lpos)); - molsel.append("-"); - } - run = true; + molsel.append(String.valueOf(lpos)); + molsel.append("-"); } - lpos = pdbResNum; + run = true; } + lpos = pdbResNum; + nextColumnMatch = matched.nextSetBit(nextColumnMatch + 1); } /* @@ -500,14 +516,16 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel if (debug) { System.out.println("Select regions:\n" + selectioncom.toString()); - System.out.println("Superimpose command(s):\n" - + command.toString()); + System.out.println( + "Superimpose command(s):\n" + command.toString()); } allComs.append("~display all; chain @CA|P; ribbon ") .append(selectioncom.toString()) .append(";" + command.toString()); } } + + String error = null; if (selectioncom.length() > 0) { // TODO: visually distinguish regions that were superposed @@ -521,9 +539,17 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel } allComs.append("; ~display all; chain @CA|P; ribbon ") .append(selectioncom.toString()).append("; focus"); - sendChimeraCommand(allComs.toString(), false); + List chimeraReplies = sendChimeraCommand(allComs.toString(), + true); + for (String reply : chimeraReplies) + { + if (reply.toLowerCase().contains("unequal numbers of atoms")) + { + error = reply; + } + } } - + return error; } /** @@ -552,30 +578,36 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel * to the Chimera command 'list models type molecule', see * ChimeraManager.getModelList(). */ - List maps = chimeraMaps.get(getPdbFile()[pdbfnum]); + List maps = chimeraMaps.get(getStructureFiles()[pdbfnum]); boolean hasSubModels = maps != null && maps.size() > 1; return "#" + String.valueOf(pdbfnum) + (hasSubModels ? ".1" : ""); } /** * Launch Chimera, unless an instance linked to this object is already - * running. Returns true if chimera is successfully launched, or already + * running. Returns true if Chimera is successfully launched, or already * running, else false. * * @return */ public boolean launchChimera() { - if (!viewer.isChimeraLaunched()) - { - return viewer.launchChimera(StructureManager.getChimeraPaths()); - } if (viewer.isChimeraLaunched()) { return true; } - log("Failed to launch Chimera!"); - return false; + + boolean launched = viewer + .launchChimera(StructureManager.getChimeraPaths()); + if (launched) + { + startChimeraProcessMonitor(); + } + else + { + log("Failed to launch Chimera!"); + } + return launched; } /** @@ -639,39 +671,35 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel String progressMsg); /** - * colour any structures associated with sequences in the given alignment - * using the getFeatureRenderer() and getSequenceRenderer() renderers but only - * if colourBySequence is enabled. + * Sends a set of colour commands to the structure viewer + * + * @param colourBySequenceCommands */ - public void colourBySequence(boolean showFeatures, - jalview.api.AlignmentViewPanel alignmentv) + @Override + protected void colourBySequence( + StructureMappingcommandSet[] colourBySequenceCommands) { - if (!colourBySequence || !loadingFinished) + for (StructureMappingcommandSet cpdbbyseq : colourBySequenceCommands) { - return; - } - if (getSsm() == null) - { - return; - } - String[] files = getPdbFile(); - - SequenceRenderer sr = getSequenceRenderer(alignmentv); - - FeatureRenderer fr = null; - if (showFeatures) - { - fr = getFeatureRenderer(alignmentv); + for (String command : cpdbbyseq.commands) + { + sendAsynchronousCommand(command, COLOURING_CHIMERA); + } } - AlignmentI alignment = alignmentv.getAlignment(); + } - StructureMappingcommandSet colourBySequenceCommands = ChimeraCommands - .getColourBySequenceCommand(getSsm(), files, getSequence(), sr, - fr, alignment); - for (String command : colourBySequenceCommands.commands) - { - sendAsynchronousCommand(command, COLOURING_CHIMERA); - } + /** + * @param files + * @param sr + * @param viewPanel + * @return + */ + @Override + protected StructureMappingcommandSet[] getColourBySequenceCommands( + String[] files, SequenceRenderer sr, AlignmentViewPanel viewPanel) + { + return ChimeraCommands.getColourBySequenceCommand(getSsm(), files, + getSequence(), sr, viewPanel); } /** @@ -701,40 +729,12 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel // ////////////////////////// /** - * returns the current featureRenderer that should be used to colour the - * structures - * - * @param alignment - * - * @return - */ - public abstract FeatureRenderer getFeatureRenderer( - AlignmentViewPanel alignment); - - /** * instruct the Jalview binding to update the pdbentries vector if necessary * prior to matching the viewer's contents to the list of structure files * Jalview knows about. */ public abstract void refreshPdbEntries(); - 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 - @@ -745,39 +745,16 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel // //////////////////////////////// // /StructureListener @Override - public synchronized String[] getPdbFile() + 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()]); - } - /** - * returns the current sequenceRenderer that should be used to colour the - * structures - * - * @param alignment - * - * @return - */ - public abstract SequenceRenderer getSequenceRenderer( - AlignmentViewPanel alignment); + return chimeraMaps.keySet() + .toArray(modelFileNames = new String[chimeraMaps.size()]); + } /** * Construct and send a command to highlight zero, one or more atoms. We do @@ -860,7 +837,8 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel * Parse model number, residue and chain for each selected position, * formatted as #0:123.A or #1.2:87.B (#model.submodel:residue.chain) */ - List atomSpecs = convertStructureResiduesToAlignment(selection); + List atomSpecs = convertStructureResiduesToAlignment( + selection); /* * Broadcast the selection (which may be empty, if the user just cleared all @@ -882,51 +860,42 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel List atomSpecs = new ArrayList(); for (String atomSpec : structureSelection) { - int colonPos = atomSpec.indexOf(":"); - if (colonPos == -1) - { - 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) + AtomSpec spec = AtomSpec.fromChimeraAtomspec(atomSpec); + String pdbfilename = getPdbFileForModel(spec.getModelNumber()); + spec.setPdbFile(pdbfilename); + atomSpecs.add(spec); + } catch (IllegalArgumentException e) { - // ignore, default to model 0 + System.err.println("Failed to parse atomspec: " + atomSpec); } + } + return atomSpecs; + } - 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[0]; - findfileloop: for (String pdbfile : this.chimeraMaps.keySet()) + /** + * @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()) + { + for (ChimeraModel cm : chimeraMaps.get(pdbfile)) { - for (ChimeraModel cm : chimeraMaps.get(pdbfile)) + if (cm.getModelNumber() == modelId) { - if (cm.getModelNumber() == modelId) - { - pdbfilename = pdbfile; - break findfileloop; - } + pdbfilename = pdbfile; + break findfileloop; } } - atomSpecs.add(new AtomSpec(pdbfilename, chainId, pdbResNum, 0)); } - return atomSpecs; + return pdbfilename; } private void log(String message) @@ -945,6 +914,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel return loadNotifiesHandled; } + @Override public void setJalviewColourScheme(ColourSchemeI cs) { colourBySequence = false; @@ -961,12 +931,15 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel List residueSet = ResidueProperties.getResidues(isNucleotide(), false); - for (String res : residueSet) + for (String resName : residueSet) { - Color col = cs.findColour(res.charAt(0)); + char res = resName.length() == 3 + ? ResidueProperties.getSingleCharacterCode(resName) + : resName.charAt(0); + Color col = cs.findColour(res, 0, null, null, 0f); command.append("color " + col.getRed() / normalise + "," - + col.getGreen() / normalise + "," + col.getBlue() - / normalise + " ::" + res + ";"); + + col.getGreen() / normalise + "," + col.getBlue() / normalise + + " ::" + resName + ";"); } sendAsynchronousCommand(command.toString(), COLOURING_CHIMERA); @@ -1012,18 +985,19 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel /** * Send the Chimera 'background solid " command. * - * @see https + * @see https * ://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/background * .html * @param col */ + @Override public void setBackgroundColour(Color col) { viewerCommandHistory(false); double normalise = 255D; final String command = "background solid " + col.getRed() / normalise - + "," + col.getGreen() / normalise + "," + col.getBlue() - / normalise + ";"; + + "," + col.getGreen() / normalise + "," + + col.getBlue() / normalise + ";"; viewer.sendChimeraCommand(command, false); viewerCommandHistory(true); } @@ -1074,27 +1048,10 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel * * @return */ + @Override public List getChainNames() { - List names = new ArrayList(); - String[][] allNames = getChains(); - if (allNames != null) - { - for (String[] chainsForPdb : allNames) - { - if (chainsForPdb != null) - { - for (String chain : chainsForPdb) - { - if (chain != null && !names.contains(chain)) - { - names.add(chain); - } - } - } - } - } - return names; + return chainNames; } /** @@ -1138,30 +1095,22 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel * features visible in Jalview * * @param avp + * @return */ - public void sendFeaturesToViewer(AlignmentViewPanel avp) + public int sendFeaturesToViewer(AlignmentViewPanel avp) { // TODO refactor as required to pull up to an interface AlignmentI alignment = avp.getAlignment(); - FeatureRenderer fr = getFeatureRenderer(avp); - /* - * fr is null if feature display is turned off - */ - if (fr == null) - { - return; - } - - String[] files = getPdbFile(); + String[] files = getStructureFiles(); if (files == null) { - return; + return 0; } StructureMappingcommandSet commandSet = ChimeraCommands .getSetAttributeCommandsForFeatures(getSsm(), files, - getSequence(), fr, alignment); + getSequence(), avp); String[] commands = commandSet.commands; if (commands.length > 10) { @@ -1174,6 +1123,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel sendAsynchronousCommand(command, null); } } + return commands.length; } /** @@ -1200,9 +1150,8 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel sendAsynchronousCommand("open cmd:" + path, null); } catch (IOException e) { - System.err - .println("Sending commands to Chimera via file failed with " - + e.getMessage()); + System.err.println("Sending commands to Chimera via file failed with " + + e.getMessage()); } } @@ -1217,87 +1166,115 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel AlignmentViewPanel alignmentPanel) { // todo pull up to AAStructureBindingModel (and interface?) - + /* * ask Chimera to list residues with the attribute, reporting its value */ - String cmd = "list residues spec ':*/" + attName + "' attr " + attName; + // 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); - /* - * TODO check if Jalview already has this feature name, if so give it a - * distinguishing prefix e.g. chim_ - */ - FeatureRenderer fr = alignmentPanel.getFeatureRenderer(); - fr.getFeaturesDisplayed().getVisibleFeatureCount(); + 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(); - /* - * Expect 0, 1 or more reply lines of the format (chi2 is attName): - * residue id #0:5.A chi2 -155.000836316 index 5 - */ - Map>> attsMap = new HashMap>>(); for (String residue : residues) { + AtomSpec spec = null; String[] tokens = residue.split(" "); - if (tokens.length > 4) + if (tokens.length < 5) { - String atomSpec = tokens[2]; - String attValue = tokens[4]; - // TODO find mapping of atomspec to Jalview residue if any - // build a map of { attValue, Map> } - // sort the integer lists - // and create a feature for each contiguous integer range - SequenceI seq = null; // mapped-to sequence - int seqPos = 0; // mapped-to sequence position + continue; + } + String atomSpec = tokens[2]; + String attValue = tokens[4]; - /* - * record attribute value / sequence / sequence position - */ - Map> seqMap = attsMap.get(attValue); - if (seqMap == null) - { - seqMap = new HashMap>(); - attsMap.put(attValue, seqMap); - } - List seqPositions = seqMap.get(seq); - if (seqPositions == null) - { - seqPositions = new ArrayList(); - seqMap.put(seq, seqPositions); - } - seqPositions.add(seqPos); + /* + * ignore 'None' (e.g. for phi) or 'False' (e.g. for isHelix) + */ + if ("None".equalsIgnoreCase(attValue) + || "False".equalsIgnoreCase(attValue)) + { + continue; } - } - /* - * traverse values and sequences - */ - for (String val : attsMap.keySet()) - { - for (SequenceI seq : attsMap.get(val).keySet()) + try { - List positions = attsMap.get(val).get(seq); - Collections.sort(positions); - // TODO find reusable code that compacts the list - List ranges = null;// compacted list - for (int[] range : ranges) - { - float score = Float.NaN; - try - { - score = Float.valueOf(val); - } catch (NumberFormatException e) - { - // was not a float value - } - String featureGroup = getViewerFeatureGroup(); - SequenceFeature sf = new SequenceFeature(attName, val, range[0], - range[1], score, featureGroup); - // note: repeating the action shouldn't duplicate features - seq.addSequenceFeature(sf); - } + 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; } /** @@ -1309,6 +1286,26 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel protected String getViewerFeatureGroup() { // todo pull up to interface - return "Chimera"; + 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; } }