X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Frbvi%2Fchimera%2FJalviewChimeraBinding.java;h=75ddc9c2f04e986fcd79df952c8b754874ffa904;hb=abd0918cc633b946cfea588ef4b4d666edf9fc8b;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..75ddc9c 100644 --- a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java +++ b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java @@ -23,13 +23,17 @@ 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.PDBEntry; +import jalview.datamodel.SearchResultMatchI; +import jalview.datamodel.SearchResults; 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; @@ -46,7 +50,7 @@ import java.io.PrintWriter; import java.net.BindException; import java.util.ArrayList; 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 */ @@ -109,6 +119,8 @@ 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. * @@ -186,16 +198,44 @@ 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(); } /** @@ -243,11 +283,14 @@ 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 +299,7 @@ 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); } @@ -279,6 +322,10 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel } viewer = null; + if (chimeraMonitor != null) + { + chimeraMonitor.interrupt(); + } releaseUIResources(); } @@ -559,23 +606,29 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel /** * 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; } /** @@ -718,30 +771,6 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel */ 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 - - * use getPdbFile to get number of unique models. - */ - private int _modelFileNameMap[]; - // //////////////////////////////// // /StructureListener @Override @@ -751,18 +780,6 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel { 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()]); @@ -882,51 +899,42 @@ 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) @@ -1074,27 +1082,10 @@ 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; } /** @@ -1217,87 +1208,115 @@ 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) + */ + SearchResults 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 +1328,27 @@ 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; } }