X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Frbvi%2Fchimera%2FJalviewChimeraBinding.java;h=00446f2ab334d297adb824bfed7a4370a55dee21;hb=947109cebef3e98693ffc0a70b5bffcbd32217e2;hp=2042ac4f7398df8d0b64b355414c99c016ef6858;hpb=4762b29420ed4df01b55a8afe5ab05467aaf41a9;p=jalview.git diff --git a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java index 2042ac4..00446f2 100644 --- a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java +++ b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java @@ -21,15 +21,14 @@ 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.SearchResults; +import jalview.datamodel.SearchResultsI; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; import jalview.httpserver.AbstractRequestHandler; @@ -49,6 +48,7 @@ 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; @@ -79,7 +79,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel private List chainNames = new ArrayList(); private Hashtable chainFile = new Hashtable(); - + /* * Object through which we talk to Chimera */ @@ -172,13 +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) @@ -199,7 +192,8 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel * @param protocol */ public JalviewChimeraBinding(StructureSelectionManager ssm, - PDBEntry[] pdbentry, SequenceI[][] sequenceIs, DataSourceType protocol) + PDBEntry[] pdbentry, SequenceI[][] sequenceIs, + DataSourceType protocol) { super(ssm, pdbentry, sequenceIs, protocol); viewer = new ChimeraManager(new StructureManager(true)); @@ -248,8 +242,8 @@ 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()); } } @@ -270,8 +264,8 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel for (String chain : toshow) { int modelNumber = getModelNoForChain(chain); - String showChainCmd = modelNumber == -1 ? "" : modelNumber + ":." - + chain.split(":")[1]; + String showChainCmd = modelNumber == -1 ? "" + : modelNumber + ":." + chain.split(":")[1]; if (!first) { cmd.append(","); @@ -296,7 +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(); @@ -340,29 +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} */ @Override - public void superposeStructures(AlignmentI[] _alignment, - int[] _refStructure, ColumnSelection[] _hiddenCols) + 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(); @@ -371,7 +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) { @@ -381,13 +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]; @@ -411,17 +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); } /* @@ -434,41 +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); } /* @@ -536,14 +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 @@ -557,9 +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; } /** @@ -588,7 +578,7 @@ 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" : ""); } @@ -607,8 +597,8 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel return true; } - boolean launched = viewer.launchChimera(StructureManager - .getChimeraPaths()); + boolean launched = viewer + .launchChimera(StructureManager.getChimeraPaths()); if (launched) { startChimeraProcessMonitor(); @@ -701,17 +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); } /** @@ -754,19 +742,18 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel */ private int _modelFileNameMap[]; - // //////////////////////////////// // /StructureListener @Override - public synchronized String[] getPdbFile() + public synchronized String[] getStructureFiles() { if (viewer == null) { return new String[0]; } - return chimeraMaps.keySet().toArray( - modelFileNames = new String[chimeraMaps.size()]); + return chimeraMaps.keySet() + .toArray(modelFileNames = new String[chimeraMaps.size()]); } /** @@ -850,7 +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 @@ -945,12 +933,13 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel false); for (String resName : residueSet) { - char res = resName.length() == 3 ? ResidueProperties - .getSingleCharacterCode(resName) : resName.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 + " ::" + resName + ";"); + + col.getGreen() / normalise + "," + col.getBlue() / normalise + + " ::" + resName + ";"); } sendAsynchronousCommand(command.toString(), COLOURING_CHIMERA); @@ -996,7 +985,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel /** * Send the Chimera 'background solid " command. * - * @see https + * @see https * ://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/background * .html * @param col @@ -1007,8 +996,8 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel viewerCommandHistory(false); double normalise = 255D; final String command = "background solid " + col.getRed() / normalise - + "," + col.getGreen() / normalise + "," + col.getBlue() - / normalise + ";"; + + "," + col.getGreen() / normalise + "," + + col.getBlue() / normalise + ";"; viewer.sendChimeraCommand(command, false); viewerCommandHistory(true); } @@ -1106,30 +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) { @@ -1142,6 +1123,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel sendAsynchronousCommand(command, null); } } + return commands.length; } /** @@ -1168,9 +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()); } } @@ -1274,7 +1255,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel /* * locate the mapped position in the alignment (if any) */ - SearchResults sr = getSsm() + SearchResultsI sr = getSsm() .findAlignmentPositionsForStructurePositions(atoms); /* @@ -1308,7 +1289,6 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel return CHIMERA_FEATURE_GROUP; } - public Hashtable getChainFile() { return chainFile;