X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Frbvi%2Fchimera%2FJalviewChimeraBinding.java;h=2534421761f6f4a08889019e945a8225c4557b07;hb=23e1ca45f5adac64d191f1e3e7d4d64ae52eaa03;hp=1ce0d2b05934599faa99ca8a0b201cda7de5ef19;hpb=f3b39605256b4803fef19117e7e8bd682bb51758;p=jalview.git diff --git a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java index 1ce0d2b..2534421 100644 --- a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java +++ b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java @@ -27,14 +27,17 @@ import jalview.bin.Cache; import jalview.datamodel.AlignmentI; import jalview.datamodel.ColumnSelection; import jalview.datamodel.PDBEntry; +import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; import jalview.httpserver.AbstractRequestHandler; 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; @@ -101,17 +104,8 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel private String lastCommand; - private boolean loadedInline; - - /** - * current set of model filenames loaded - */ - String[] modelFileNames = null; - String lastHighlightCommand; - private List lastReply; - /* * incremented every time a load notification is successfully handled - * lightweight mechanism for other threads to detect when they can start @@ -617,7 +611,8 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel if (lastCommand == null || !lastCommand.equals(command)) { // trim command or it may never find a match in the replyLog!! - lastReply = viewer.sendChimeraCommand(command.trim(), logResponse); + List lastReply = viewer.sendChimeraCommand(command.trim(), + logResponse); if (logResponse && debug) { log("Response from command ('" + command + "') was:\n" + lastReply); @@ -715,17 +710,6 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel // 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 @@ -795,15 +779,6 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel } /** - * map from string to applet - */ - public Map getRegistryInfo() - { - // TODO Auto-generated method stub - return null; - } - - /** * returns the current sequenceRenderer that should be used to colour the * structures * @@ -815,20 +790,18 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel AlignmentViewPanel alignment); /** - * Construct and send a command to highlight zero, one or more atoms. - * - * 
-   * Done by generating a command like (to 'highlight' positions 44 and 46)
-   *   show #0:44,46.C
-   *
+ * 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. */ @Override public void highlightAtoms(List atoms) { - if (atoms == null) + if (atoms == null || atoms.size() == 0) { return; } + StringBuilder cmd = new StringBuilder(128); boolean first = true; boolean found = false; @@ -843,7 +816,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel { if (first) { - cmd.append("show #").append(cms.get(0).getModelNumber()) + cmd.append("rlabel #").append(cms.get(0).getModelNumber()) .append(":"); } else @@ -851,7 +824,6 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel cmd.append(","); } first = false; - cmd.append(cms.get(0).getModelNumber()).append(":"); cmd.append(pdbResNum); if (!chain.equals(" ")) { @@ -863,19 +835,24 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel String command = cmd.toString(); /* - * Avoid repeated commands for the same residue + * avoid repeated commands for the same residue */ if (command.equals(lastHighlightCommand)) { return; } - viewerCommandHistory(false); + /* + * unshow the label for the previous residue + */ + if (lastHighlightCommand != null) + { + viewer.sendChimeraCommand("~" + lastHighlightCommand, false); + } if (found) { - viewer.sendChimeraCommand(command.toString(), false); + viewer.sendChimeraCommand(command, false); } - viewerCommandHistory(true); this.lastHighlightCommand = command; } @@ -1151,4 +1128,87 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel sm.highlightStructure(this, seq, positions); } } + + /** + * Constructs and send commands to Chimera to set attributes on residues for + * features visible in Jalview + * + * @param avp + */ + public void sendFeaturesToChimera(AlignmentViewPanel avp) + { + // TODO send a command per feature with the range of residues it applies to + AlignmentI alignment = avp.getAlignment(); + FeatureRenderer fr = getFeatureRenderer(avp); + + /* + * fr is null if feature display is turned off + */ + if (fr == null) + { + return; + } + + String[] files = getPdbFile(); + if (files == null) + { + return; + } + for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) + { + StructureMapping[] mapping = getSsm().getMapping(files[pdbfnum]); + + if (mapping == null || mapping.length < 1) + { + continue; + } + + int lastPos = -1; + for (int seqNo = 0; seqNo < getSequence()[pdbfnum].length; seqNo++) + { + for (int m = 0; m < mapping.length; m++) + { + final SequenceI seq = getSequence()[pdbfnum][seqNo]; + int sp = alignment.findIndex(seq); + if (mapping[m].getSequence() == seq && sp > -1) + { + SequenceI asp = alignment.getSequenceAt(sp); + for (int r = 0; r < asp.getLength(); r++) + { + // no mapping to gaps in sequence + if (Comparison.isGap(asp.getCharAt(r))) + { + continue; + } + int residuePos = asp.findPosition(r); + int pos = mapping[m].getPDBResNum(residuePos); + + if (pos < 1 || pos == lastPos) + { + continue; + } + final String chain = mapping[m].getChain(); + List features = fr.findFeaturesAtRes(asp, + residuePos); + for (SequenceFeature feature : features) + { + String desc = feature.getDescription(); + float score = feature.getScore(); + if (score != 0 && score != Float.NaN) + { + desc = Float.toString(score); + } + String attName = "jv:" + + feature.getType().replace(" ", "_"); + String cmd = "setattr r " + attName + " \"" + + desc + "\" #" + pdbfnum + ":" + pos + "." + chain; + System.out.println(cmd); + sendAsynchronousCommand(cmd, null); + } + } + } + } + } + } + } }