X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fext%2Frbvi%2Fchimera%2FJalviewChimeraBinding.java;h=00446f2ab334d297adb824bfed7a4370a55dee21;hb=refs%2Fheads%2FJAL-3253-applet-SwingJS-omnibus;hp=ffce90cadc973bb1d6ae79ec3bf64e3238293dc8;hpb=c72ef272fa17501a5677e8569d02195d500487e8;p=jalview.git diff --git a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java index ffce90c..00446f2 100644 --- a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java +++ b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java @@ -25,7 +25,7 @@ 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; @@ -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 */ @@ -192,7 +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)); @@ -241,8 +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()); } } @@ -263,8 +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(","); @@ -289,7 +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(); @@ -337,10 +338,10 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel */ @Override public String superposeStructures(AlignmentI[] _alignment, - int[] _refStructure, ColumnSelection[] _hiddenCols) + int[] _refStructure, HiddenColumns[] _hiddenCols) { StringBuilder allComs = new StringBuilder(128); - String[] files = getPdbFile(); + String[] files = getStructureFiles(); if (!waitForFileLoad(files)) { @@ -353,7 +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) { @@ -515,8 +516,8 @@ 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()) @@ -577,7 +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" : ""); } @@ -596,8 +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(); @@ -741,19 +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()]); } /** @@ -837,7 +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 @@ -932,12 +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); @@ -983,7 +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 @@ -994,8 +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); } @@ -1100,7 +1102,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel // TODO refactor as required to pull up to an interface AlignmentI alignment = avp.getAlignment(); - String[] files = getPdbFile(); + String[] files = getStructureFiles(); if (files == null) { return 0; @@ -1148,9 +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()); } } @@ -1288,7 +1289,6 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel return CHIMERA_FEATURE_GROUP; } - public Hashtable getChainFile() { return chainFile;