X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fjmol%2FJalviewJmolBinding.java;h=2f3464be0c7af6ec58d6e186019ec2ffc88803c2;hb=e97cd6659f6bcac55dc030e770192b0044960dc5;hp=fc86e1c1669a9898f71c9ca8c4f8730ce88b6383;hpb=71dddf0df3cc5295d8832ee7a95430530bd515a3;p=jalview.git diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java index fc86e1c..2f3464b 100644 --- a/src/jalview/ext/jmol/JalviewJmolBinding.java +++ b/src/jalview/ext/jmol/JalviewJmolBinding.java @@ -28,6 +28,7 @@ import jalview.datamodel.ColumnSelection; import jalview.datamodel.PDBEntry; import jalview.datamodel.SequenceI; import jalview.io.AppletFormatAdapter; +import jalview.io.StructureFile; import jalview.schemes.ColourSchemeI; import jalview.schemes.ResidueProperties; import jalview.structure.AtomSpec; @@ -55,20 +56,13 @@ import org.jmol.api.JmolSelectionListener; import org.jmol.api.JmolStatusListener; import org.jmol.api.JmolViewer; import org.jmol.c.CBK; -import org.jmol.popup.JmolGenericPopup; import org.jmol.script.T; -import org.jmol.viewer.JC; import org.jmol.viewer.Viewer; public abstract class JalviewJmolBinding extends AAStructureBindingModel implements JmolStatusListener, JmolSelectionListener, ComponentListener { - /* - * state flag used to check if the Jmol viewer's paint method can be called - */ - private boolean finishedInit = false; - boolean allChainsSelected = false; /* @@ -77,13 +71,11 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel */ private boolean associateNewStructs = false; - Vector atomsPicked = new Vector(); - - public Vector chainNames; + Vector atomsPicked = new Vector(); - Hashtable chainFile; + public Vector chainNames; - StringBuffer eval = new StringBuffer(); + Hashtable chainFile; public String fileLoadingError; @@ -93,7 +85,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel */ int frameNo = 0; - protected JmolGenericPopup jmolpopup; + // protected JmolGenericPopup jmolpopup; // not used - remove? String lastCommand; @@ -152,15 +144,13 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel * @param chainList * list of chains to make visible */ - public void centerViewer(Vector chainList) + public void centerViewer(Vector chainList) { - StringBuffer cmd = new StringBuffer(); - String lbl; + StringBuilder cmd = new StringBuilder(128); int mlength, p; - for (int i = 0, iSize = chainList.size(); i < iSize; i++) + for (String lbl : chainList) { mlength = 0; - lbl = (String) chainList.elementAt(i); do { p = mlength; @@ -168,7 +158,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel } while (p < mlength && mlength < (lbl.length() - 2)); // TODO: lookup each pdb id and recover proper model number for it. cmd.append(":" + lbl.substring(mlength + 1) + " /" - + (1 + getModelNum((String) chainFile.get(lbl))) + " or "); + + (1 + getModelNum(chainFile.get(lbl))) + " or "); } if (cmd.length() > 0) { @@ -179,12 +169,9 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel public void closeViewer() { - viewer.acm.setModeMouse(JC.MOUSE_NONE); // remove listeners for all structures in viewer getSsm().removeStructureViewerListener(this, this.getPdbFile()); - // and shut down jmol - viewer.evalStringQuiet("zap"); - viewer.setJmolStatusListener(null); + viewer.dispose(); lastCommand = null; viewer = null; releaseUIResources(); @@ -241,10 +228,9 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel public void superposeStructures(AlignmentI alignment, int refStructure, ColumnSelection hiddenCols) { - superposeStructures(new AlignmentI[] - { alignment }, new int[] - { refStructure }, new ColumnSelection[] - { hiddenCols }); + superposeStructures(new AlignmentI[] { alignment }, + new int[] { refStructure }, + new ColumnSelection[] { hiddenCols }); } /** @@ -264,8 +250,17 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel public void superposeStructures(AlignmentI[] _alignment, int[] _refStructure, ColumnSelection[] _hiddenCols) { + while (viewer.isScriptExecuting()) + { + try + { + Thread.sleep(10); + } catch (InterruptedException i) + { + } + ; + } String[] files = getPdbFile(); - if (!waitForFileLoad(files)) { return; @@ -277,7 +272,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel String nSeconds = " "; if (files.length > 10) { - nSeconds = " 0.00001 "; + nSeconds = " 0.005 "; } else { @@ -286,7 +281,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel } // see JAL-1345 - should really automatically turn off the animation for // large numbers of structures, but Jmol doesn't seem to allow that. - nSeconds = " "; + // nSeconds = " "; // union of all aligned positions are collected together. for (int a = 0; a < _alignment.length; a++) { @@ -454,13 +449,12 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel } if (selectioncom.length() > 0) { - System.out.println("Select regions:\n" + selectioncom.toString()); + // System.out.println("Select regions:\n" + selectioncom.toString()); evalStateCommand("select *; cartoons off; backbone; select (" + selectioncom.toString() + "); cartoons; "); // selcom.append("; ribbons; "); String cmdString = command.toString(); - System.out -.println("Superimpose command(s):\n" + cmdString); + // System.out.println("Superimpose command(s):\n" + cmdString); evalStateCommand(cmdString); } @@ -471,7 +465,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel { selectioncom.setLength(selectioncom.length() - 1); } - System.out.println("Select regions:\n" + selectioncom.toString()); + // System.out.println("Select regions:\n" + selectioncom.toString()); evalStateCommand("select *; cartoons off; backbone; select (" + selectioncom.toString() + "); cartoons; "); // evalStateCommand("select *; backbone; select "+selcom.toString()+"; cartoons; center "+selcom.toString()); @@ -494,9 +488,10 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel * using the getFeatureRenderer() and getSequenceRenderer() renderers but only * if colourBySequence is enabled. */ - public void colourBySequence(boolean showFeatures, - jalview.api.AlignmentViewPanel alignmentv) + public void colourBySequence(AlignmentViewPanel alignmentv) { + boolean showFeatures = alignmentv.getAlignViewport() + .isShowSequenceFeatures(); if (!colourBySequence || !isLoadingFinished()) { return; @@ -516,7 +511,8 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel } AlignmentI alignment = alignmentv.getAlignment(); - for (jalview.structure.StructureMappingcommandSet cpdbbyseq : getColourBySequenceCommands(files, sr, fr, alignment)) + for (jalview.structure.StructureMappingcommandSet cpdbbyseq : getColourBySequenceCommands( + files, sr, fr, alignment)) { for (String cbyseq : cpdbbyseq.commands) { @@ -536,10 +532,8 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel String[] files, SequenceRenderer sr, FeatureRenderer fr, AlignmentI alignment) { - return JmolCommands - .getColourBySequenceCommand(getSsm(), files, getSequence(), sr, - fr, - alignment); + return JmolCommands.getColourBySequenceCommand(getSsm(), files, + getSequence(), sr, fr, alignment); } /** @@ -555,6 +549,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel System.out.println("JMOL CREATE IMAGE"); } + @Override public String createImage(String fileName, String type, Object textOrBytes, int quality) { @@ -562,6 +557,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel return null; } + @Override public String eval(String strEval) { // System.out.println(strEval); @@ -572,11 +568,13 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel // End StructureListener // ////////////////////////// + @Override public float[][] functionXY(String functionName, int x, int y) { return null; } + @Override public float[][][] functionXYZ(String functionName, int nx, int ny, int nz) { // TODO Auto-generated method stub @@ -592,8 +590,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel } // TODO: verify atomIndex is selecting correct model. // return new Color(viewer.getAtomArgb(atomIndex)); Jmol 12.2.4 - int colour = viewer.ms.at[atomIndex] - .atomPropertyInt(T.color); + int colour = viewer.ms.at[atomIndex].atomPropertyInt(T.color); return new Color(colour); } @@ -671,6 +668,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel // applet path with docroot - discard as format won't match pdbfile mset[0] = m; } + _modelFileNameMap[0] = 0; // filename index for first model is always 0. } int j = 1; for (int i = 1; i < mset.length; i++) @@ -729,7 +727,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel public void handlePopupMenu(int x, int y) { // jmolpopup.show(x, y); - jmolpopup.jpiShow(x, y); + // jmolpopup.jpiShow(x, y); } /** @@ -740,6 +738,11 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel { if (atoms != null) { + if (resetLastRes.length() > 0) + { + viewer.evalStringQuiet(resetLastRes.toString()); + resetLastRes.setLength(0); + } for (AtomSpec atom : atoms) { highlightAtom(atom.getAtomIndex(), atom.getPdbResNum(), @@ -759,12 +762,10 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel // look up file model number for this pdbfile int mdlNum = 0; - String fn; // may need to adjust for URLencoding here - we don't worry about that yet. while (mdlNum < modelFileNames.length && !pdbfile.equals(modelFileNames[mdlNum])) { - // System.out.println("nomatch:"+pdbfile+"\nmodelfn:"+fn); mdlNum++; } if (mdlNum == modelFileNames.length) @@ -773,38 +774,31 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel } jmolHistory(false); - // if (!pdbfile.equals(pdbentry.getFile())) - // return; - if (resetLastRes.length() > 0) - { - viewer.evalStringQuiet(resetLastRes.toString()); - } - eval.setLength(0); - eval.append("select " + pdbResNum); // +modelNum + StringBuilder cmd = new StringBuilder(64); + cmd.append("select " + pdbResNum); // +modelNum - resetLastRes.setLength(0); resetLastRes.append("select " + pdbResNum); // +modelNum - eval.append(":"); + cmd.append(":"); resetLastRes.append(":"); if (!chain.equals(" ")) { - eval.append(chain); + cmd.append(chain); resetLastRes.append(chain); } { - eval.append(" /" + (mdlNum + 1)); + cmd.append(" /" + (mdlNum + 1)); resetLastRes.append("/" + (mdlNum + 1)); } - eval.append(";wireframe 100;" + eval.toString() + " and not hetero;"); + cmd.append(";wireframe 100;" + cmd.toString() + " and not hetero;"); resetLastRes.append(";wireframe 0;" + resetLastRes.toString() + " and not hetero; spacefill 0;"); - eval.append("spacefill 200;select none"); + cmd.append("spacefill 200;select none"); - viewer.evalStringQuiet(eval.toString()); + viewer.evalStringQuiet(cmd.toString()); jmolHistory(true); } @@ -892,8 +886,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel pdbfilename = modelFileNames[_mp]; if (pdbfilename == null) { - pdbfilename = new File( - viewer.ms.getModelFileName(mnumber)) + pdbfilename = new File(viewer.ms.getModelFileName(mnumber)) .getAbsolutePath(); } @@ -948,7 +941,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel String mdlString = ""; if ((p = strInfo.indexOf(":")) > -1) { - picked += strInfo.substring(p + 1, strInfo.indexOf(".")); + picked += strInfo.substring(p, strInfo.indexOf(".")); } if ((p = strInfo.indexOf("/")) > -1) @@ -1081,8 +1074,8 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel fileLoadingError = null; String[] oldmodels = modelFileNames; modelFileNames = null; - chainNames = new Vector(); - chainFile = new Hashtable(); + chainNames = new Vector(); + chainFile = new Hashtable(); boolean notifyLoaded = false; String[] modelfilenames = getPdbFile(); // first check if we've lost any structures @@ -1125,8 +1118,8 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel { String fileName = modelfilenames[modelnum]; boolean foundEntry = false; - MCview.PDBfile pdb = null; - String pdbfile = null, pdbfhash = null; + StructureFile pdb = null; + String pdbfile = null; // model was probably loaded inline - so check the pdb file hashcode if (loadedInline) { @@ -1135,10 +1128,9 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel // 'best guess' pdbfile = viewer.getData("" + (1 + _modelFileNameMap[modelnum]) + ".0", "PDB"); - pdbfhash = "" + pdbfile.hashCode(); } - // search pdbentries and sequences to find correct pdbentry for this - // model + // search pdbentries and sequences to find correct pdbentry for this + // model for (int pe = 0; pe < getPdbCount(); pe++) { boolean matches = false; @@ -1149,7 +1141,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel { pdb = getSsm().setMapping(getSequence()[pe], getChains()[pe], pdbfile, AppletFormatAdapter.PASTE); - getPdbEntry(modelnum).setFile("INLINE" + pdb.id); + getPdbEntry(modelnum).setFile("INLINE" + pdb.getId()); matches = true; foundEntry = true; } @@ -1188,10 +1180,10 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel if (matches) { // add an entry for every chain in the model - for (int i = 0; i < pdb.chains.size(); i++) + for (int i = 0; i < pdb.getChains().size(); i++) { - String chid = new String(pdb.id + ":" - + pdb.chains.elementAt(i).id); + String chid = new String(pdb.getId() + ":" + + pdb.getChains().elementAt(i).id); chainFile.put(chid, fileName); chainNames.addElement(chid); } @@ -1216,14 +1208,14 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel } // FILE LOADED OK // so finally, update the jmol bits and pieces - if (jmolpopup != null) - { - // potential for deadlock here: - // jmolpopup.updateComputedMenus(); - } + // if (jmolpopup != null) + // { + // // potential for deadlock here: + // // jmolpopup.updateComputedMenus(); + // } if (!isLoadingFromArchive()) { - viewer.evalStringQuiet("model 0; select backbone;restrict;cartoon;wireframe off;spacefill off"); + viewer.evalStringQuiet("model *; select backbone;restrict;cartoon;wireframe off;spacefill off"); } // register ourselves as a listener and notify the gui that it needs to // update itself. @@ -1271,6 +1263,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel */ public abstract void sendConsoleMessage(String strStatus); + @Override public void setCallbackFunction(String callbackType, String callbackFunction) { @@ -1408,16 +1401,6 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel return null; } - public boolean isFinishedInit() - { - return finishedInit; - } - - public void setFinishedInit(boolean finishedInit) - { - this.finishedInit = finishedInit; - } - /** * */ @@ -1472,4 +1455,3 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel showConsole(false); } } -