X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fjmol%2FJalviewJmolBinding.java;h=b464c94b66b8f0c8902686d91f8045b3adc3a676;hb=4d7f98a6dd54d9863ba449ec79dcd95d25ed863d;hp=cdd137b8e2bc3946785d9b6c28361553b8ec4a17;hpb=3bc2fbe640abb0d8941aead117c9624dd16773a3;p=jalview.git diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java index cdd137b..b464c94 100644 --- a/src/jalview/ext/jmol/JalviewJmolBinding.java +++ b/src/jalview/ext/jmol/JalviewJmolBinding.java @@ -20,6 +20,21 @@ */ package jalview.ext.jmol; +import jalview.api.AlignmentViewPanel; +import jalview.api.FeatureRenderer; +import jalview.api.SequenceRenderer; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.ColumnSelection; +import jalview.datamodel.PDBEntry; +import jalview.datamodel.SequenceI; +import jalview.io.AppletFormatAdapter; +import jalview.schemes.ColourSchemeI; +import jalview.schemes.ResidueProperties; +import jalview.structure.AtomSpec; +import jalview.structure.StructureMappingcommandSet; +import jalview.structure.StructureSelectionManager; +import jalview.structures.models.AAStructureBindingModel; + import java.awt.Color; import java.awt.Container; import java.awt.event.ComponentEvent; @@ -32,38 +47,22 @@ import java.util.List; import java.util.Map; import java.util.Vector; +import javajs.awt.Dimension; + import org.jmol.adapter.smarter.SmarterJmolAdapter; import org.jmol.api.JmolAppConsoleInterface; import org.jmol.api.JmolSelectionListener; import org.jmol.api.JmolStatusListener; import org.jmol.api.JmolViewer; -import org.jmol.constant.EnumCallback; -import org.jmol.popup.JmolPopup; - -import jalview.api.AlignmentViewPanel; -import jalview.api.FeatureRenderer; -import jalview.api.SequenceRenderer; -import jalview.datamodel.AlignmentI; -import jalview.datamodel.ColumnSelection; -import jalview.datamodel.PDBEntry; -import jalview.datamodel.SequenceI; -import jalview.io.AppletFormatAdapter; -import jalview.schemes.ColourSchemeI; -import jalview.schemes.ResidueProperties; -import jalview.structure.AtomSpec; -import jalview.structure.StructureMappingcommandSet; -import jalview.structure.StructureSelectionManager; -import jalview.structures.models.AAStructureBindingModel; +import org.jmol.c.CBK; +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; /* @@ -72,13 +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; @@ -88,7 +85,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel */ int frameNo = 0; - protected JmolPopup jmolpopup; + // protected JmolGenericPopup jmolpopup; // not used - remove? String lastCommand; @@ -103,7 +100,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel StringBuffer resetLastRes = new StringBuffer(); - public JmolViewer viewer; + public Viewer viewer; public JalviewJmolBinding(StructureSelectionManager ssm, PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains, @@ -120,7 +117,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel } public JalviewJmolBinding(StructureSelectionManager ssm, - SequenceI[][] seqs, JmolViewer theViewer) + SequenceI[][] seqs, Viewer theViewer) { super(ssm, seqs); @@ -137,7 +134,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel */ public String getViewerTitle() { - return getViewerTitle("JMol", true); + return getViewerTitle("Jmol", true); } /** @@ -147,15 +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; @@ -163,7 +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) { @@ -174,7 +169,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel public void closeViewer() { - viewer.setModeMouse(org.jmol.viewer.JmolConstants.MOUSE_NONE); + viewer.acm.setModeMouse(JC.MOUSE_NONE); // remove listeners for all structures in viewer getSsm().removeStructureViewerListener(this, this.getPdbFile()); // and shut down jmol @@ -236,10 +231,9 @@ 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 }); } /** @@ -259,8 +253,17 @@ 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; @@ -272,7 +275,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel String nSeconds = " "; if (files.length > 10) { - nSeconds = " 0.00001 "; + nSeconds = " 0.005 "; } else { @@ -281,7 +284,7 @@ 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++) { @@ -454,8 +457,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel + 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); } @@ -489,9 +491,10 @@ 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; @@ -511,7 +514,8 @@ 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) { @@ -531,10 +535,8 @@ 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); } /** @@ -586,7 +588,9 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel return null; } // TODO: verify atomIndex is selecting correct model. - return new Color(viewer.getAtomArgb(atomIndex)); + // return new Color(viewer.getAtomArgb(atomIndex)); Jmol 12.2.4 + int colour = viewer.ms.at[atomIndex].atomPropertyInt(T.color); + return new Color(colour); } /** @@ -642,26 +646,34 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel } if (modelFileNames == null) { - - String mset[] = new String[viewer.getModelCount()]; + String mset[] = new String[viewer.ms.mc]; _modelFileNameMap = new int[mset.length]; - int j = 1; - String m = viewer.getModelFileName(0); + String m = viewer.ms.getModelFileName(0); if (m != null) { + mset[0] = m; try { mset[0] = new File(m).getAbsolutePath(); } catch (AccessControlException x) { - // usually not allowed to do this in applet, so keep raw handle + // usually not allowed to do this in applet + System.err + .println("jmolBinding: Using local file string from Jmol: " + + m); + } + if (mset[0].indexOf("/file:") != -1) + { + // applet path with docroot - discard as format won't match pdbfile mset[0] = m; - // System.err.println("jmolBinding: Using local file string from Jmol: "+m); } + _modelFileNameMap[0] = 0; // filename index for first model is always 0. } + int j = 1; for (int i = 1; i < mset.length; i++) { - m = viewer.getModelFileName(i); + m = viewer.ms.getModelFileName(i); + mset[j] = m; if (m != null) { try @@ -670,7 +682,6 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel } catch (AccessControlException x) { // usually not allowed to do this in applet, so keep raw handle - mset[j] = m; // System.err.println("jmolBinding: Using local file string from Jmol: "+m); } } @@ -714,7 +725,8 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel public void handlePopupMenu(int x, int y) { - jmolpopup.show(x, y); + // jmolpopup.show(x, y); + // jmolpopup.jpiShow(x, y); } /** @@ -744,12 +756,10 @@ 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) @@ -765,31 +775,31 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel 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); } @@ -877,7 +887,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel pdbfilename = modelFileNames[_mp]; if (pdbfilename == null) { - pdbfilename = new File(viewer.getModelFileName(mnumber)) + pdbfilename = new File(viewer.ms.getModelFileName(mnumber)) .getAbsolutePath(); } @@ -932,7 +942,7 @@ 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) @@ -965,7 +975,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel } @Override - public void notifyCallback(EnumCallback type, Object[] data) + public void notifyCallback(CBK type, Object[] data) { try { @@ -1019,7 +1029,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel } @Override - public boolean notifyEnabled(EnumCallback callbackPick) + public boolean notifyEnabled(CBK callbackPick) { switch (callbackPick) { @@ -1032,13 +1042,9 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel case HOVER: case ERROR: return true; - case RESIZE: - case SYNC: - case CLICK: - case ANIMFRAME: - case MINIMIZATION: + default: + return false; } - return false; } // incremented every time a load notification is successfully handled - @@ -1069,8 +1075,8 @@ 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 @@ -1114,7 +1120,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel String fileName = modelfilenames[modelnum]; boolean foundEntry = false; MCview.PDBfile pdb = null; - String pdbfile = null, pdbfhash = null; + String pdbfile = null; // model was probably loaded inline - so check the pdb file hashcode if (loadedInline) { @@ -1123,10 +1129,9 @@ 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; @@ -1144,9 +1149,9 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel } else { - File fl; - if (matches = (fl = new File(getPdbEntry(pe).getFile())) - .equals(new File(fileName))) + File fl = new File(getPdbEntry(pe).getFile()); + matches = fl.equals(new File(fileName)); + if (matches) { foundEntry = true; // TODO: Jmol can in principle retrieve from CLASSLOADER but @@ -1204,14 +1209,14 @@ 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. @@ -1360,12 +1365,14 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel { commandOptions = ""; } - viewer = JmolViewer.allocateViewer(renderPanel, + viewer = (Viewer) JmolViewer.allocateViewer(renderPanel, (jmolfileio ? new SmarterJmolAdapter() : null), htmlName + ((Object) this).toString(), documentBase, codeBase, commandOptions, this); - console = createJmolConsole(viewer, consolePanel, buttonsToShow); + viewer.setJmolStatusListener(this); // extends JmolCallbackListener + + console = createJmolConsole(consolePanel, buttonsToShow); if (consolePanel != null) { consolePanel.addComponentListener(this); @@ -1375,7 +1382,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel } protected abstract JmolAppConsoleInterface createJmolConsole( - JmolViewer viewer2, Container consolePanel, String buttonsToShow); + Container consolePanel, String buttonsToShow); protected org.jmol.api.JmolAppConsoleInterface console = null; @@ -1388,20 +1395,10 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel } @Override - public void resizeInnerPanel(String data) + public Dimension resizeInnerPanel(String data) { // Jalview doesn't honour resize panel requests - - } - - public boolean isFinishedInit() - { - return finishedInit; - } - - public void setFinishedInit(boolean finishedInit) - { - this.finishedInit = finishedInit; + return null; } /**