X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fjmol%2FJalviewJmolBinding.java;h=58325fdc7791302b2c3bdfc38db3b94aed86e0a7;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=45fc37849f6e17345c558a25924649d6d167cb22;hpb=17fe82c9d7f9da1b17f3091e4b3992a35e3e411e;p=jalview.git diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java index 45fc378..58325fd 100644 --- a/src/jalview/ext/jmol/JalviewJmolBinding.java +++ b/src/jalview/ext/jmol/JalviewJmolBinding.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) - * Copyright (C) $$Year-Rel$$ The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9) + * Copyright (C) 2015 The Jalview Authors * * This file is part of Jalview. * @@ -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; @@ -32,39 +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.StructureMapping; -import jalview.structure.StructureMappingcommandSet; -import jalview.structure.StructureSelectionManager; -import jalview.structures.models.AAStructureBindingModel; -import jalview.util.MessageManager; +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; /* @@ -73,13 +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; @@ -89,7 +85,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel */ int frameNo = 0; - protected JmolPopup jmolpopup; + // protected JmolGenericPopup jmolpopup; // not used - remove? String lastCommand; @@ -104,7 +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, @@ -121,7 +117,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel } public JalviewJmolBinding(StructureSelectionManager ssm, - SequenceI[][] seqs, JmolViewer theViewer) + SequenceI[][] seqs, Viewer theViewer) { super(ssm, seqs); @@ -138,7 +134,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel */ public String getViewerTitle() { - return getViewerTitle("JMol", true); + return getViewerTitle("Jmol", true); } /** @@ -148,15 +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; @@ -164,7 +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) { @@ -175,7 +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 @@ -237,59 +231,51 @@ 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 }); } + /** + * 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 + */ public void superposeStructures(AlignmentI[] _alignment, int[] _refStructure, ColumnSelection[] _hiddenCols) { - assert (_alignment.length == _refStructure.length && _alignment.length != _hiddenCols.length); - - String[] files = getPdbFile(); - // check to see if we are still waiting for Jmol files - long starttime = System.currentTimeMillis(); - boolean waiting = true; - do + while (viewer.isScriptExecuting()) { - waiting = false; - for (String file : files) + try + { + Thread.sleep(10); + } catch (InterruptedException i) { - try - { - // HACK - in Jalview 2.8 this call may not be threadsafe so we catch - // every possible exception - StructureMapping[] sm = getSsm().getMapping(file); - if (sm == null || sm.length == 0) - { - waiting = true; - } - } catch (Exception x) - { - waiting = true; - } catch (Error q) - { - waiting = true; - } } - // we wait around for a reasonable time before we give up - } while (waiting - && System.currentTimeMillis() < (10000 + 1000 * files.length + starttime)); - if (waiting) + ; + } + String[] files = getPdbFile(); + if (!waitForFileLoad(files)) { - System.err - .println("RUNTIME PROBLEM: Jmol seems to be taking a long time to process all the structures."); return; } - StringBuffer selectioncom = new StringBuffer(); + + StringBuilder selectioncom = new StringBuilder(256); // In principle - nSeconds specifies the speed of animation for each // superposition - but is seems to behave weirdly, so we don't specify it. String nSeconds = " "; if (files.length > 10) { - nSeconds = " 0.00001 "; + nSeconds = " 0.005 "; } else { @@ -298,7 +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++) { @@ -319,134 +305,78 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel + refStructure); refStructure = -1; } - if (refStructure < -1) - { - refStructure = -1; - } - StringBuffer command = new StringBuffer(); + /* + * 'matched' array will hold 'true' for visible alignment columns 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++) { - matched[m] = (hiddenCols != null) ? hiddenCols.isVisible(m) : true; } - int commonrpositions[][] = new int[files.length][alignment.getWidth()]; - String isel[] = new String[files.length]; - // reference structure - all others are superposed in it - String[] targetC = new String[files.length]; - String[] chainNames = new String[files.length]; - for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) + SuperposeData[] structures = new SuperposeData[files.length]; + for (int f = 0; f < files.length; f++) { - StructureMapping[] mapping = getSsm().getMapping(files[pdbfnum]); - // RACE CONDITION - getMapping only returns Jmol loaded filenames once - // Jmol callback has completed. - if (mapping == null || mapping.length < 1) - { - throw new Error(MessageManager.getString("error.implementation_error_jmol_getting_data")); - } - int lastPos = -1; - final int sequenceCountForPdbFile = getSequence()[pdbfnum].length; - for (int s = 0; s < sequenceCountForPdbFile; s++) - { - for (int sp, m = 0; m < mapping.length; m++) - { - if (mapping[m].getSequence() == getSequence()[pdbfnum][s] - && (sp = alignment.findIndex(getSequence()[pdbfnum][s])) > -1) - { - if (refStructure == -1) - { - refStructure = pdbfnum; - } - SequenceI asp = alignment.getSequenceAt(sp); - for (int r = 0; r < matched.length; r++) - { - if (!matched[r]) - { - continue; - } - matched[r] = false; // assume this is not a good site - if (r >= asp.getLength()) - { - continue; - } - - if (jalview.util.Comparison.isGap(asp.getCharAt(r))) - { - // no mapping to gaps in sequence - continue; - } - int t = asp.findPosition(r); // sequence position - int apos = mapping[m].getAtomNum(t); - int pos = mapping[m].getPDBResNum(t); - - if (pos < 1 || pos == lastPos) - { - // can't align unmapped sequence - continue; - } - matched[r] = true; // this is a good ite - lastPos = pos; - // just record this residue position - commonrpositions[pdbfnum][r] = pos; - } - // create model selection suffix - isel[pdbfnum] = "/" + (pdbfnum + 1) + ".1"; - if (mapping[m].getChain() == null - || mapping[m].getChain().trim().length() == 0) - { - targetC[pdbfnum] = ""; - } - else - { - targetC[pdbfnum] = ":" + mapping[m].getChain(); - } - chainNames[pdbfnum] = mapping[m].getPdbId() - + targetC[pdbfnum]; - // move on to next pdb file - s = getSequence()[pdbfnum].length; - break; - } - } - } + structures[f] = new SuperposeData(alignment.getWidth()); } - // TODO: consider bailing if nmatched less than 4 because superposition - // not - // well defined. - // TODO: refactor superposable position search (above) from jmol selection - // construction (below) + /* + * Calculate the superposable alignment columns ('matched'), and the + * corresponding structure residue positions (structures.pdbResNo) + */ + int candidateRefStructure = findSuperposableResidues(alignment, + matched, structures); + if (refStructure < 0) + { + /* + * If no reference structure was specified, pick the first one that has + * a mapping in the alignment + */ + refStructure = candidateRefStructure; + } String[] selcom = new String[files.length]; int nmatched = 0; - // generate select statements to select regions to superimpose structures + for (boolean b : matched) + { + if (b) + { + nmatched++; + } + } + if (nmatched < 4) + { + // TODO: bail out here because superposition illdefined? + } + + /* + * generate select statements to select regions to superimpose structures + */ { for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) { - String chainCd = targetC[pdbfnum]; + String chainCd = ":" + structures[pdbfnum].chain; int lpos = -1; boolean run = false; - StringBuffer molsel = new StringBuffer(); + StringBuilder molsel = new StringBuilder(); molsel.append("{"); for (int r = 0; r < matched.length; r++) { if (matched[r]) { - if (pdbfnum == 0) - { - nmatched++; - } - if (lpos != commonrpositions[pdbfnum][r] - 1) + int pdbResNo = structures[pdbfnum].pdbResNo[r]; + if (lpos != pdbResNo - 1) { // discontinuity if (lpos != -1) { molsel.append(lpos); molsel.append(chainCd); - // molsel.append("} {"); molsel.append("|"); } + run = false; } else { @@ -459,11 +389,12 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel } run = true; } - lpos = commonrpositions[pdbfnum][r]; - // molsel.append(lpos); + lpos = pdbResNo; } } - // add final selection phrase + /* + * add final selection phrase + */ if (lpos != -1) { molsel.append(lpos); @@ -490,6 +421,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel } } } + StringBuilder command = new StringBuilder(256); for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) { if (pdbfnum == refStructure || selcom[pdbfnum] == null @@ -499,22 +431,23 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel } command.append("echo "); command.append("\"Superposing ("); - command.append(chainNames[pdbfnum]); + command.append(structures[pdbfnum].pdbId); command.append(") against reference ("); - command.append(chainNames[refStructure]); + command.append(structures[refStructure].pdbId); command.append(")\";\ncompare " + nSeconds); command.append("{"); - command.append(1 + pdbfnum); + command.append(Integer.toString(1 + pdbfnum)); command.append(".1} {"); - command.append(1 + refStructure); - command.append(".1} SUBSET {*.CA | *.P} ATOMS "); - - // form the matched pair strings - String sep = ""; - for (int s = 0; s < 2; s++) - { - command.append(selcom[(s == 0 ? pdbfnum : refStructure)]); - } + command.append(Integer.toString(1 + refStructure)); + // conformation=1 excludes alternate locations for CA (JAL-1757) + command.append(".1} SUBSET {(*.CA | *.P) and conformation=1} ATOMS "); + + // for (int s = 0; s < 2; s++) + // { + // command.append(selcom[(s == 0 ? pdbfnum : refStructure)]); + // } + command.append(selcom[pdbfnum]); + command.append(selcom[refStructure]); command.append(" ROTATE TRANSLATE;\n"); } if (selectioncom.length() > 0) @@ -523,10 +456,10 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel evalStateCommand("select *; cartoons off; backbone; select (" + selectioncom.toString() + "); cartoons; "); // selcom.append("; ribbons; "); - System.out - .println("Superimpose command(s):\n" + command.toString()); + String cmdString = command.toString(); + System.out.println("Superimpose command(s):\n" + cmdString); - evalStateCommand(command.toString()); + evalStateCommand(cmdString); } } if (selectioncom.length() > 0) @@ -558,9 +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; @@ -580,7 +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) { @@ -600,10 +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); } /** @@ -655,7 +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); } /** @@ -702,6 +637,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel // //////////////////////////////// // /StructureListener + @Override public synchronized String[] getPdbFile() { if (viewer == null) @@ -710,26 +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 @@ -738,7 +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); } } @@ -782,7 +725,24 @@ 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); + } + + /** + * Highlight zero, one or more atoms on the structure + */ + @Override + public void highlightAtoms(List atoms) + { + if (atoms != null) + { + for (AtomSpec atom : atoms) + { + highlightAtom(atom.getAtomIndex(), atom.getPdbResNum(), + atom.getChain(), atom.getPdbFile()); + } + } } // jmol/ssm only @@ -796,12 +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) @@ -817,31 +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); } @@ -929,7 +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(); } @@ -984,7 +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) @@ -1017,7 +975,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel } @Override - public void notifyCallback(EnumCallback type, Object[] data) + public void notifyCallback(CBK type, Object[] data) { try { @@ -1071,7 +1029,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel } @Override - public boolean notifyEnabled(EnumCallback callbackPick) + public boolean notifyEnabled(CBK callbackPick) { switch (callbackPick) { @@ -1084,13 +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 - @@ -1121,8 +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 @@ -1166,7 +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) { @@ -1175,10 +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; @@ -1196,9 +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 @@ -1256,14 +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. @@ -1412,12 +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); @@ -1427,7 +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; @@ -1439,32 +1394,11 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel jmolHistory(true); } - /** - * - * @param pdbfile - * @return text report of alignment between pdbfile and any associated - * alignment sequences - */ - public String printMapping(String pdbfile) - { - return getSsm().printMapping(pdbfile); - } - @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; } /**