X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fext%2Fjmol%2FJalviewJmolBinding.java;h=93a56334ec0176d7e5506fb10595ad5ddeeb76ec;hb=4a28fee3e0c129a01268d26e1396b045bd893fb8;hp=061271af8395ba3575029afa04c5ecdae5511af1;hpb=f236e4e9e66583ca15dce3c3ef0cc43b02bf092e;p=jalview.git diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java index 061271a..93a5633 100644 --- a/src/jalview/ext/jmol/JalviewJmolBinding.java +++ b/src/jalview/ext/jmol/JalviewJmolBinding.java @@ -26,11 +26,15 @@ import java.awt.event.ComponentListener; import java.io.File; import java.net.URL; import java.util.ArrayList; +import java.util.Arrays; +import java.util.HashMap; import java.util.List; import java.util.Map; import java.util.StringTokenizer; import java.util.Vector; +import javax.swing.SwingUtilities; + import org.jmol.adapter.smarter.SmarterJmolAdapter; import org.jmol.api.JmolAppConsoleInterface; import org.jmol.api.JmolSelectionListener; @@ -39,9 +43,14 @@ import org.jmol.api.JmolViewer; import org.jmol.c.CBK; import org.jmol.viewer.Viewer; +import jalview.api.AlignmentViewPanel; import jalview.api.FeatureRenderer; +import jalview.api.FeatureSettingsModelI; +import jalview.api.SequenceRenderer; +import jalview.bin.Console; import jalview.datamodel.PDBEntry; import jalview.datamodel.SequenceI; +import jalview.gui.AppJmol; import jalview.gui.IProgressIndicator; import jalview.gui.StructureViewer.ViewerType; import jalview.io.DataSourceType; @@ -51,6 +60,8 @@ import jalview.structure.StructureCommand; import jalview.structure.StructureCommandI; import jalview.structure.StructureSelectionManager; import jalview.structures.models.AAStructureBindingModel; +import jalview.ws.dbsources.Pdb; +import javajs.util.BS; public abstract class JalviewJmolBinding extends AAStructureBindingModel implements JmolStatusListener, JmolSelectionListener, @@ -82,8 +93,8 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel setStructureCommands(new JmolCommands()); /* * viewer = JmolViewer.allocateViewer(renderPanel, new SmarterJmolAdapter(), - * "jalviewJmol", ap.av.applet .getDocumentBase(), - * ap.av.applet.getCodeBase(), "", this); + * "jalviewJmol", ap.av.applet .getDocumentBase(), ap.av.applet.getCodeBase(), + * "", this); * * jmolpopup = JmolPopup.newJmolPopup(viewer, true, "Jmol", true); */ @@ -111,14 +122,26 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel return getViewerTitle("Jmol", true); } - public void closeViewer() + private String jmolScript(String script) + { + return jmolScript(script, false); + } + + private String jmolScript(String script, boolean useScriptWait) { - // remove listeners for all structures in viewer - getSsm().removeStructureViewerListener(this, this.getStructureFiles()); - jmolViewer.dispose(); - lastCommand = null; - jmolViewer = null; - releaseUIResources(); + Console.debug(">>Jmol>> " + script); + String s; + if (useScriptWait) + { + s = jmolViewer.scriptWait(script); + } + else + { + s = jmolViewer.evalStringQuiet(script); // scriptWait(script); BH + } + Console.debug("< getHetatmNames() + { + HashMap hetlist = new HashMap(); + for (int mc = 0; mc < jmolViewer.ms.mc; mc++) + { + Map hets = jmolViewer.ms.getHeteroList(mc); + if (hets != null) + { + hetlist.putAll(hets); + } + } + return hetlist; + } + // + //////////////////////////// + @Override public float[][] functionXY(String functionName, int x, int y) { @@ -201,8 +245,8 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel for (int i = 0; i < modelCount; ++i) { /* - * defensive check for null as getModelFileName can return null - * even when model count ms.mc is > 0 + * defensive check for null as getModelFileName can return null even when model + * count ms.mc is > 0 */ filePath = jmolViewer.ms.getModelFileName(i); if (filePath != null && !mset.contains(filePath)) @@ -210,7 +254,10 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel mset.add(filePath); } } - modelFileNames = mset.toArray(new String[mset.size()]); + if (!mset.isEmpty()) + { + modelFileNames = mset.toArray(new String[mset.size()]); + } } return modelFileNames; @@ -245,74 +292,99 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel { if (resetLastRes.length() > 0) { - jmolViewer.evalStringQuiet(resetLastRes.toString()); + jmolScript(resetLastRes.toString()); resetLastRes.setLength(0); } + StringBuilder highlightCommands = null; for (AtomSpec atom : atoms) { - highlightAtom(atom.getAtomIndex(), atom.getPdbResNum(), - atom.getChain(), atom.getPdbFile()); + StringBuilder thisAtom = highlightAtom(atom.getAtomIndex(), + atom.getPdbResNum(), atom.getChain(), atom.getPdbFile()); + if (thisAtom != null) + { + if (highlightCommands == null) + { + highlightCommands = thisAtom; + } + else + { + highlightCommands.append(thisAtom); + } + } } + if (highlightCommands != null) + { + jmolHistory(false); + jmolScript(highlightCommands.toString()); + jmolHistory(true); + } + // Highlight distances between atoms with a 'measure' command - not yet + // working + // if (atoms.size() >= 2) + // { + // StringBuilder sb = new StringBuilder(); + // for (int a = 0; a < atoms.size(); a++) + // { + // AtomSpec speca = atoms.get(a); + // String a_model = getModelIdForFile(speca.getPdbFile()); + // for (int b = a + 1; b < atoms.size(); b++) + // { + // AtomSpec specb = atoms.get(b); + // String b_model = getModelIdForFile(speca.getPdbFile()); + // sb.append("measure ALL (" + speca.getAtomIndex() + " and */" + // + a_model + ") (" + specb.getAtomIndex() + " and */" + // + b_model + ");"); + // } + // } + // jmolHistory(false, useScriptWait); + // jmolScript(sb.toString(), useScriptWait); + // jmolHistory(true, useScriptWait); + // } + } + } // jmol/ssm only - public void highlightAtom(int atomIndex, int pdbResNum, String chain, - String pdbfile) + private StringBuilder highlightAtom(int atomIndex, int pdbResNum, + String chain, String pdbfile) { - if (modelFileNames == null) - { - return; - } - - // look up file model number for this pdbfile - int mdlNum = 0; - // may need to adjust for URLencoding here - we don't worry about that yet. - while (mdlNum < modelFileNames.length - && !pdbfile.equals(modelFileNames[mdlNum])) + String modelId = getModelIdForFile(pdbfile); + if (modelId.isEmpty()) { - mdlNum++; - } - if (mdlNum == modelFileNames.length) - { - return; + return null; } - jmolHistory(false); - + StringBuilder selection = new StringBuilder(32); StringBuilder cmd = new StringBuilder(64); - cmd.append("select ").append(String.valueOf(pdbResNum)); // +modelNum - - resetLastRes.append("select ").append(String.valueOf(pdbResNum)); // +modelNum - - cmd.append(":"); - resetLastRes.append(":"); + selection.append("select ").append(String.valueOf(pdbResNum)); + selection.append(":"); if (!chain.equals(" ")) { - cmd.append(chain); - resetLastRes.append(chain); + selection.append(chain); } - { - cmd.append(" /").append(String.valueOf(mdlNum + 1)); - resetLastRes.append("/").append(String.valueOf(mdlNum + 1)); - } - cmd.append(";wireframe 100;" + cmd.toString() + " and not hetero;"); - - resetLastRes.append(";wireframe 0;" + resetLastRes.toString() - + " and not hetero; spacefill 0;"); + selection.append(" /").append(modelId); - cmd.append("spacefill 200;select none"); + cmd.append(selection).append(";wireframe 100;").append(selection) + .append(" and not hetero;").append("spacefill 200;select none"); - jmolViewer.evalStringQuiet(cmd.toString()); - jmolHistory(true); + resetLastRes.append(selection).append(";wireframe 0;").append(selection) + .append(" and not hetero; spacefill 0;"); + return cmd; } private boolean debug = true; private void jmolHistory(boolean enable) { - jmolViewer.evalStringQuiet("History " + ((debug || enable) ? "on" : "off")); + jmolHistory(enable, false); + } + + private void jmolHistory(boolean enable, boolean useScriptWait) + { + jmolScript("History " + ((debug || enable) ? "on" : "off"), + useScriptWait); } public void loadInline(String string) @@ -412,8 +484,8 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel } /* - * highlight position on alignment(s); if some text is returned, - * show this as a second line on the structure hover tooltip + * highlight position on alignment(s); if some text is returned, show this as a + * second line on the structure hover tooltip */ String label = getSsm().mouseOverStructure(pdbResNum, chainId, pdbfilename); @@ -441,16 +513,17 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel lastMessage = strInfo; if (data != null) { - System.err.println("Ignoring additional hover info: " + data - + " (other info: '" + strInfo + "' pos " + atomIndex + ")"); + jalview.bin.Console.errPrintln( + "Ignoring additional hover info: " + data + " (other info: '" + + strInfo + "' pos " + atomIndex + ")"); } mouseOverStructure(atomIndex, strInfo); } /* * { if (history != null && strStatus != null && - * !strStatus.equals("Script completed")) { history.append("\n" + strStatus); - * } } + * !strStatus.equals("Script completed")) { history.append("\n" + strStatus); } + * } */ public void notifyAtomPicked(int atomIndex, String strInfo, @@ -458,11 +531,12 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel { /** * this implements the toggle label behaviour copied from the original - * structure viewer, MCView + * structure viewer, mc_view */ if (strData != null) { - System.err.println("Ignoring additional pick data string " + strData); + jalview.bin.Console.errPrintln( + "Ignoring additional pick data string " + strData); } int chainSeparator = strInfo.indexOf(":"); int p = 0; @@ -489,7 +563,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel if (!atomsPicked.contains(picked)) { - jmolViewer.evalStringQuiet("select " + picked + ";label %n %r:%c"); + jmolScript("select " + picked + ";label %n %r:%c"); atomsPicked.addElement(picked); } else @@ -511,6 +585,28 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel @Override public void notifyCallback(CBK type, Object[] data) { + /* + * ensure processed in AWT thread to avoid risk of deadlocks + */ + SwingUtilities.invokeLater(new Runnable() + { + + @Override + public void run() + { + processCallback(type, data); + } + }); + } + + /** + * Processes one callback notification from Jmol + * + * @param type + * @param data + */ + protected void processCallback(CBK type, Object[] data) + { try { switch (type) @@ -542,7 +638,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel (data == null) ? ((String) null) : (String) data[1]); break; case ERROR: - // System.err.println("Ignoring error callback."); + // jalview.bin.Console.errPrintln("Ignoring error callback."); break; case SYNC: case RESIZE: @@ -552,13 +648,14 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel case CLICK: default: - System.err.println( + jalview.bin.Console.errPrintln( "Unhandled callback " + type + " " + data[1].toString()); break; } } catch (Exception e) { - System.err.println("Squashed Jmol callback handler error:"); + jalview.bin.Console + .errPrintln("Squashed Jmol callback handler error:"); e.printStackTrace(); } } @@ -612,6 +709,11 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel modelFileNames = null; boolean notifyLoaded = false; String[] modelfilenames = getStructureFiles(); + if (modelfilenames == null) + { + // Jmol is still loading files! + return; + } // first check if we've lost any structures if (oldmodels != null && oldmodels.length > 0) { @@ -675,8 +777,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel // see JAL-623 - need method of matching pasted data up { pdb = getSsm().setMapping(getSequence()[pe], getChains()[pe], - pdbfile, DataSourceType.PASTE, - getIProgressIndicator()); + pdbfile, DataSourceType.PASTE, getIProgressIndicator()); getPdbEntry(modelnum).setFile("INLINE" + pdb.getId()); matches = true; foundEntry = true; @@ -744,7 +845,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel // } if (!isLoadingFromArchive()) { - jmolViewer.evalStringQuiet( + jmolScript( "model *; select backbone;restrict;cartoon;wireframe off;spacefill off"); } // register ourselves as a listener and notify the gui that it needs to @@ -755,7 +856,9 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel FeatureRenderer fr = getFeatureRenderer(null); if (fr != null) { - fr.featuresAdded(); + FeatureSettingsModelI colours = new Pdb().getFeatureColourScheme(); + ((AppJmol) getViewer()).getAlignmentPanel().av + .applyFeaturesStyle(colours); } refreshGUI(); loadNotifiesHandled++; @@ -784,8 +887,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel public abstract void sendConsoleEcho(String strEcho); /* * { showConsole(true); * - * history.append("\n" + - * strEcho); } + * history.append("\n" + strEcho); } */ // /End JmolStatusListener @@ -802,14 +904,17 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel public void setCallbackFunction(String callbackType, String callbackFunction) { - System.err.println("Ignoring set-callback request to associate " - + callbackType + " with function " + callbackFunction); + jalview.bin.Console + .errPrintln("Ignoring set-callback request to associate " + + callbackType + " with function " + callbackFunction); } public void showHelp() { - showUrl("http://jmol.sourceforge.net/docs/JmolUserGuide/", "jmolHelp"); + showUrl("http://wiki.jmol.org" + // BH 2018 "http://jmol.sourceforge.net/docs/JmolUserGuide/" + , "jmolHelp"); } /** @@ -826,7 +931,16 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel */ public abstract void showConsole(boolean show); + public static Viewer getJmolData(JmolParser jmolParser) + { + return (Viewer) JmolViewer.allocateViewer(null, null, null, null, null, + "-x -o -n", jmolParser); + } + /** + * + * + * * @param renderPanel * @param jmolfileio * - when true will initialise jmol's file IO system (should be false @@ -857,13 +971,17 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel * @param consolePanel * - panel to contain Jmol console * @param buttonsToShow - * - buttons to show on the console, in ordr + * - buttons to show on the console, in order */ public void allocateViewer(Container renderPanel, boolean jmolfileio, String htmlName, URL documentBase, URL codeBase, String commandOptions, final Container consolePanel, String buttonsToShow) { + + jalview.bin.Console + .errPrintln("Allocating Jmol Viewer: " + commandOptions); + if (commandOptions == null) { commandOptions = ""; @@ -875,7 +993,16 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel jmolViewer.setJmolStatusListener(this); // extends JmolCallbackListener - console = createJmolConsole(consolePanel, buttonsToShow); + try + { + console = createJmolConsole(consolePanel, buttonsToShow); + } catch (Throwable e) + { + jalview.bin.Console + .errPrintln("Could not create Jmol application console. " + + e.getMessage()); + e.printStackTrace(); + } if (consolePanel != null) { consolePanel.addComponentListener(this); @@ -887,6 +1014,9 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel protected abstract JmolAppConsoleInterface createJmolConsole( Container consolePanel, String buttonsToShow); + // BH 2018 -- Jmol console is not working due to problems with styled + // documents. + protected org.jmol.api.JmolAppConsoleInterface console = null; @Override @@ -990,4 +1120,23 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel { return ".spt"; } + + @Override + public void selectionChanged(BS arg0) + { + // TODO Auto-generated method stub + + } + + @Override + public SequenceRenderer getSequenceRenderer(AlignmentViewPanel avp) + { + return new jalview.gui.SequenceRenderer(avp.getAlignViewport()); + } + + @Override + public String getHelpURL() + { + return "http://wiki.jmol.org"; // BH 2018 + } }