X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fjmol%2FJalviewJmolBinding.java;h=21a19ae36fdcad3666da1b3c84edbb27287d6318;hb=c0e43acd458a2e19a5ab3be56a53bc88932657c4;hp=63c1fd3b6d3b158e5433dc5e7e21edd70a2f8578;hpb=7720585dc8cc56cdad2486b330ed37ddd0133531;p=jalview.git diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java index 63c1fd3..21a19ae 100644 --- a/src/jalview/ext/jmol/JalviewJmolBinding.java +++ b/src/jalview/ext/jmol/JalviewJmolBinding.java @@ -31,6 +31,8 @@ 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; @@ -41,10 +43,12 @@ import org.jmol.viewer.Viewer; import jalview.api.AlignmentViewPanel; import jalview.api.FeatureRenderer; +import jalview.api.FeatureSettingsModelI; import jalview.api.SequenceRenderer; -import jalview.bin.Cache; +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; @@ -54,6 +58,7 @@ 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 @@ -86,8 +91,8 @@ 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); */ @@ -117,9 +122,22 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel private String jmolScript(String script) { - Cache.log.debug(">>Jmol>> " + script); - String s = jmolViewer.scriptWait(script); - Cache.log.debug("<>Jmol>> " + script); + String s; + if (useScriptWait) + { + s = jmolViewer.scriptWait(script); + } + else + { + s = jmolViewer.evalStringQuiet(script); // scriptWait(script); BH + } + Console.debug("< 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)) @@ -249,22 +267,47 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel { if (atoms != null) { + boolean useScriptWait = atoms.size() > 1; if (resetLastRes.length() > 0) { - jmolScript(resetLastRes.toString()); + jmolScript(resetLastRes.toString(), useScriptWait); resetLastRes.setLength(0); } for (AtomSpec atom : atoms) { highlightAtom(atom.getAtomIndex(), atom.getPdbResNum(), - atom.getChain(), atom.getPdbFile()); + atom.getChain(), atom.getPdbFile(), useScriptWait); } + // 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) + String pdbfile, boolean useScriptWait) { String modelId = getModelIdForFile(pdbfile); if (modelId.isEmpty()) @@ -272,7 +315,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel return; } - jmolHistory(false); + jmolHistory(false, useScriptWait); StringBuilder selection = new StringBuilder(32); StringBuilder cmd = new StringBuilder(64); @@ -290,15 +333,21 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel resetLastRes.append(selection).append(";wireframe 0;").append(selection) .append(" and not hetero; spacefill 0;"); - jmolScript(cmd.toString()); - jmolHistory(true); + jmolScript(cmd.toString(), useScriptWait); + jmolHistory(true, useScriptWait); } private boolean debug = true; private void jmolHistory(boolean enable) { - jmolScript("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) @@ -398,8 +447,8 @@ 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); @@ -435,8 +484,8 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel /* * { 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, @@ -497,6 +546,28 @@ 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) @@ -745,7 +816,9 @@ 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++; @@ -774,8 +847,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel public abstract void sendConsoleEcho(String strEcho); /* * { showConsole(true); * - * history.append("\n" + - * strEcho); } + * history.append("\n" + strEcho); } */ // /End JmolStatusListener