X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fjmol%2FJalviewJmolBinding.java;h=cfb30b3b8ef705d8d2282457ccd91b197a360452;hb=772f645f8a2cb3c5d25eab36d875f2e09ceca48f;hp=258d80660e23ac3940a372eea7dc8dad576a4b3e;hpb=b513684c725997c77341f30ce4e584cf9f7cdfed;p=jalview.git diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java index 258d806..cfb30b3 100644 --- a/src/jalview/ext/jmol/JalviewJmolBinding.java +++ b/src/jalview/ext/jmol/JalviewJmolBinding.java @@ -44,12 +44,12 @@ import java.awt.event.ComponentEvent; import java.awt.event.ComponentListener; import java.io.File; import java.net.URL; -import java.security.AccessControlException; import java.util.ArrayList; import java.util.BitSet; import java.util.Hashtable; import java.util.List; import java.util.Map; +import java.util.StringTokenizer; import java.util.Vector; import org.jmol.adapter.smarter.SmarterJmolAdapter; @@ -65,6 +65,8 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel implements JmolStatusListener, JmolSelectionListener, ComponentListener { + private String lastMessage; + boolean allChainsSelected = false; /* @@ -89,8 +91,6 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel String lastCommand; - String lastMessage; - boolean loadedInline; StringBuffer resetLastRes = new StringBuffer(); @@ -167,7 +167,9 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel // remove listeners for all structures in viewer getSsm().removeStructureViewerListener(this, this.getStructureFiles()); if (viewer != null) + { viewer.dispose(); + } lastCommand = null; viewer = null; releaseUIResources(); @@ -473,13 +475,14 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel jmolHistory(false); if (lastCommand == null || !lastCommand.equals(command)) { - viewer.evalStringQuiet(command + "\n"); + jmolScript(command + "\n"); } jmolHistory(true); lastCommand = command; } Thread colourby = null; + /** * Sends a set of colour commands to the structure viewer * @@ -494,7 +497,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel colourby.interrupt(); colourby = null; } - colourby = new Thread(new Runnable() + Thread colourby = new Thread(new Runnable() { @Override public void run() @@ -509,6 +512,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel } }); colourby.start(); + this.colourby = colourby; } /** @@ -615,74 +619,6 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel */ private int _modelFileNameMap[]; - // //////////////////////////////// - // /StructureListener - // @Override - public synchronized String[] getPdbFilex() - { - if (viewer == null) - { - return new String[0]; - } - if (modelFileNames == null) - { - List mset = new ArrayList<>(); - _modelFileNameMap = new int[viewer.ms.mc]; - String m = viewer.ms.getModelFileName(0); - if (m != null) - { - String filePath = m; - try - { - filePath = new File(m).getAbsolutePath(); - } catch (AccessControlException x) - { - // usually not allowed to do this in applet - System.err.println( - "jmolBinding: Using local file string from Jmol: " + m); - } - if (filePath.indexOf("/file:") != -1) - { - // applet path with docroot - discard as format won't match pdbfile - filePath = m; - } - mset.add(filePath); - _modelFileNameMap[0] = 0; // filename index for first model is always 0. - } - int j = 1; - for (int i = 1; i < viewer.ms.mc; i++) - { - m = viewer.ms.getModelFileName(i); - String filePath = m; - if (m != null) - { - try - { - filePath = new File(m).getAbsolutePath(); - } catch (AccessControlException x) - { - // usually not allowed to do this in applet, so keep raw handle - // System.err.println("jmolBinding: Using local file string from - // Jmol: "+m); - } - } - - /* - * add this model unless it is read from a structure file we have - * already seen (example: 2MJW is an NMR structure with 10 models) - */ - if (!mset.contains(filePath)) - { - mset.add(filePath); - _modelFileNameMap[j] = i; // record the model index for the filename - j++; - } - } - modelFileNames = mset.toArray(new String[mset.size()]); - } - return modelFileNames; - } - @Override public synchronized String[] getStructureFiles() { @@ -739,7 +675,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel { if (resetLastRes.length() > 0) { - viewer.evalStringQuiet(resetLastRes.toString()); + jmolScript(resetLastRes.toString()); resetLastRes.setLength(0); } for (AtomSpec atom : atoms) @@ -797,7 +733,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel cmd.append("spacefill 200;select none"); - viewer.evalStringQuiet(cmd.toString()); + jmolScript(cmd.toString()); jmolHistory(true); } @@ -806,7 +742,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel private void jmolHistory(boolean enable) { - viewer.evalStringQuiet("History " + ((debug || enable) ? "on" : "off")); + jmolScript("History " + ((debug || enable) ? "on" : "off")); } public void loadInline(String string) @@ -823,7 +759,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel viewer.openStringInline(string); } - public void mouseOverStructure(int atomIndex, String strInfo) + protected void mouseOverStructure(int atomIndex, final String strInfo) { int pdbResNum; int alocsep = strInfo.indexOf("^"); @@ -877,7 +813,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel try { // recover PDB filename for the model hovered over. - int mnumber = new Integer(mdlId).intValue() - 1; + int mnumber = Integer.valueOf(mdlId).intValue() - 1; if (_modelFileNameMap != null) { int _mp = _modelFileNameMap.length - 1; @@ -904,18 +840,36 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel } catch (Exception e) { } - ; } - if (lastMessage == null || !lastMessage.equals(strInfo)) + + /* + * 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); + if (label != null) { - getSsm().mouseOverStructure(pdbResNum, chainId, pdbfilename); + // change comma to pipe separator (newline token for Jmol) + label = label.replace(',', '|'); + StringTokenizer toks = new StringTokenizer(strInfo, " "); + StringBuilder sb = new StringBuilder(); + sb.append("select ").append(String.valueOf(pdbResNum)).append(":") + .append(chainId).append("/1"); + sb.append(";set hoverLabel \"").append(toks.nextToken()).append(" ") + .append(toks.nextToken()); + sb.append("|").append(label).append("\""); + evalStateCommand(sb.toString()); } - - lastMessage = strInfo; } public void notifyAtomHovered(int atomIndex, String strInfo, String data) { + if (strInfo.equals(lastMessage)) + { + return; + } + lastMessage = strInfo; if (data != null) { System.err.println("Ignoring additional hover info: " + data @@ -935,7 +889,7 @@ 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) { @@ -966,7 +920,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel if (!atomsPicked.contains(picked)) { - viewer.evalStringQuiet("select " + picked + ";label %n %r:%c"); + jmolScript("select " + picked + ";label %n %r:%c"); atomsPicked.addElement(picked); } else @@ -1154,8 +1108,7 @@ 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; @@ -1230,7 +1183,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel // } if (!isLoadingFromArchive()) { - viewer.evalStringQuiet( + jmolScript( "model *; select backbone;restrict;cartoon;wireframe off;spacefill off"); } // register ourselves as a listener and notify the gui that it needs to @@ -1255,7 +1208,10 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel return chainNames; } - protected abstract IProgressIndicator getIProgressIndicator(); + protected IProgressIndicator getIProgressIndicator() + { + return null; + } public void notifyNewPickingModeMeasurement(int iatom, String strMeasure) { @@ -1327,7 +1283,9 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel 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"); } /** @@ -1351,7 +1309,16 @@ 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 @@ -1382,13 +1349,16 @@ 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) { + + System.err.println("Allocating Jmol Viewer: " + commandOptions); + if (commandOptions == null) { commandOptions = ""; @@ -1398,9 +1368,19 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel htmlName + ((Object) this).toString(), documentBase, codeBase, commandOptions, this); - viewer.setJmolStatusListener(this); // extends JmolCallbackListener + viewer.setJmolStatusListener(this); + + // BH how about extending Jmol's status listener? - console = createJmolConsole(consolePanel, buttonsToShow); + try + { + console = createJmolConsole(consolePanel, buttonsToShow); + } catch (Throwable e) + { + System.err.println("Could not create Jmol application console. " + + e.getMessage()); + e.printStackTrace(); + } if (consolePanel != null) { consolePanel.addComponentListener(this); @@ -1412,17 +1392,32 @@ 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 public void setBackgroundColour(java.awt.Color col) { jmolHistory(false); - viewer.evalStringQuiet("background [" + col.getRed() + "," - + col.getGreen() + "," + col.getBlue() + "];"); + jmolScript("background [" + col.getRed() + "," + col.getGreen() + "," + + col.getBlue() + "];"); jmolHistory(true); } + private String jmolScript(String script) + { + + System.err.println(">>Jmol>> " + script); + + String s = viewer.scriptWait(script); + + System.err.println("<