X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fjmol%2FJalviewJmolBinding.java;h=3bac3bc1f9bb67c082b371fca52f54c9697f41f3;hb=1b5f1de68f3f4dadcd4eecc80a5db17441eb7ab6;hp=f27b533982a47fc74ce61676df4daf893cfe865c;hpb=b40e588eda6f640aa69ded711e49f8590bdc78b6;p=jalview.git diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java index f27b533..3bac3bc 100644 --- a/src/jalview/ext/jmol/JalviewJmolBinding.java +++ b/src/jalview/ext/jmol/JalviewJmolBinding.java @@ -24,6 +24,8 @@ import java.applet.Applet; import java.awt.*; import java.awt.event.*; +import javax.swing.JPanel; + import jalview.api.FeatureRenderer; import jalview.api.SequenceRenderer; import jalview.api.SequenceStructureBinding; @@ -36,11 +38,13 @@ import org.jmol.adapter.smarter.SmarterJmolAdapter; import org.jmol.popup.*; import org.jmol.viewer.JmolConstants; +import org.jmol.viewer.Viewer; import jalview.schemes.*; public abstract class JalviewJmolBinding implements StructureListener, - JmolStatusListener, SequenceStructureBinding, JmolSelectionListener + JmolStatusListener, SequenceStructureBinding, + JmolSelectionListener, ComponentListener { /** @@ -77,6 +81,8 @@ public abstract class JalviewJmolBinding implements StructureListener, public Vector chainNames; + Hashtable chainFile; + /** * array of target chains for seuqences - tied to pdbentry and sequence[] */ @@ -207,8 +213,9 @@ public abstract class JalviewJmolBinding implements StructureListener, p = mlength; mlength = lbl.indexOf(":", p); } 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) + " /" - + getModelNum(lbl.substring(0, mlength)) + " or "); + + (1 + getModelNum((String) chainFile.get(lbl))) + " or "); } if (cmd.length() > 0) cmd.setLength(cmd.length() - 4); @@ -226,8 +233,15 @@ public abstract class JalviewJmolBinding implements StructureListener, viewer.setJmolStatusListener(null); lastCommand = null; viewer = null; + releaseUIResources(); } + /** + * called by JalviewJmolbinding after closeViewer is called - release any + * resources and references so they can be garbage collected. + */ + protected abstract void releaseUIResources(); + public void colourByChain() { colourBySequence = false; @@ -373,6 +387,7 @@ public abstract class JalviewJmolBinding implements StructureListener, } } String[] selcom = new String[files.length]; + int nmatched = 0; // generate select statements to select regions to superimpose structures { for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) @@ -386,7 +401,10 @@ public abstract class JalviewJmolBinding implements StructureListener, { if (matched[r]) { - + if (pdbfnum == 0) + { + nmatched++; + } if (lpos != commonrpositions[pdbfnum][r] - 1) { // discontinuity @@ -433,7 +451,10 @@ public abstract class JalviewJmolBinding implements StructureListener, } } } - + // TODO: consider bailing if nmatched less than 4 because superposition not + // well defined. + // TODO: refactor superposable position search (above) from jmol selection + // construction (below) for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) { if (pdbfnum == refStructure) @@ -533,7 +554,7 @@ public abstract class JalviewJmolBinding implements StructureListener, Color col = sr.getResidueBoxColour(sequence[pdbfnum][s], r); - if (showFeatures) + if (showFeatures && fr != null) col = fr.findFeatureColour(col, sequence[pdbfnum][s], r); String newSelcom = (mapping[m].getChain() != " " ? ":" + mapping[m].getChain() : "") @@ -682,6 +703,10 @@ public abstract class JalviewJmolBinding implements StructureListener, // /StructureListener public synchronized String[] getPdbFile() { + if (viewer == null) + { + return new String[0]; + } if (modelFileNames == null) { @@ -694,8 +719,8 @@ public abstract class JalviewJmolBinding implements StructureListener, mset[j] = viewer.getModelFileName(i); _modelFileNameMap[j] = i; // record the model index for the filename // skip any additional models in the same file (NMR structures) - if ((mset[j] == null ? mset[j] != mset[j - 1] : (mset[j - 1] == null - || !mset[j].equals(mset[j - 1])))) + if ((mset[j] == null ? mset[j] != mset[j - 1] + : (mset[j - 1] == null || !mset[j].equals(mset[j - 1])))) { j++; } @@ -974,7 +999,6 @@ public abstract class JalviewJmolBinding implements StructureListener, case JmolConstants.CALLBACK_MEASURE: case JmolConstants.CALLBACK_CLICK: - default: System.err.println("Unhandled callback " + type + " " + data[1].toString()); @@ -1009,6 +1033,16 @@ public abstract class JalviewJmolBinding implements StructureListener, return false; } + // incremented every time a load notification is successfully handled - + // lightweight mechanism for other threads to detect when they can start + // referrring to new structures. + private long loadNotifiesHandled = 0; + + public long getLoadNotifiesHandled() + { + return loadNotifiesHandled; + } + public void notifyFileLoaded(String fullPathName, String fileName2, String modelName, String errorMsg, int modelParts) { @@ -1028,6 +1062,7 @@ public abstract class JalviewJmolBinding implements StructureListener, String[] oldmodels = modelFileNames; modelFileNames = null; chainNames = new Vector(); + chainFile = new Hashtable(); boolean notifyLoaded = false; String[] modelfilenames = getPdbFile(); ssm = StructureSelectionManager.getStructureSelectionManager(); @@ -1077,9 +1112,10 @@ public abstract class JalviewJmolBinding implements StructureListener, if (loadedInline) { // calculate essential attributes for the pdb data imported inline. - // prolly need to resolve modelnumber properly - for now just use our 'best guess' - pdbfile = viewer.getData(""+(1+_modelFileNameMap[modelnum])+".0", - "PDB"); + // prolly need to resolve modelnumber properly - for now just use our + // 'best guess' + pdbfile = viewer.getData("" + (1 + _modelFileNameMap[modelnum]) + + ".0", "PDB"); pdbfhash = "" + pdbfile.hashCode(); } if (pdbentry != null) @@ -1091,8 +1127,8 @@ public abstract class JalviewJmolBinding implements StructureListener, boolean matches = false; if (fileName == null) { - if (false) - // see JAL-623 - need method of matching pasted data up + if (false) + // see JAL-623 - need method of matching pasted data up { pdb = ssm.setMapping(sequence[pe], chains[pe], pdbfile, AppletFormatAdapter.PASTE); @@ -1128,7 +1164,6 @@ public abstract class JalviewJmolBinding implements StructureListener, pdb = ssm.setMapping(sequence[pe], chains[pe], pdbentry[pe].getFile(), protocol); - } } if (matches) @@ -1137,8 +1172,10 @@ public abstract class JalviewJmolBinding implements StructureListener, // add an entry for every chain in the model for (int i = 0; i < pdb.chains.size(); i++) { - chainNames.addElement(new String(pdb.id + ":" - + ((MCview.PDBChain) pdb.chains.elementAt(i)).id)); + String chid = new String(pdb.id + ":" + + ((MCview.PDBChain) pdb.chains.elementAt(i)).id); + chainFile.put(chid, pdbentry[pe].getFile()); + chainNames.addElement(chid); } notifyLoaded = true; } @@ -1146,19 +1183,19 @@ public abstract class JalviewJmolBinding implements StructureListener, } if (!foundEntry && associateNewStructs) { - // this is a foreign pdb file that jalview doesn't know about - add - // it to the dataset and try to find a home - either on a matching - // sequence or as a new sequence. - String pdbcontent = viewer.getData("/" + (modelnum + 1) + ".1", - "PDB"); - // parse pdb file into a chain, etc. - // locate best match for pdb in associated views and add mapping to - // ssm - // if properly registered then - notifyLoaded = true; + // this is a foreign pdb file that jalview doesn't know about - add + // it to the dataset and try to find a home - either on a matching + // sequence or as a new sequence. + String pdbcontent = viewer.getData("/" + (modelnum + 1) + ".1", + "PDB"); + // parse pdb file into a chain, etc. + // locate best match for pdb in associated views and add mapping to + // ssm + // if properly registered then + notifyLoaded = true; - } } + } // FILE LOADED OK // so finally, update the jmol bits and pieces if (jmolpopup != null) @@ -1182,6 +1219,7 @@ public abstract class JalviewJmolBinding implements StructureListener, fr.featuresAdded(); } refreshGUI(); + loadNotifiesHandled++; } } @@ -1274,6 +1312,13 @@ public abstract class JalviewJmolBinding implements StructureListener, public abstract void refreshGUI(); /** + * called to show or hide the associated console window container. + * + * @param show + */ + public abstract void showConsole(boolean show); + + /** * @param renderPanel * @param jmolfileio * - when true will initialise jmol's file IO system (should be false @@ -1283,14 +1328,75 @@ public abstract class JalviewJmolBinding implements StructureListener, * @param codeBase * @param commandOptions */ - public void allocateViewer(Component renderPanel, boolean jmolfileio, + public void allocateViewer(Container renderPanel, boolean jmolfileio, String htmlName, URL documentBase, URL codeBase, String commandOptions) { + allocateViewer(renderPanel, jmolfileio, htmlName, documentBase, + codeBase, commandOptions, null, null); + } + + /** + * + * @param renderPanel + * @param jmolfileio + * - when true will initialise jmol's file IO system (should be false + * in applet context) + * @param htmlName + * @param documentBase + * @param codeBase + * @param commandOptions + * @param consolePanel + * - panel to contain Jmol console + * @param buttonsToShow + * - buttons to show on the console, in ordr + */ + public void allocateViewer(Container renderPanel, boolean jmolfileio, + String htmlName, URL documentBase, URL codeBase, + String commandOptions, final Container consolePanel, + String buttonsToShow) + { viewer = JmolViewer.allocateViewer(renderPanel, (jmolfileio ? new SmarterJmolAdapter() : null), htmlName + ((Object) this).toString(), documentBase, codeBase, commandOptions, this); + + console = createJmolConsole(viewer, consolePanel, buttonsToShow); + if (consolePanel != null) + { + consolePanel.addComponentListener(this); + + } + + } + + protected abstract JmolAppConsoleInterface createJmolConsole( + JmolViewer viewer2, Container consolePanel, String buttonsToShow); + + protected org.jmol.api.JmolAppConsoleInterface console = null; + + @Override + public void componentResized(ComponentEvent e) + { + + } + + @Override + public void componentMoved(ComponentEvent e) + { + + } + + @Override + public void componentShown(ComponentEvent e) + { + showConsole(true); + } + + @Override + public void componentHidden(ComponentEvent e) + { + showConsole(false); } public void setLoadingFromArchive(boolean loadingFromArchive)