X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fjmol%2FJalviewJmolBinding.java;h=67327c13b26aed3f956a86c4c5b7bbf9e3c251e6;hb=c8f5deb89ce327cd4a103025122e2ee11a4c97fb;hp=f8fe17b5fb200e56091903842bfb30245aaf4895;hpb=4de8dbdccf508589bec18d9a8af5799531c5807b;p=jalview.git diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java index f8fe17b..67327c1 100644 --- a/src/jalview/ext/jmol/JalviewJmolBinding.java +++ b/src/jalview/ext/jmol/JalviewJmolBinding.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle * * This file is part of Jalview. @@ -24,6 +24,9 @@ import java.applet.Applet; import java.awt.*; import java.awt.event.*; +import javax.swing.JPanel; + +import jalview.api.AlignmentViewPanel; import jalview.api.FeatureRenderer; import jalview.api.SequenceRenderer; import jalview.api.SequenceStructureBinding; @@ -36,11 +39,13 @@ 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 +82,8 @@ public abstract class JalviewJmolBinding implements StructureListener, public Vector chainNames; + Hashtable chainFile; + /** * array of target chains for seuqences - tied to pdbentry and sequence[] */ @@ -110,7 +117,7 @@ public abstract class JalviewJmolBinding implements StructureListener, public PDBEntry[] pdbentry; /** - * datasource protocol for access to PDBEntry + * datasource protocol for access to PDBEntrylatest */ String protocol = null; @@ -161,10 +168,12 @@ public abstract class JalviewJmolBinding implements StructureListener, public String getViewerTitle() { if (sequence == null || pdbentry == null || sequence.length < 1 - || pdbentry.length < 1) + || pdbentry.length < 1 || sequence[0].length < 1) { return ("Jalview Jmol Window"); } + // TODO: give a more informative title when multiple structures are + // displayed. StringBuffer title = new StringBuffer(sequence[0][0].getName() + ":" + pdbentry[0].getId()); @@ -205,8 +214,9 @@ 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); @@ -224,11 +234,21 @@ 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; + // TODO: colour by chain should colour each chain distinctly across all + // visible models + // TODO: http://issues.jalview.org/browse/JAL-628 evalStateCommand("select *;color chain"); } @@ -264,195 +284,252 @@ public abstract class JalviewJmolBinding implements StructureListener, /** * superpose the structures associated with sequences in the alignment * according to their corresponding positions. ded) + * * @param refStructure * - select which pdb file to use as reference (default is -1 - the * first structure in the alignment) - * @param hiddenCols TODO + * @param hiddenCols + * TODO */ - public void superposeStructures(AlignmentI alignment, int refStructure, ColumnSelection hiddenCols) + public void superposeStructures(AlignmentI alignment, int refStructure, + ColumnSelection hiddenCols) + { + superposeStructures(new AlignmentI[] + { alignment }, new int[] + { refStructure }, new ColumnSelection[] + { hiddenCols }); + } + + public void superposeStructures(AlignmentI[] _alignment, + int[] _refStructure, ColumnSelection[] _hiddenCols) { String[] files = getPdbFile(); - if (refStructure>=files.length) - { - System.err.println("Invalid reference structure value "+refStructure); - refStructure= -1; - } - if (refStructure<-1) - { - refStructure=-1; - } - StringBuffer command = new StringBuffer(), selectioncom = new StringBuffer(); - - 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]; - for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) + StringBuffer selectioncom = new StringBuffer(); + assert (_alignment.length == _refStructure.length && _alignment.length != _hiddenCols.length); + // union of all aligned positions are collected together. + for (int a = 0; a < _alignment.length; a++) { - StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]); + int refStructure = _refStructure[a]; + AlignmentI alignment = _alignment[a]; + ColumnSelection hiddenCols = _hiddenCols[a]; + if (a > 0 + && selectioncom.length() > 0 + && !selectioncom.substring(selectioncom.length() - 1).equals( + "|")) + { + selectioncom.append("|"); + } + // process this alignment + if (refStructure >= files.length) + { + System.err.println("Invalid reference structure value " + + refStructure); + refStructure = -1; + } + if (refStructure < -1) + { + refStructure = -1; + } + StringBuffer command = new StringBuffer(); - if (mapping == null || mapping.length < 1) - continue; + boolean matched[] = new boolean[alignment.getWidth()]; + for (int m = 0; m < matched.length; m++) + { - int lastPos = -1; - for (int s = 0; s < sequence[pdbfnum].length; s++) + 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++) { - for (int sp, m = 0; m < mapping.length; m++) + StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]); + + if (mapping == null || mapping.length < 1) + continue; + + int lastPos = -1; + for (int s = 0; s < sequence[pdbfnum].length; s++) { - if (mapping[m].getSequence() == sequence[pdbfnum][s] - && (sp = alignment.findIndex(sequence[pdbfnum][s])) > -1) + for (int sp, m = 0; m < mapping.length; m++) { - if (refStructure == -1) - { - refStructure = pdbfnum; - } - SequenceI asp = alignment.getSequenceAt(sp); - for (int r = 0; r < matched.length; r++) + if (mapping[m].getSequence() == sequence[pdbfnum][s] + && (sp = alignment.findIndex(sequence[pdbfnum][s])) > -1) { - if (!matched[r]) + if (refStructure == -1) { - continue; + refStructure = pdbfnum; } - matched[r] = false; // assume this is not a good site - if (r >= asp.getLength()) + SequenceI asp = alignment.getSequenceAt(sp); + for (int r = 0; r < matched.length; r++) { - continue; - } + 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))) + 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) { - // no mapping to gaps in sequence - continue; + targetC[pdbfnum] = ""; } - int t = asp.findPosition(r); // sequence position - int apos = mapping[m].getAtomNum(t); - int pos = mapping[m].getPDBResNum(t); - - if (pos < 1 || pos == lastPos) + else { - // can't align unmapped sequence - continue; + targetC[pdbfnum] = ":" + mapping[m].getChain(); } - 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] = ""; + chainNames[pdbfnum] = mapping[m].getPdbId() + + targetC[pdbfnum]; + // move on to next pdb file + s = sequence[pdbfnum].length; + break; } - else - { - targetC[pdbfnum] = ":" + mapping[m].getChain(); - } - // move on to next pdb file - s = sequence[pdbfnum].length; - break; } } } - } - String[] selcom = new String[files.length]; - // generate select statements to select regions to superimpose structures - { - for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) + String[] selcom = new String[files.length]; + int nmatched = 0; + // generate select statements to select regions to superimpose structures { - String chainCd = targetC[pdbfnum]; - int lpos = -1; - boolean run = false; - StringBuffer molsel = new StringBuffer(); - molsel.append("{"); - for (int r = 0; r < matched.length; r++) + for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) { - if (matched[r]) + String chainCd = targetC[pdbfnum]; + int lpos = -1; + boolean run = false; + StringBuffer molsel = new StringBuffer(); + molsel.append("{"); + for (int r = 0; r < matched.length; r++) { - - if (lpos != commonrpositions[pdbfnum][r] - 1) + if (matched[r]) { - // discontinuity - if (lpos != -1) + if (pdbfnum == 0) { - molsel.append(lpos); - molsel.append(chainCd); - // molsel.append("} {"); - molsel.append("|"); + nmatched++; } - } - else - { - // continuous run - and lpos >-1 - if (!run) + if (lpos != commonrpositions[pdbfnum][r] - 1) + { + // discontinuity + if (lpos != -1) + { + molsel.append(lpos); + molsel.append(chainCd); + // molsel.append("} {"); + molsel.append("|"); + } + } + else { - // at the beginning, so add dash - molsel.append(lpos); - molsel.append("-"); + // continuous run - and lpos >-1 + if (!run) + { + // at the beginning, so add dash + molsel.append(lpos); + molsel.append("-"); + } + run = true; } - run = true; + lpos = commonrpositions[pdbfnum][r]; + // molsel.append(lpos); } - lpos = commonrpositions[pdbfnum][r]; - // molsel.append(lpos); + } + // add final selection phrase + if (lpos != -1) + { + molsel.append(lpos); + molsel.append(chainCd); + molsel.append("}"); + } + selcom[pdbfnum] = molsel.toString(); + selectioncom.append("(("); + selectioncom.append(selcom[pdbfnum].substring(1, + selcom[pdbfnum].length() - 1)); + selectioncom.append(" )& "); + selectioncom.append(pdbfnum + 1); + selectioncom.append(".1)"); + if (pdbfnum < files.length - 1) + { + selectioncom.append("|"); } } - // add final selection phrase - if (lpos != -1) + } + // 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) { - molsel.append(lpos); - molsel.append(chainCd); - molsel.append("}"); + continue; } - selcom[pdbfnum] = molsel.toString(); - selectioncom.append("(("); - selectioncom.append(selcom[pdbfnum].substring(1, selcom[pdbfnum].length()-1)); - selectioncom.append(" )& "); - selectioncom.append(pdbfnum+1); - selectioncom.append(".1)"); - if (pdbfnum 0) + {// finally, mark all regions that were superposed. + if (selectioncom.substring(selectioncom.length() - 1).equals("|")) { - command.append(selcom[(s == 0 ? pdbfnum : refStructure)]); + selectioncom.setLength(selectioncom.length() - 1); } - command.append(" ROTATE TRANSLATE;\n"); + System.out.println("Select regions:\n" + selectioncom.toString()); + evalStateCommand("select *; cartoons off; backbone; select (" + + selectioncom.toString() + "); cartoons; "); + // evalStateCommand("select *; backbone; select "+selcom.toString()+"; cartoons; center "+selcom.toString()); } - System.out.println("Select regions:\n" + selectioncom.toString()); - evalStateCommand("select *; cartoons off; backbone; select ("+selectioncom.toString()+"); cartoons; "); - // selcom.append("; ribbons; "); - System.out.println("Superimpose command(s):\n" + command.toString()); - - evalStateCommand(command.toString()); - - // evalStateCommand("select *; backbone; select "+selcom.toString()+"; cartoons; center "+selcom.toString()); } public void evalStateCommand(String command) @@ -471,7 +548,8 @@ public abstract class JalviewJmolBinding implements StructureListener, * using the getFeatureRenderer() and getSequenceRenderer() renderers but only * if colourBySequence is enabled. */ - public void colourBySequence(boolean showFeatures, AlignmentI alignment) + public void colourBySequence(boolean showFeatures, + jalview.api.AlignmentViewPanel alignmentv) { if (!colourBySequence) return; @@ -480,14 +558,15 @@ public abstract class JalviewJmolBinding implements StructureListener, return; } String[] files = getPdbFile(); - SequenceRenderer sr = getSequenceRenderer(); + + SequenceRenderer sr = getSequenceRenderer(alignmentv); FeatureRenderer fr = null; if (showFeatures) { - fr = getFeatureRenderer(); + fr = getFeatureRenderer(alignmentv); } - + AlignmentI alignment = alignmentv.getAlignment(); StringBuffer command = new StringBuffer(); for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) @@ -522,7 +601,7 @@ 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() : "") @@ -634,9 +713,12 @@ public abstract class JalviewJmolBinding implements StructureListener, * returns the current featureRenderer that should be used to colour the * structures * + * @param alignment + * * @return */ - public abstract FeatureRenderer getFeatureRenderer(); + public abstract FeatureRenderer getFeatureRenderer( + AlignmentViewPanel alignment); /** * instruct the Jalview binding to update the pdbentries vector if necessary @@ -660,18 +742,41 @@ public abstract class JalviewJmolBinding implements StructureListener, return -1; } + /** + * map between index of model filename returned from getPdbFile and the first + * index of models from this file in the viewer. Note - this is not trimmed - + * use getPdbFile to get number of unique models. + */ + private int _modelFileNameMap[]; + // //////////////////////////////// // /StructureListener - public String[] getPdbFile() + public synchronized String[] getPdbFile() { + if (viewer == null) + { + return new String[0]; + } if (modelFileNames == null) { + String mset[] = new String[viewer.getModelCount()]; - for (int i = 0; i < mset.length; i++) + _modelFileNameMap = new int[mset.length]; + int j = 1; + mset[0] = viewer.getModelFileName(0); + for (int i = 1; i < mset.length; i++) { - mset[i] = viewer.getModelFileName(i); + 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])))) + { + j++; + } } - modelFileNames = mset; + modelFileNames = new String[j]; + System.arraycopy(mset, 0, modelFileNames, 0, j); } return modelFileNames; } @@ -689,9 +794,12 @@ public abstract class JalviewJmolBinding implements StructureListener, * returns the current sequenceRenderer that should be used to colour the * structures * + * @param alignment + * * @return */ - public abstract SequenceRenderer getSequenceRenderer(); + public abstract SequenceRenderer getSequenceRenderer( + AlignmentViewPanel alignment); // /////////////////////////////// // JmolStatusListener @@ -772,12 +880,21 @@ public abstract class JalviewJmolBinding implements StructureListener, public void loadInline(String string) { loadedInline = true; + // TODO: re JAL-623 + // viewer.loadInline(strModel, isAppend); + // could do this: + // construct fake fullPathName and fileName so we can identify the file + // later. + // Then, construct pass a reader for the string to Jmol. + // ((org.jmol.Viewer.Viewer) viewer).loadModelFromFile(fullPathName, + // fileName, null, reader, false, null, null, 0); viewer.openStringInline(string); } public void mouseOverStructure(int atomIndex, String strInfo) { int pdbResNum; + int alocsep = strInfo.indexOf("^"); int mdlSep = strInfo.indexOf("/"); int chainSeparator = strInfo.indexOf(":"), chainSeparator1 = -1; @@ -790,9 +907,18 @@ public abstract class JalviewJmolBinding implements StructureListener, chainSeparator = mdlSep; } } - pdbResNum = Integer.parseInt(strInfo.substring( - strInfo.indexOf("]") + 1, chainSeparator)); + // handle insertion codes + if (alocsep != -1) + { + pdbResNum = Integer.parseInt(strInfo.substring( + strInfo.indexOf("]") + 1, alocsep)); + } + else + { + pdbResNum = Integer.parseInt(strInfo.substring( + strInfo.indexOf("]") + 1, chainSeparator)); + } String chainId; if (strInfo.indexOf(":") > -1) @@ -936,7 +1062,6 @@ public abstract class JalviewJmolBinding implements StructureListener, case JmolConstants.CALLBACK_MEASURE: case JmolConstants.CALLBACK_CLICK: - default: System.err.println("Unhandled callback " + type + " " + data[1].toString()); @@ -971,6 +1096,16 @@ 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) { @@ -980,6 +1115,9 @@ public abstract class JalviewJmolBinding implements StructureListener, refreshGUI(); return; } + // TODO: deal sensibly with models loaded inLine: + // modelName will be null, as will fullPathName. + // the rest of this routine ignores the arguments, and simply interrogates // the Jmol view to find out what structures it contains, and adds them to // the structure selection manager. @@ -987,6 +1125,7 @@ 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(); @@ -1029,84 +1168,103 @@ public abstract class JalviewJmolBinding implements StructureListener, for (int modelnum = 0; modelnum < modelfilenames.length; modelnum++) { String fileName = modelfilenames[modelnum]; - if (fileName != null) + boolean foundEntry = false; + MCview.PDBfile pdb = null; + String pdbfile = null, pdbfhash = null; + // model was probably loaded inline - so check the pdb file hashcode + 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"); + pdbfhash = "" + pdbfile.hashCode(); + } + if (pdbentry != null) { - boolean foundEntry = false; - // search pdbentries and sequences to find correct pdbentry and - // sequence[] pair for this filename - if (pdbentry != null) + // search pdbentries and sequences to find correct pdbentry for this + // model + for (int pe = 0; pe < pdbentry.length; pe++) { - for (int pe = 0; pe < pdbentry.length; pe++) + boolean matches = false; + if (fileName == null) { - if (pdbentry[pe].getFile().equals(fileName)) + if (false) + // see JAL-623 - need method of matching pasted data up { + pdb = ssm.setMapping(sequence[pe], chains[pe], pdbfile, + AppletFormatAdapter.PASTE); + pdbentry[modelnum].setFile("INLINE" + pdb.id); + matches = true; foundEntry = true; - MCview.PDBfile pdb; - if (loadedInline) - { - // TODO: replace with getData ? - pdb = ssm.setMapping(sequence[pe], chains[pe], - pdbentry[pe].getFile(), AppletFormatAdapter.PASTE); - pdbentry[pe].setFile("INLINE" + pdb.id); - } - else + } + } + else + { + if (matches = pdbentry[pe].getFile().equals(fileName)) + { + foundEntry = true; + // TODO: Jmol can in principle retrieve from CLASSLOADER but + // this + // needs + // to be tested. See mantis bug + // https://mantis.lifesci.dundee.ac.uk/view.php?id=36605 + String protocol = AppletFormatAdapter.URL; + try { - // TODO: Jmol can in principle retrieve from CLASSLOADER but - // this - // needs - // to be tested. See mantis bug - // https://mantis.lifesci.dundee.ac.uk/view.php?id=36605 - String protocol = AppletFormatAdapter.URL; - try - { - File fl = new java.io.File(pdbentry[pe].getFile()); - if (fl.exists()) - { - protocol = AppletFormatAdapter.FILE; - } - } catch (Exception e) - { - } catch (Error e) + File fl = new java.io.File(pdbentry[pe].getFile()); + if (fl.exists()) { + protocol = AppletFormatAdapter.FILE; } - ; - pdb = ssm.setMapping(sequence[pe], chains[pe], - pdbentry[pe].getFile(), protocol); - - } - - pdbentry[pe].setId(pdb.id); - - for (int i = 0; i < pdb.chains.size(); i++) + } catch (Exception e) + { + } catch (Error e) { - chainNames.addElement(new String(pdb.id + ":" - + ((MCview.PDBChain) pdb.chains.elementAt(i)).id)); } - notifyLoaded = true; + ; + pdb = ssm.setMapping(sequence[pe], chains[pe], + pdbentry[pe].getFile(), protocol); + + } + } + if (matches) + { + pdbentry[pe].setId(pdb.id); + // add an entry for every chain in the model + for (int i = 0; i < pdb.chains.size(); i++) + { + String chid = new String(pdb.id + ":" + + ((MCview.PDBChain) pdb.chains.elementAt(i)).id); + chainFile.put(chid, pdbentry[pe].getFile()); + chainNames.addElement(chid); } + notifyLoaded = true; } } - 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; + } + 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; - } } } // FILE LOADED OK // so finally, update the jmol bits and pieces if (jmolpopup != null) { - jmolpopup.updateComputedMenus(); + // potential for deadlock here: + // jmolpopup.updateComputedMenus(); } if (!isLoadingFromArchive()) { @@ -1118,12 +1276,13 @@ public abstract class JalviewJmolBinding implements StructureListener, ssm.addStructureViewerListener(this); if (notifyLoaded) { - FeatureRenderer fr = getFeatureRenderer(); + FeatureRenderer fr = getFeatureRenderer(null); if (fr != null) { fr.featuresAdded(); } refreshGUI(); + loadNotifiesHandled++; } } @@ -1216,6 +1375,13 @@ 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 @@ -1225,14 +1391,71 @@ 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; + + public void componentResized(ComponentEvent e) + { + + } + + public void componentMoved(ComponentEvent e) + { + + } + + public void componentShown(ComponentEvent e) + { + showConsole(true); + } + + public void componentHidden(ComponentEvent e) + { + showConsole(false); } public void setLoadingFromArchive(boolean loadingFromArchive) @@ -1252,4 +1475,142 @@ public abstract class JalviewJmolBinding implements StructureListener, + col.getGreen() + "," + col.getBlue() + "];"); jmolHistory(true); } + + /** + * add structures and any known sequence associations + * + * @returns the pdb entries added to the current set. + */ + public synchronized PDBEntry[] addSequenceAndChain(PDBEntry[] pdbe, + SequenceI[][] seq, String[][] chns) + { + int pe = -1; + Vector v = new Vector(); + Vector rtn = new Vector(); + for (int i = 0; i < pdbentry.length; i++) + { + v.addElement(pdbentry[i]); + } + for (int i = 0; i < pdbe.length; i++) + { + int r = v.indexOf(pdbe[i]); + if (r == -1 || r >= pdbentry.length) + { + rtn.addElement(new int[] + { v.size(), i }); + v.addElement(pdbe[i]); + } + else + { + // just make sure the sequence/chain entries are all up to date + addSequenceAndChain(r, seq[i], chns[i]); + } + } + pdbe = new PDBEntry[v.size()]; + v.copyInto(pdbe); + pdbentry = pdbe; + if (rtn.size() > 0) + { + // expand the tied seuqence[] and string[] arrays + SequenceI[][] sqs = new SequenceI[pdbentry.length][]; + String[][] sch = new String[pdbentry.length][]; + System.arraycopy(sequence, 0, sqs, 0, sequence.length); + System.arraycopy(chains, 0, sch, 0, this.chains.length); + sequence = sqs; + chains = sch; + pdbe = new PDBEntry[rtn.size()]; + for (int r = 0; r < pdbe.length; r++) + { + int[] stri = ((int[]) rtn.elementAt(r)); + // record the pdb file as a new addition + pdbe[r] = pdbentry[stri[0]]; + // and add the new sequence/chain entries + addSequenceAndChain(stri[0], seq[stri[1]], chns[stri[1]]); + } + } + else + { + pdbe = null; + } + return pdbe; + } + + public void addSequence(int pe, SequenceI[] seq) + { + // add sequences to the pe'th pdbentry's seuqence set. + addSequenceAndChain(pe, seq, null); + } + + private void addSequenceAndChain(int pe, SequenceI[] seq, String[] tchain) + { + if (pe < 0 || pe >= pdbentry.length) + { + throw new Error( + "Implementation error - no corresponding pdbentry (for index " + + pe + ") to add sequences mappings to"); + } + final String nullChain = "TheNullChain"; + Vector s = new Vector(); + Vector c = new Vector(); + if (chains == null) + { + chains = new String[pdbentry.length][]; + } + if (sequence[pe] != null) + { + for (int i = 0; i < sequence[pe].length; i++) + { + s.addElement(sequence[pe][i]); + if (chains[pe] != null) + { + if (i < chains[pe].length) + { + c.addElement(chains[pe][i]); + } + else + { + c.addElement(nullChain); + } + } + else + { + if (tchain != null && tchain.length > 0) + { + c.addElement(nullChain); + } + } + } + } + for (int i = 0; i < seq.length; i++) + { + if (!s.contains(seq[i])) + { + s.addElement(seq[i]); + if (tchain != null && i < tchain.length) + { + c.addElement(tchain[i] == null ? nullChain : tchain[i]); + } + } + } + SequenceI[] tmp = new SequenceI[s.size()]; + s.copyInto(tmp); + sequence[pe] = tmp; + if (c.size() > 0) + { + String[] tch = new String[c.size()]; + c.copyInto(tch); + for (int i = 0; i < tch.length; i++) + { + if (tch[i] == nullChain) + { + tch[i] = null; + } + } + chains[pe] = tch; + } + else + { + chains[pe] = null; + } + } }