X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fjmol%2FJalviewJmolBinding.java;h=895db9ab8339b59b63859131cd3c96f4078bcaea;hb=cb8e52fbbc5f725e3f7f48c672cdddb0690bd978;hp=80eed4f1ce68ad0f86e76ddacafd5f8cdb6449db;hpb=1fcc59559aec3e57268d4175f9ff3dbf9a3e16e5;p=jalview.git diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java index 80eed4f..895db9a 100644 --- a/src/jalview/ext/jmol/JalviewJmolBinding.java +++ b/src/jalview/ext/jmol/JalviewJmolBinding.java @@ -20,52 +20,52 @@ */ package jalview.ext.jmol; -import jalview.api.AlignmentViewPanel; -import jalview.api.FeatureRenderer; -import jalview.api.SequenceRenderer; -import jalview.datamodel.AlignmentI; -import jalview.datamodel.HiddenColumns; -import jalview.datamodel.PDBEntry; -import jalview.datamodel.SequenceI; -import jalview.gui.IProgressIndicator; -import jalview.io.DataSourceType; -import jalview.io.StructureFile; -import jalview.schemes.ColourSchemeI; -import jalview.schemes.ResidueProperties; -import jalview.structure.AtomSpec; -import jalview.structure.StructureMappingcommandSet; -import jalview.structure.StructureSelectionManager; -import jalview.structures.models.AAStructureBindingModel; -import jalview.util.MessageManager; - -import java.awt.Color; import java.awt.Container; 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 javax.swing.SwingUtilities; + import org.jmol.adapter.smarter.SmarterJmolAdapter; import org.jmol.api.JmolAppConsoleInterface; import org.jmol.api.JmolSelectionListener; import org.jmol.api.JmolStatusListener; import org.jmol.api.JmolViewer; import org.jmol.c.CBK; -import org.jmol.script.T; 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; +import jalview.io.StructureFile; +import jalview.structure.AtomSpec; +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, ComponentListener { - boolean allChainsSelected = false; + private String lastMessage; /* * when true, try to search the associated datamodel for sequences that are @@ -73,39 +73,26 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel */ private boolean associateNewStructs = false; - Vector atomsPicked = new Vector<>(); - - private List chainNames; + private Vector atomsPicked = new Vector<>(); - Hashtable chainFile; - - /* - * the default or current model displayed if the model cannot be identified - * from the selection message - */ - int frameNo = 0; + private String lastCommand; - // protected JmolGenericPopup jmolpopup; // not used - remove? + private boolean loadedInline; - String lastCommand; + private StringBuffer resetLastRes = new StringBuffer(); - String lastMessage; - - boolean loadedInline; - - StringBuffer resetLastRes = new StringBuffer(); - - public Viewer viewer; + public Viewer jmolViewer; public JalviewJmolBinding(StructureSelectionManager ssm, PDBEntry[] pdbentry, SequenceI[][] sequenceIs, DataSourceType protocol) { super(ssm, pdbentry, sequenceIs, protocol); + 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); */ @@ -116,9 +103,10 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel { super(ssm, seqs); - viewer = theViewer; - viewer.setJmolStatusListener(this); - viewer.addSelectionListener(this); + jmolViewer = theViewer; + jmolViewer.setJmolStatusListener(this); + jmolViewer.addSelectionListener(this); + setStructureCommands(new JmolCommands()); } /** @@ -132,405 +120,32 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel return getViewerTitle("Jmol", true); } - /** - * prepare the view for a given set of models/chains. chainList contains - * strings of the form 'pdbfilename:Chaincode' - * - * @param chainList - * list of chains to make visible - */ - public void centerViewer(Vector chainList) - { - StringBuilder cmd = new StringBuilder(128); - int mlength, p; - for (String lbl : chainList) - { - mlength = 0; - do - { - 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) + " /" - + (1 + getModelNum(chainFile.get(lbl))) + " or "); - } - if (cmd.length() > 0) - { - cmd.setLength(cmd.length() - 4); - } - evalStateCommand("select *;restrict " + cmd + ";cartoon;center " + cmd); - } - - public void closeViewer() - { - // remove listeners for all structures in viewer - getSsm().removeStructureViewerListener(this, this.getStructureFiles()); - if (viewer != null) - viewer.dispose(); - lastCommand = null; - viewer = null; - releaseUIResources(); - } - - @Override - 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"); - } - - @Override - public void colourByCharge() - { - colourBySequence = false; - evalStateCommand("select *;color white;select ASP,GLU;color red;" - + "select LYS,ARG;color blue;select CYS;color yellow"); - } - - /** - * superpose the structures associated with sequences in the alignment - * according to their corresponding positions. - */ - public void superposeStructures(AlignmentI alignment) - { - superposeStructures(alignment, -1, null); - } - - /** - * 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) - */ - public void superposeStructures(AlignmentI alignment, int refStructure) + private String jmolScript(String script) { - superposeStructures(alignment, refStructure, null); - } + Console.debug(">>Jmol>> " + script); + String s = jmolViewer.evalStringQuiet(script); // scriptWait(script); BH + Console.debug("< executeCommand(StructureCommandI command, + boolean getReply) { - while (viewer.isScriptExecuting()) - { - try - { - Thread.sleep(10); - } catch (InterruptedException i) - { - } - } - - /* - * get the distinct structure files modelled - * (a file with multiple chains may map to multiple sequences) - */ - String[] files = getStructureFiles(); - if (!waitForFileLoad(files)) + if (command == null) { return null; } - - StringBuilder selectioncom = new StringBuilder(256); - // In principle - nSeconds specifies the speed of animation for each - // superposition - but is seems to behave weirdly, so we don't specify it. - String nSeconds = " "; - if (files.length > 10) - { - nSeconds = " 0.005 "; - } - else - { - nSeconds = " " + (2.0 / files.length) + " "; - // if (nSeconds).substring(0,5)+" "; - } - - // see JAL-1345 - should really automatically turn off the animation for - // large numbers of structures, but Jmol doesn't seem to allow that. - // nSeconds = " "; - // union of all aligned positions are collected together. - for (int a = 0; a < _alignment.length; a++) - { - int refStructure = _refStructure[a]; - AlignmentI alignment = _alignment[a]; - HiddenColumns 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; - } - - /* - * 'matched' bit j will be set for visible alignment columns j where - * all sequences have a residue with a mapping to the PDB structure - */ - BitSet matched = new BitSet(); - for (int m = 0; m < alignment.getWidth(); m++) - { - if (hiddenCols == null || hiddenCols.isVisible(m)) - { - matched.set(m); - } - } - - SuperposeData[] structures = new SuperposeData[files.length]; - for (int f = 0; f < files.length; f++) - { - structures[f] = new SuperposeData(alignment.getWidth()); - } - - /* - * Calculate the superposable alignment columns ('matched'), and the - * corresponding structure residue positions (structures.pdbResNo) - */ - int candidateRefStructure = findSuperposableResidues(alignment, - matched, structures); - if (refStructure < 0) - { - /* - * If no reference structure was specified, pick the first one that has - * a mapping in the alignment - */ - refStructure = candidateRefStructure; - } - - String[] selcom = new String[files.length]; - int nmatched = matched.cardinality(); - if (nmatched < 4) - { - return (MessageManager.formatMessage("label.insufficient_residues", - nmatched)); - } - - /* - * generate select statements to select regions to superimpose structures - */ - { - // TODO extract method to construct selection statements - for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) - { - String chainCd = ":" + structures[pdbfnum].chain; - int lpos = -1; - boolean run = false; - StringBuilder molsel = new StringBuilder(); - molsel.append("{"); - - int nextColumnMatch = matched.nextSetBit(0); - while (nextColumnMatch != -1) - { - int pdbResNo = structures[pdbfnum].pdbResNo[nextColumnMatch]; - if (lpos != pdbResNo - 1) - { - // discontinuity - if (lpos != -1) - { - molsel.append(lpos); - molsel.append(chainCd); - molsel.append("|"); - } - run = false; - } - else - { - // continuous run - and lpos >-1 - if (!run) - { - // at the beginning, so add dash - molsel.append(lpos); - molsel.append("-"); - } - run = true; - } - lpos = pdbResNo; - nextColumnMatch = matched.nextSetBit(nextColumnMatch + 1); - } - /* - * add final selection phrase - */ - if (lpos != -1) - { - molsel.append(lpos); - molsel.append(chainCd); - molsel.append("}"); - } - if (molsel.length() > 1) - { - 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("|"); - } - } - else - { - selcom[pdbfnum] = null; - } - } - } - StringBuilder command = new StringBuilder(256); - // command.append("set spinFps 10;\n"); - - for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) - { - if (pdbfnum == refStructure || selcom[pdbfnum] == null - || selcom[refStructure] == null) - { - continue; - } - command.append("echo "); - command.append("\"Superposing ("); - command.append(structures[pdbfnum].pdbId); - command.append(") against reference ("); - command.append(structures[refStructure].pdbId); - command.append(")\";\ncompare " + nSeconds); - command.append("{"); - command.append(Integer.toString(1 + pdbfnum)); - command.append(".1} {"); - command.append(Integer.toString(1 + refStructure)); - // conformation=1 excludes alternate locations for CA (JAL-1757) - command.append( - ".1} SUBSET {(*.CA | *.P) and conformation=1} ATOMS "); - - // for (int s = 0; s < 2; s++) - // { - // command.append(selcom[(s == 0 ? pdbfnum : refStructure)]); - // } - command.append(selcom[pdbfnum]); - command.append(selcom[refStructure]); - command.append(" ROTATE TRANSLATE;\n"); - } - if (selectioncom.length() > 0) - { - // TODO is performing selectioncom redundant here? is done later on - // System.out.println("Select regions:\n" + selectioncom.toString()); - evalStateCommand("select *; cartoons off; backbone; select (" - + selectioncom.toString() + "); cartoons; "); - // selcom.append("; ribbons; "); - String cmdString = command.toString(); - // System.out.println("Superimpose command(s):\n" + cmdString); - - evalStateCommand(cmdString); - } - } - if (selectioncom.length() > 0) - {// finally, mark all regions that were superposed. - if (selectioncom.substring(selectioncom.length() - 1).equals("|")) - { - selectioncom.setLength(selectioncom.length() - 1); - } - // 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()); - } - - return null; - } - - public void evalStateCommand(String command) - { + String cmd = command.getCommand(); jmolHistory(false); - if (lastCommand == null || !lastCommand.equals(command)) + if (lastCommand == null || !lastCommand.equals(cmd)) { - jmolScript(command + "\n"); + jmolScript(cmd + "\n"); } jmolHistory(true); - lastCommand = command; - } - - Thread colourby = null; - /** - * Sends a set of colour commands to the structure viewer - * - * @param colourBySequenceCommands - */ - @Override - protected void colourBySequence( - final StructureMappingcommandSet[] colourBySequenceCommands) - { - if (colourby != null) - { - colourby.interrupt(); - colourby = null; - } - colourby = new Thread(new Runnable() - { - @Override - public void run() - { - for (StructureMappingcommandSet cpdbbyseq : colourBySequenceCommands) - { - for (String cbyseq : cpdbbyseq.commands) - { - executeWhenReady(cbyseq); - } - } - } - }); - colourby.start(); - } - - /** - * @param files - * @param sr - * @param viewPanel - * @return - */ - @Override - protected StructureMappingcommandSet[] getColourBySequenceCommands( - String[] files, SequenceRenderer sr, AlignmentViewPanel viewPanel) - { - return JmolCommands.getColourBySequenceCommand(getSsm(), files, - getSequence(), sr, viewPanel); - } - - /** - * @param command - */ - protected void executeWhenReady(String command) - { - evalStateCommand(command); + lastCommand = cmd; + return null; } public void createImage(String file, String type, int quality) @@ -571,43 +186,6 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel return null; } - public Color getColour(int atomIndex, int pdbResNum, String chain, - String pdbfile) - { - if (getModelNum(pdbfile) < 0) - { - return null; - } - // TODO: verify atomIndex is selecting correct model. - // return new Color(viewer.getAtomArgb(atomIndex)); Jmol 12.2.4 - int colour = viewer.ms.at[atomIndex].atomPropertyInt(T.color); - return new Color(colour); - } - - /** - * instruct the Jalview binding to update the pdbentries vector if necessary - * prior to matching the jmol view's contents to the list of structure files - * Jalview knows about. - */ - public abstract void refreshPdbEntries(); - - private int getModelNum(String modelFileName) - { - String[] mfn = getStructureFiles(); - if (mfn == null) - { - return -1; - } - for (int i = 0; i < mfn.length; i++) - { - if (mfn[i].equalsIgnoreCase(modelFileName)) - { - return i; - } - } - 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 - @@ -615,96 +193,35 @@ 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() { - List mset = new ArrayList<>(); - if (viewer == null) + if (jmolViewer == null) { return new String[0]; } if (modelFileNames == null) { - int modelCount = viewer.ms.mc; + int modelCount = jmolViewer.ms.mc; String filePath = null; + List mset = new ArrayList<>(); for (int i = 0; i < modelCount; ++i) { - filePath = viewer.ms.getModelFileName(i); - if (!mset.contains(filePath)) + /* + * 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)) { mset.add(filePath); } } - modelFileNames = mset.toArray(new String[mset.size()]); + if (!mset.isEmpty()) + { + modelFileNames = mset.toArray(new String[mset.size()]); + } } return modelFileNames; @@ -754,55 +271,35 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel public void 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])) - { - mdlNum++; - } - if (mdlNum == modelFileNames.length) + String modelId = getModelIdForFile(pdbfile); + if (modelId.isEmpty()) { return; } jmolHistory(false); + StringBuilder selection = new StringBuilder(32); StringBuilder cmd = new StringBuilder(64); - cmd.append("select " + pdbResNum); // +modelNum - - resetLastRes.append("select " + 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(" /" + (mdlNum + 1)); - resetLastRes.append("/" + (mdlNum + 1)); - } - cmd.append(";wireframe 100;" + cmd.toString() + " and not hetero;"); + selection.append(" /").append(modelId); - resetLastRes.append(";wireframe 0;" + resetLastRes.toString() - + " and not hetero; spacefill 0;"); + cmd.append(selection).append(";wireframe 100;").append(selection) + .append(" and not hetero;").append("spacefill 200;select none"); - cmd.append("spacefill 200;select none"); + resetLastRes.append(selection).append(";wireframe 0;").append(selection) + .append(" and not hetero; spacefill 0;"); jmolScript(cmd.toString()); jmolHistory(true); - } - boolean debug = true; + private boolean debug = true; private void jmolHistory(boolean enable) { @@ -820,10 +317,10 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel // 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); + jmolViewer.openStringInline(string); } - public void mouseOverStructure(int atomIndex, String strInfo) + protected void mouseOverStructure(int atomIndex, final String strInfo) { int pdbResNum; int alocsep = strInfo.indexOf("^"); @@ -863,8 +360,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel chainId = " "; } - String pdbfilename = modelFileNames[frameNo]; // default is first or current - // model + String pdbfilename = modelFileNames[0]; // default is first model if (mdlSep > -1) { if (chainSeparator1 == -1) @@ -877,7 +373,7 @@ 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; @@ -897,25 +393,43 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel if (pdbfilename == null) { - pdbfilename = new File(viewer.ms.getModelFileName(mnumber)) + pdbfilename = new File(jmolViewer.ms.getModelFileName(mnumber)) .getAbsolutePath(); } } } 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("\""); + executeCommand(new StructureCommand(sb.toString()), false); } - - 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 @@ -926,8 +440,8 @@ 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, @@ -971,7 +485,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel } else { - viewer.evalString("select " + picked + ";label off"); + jmolViewer.evalString("select " + picked + ";label off"); atomsPicked.removeElement(picked); } jmolHistory(true); @@ -988,6 +502,28 @@ 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) @@ -1087,10 +623,13 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel fileLoadingError = null; String[] oldmodels = modelFileNames; modelFileNames = null; - chainNames = new ArrayList<>(); - chainFile = new Hashtable<>(); 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) { @@ -1139,7 +678,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel // 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( + pdbfile = jmolViewer.getData( "" + (1 + _modelFileNameMap[modelnum]) + ".0", "PDB"); } // search pdbentries and sequences to find correct pdbentry for this @@ -1154,8 +693,7 @@ 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; @@ -1194,14 +732,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel } if (matches) { - // add an entry for every chain in the model - for (int i = 0; i < pdb.getChains().size(); i++) - { - String chid = new String( - pdb.getId() + ":" + pdb.getChains().elementAt(i).id); - chainFile.put(chid, fileName); - chainNames.add(chid); - } + stashFoundChains(pdb, fileName); notifyLoaded = true; } } @@ -1211,7 +742,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel // 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", + String pdbcontent = jmolViewer.getData("/" + (modelnum + 1) + ".1", "PDB"); // parse pdb file into a chain, etc. // locate best match for pdb in associated views and add mapping to @@ -1241,7 +772,9 @@ 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++; @@ -1249,12 +782,6 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel setLoadingFromArchive(false); } - @Override - public List getChainNames() - { - return chainNames; - } - protected IProgressIndicator getIProgressIndicator() { return null; @@ -1276,8 +803,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel public abstract void sendConsoleEcho(String strEcho); /* * { showConsole(true); * - * history.append("\n" + - * strEcho); } + * history.append("\n" + strEcho); } */ // /End JmolStatusListener @@ -1299,38 +825,11 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel } - @Override - public void setJalviewColourScheme(ColourSchemeI cs) - { - colourBySequence = false; - - if (cs == null) - { - return; - } - - jmolHistory(false); - StringBuilder command = new StringBuilder(128); - command.append("select *;color white;"); - List residueSet = ResidueProperties.getResidues(isNucleotide(), - false); - for (String resName : residueSet) - { - char res = resName.length() == 3 - ? ResidueProperties.getSingleCharacterCode(resName) - : resName.charAt(0); - Color col = cs.findColour(res, 0, null, null, 0f); - command.append("select " + resName + ";color[" + col.getRed() + "," - + col.getGreen() + "," + col.getBlue() + "];"); - } - - evalStateCommand(command.toString()); - jmolHistory(true); - } - 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"); } /** @@ -1341,20 +840,12 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel public abstract void showUrl(String url, String target); /** - * called when the binding thinks the UI needs to be refreshed after a Jmol - * state change. this could be because structures were loaded, or because an - * error has occured. - */ - public abstract void refreshGUI(); - - /** * called to show or hide the associated console window container. * * @param show */ public abstract void showConsole(boolean show); - public static Viewer getJmolData(JmolParser jmolParser) { return (Viewer) JmolViewer.allocateViewer(null, null, null, null, null, @@ -1402,24 +893,27 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel String commandOptions, final Container consolePanel, String buttonsToShow) { - + System.err.println("Allocating Jmol Viewer: " + commandOptions); - + if (commandOptions == null) { commandOptions = ""; } - viewer = (Viewer) JmolViewer.allocateViewer(renderPanel, + jmolViewer = (Viewer) JmolViewer.allocateViewer(renderPanel, (jmolfileio ? new SmarterJmolAdapter() : null), htmlName + ((Object) this).toString(), documentBase, codeBase, commandOptions, this); - viewer.setJmolStatusListener(this); // extends JmolCallbackListener + jmolViewer.setJmolStatusListener(this); // extends JmolCallbackListener - try { + try + { console = createJmolConsole(consolePanel, buttonsToShow); - } catch (Throwable e) { - System.err.println("Could not create Jmol application console. " + e.getMessage()); + } catch (Throwable e) + { + System.err.println("Could not create Jmol application console. " + + e.getMessage()); e.printStackTrace(); } if (consolePanel != null) @@ -1433,33 +927,12 @@ 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. - + // 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); - 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("<