X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Frbvi%2Fchimera%2FJalviewChimeraBinding.java;h=9d1ed43df1ef8b06d9050f97bfeffbe9ed31b971;hb=be32c14cd8e48fe0a207cd7030cb9cd46f894678;hp=11aa5c0edea37371a8593f86f20b4de086df75cc;hpb=a91adcb6c9a9bd7ed9946215e09ca3af4f7e6080;p=jalview.git diff --git a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java index 11aa5c0..9d1ed43 100644 --- a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java +++ b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -23,168 +23,152 @@ package jalview.ext.rbvi.chimera; import jalview.api.AlignmentViewPanel; import jalview.api.FeatureRenderer; import jalview.api.SequenceRenderer; -import jalview.api.SequenceStructureBinding; -import jalview.api.StructureSelectionManagerProvider; +import jalview.bin.Cache; import jalview.datamodel.AlignmentI; import jalview.datamodel.ColumnSelection; import jalview.datamodel.PDBEntry; import jalview.datamodel.SequenceI; -import jalview.io.AppletFormatAdapter; import jalview.schemes.ColourSchemeI; import jalview.schemes.ResidueProperties; -import jalview.structure.StructureListener; import jalview.structure.StructureMapping; +import jalview.structure.StructureMappingcommandSet; import jalview.structure.StructureSelectionManager; -import jalview.structures.models.SequenceStructureBindingModel; +import jalview.structures.models.AAStructureBindingModel; +import jalview.util.Comparison; +import jalview.util.MessageManager; import java.awt.Color; -import java.awt.event.ComponentEvent; -import java.io.File; import java.util.ArrayList; -import java.util.Enumeration; import java.util.HashMap; -import java.util.Hashtable; +import java.util.LinkedHashMap; import java.util.List; import java.util.Map; -import java.util.Vector; import ext.edu.ucsf.rbvi.strucviz2.ChimeraManager; import ext.edu.ucsf.rbvi.strucviz2.ChimeraModel; import ext.edu.ucsf.rbvi.strucviz2.StructureManager; import ext.edu.ucsf.rbvi.strucviz2.StructureManager.ModelType; -public abstract class JalviewChimeraBinding extends - SequenceStructureBindingModel implements StructureListener, - SequenceStructureBinding, StructureSelectionManagerProvider - +public abstract class JalviewChimeraBinding extends AAStructureBindingModel { + + private static final boolean debug = false; + + private static final String PHOSPHORUS = "P"; + + private static final String ALPHACARBON = "CA"; + private StructureManager csm; private ChimeraManager viewer; - /** + /* * set if chimera state is being restored from some source - instructs binding * not to apply default display style when structure set is updated for first * time. */ private boolean loadingFromArchive = false; - /** - * second flag to indicate if the jmol viewer should ignore sequence colouring + /* + * flag to indicate if the Chimera viewer should ignore sequence colouring * events from the structure manager because the GUI is still setting up */ private boolean loadingFinished = true; - /** - * state flag used to check if the Jmol viewer's paint method can be called + /* + * state flag used to check if the Chimera viewer's paint method can be called */ private boolean finishedInit = false; - public boolean isFinishedInit() - { - return finishedInit; - } - - public void setFinishedInit(boolean finishedInit) - { - this.finishedInit = finishedInit; - } - - boolean allChainsSelected = false; + private List atomsPicked = new ArrayList(); - /** - * when true, try to search the associated datamodel for sequences that are - * associated with any unknown structures in the Jmol view. - */ - private boolean associateNewStructs = false; - - Vector atomsPicked = new Vector(); + private List chainNames; - public Vector chainNames; + private Map chainFile; - Hashtable chainFile; + public String fileLoadingError; - /** - * array of target chains for seuqences - tied to pdbentry and sequence[] + /* + * Map of ChimeraModel objects keyed by PDB full local file name */ - protected String[][] chains; + private Map> chimeraMaps = new LinkedHashMap>(); - boolean colourBySequence = true; - - StringBuffer eval = new StringBuffer(); + /* + * the default or current model displayed if the model cannot be identified + * from the selection message + */ + private int frameNo = 0; - public String fileLoadingError; + private String lastCommand; - private Map> chimmaps = new HashMap>(); + private String lastMessage; - private List mdlToFile = new ArrayList(); + private boolean loadedInline; /** - * the default or current model displayed if the model cannot be identified - * from the selection message + * current set of model filenames loaded */ - int frameNo = 0; - - String lastCommand; + String[] modelFileNames = null; - String lastMessage; + String lastMousedOverAtomSpec; - boolean loadedInline; + private List lastReply; + /** + * Open a PDB structure file in Chimera and set up mappings from Jalview. + * + * We check if the PDB model id is already loaded in Chimera, if so don't + * reopen it. This is the case if Chimera has opened a saved session file. + * + * @param pe + * @return + */ public boolean openFile(PDBEntry pe) { String file = pe.getFile(); try { + List modelsToMap = new ArrayList(); List oldList = viewer.getModelList(); - viewer.openModel(file, ModelType.PDB_MODEL); - List newList = viewer.getModelList(); - if (oldList.size() < newList.size()) + boolean alreadyOpen = false; + + /* + * If Chimera already has this model, don't reopen it, but do remap it. + */ + for (ChimeraModel open : oldList) { - while (oldList.size() > 0) + if (open.getModelName().equals(pe.getId())) { - oldList.remove(0); - newList.remove(0); - } - chimmaps.put(file, newList); - for (ChimeraModel cm : newList) - { - while (mdlToFile.size() < 1 + cm.getModelNumber()) - { - mdlToFile.add(new String("")); - } - mdlToFile.set(cm.getModelNumber(), file); + alreadyOpen = true; + modelsToMap.add(open); } + } - File fl = new File(file); - String protocol = AppletFormatAdapter.URL; - try - { - if (fl.exists()) - { - protocol = AppletFormatAdapter.FILE; - } - } catch (Exception e) - { - } catch (Error e) - { - } - // Explicitly map to the filename used by Jmol ; - // pdbentry[pe].getFile(), protocol); + /* + * If Chimera doesn't yet have this model, ask it to open it, and retrieve + * the model names added by Chimera. + */ + if (!alreadyOpen) + { + viewer.openModel(file, pe.getId(), ModelType.PDB_MODEL); + modelsToMap = viewer.getModelList(); + modelsToMap.removeAll(oldList); + } - if (ssm != null) + chimeraMaps.put(file, modelsToMap); + + if (getSsm() != null) + { + getSsm().addStructureViewerListener(this); + // ssm.addSelectionListener(this); + FeatureRenderer fr = getFeatureRenderer(null); + if (fr != null) { - ssm.addStructureViewerListener(this); - // ssm.addSelectionListener(this); - FeatureRenderer fr = getFeatureRenderer(null); - if (fr != null) - { - fr.featuresAdded(); - } - refreshGUI(); + fr.featuresAdded(); } - return true; + refreshGUI(); } + return true; } catch (Exception q) { log("Exception when trying to open model " + file + "\n" @@ -195,157 +179,109 @@ public abstract class JalviewChimeraBinding extends } /** - * current set of model filenames loaded - */ - String[] modelFileNames = null; - - public PDBEntry[] pdbentry; - - /** - * datasource protocol for access to PDBEntrylatest - */ - String protocol = null; - - StringBuffer resetLastRes = new StringBuffer(); - - /** - * sequences mapped to each pdbentry + * Constructor + * + * @param ssm + * @param pdbentry + * @param sequenceIs + * @param chains + * @param protocol */ - public SequenceI[][] sequence; - - public StructureSelectionManager ssm; - - private List lastReply; - public JalviewChimeraBinding(StructureSelectionManager ssm, PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains, String protocol) { - this.ssm = ssm; - this.sequence = sequenceIs; - this.chains = chains; - this.pdbentry = pdbentry; - this.protocol = protocol; - if (chains == null) - { - this.chains = new String[pdbentry.length][]; - } + super(ssm, pdbentry, sequenceIs, chains, protocol); viewer = new ChimeraManager( csm = new ext.edu.ucsf.rbvi.strucviz2.StructureManager(true)); - /* - * viewer = JmolViewer.allocateViewer(renderPanel, new SmarterJmolAdapter(), - * "jalviewJmol", ap.av.applet .getDocumentBase(), - * ap.av.applet.getCodeBase(), "", this); - * - * jmolpopup = JmolPopup.newJmolPopup(viewer, true, "Jmol", true); - */ } + /** + * Constructor + * + * @param ssm + * @param theViewer + */ public JalviewChimeraBinding(StructureSelectionManager ssm, - ChimeraManager viewer2) + ChimeraManager theViewer) { - this.ssm = ssm; - viewer = viewer2; + super(ssm, null); + viewer = theViewer; csm = viewer.getStructureManager(); } /** - * construct a title string for the viewer window based on the data jalview + * Construct a title string for the viewer window based on the data Jalview * knows about * + * @param verbose * @return */ - public String getViewerTitle() + public String getViewerTitle(boolean verbose) { - if (sequence == null || pdbentry == null || sequence.length < 1 - || pdbentry.length < 1 || sequence[0].length < 1) - { - return ("Jalview Chimera Window"); - } - // TODO: give a more informative title when multiple structures are - // displayed. - StringBuffer title = new StringBuffer("Chimera view for " - + sequence[0][0].getName() + ":" + pdbentry[0].getId()); - - if (pdbentry[0].getProperty() != null) - { - if (pdbentry[0].getProperty().get("method") != null) - { - title.append(" Method: "); - title.append(pdbentry[0].getProperty().get("method")); - } - if (pdbentry[0].getProperty().get("chains") != null) - { - title.append(" Chain:"); - title.append(pdbentry[0].getProperty().get("chains")); - } - } - return title.toString(); + return getViewerTitle("Chimera", verbose); } /** * prepare the view for a given set of models/chains. chainList contains * strings of the form 'pdbfilename:Chaincode' * - * @param chainList + * @param toshow * list of chains to make visible */ - public void centerViewer(Vector chainList) + public void centerViewer(List toshow) { - StringBuffer cmd = new StringBuffer(); - String lbl; + StringBuilder cmd = new StringBuilder(64); int mlength, p; - for (int i = 0, iSize = chainList.size(); i < iSize; i++) + for (String lbl : toshow) { mlength = 0; - lbl = (String) chainList.elementAt(i); 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("#" + getModelNum((String) chainFile.get(lbl)) + "." + cmd.append("#" + getModelNum(chainFile.get(lbl)) + "." + lbl.substring(mlength + 1) + " or "); } if (cmd.length() > 0) + { cmd.setLength(cmd.length() - 4); - evalStateCommand("~display #*; ~ribbon #*; ribbon " + cmd + ";focus " - + cmd,false); + } + String cmdstring = cmd.toString(); + evalStateCommand("~display #*; ~ribbon #*; ribbon " + cmdstring + + ";focus " + cmdstring, false); } - public void closeViewer() + /** + * Close down the Jalview viewer, and (optionally) the associated Chimera + * window. + */ + public void closeViewer(boolean closeChimera) { - ssm.removeStructureViewerListener(this, this.getPdbFile()); - // and shut down Chimera - viewer.exitChimera(); - // viewer.evalStringQuiet("zap"); - // viewer.setJmolStatusListener(null); + getSsm().removeStructureViewerListener(this, this.getPdbFile()); + if (closeChimera) + { + viewer.exitChimera(); + } 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",false); + evalStateCommand("rainbow chain", false); } public void colourByCharge() { colourBySequence = false; - evalStateCommand("colour *;color white;select ASP,GLU;color red;" - + "select LYS,ARG;color blue;select CYS;color yellow", false); + evalStateCommand( + "color white;color red ::ASP;color red ::GLU;color blue ::LYS;color blue ::ARG;color yellow ::CYS", + false); } /** @@ -393,9 +329,9 @@ public abstract class JalviewChimeraBinding extends int[] _refStructure, ColumnSelection[] _hiddenCols) { assert (_alignment.length == _refStructure.length && _alignment.length != _hiddenCols.length); - StringBuffer allComs = new StringBuffer(); // whole shebang for superposition + StringBuilder allComs = new StringBuilder(128); // Chimera superposition cmd String[] files = getPdbFile(); - // check to see if we are still waiting for Jmol files + // check to see if we are still waiting for Chimera files long starttime = System.currentTimeMillis(); boolean waiting = true; do @@ -407,7 +343,7 @@ public abstract class JalviewChimeraBinding extends { // HACK - in Jalview 2.8 this call may not be threadsafe so we catch // every possible exception - StructureMapping[] sm = ssm.getMapping(file); + StructureMapping[] sm = getSsm().getMapping(file); if (sm == null || sm.length == 0) { waiting = true; @@ -426,7 +362,7 @@ public abstract class JalviewChimeraBinding extends if (waiting) { System.err - .println("RUNTIME PROBLEM: Jmol seems to be taking a long time to process all the structures."); + .println("RUNTIME PROBLEM: Chimera seems to be taking a long time to process all the structures."); return; } refreshPdbEntries(); @@ -454,7 +390,6 @@ public abstract class JalviewChimeraBinding extends { refStructure = -1; } - StringBuffer command = new StringBuffer(); boolean matched[] = new boolean[alignment.getWidth()]; for (int m = 0; m < matched.length; m++) @@ -465,27 +400,27 @@ public abstract class JalviewChimeraBinding extends 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]; - String[] atomS = new String[files.length]; + String[] atomSpec = new String[files.length]; for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) { - StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]); + StructureMapping[] mapping = getSsm().getMapping(files[pdbfnum]); // RACE CONDITION - getMapping only returns Jmol loaded filenames once // Jmol callback has completed. if (mapping == null || mapping.length < 1) { - throw new Error( - "Implementation error - Chimera seems to be still working on getting its data - report at http://issues.jalview.org/browse/JAL-1016"); + throw new Error(MessageManager.getString("error.implementation_error_chimera_getting_data")); } int lastPos = -1; - for (int s = 0; s < sequence[pdbfnum].length; s++) + final int seqCountForPdbFile = getSequence()[pdbfnum].length; + for (int s = 0; s < seqCountForPdbFile; s++) { for (int sp, m = 0; m < mapping.length; m++) { - if (mapping[m].getSequence() == sequence[pdbfnum][s] - && (sp = alignment.findIndex(sequence[pdbfnum][s])) > -1) + final SequenceI theSequence = getSequence()[pdbfnum][s]; + if (mapping[m].getSequence() == theSequence + && (sp = alignment.findIndex(theSequence)) > -1) { if (refStructure == -1) { @@ -504,7 +439,7 @@ public abstract class JalviewChimeraBinding extends continue; } - if (jalview.util.Comparison.isGap(asp.getCharAt(r))) + if (Comparison.isGap(asp.getCharAt(r))) { // no mapping to gaps in sequence continue; @@ -536,9 +471,9 @@ public abstract class JalviewChimeraBinding extends } chainNames[pdbfnum] = mapping[m].getPdbId() + targetC[pdbfnum]; - atomS[pdbfnum] = asp.getRNA()!=null ? "P" : "CA"; + atomSpec[pdbfnum] = asp.getRNA() != null ? PHOSPHORUS : ALPHACARBON; // move on to next pdb file - s = sequence[pdbfnum].length; + s = seqCountForPdbFile; break; } } @@ -619,6 +554,7 @@ public abstract class JalviewChimeraBinding extends } } } + StringBuilder command = new StringBuilder(256); for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) { if (pdbfnum == refStructure || selcom[pdbfnum] == null @@ -626,26 +562,36 @@ public abstract class JalviewChimeraBinding extends { continue; } - if (command.length()>0) + if (command.length() > 0) { command.append(";"); } - command.append("match"); - // form the matched pair strings - for (int s = 0; s < 2; s++) - { - command.append(" #"+(s == 0 ? pdbfnum : refStructure)+".1"); - // note - need to select on first model, otherwise it all goes wrong! - command.append(selcom[(s == 0 ? pdbfnum : refStructure)]); - command.append("@"+atomS[(s == 0 ? pdbfnum : refStructure)]); // match on backbone alpha/polyphosphate - } + /* + * Form Chimera match command, from the 'new' structure to the + * 'reference' structure e.g. (residues 1-91, chain B/A, alphacarbons): + * + * match #1:1-91.B@CA #0:1-91.A@CA + * + * @see + * https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html + */ + command.append("match #" + pdbfnum /* +".1" */); + // TODO: handle sub-models + command.append(selcom[pdbfnum]); + command.append("@" + atomSpec[pdbfnum]); + command.append(" #" + refStructure /* +".1" */); + command.append(selcom[refStructure]); + command.append("@" + atomSpec[refStructure]); } if (selectioncom.length() > 0) { - System.out.println("Select regions:\n" + selectioncom.toString()); - System.out - .println("Superimpose command(s):\n" + command.toString()); + if (debug) + { + System.out.println("Select regions:\n" + selectioncom.toString()); + System.out.println("Superimpose command(s):\n" + + command.toString()); + } allComs.append("~display all; chain @CA|P; ribbon " + selectioncom.toString() + ";"+command.toString()); // selcom.append("; ribbons; "); @@ -657,11 +603,14 @@ public abstract class JalviewChimeraBinding extends { selectioncom.setLength(selectioncom.length() - 1); } - System.out.println("Select regions:\n" + selectioncom.toString()); + if (debug) + { + System.out.println("Select regions:\n" + selectioncom.toString()); + } allComs.append("; ~display all; chain @CA|P; ribbon " - + selectioncom.toString() + ""); + + selectioncom.toString() + "; focus"); // evalStateCommand("select *; backbone; select "+selcom.toString()+"; cartoons; center "+selcom.toString()); - evalStateCommand(allComs.toString(),false); + evalStateCommand(allComs.toString(), true /* false */); } } @@ -670,7 +619,7 @@ public abstract class JalviewChimeraBinding extends { if (!viewer.isChimeraLaunched()) { - viewer.launchChimera(csm.getChimeraPaths()); + viewer.launchChimera(StructureManager.getChimeraPaths()); } if (!viewer.isChimeraLaunched()) { @@ -678,33 +627,36 @@ public abstract class JalviewChimeraBinding extends } } - public void evalStateCommand(final String command, boolean resp) + /** + * Answers true if the Chimera process is still running, false if ended or not + * started. + * + * @return + */ + public boolean isChimeraRunning() + { + return viewer.isChimeraLaunched(); + } + + /** + * Send a command to Chimera, launching it first if necessary, and optionally + * log any responses. + * + * @param command + * @param logResponse + */ + public void evalStateCommand(final String command, boolean logResponse) { viewerCommandHistory(false); checkLaunched(); if (lastCommand == null || !lastCommand.equals(command)) { -// Thread t = new Thread(new Runnable() -// { -// @Override -// public void run() -// { - lastReply = viewer.sendChimeraCommand(command, resp); - if (debug) - { - log("Response from command ('" + command + "') was:\n" - + lastReply); - } -// } -// }); - // TODO - use j7/8 thread management -// try -// { -// t.join(); -// } catch (InterruptedException foo) -// { -// } -// ; + // trim command or it may never find a match in the replyLog!! + lastReply = viewer.sendChimeraCommand(command.trim(), logResponse); + if (debug && logResponse) + { + log("Response from command ('" + command + "') was:\n" + lastReply); + } } viewerCommandHistory(true); lastCommand = command; @@ -719,8 +671,10 @@ public abstract class JalviewChimeraBinding extends jalview.api.AlignmentViewPanel alignmentv) { if (!colourBySequence || !loadingFinished) + { return; - if (ssm == null) + } + if (getSsm() == null) { return; } @@ -735,76 +689,64 @@ public abstract class JalviewChimeraBinding extends } AlignmentI alignment = alignmentv.getAlignment(); - for (jalview.structure.StructureMappingcommandSet cpdbbyseq : ChimeraCommands - .getColourBySequenceCommand(ssm, files, sequence, sr, fr, - alignment)) - for (String cbyseq : cpdbbyseq.commands) + for (jalview.structure.StructureMappingcommandSet cpdbbyseq : getColourBySequenceCommands( + files, sr, fr, alignment)) + { + for (String command : cpdbbyseq.commands) { - waitForChimera(); - evalStateCommand(cbyseq, false); - waitForChimera(); + executeWhenReady(command); } - } - - private void waitForChimera() - { - while (viewer.isBusy()) - { - try { - Thread.sleep(15); - } catch (InterruptedException q) - {} } } - public boolean isColourBySequence() + /** + * @param files + * @param sr + * @param fr + * @param alignment + * @return + */ + protected StructureMappingcommandSet[] getColourBySequenceCommands( + String[] files, SequenceRenderer sr, FeatureRenderer fr, + AlignmentI alignment) { - return colourBySequence; + return ChimeraCommands.getColourBySequenceCommand(getSsm(), files, + getSequence(), sr, fr, alignment); } - public void setColourBySequence(boolean colourBySequence) + /** + * @param command + */ + protected void executeWhenReady(String command) { - this.colourBySequence = colourBySequence; + waitForChimera(); + evalStateCommand(command, false); + waitForChimera(); } - public void createImage(String file, String type, int quality) + private void waitForChimera() { - System.out.println("JMOL CREATE IMAGE"); + while (viewer != null && viewer.isBusy()) + { + try { + Thread.sleep(15); + } catch (InterruptedException q) + {} + } } - public String createImage(String fileName, String type, - Object textOrBytes, int quality) - { - System.out.println("JMOL CREATE IMAGE"); - return null; - } - public String eval(String strEval) - { - // System.out.println(strEval); - // "# 'eval' is implemented only for the applet."; - return null; - } // End StructureListener // ////////////////////////// - public float[][] functionXY(String functionName, int x, int y) - { - return null; - } - - public float[][][] functionXYZ(String functionName, int nx, int ny, int nz) - { - // TODO Auto-generated method stub - return null; - } - public Color getColour(int atomIndex, int pdbResNum, String chain, String pdbfile) { if (getModelNum(pdbfile) < 0) + { return null; + } log("get model / residue colour attribute unimplemented"); return null; } @@ -837,7 +779,9 @@ public abstract class JalviewChimeraBinding extends for (int i = 0; i < mfn.length; i++) { if (mfn[i].equalsIgnoreCase(modelFileName)) + { return i; + } } return -1; } @@ -870,8 +814,8 @@ public abstract class JalviewChimeraBinding extends // // System.arraycopy(mset, 0, modelFileNames, 0, j); // } - return chimmaps.keySet().toArray( - modelFileNames = new String[chimmaps.size()]); + return chimeraMaps.keySet().toArray( + modelFileNames = new String[chimeraMaps.size()]); } /** @@ -894,49 +838,47 @@ public abstract class JalviewChimeraBinding extends public abstract SequenceRenderer getSequenceRenderer( AlignmentViewPanel alignment); - // jmol/ssm only + /** + * Construct and send a command to highlight an atom. + * + * 
+   * Done by generating a command like (to 'highlight' position 44)
+   *   ~select #0:43.C;select #0:44.C
+   * Note this removes the selection from the previous position.
+   *
+ */ public void highlightAtom(int atomIndex, int pdbResNum, String chain, String pdbfile) { - List cms = chimmaps.get(pdbfile); + List cms = chimeraMaps.get(pdbfile); if (cms != null) { - int mdlNum = cms.get(0).getModelNumber(); - - viewerCommandHistory(false); - // viewer.stopListening(); - if (resetLastRes.length() > 0) + StringBuilder sb = new StringBuilder(); + sb.append(" #" + cms.get(0).getModelNumber()); + sb.append(":" + pdbResNum); + if (!chain.equals(" ")) { - eval.setLength(0); - eval.append(resetLastRes.toString() + ";"); + sb.append("." + chain); } + String atomSpec = sb.toString(); - eval.append("display "); // +modelNum - - resetLastRes.setLength(0); - resetLastRes.append("~display "); + StringBuilder command = new StringBuilder(32); + if (lastMousedOverAtomSpec != null) { - eval.append(" #" + (mdlNum)); - resetLastRes.append(" #" + (mdlNum)); + command.append("~show " + lastMousedOverAtomSpec + ";"); } - // complete select string - - eval.append(":" + pdbResNum); - resetLastRes.append(":" + pdbResNum); - if (!chain.equals(" ")) + viewerCommandHistory(false); + command.append("show ").append(atomSpec); + String cmd = command.toString(); + if (cmd.length() > 0) { - eval.append("." + chain); - resetLastRes.append("." + chain); + viewer.sendChimeraCommand(cmd, false); } - - viewer.sendChimeraCommand(eval.toString(), false); viewerCommandHistory(true); - // viewer.startListening(); + this.lastMousedOverAtomSpec = atomSpec; } } - boolean debug = true; - private void log(String message) { System.err.println("## Chimera log: " + message); @@ -944,8 +886,8 @@ public abstract class JalviewChimeraBinding extends private void viewerCommandHistory(boolean enable) { - log("(Not yet implemented) History " - + ((debug || enable) ? "on" : "off")); + // log("(Not yet implemented) History " + // + ((debug || enable) ? "on" : "off")); } public void loadInline(String string) @@ -996,8 +938,10 @@ public abstract class JalviewChimeraBinding extends String chainId; if (strInfo.indexOf(":") > -1) + { chainId = strInfo.substring(strInfo.indexOf(":") + 1, strInfo.indexOf(".")); + } else { chainId = " "; @@ -1035,7 +979,9 @@ public abstract class JalviewChimeraBinding extends ; } if (lastMessage == null || !lastMessage.equals(strInfo)) - ssm.mouseOverStructure(pdbResNum, chainId, pdbfilename); + { + getSsm().mouseOverStructure(pdbResNum, chainId, pdbfilename); + } lastMessage = strInfo; } @@ -1054,13 +1000,17 @@ public abstract class JalviewChimeraBinding extends int chainSeparator = strInfo.indexOf(":"); int p = 0; if (chainSeparator == -1) + { chainSeparator = strInfo.indexOf("."); + } String picked = strInfo.substring(strInfo.indexOf("]") + 1, chainSeparator); String mdlString = ""; if ((p = strInfo.indexOf(":")) > -1) + { picked += strInfo.substring(p + 1, strInfo.indexOf(".")); + } if ((p = strInfo.indexOf("/")) > -1) { @@ -1073,12 +1023,12 @@ public abstract class JalviewChimeraBinding extends if (!atomsPicked.contains(picked)) { viewer.select(picked); - atomsPicked.addElement(picked); + atomsPicked.add(picked); } else { viewer.select("not " + picked); - atomsPicked.removeElement(picked); + atomsPicked.remove(picked); } viewerCommandHistory(true); // TODO: in application this happens @@ -1093,7 +1043,7 @@ public abstract class JalviewChimeraBinding extends // incremented every time a load notification is successfully handled - // lightweight mechanism for other threads to detect when they can start - // referrring to new structures. + // referring to new structures. private long loadNotifiesHandled = 0; public long getLoadNotifiesHandled() @@ -1119,8 +1069,8 @@ public abstract class JalviewChimeraBinding extends fileLoadingError = null; String[] oldmodels = modelFileNames; modelFileNames = null; - chainNames = new Vector(); - chainFile = new Hashtable(); + chainNames = new ArrayList(); + chainFile = new HashMap(); boolean notifyLoaded = false; String[] modelfilenames = getPdbFile(); // first check if we've lost any structures @@ -1155,13 +1105,13 @@ public abstract class JalviewChimeraBinding extends } // deregister the Jmol instance for these structures - we'll add // ourselves again at the end for the current structure set. - ssm.removeStructureViewerListener(this, oldmfn); + getSsm().removeStructureViewerListener(this, oldmfn); } } // register ourselves as a listener and notify the gui that it needs to // update itself. - ssm.addStructureViewerListener(this); + getSsm().addStructureViewerListener(this); if (notifyLoaded) { @@ -1181,70 +1131,43 @@ public abstract class JalviewChimeraBinding extends colourBySequence = false; if (cs == null) + { return; + } - String res; int index; Color col; + // Chimera expects RBG values in the range 0-1 + final double normalise = 255D; viewerCommandHistory(false); // TODO: Switch between nucleotide or aa selection expressions - Enumeration en = ResidueProperties.aa3Hash.keys(); - StringBuffer command = new StringBuffer("select *;color white;"); - while (en.hasMoreElements()) + StringBuilder command = new StringBuilder(128); + command.append("color white;"); + for (String res : ResidueProperties.aa3Hash.keySet()) { - res = en.nextElement().toString(); - index = ((Integer) ResidueProperties.aa3Hash.get(res)).intValue(); + index = ResidueProperties.aa3Hash.get(res).intValue(); if (index > 20) + { continue; + } col = cs.findColour(ResidueProperties.aa[index].charAt(0)); - // TODO: need colour string function and res selection here - command.append("select " + res + ";color[" + col.getRed() + "," - + col.getGreen() + "," + col.getBlue() + "];"); + command.append("color " + col.getRed() / normalise + "," + + col.getGreen() / normalise + "," + col.getBlue() + / normalise + " ::" + res + ";"); } evalStateCommand(command.toString(),false); viewerCommandHistory(true); } - public void showHelp() - { - // chimera help - showUrl("http://jmol.sourceforge.net/docs/JmolUserGuide/", "jmolHelp"); - } - /** - * open the URL somehow - * - * @param target - */ - public abstract void showUrl(String url, String target); - - /** - * called when the binding thinks the UI needs to be refreshed after a Jmol + * called when the binding thinks the UI needs to be refreshed after a Chimera * state change. this could be because structures were loaded, or because an - * error has occured. + * error has occurred. */ public abstract void refreshGUI(); - public void componentResized(ComponentEvent e) - { - - } - - public void componentMoved(ComponentEvent e) - { - - } - - public void componentShown(ComponentEvent e) - { - } - - public void componentHidden(ComponentEvent e) - { - } - public void setLoadingFromArchive(boolean loadingFromArchive) { this.loadingFromArchive = loadingFromArchive; @@ -1252,8 +1175,8 @@ public abstract class JalviewChimeraBinding extends /** * - * @return true if Jmol is still restoring state or loading is still going on - * (see setFinsihedLoadingFromArchive) + * @return true if Chimeral is still restoring state or loading is still going + * on (see setFinsihedLoadingFromArchive) */ public boolean isLoadingFromArchive() { @@ -1271,163 +1194,89 @@ public abstract class JalviewChimeraBinding extends loadingFinished = finishedLoading; } - public void setBackgroundColour(java.awt.Color col) + /** + * Send the Chimera 'background solid " command. + * + * @see https + * ://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/background + * .html + * @param col + */ + public void setBackgroundColour(Color col) { viewerCommandHistory(false); - // todo set background colour - viewer.sendChimeraCommand( - "background [" + col.getRed() + "," + col.getGreen() + "," - + col.getBlue() + "];", false); + double normalise = 255D; + final String command = "background solid " + col.getRed() / normalise + "," + + col.getGreen() / normalise + "," + col.getBlue() + / normalise + ";"; + viewer.sendChimeraCommand(command, false); viewerCommandHistory(true); } /** - * add structures and any known sequence associations * - * @returns the pdb entries added to the current set. + * @param pdbfile + * @return text report of alignment between pdbfile and any associated + * alignment sequences + */ + public String printMapping(String pdbfile) + { + return getSsm().printMapping(pdbfile); + } + + /** + * Ask Chimera to save its session to the given file. Returns true if + * successful, else false. + * + * @param filepath + * @return */ - public synchronized PDBEntry[] addSequenceAndChain(PDBEntry[] pdbe, - SequenceI[][] seq, String[][] chns) + public boolean saveSession(String filepath) { - 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++) + if (isChimeraRunning()) { - int r = v.indexOf(pdbe[i]); - if (r == -1 || r >= pdbentry.length) + List reply = viewer.sendChimeraCommand("save " + filepath, + true); + if (reply.contains("Session written")) { - rtn.addElement(new int[] - { v.size(), i }); - v.addElement(pdbe[i]); + return true; } else { - // just make sure the sequence/chain entries are all up to date - addSequenceAndChain(r, seq[i], chns[i]); + Cache.log + .error("Error saving Chimera session: " + reply.toString()); } } - 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; + return false; } - public void addSequence(int pe, SequenceI[] seq) + /** + * Ask Chimera to open a session file. Returns true if successful, else false. + * The filename must have a .py extension for this command to work. + * + * @param filepath + * @return + */ + public boolean openSession(String filepath) { - // add sequences to the pe'th pdbentry's seuqence set. - addSequenceAndChain(pe, seq, null); + evalStateCommand("open " + filepath, true); + // todo: test for failure - how? + return true; } - private void addSequenceAndChain(int pe, SequenceI[] seq, String[] tchain) + public boolean isFinishedInit() { - 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; - } + return finishedInit; } - /** - * - * @param pdbfile - * @return text report of alignment between pdbfile and any associated - * alignment sequences - */ - public String printMapping(String pdbfile) + public void setFinishedInit(boolean finishedInit) + { + this.finishedInit = finishedInit; + } + + public List getChainNames() { - return ssm.printMapping(pdbfile); + return chainNames; } }