X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Frbvi%2Fchimera%2FJalviewChimeraBinding.java;h=98f2e1a7a7c406ed418b8665e234643a97823ba1;hb=85937698cb3a6d1fb8be1cfa7a1677e632da7be9;hp=3f2d5e44e939209bb357820ca4942fcb96d0b62b;hpb=8b70da73fd4073a6e28292d94c1e731878858b66;p=jalview.git diff --git a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java index 3f2d5e4..98f2e1a 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. * @@ -20,175 +20,179 @@ */ package jalview.ext.rbvi.chimera; +import java.awt.Color; +import java.net.BindException; +import java.util.ArrayList; +import java.util.LinkedHashMap; +import java.util.List; +import java.util.Map; + +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; + 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.httpserver.AbstractRequestHandler; import jalview.schemes.ColourSchemeI; import jalview.schemes.ResidueProperties; -import jalview.structure.StructureListener; +import jalview.structure.AtomSpec; 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.LinkedHashMap; -import java.util.List; -import java.util.Map; - -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 AAStructureBindingModel +{ + // Chimera clause to exclude alternate locations in atom selection + private static final String NO_ALTLOCS = "&~@.B-Z&~@.2-9"; -public abstract class JalviewChimeraBinding extends - SequenceStructureBindingModel implements StructureListener, - SequenceStructureBinding, StructureSelectionManagerProvider + private static final boolean debug = false; -{ private static final String PHOSPHORUS = "P"; private static final String ALPHACARBON = "CA"; private StructureManager csm; + /* + * Object through which we talk to Chimera + */ private ChimeraManager viewer; - /** + /* + * Object which listens to Chimera notifications + */ + private AbstractRequestHandler chimeraListener; + + /* * 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; - } + private List atomsPicked = new ArrayList(); - public void setFinishedInit(boolean finishedInit) - { - this.finishedInit = finishedInit; - } + private List chainNames; - boolean allChainsSelected = false; + private Map chainFile; - /** - * when true, try to search the associated datamodel for sequences that are - * associated with any unknown structures in the Chimera view. + public String fileLoadingError; + + /* + * Map of ChimeraModel objects keyed by PDB full local file name */ - private boolean associateNewStructs = false; + private Map> chimeraMaps = new LinkedHashMap>(); - List atomsPicked = new ArrayList(); + /* + * the default or current model displayed if the model cannot be identified + * from the selection message + */ + private int frameNo = 0; - public List chainNames; + private String lastCommand; - private Map chainFile; + private boolean loadedInline; /** - * array of target chains for sequences - tied to pdbentry and sequence[] + * current set of model filenames loaded */ - protected String[][] chains; - - boolean colourBySequence = true; - - StringBuffer eval = new StringBuffer(); + String[] modelFileNames = null; - public String fileLoadingError; + String lastMousedOverAtomSpec; - private Map> chimmaps = new LinkedHashMap>(); + private List lastReply; - private List mdlToFile = new ArrayList(); + /* + * incremented every time a load notification is successfully handled - + * lightweight mechanism for other threads to detect when they can start + * referring to new structures. + */ + private long loadNotifiesHandled = 0; /** - * the default or current model displayed if the model cannot be identified - * from the selection message + * 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 */ - int frameNo = 0; - - String lastCommand; - - String lastMessage; - - boolean loadedInline; - public boolean openFile(PDBEntry pe) { String file = pe.getFile(); try { + List modelsToMap = new ArrayList(); List oldList = viewer.getModelList(); - viewer.openModel(file, pe.getId(), 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); + alreadyOpen = true; + modelsToMap.add(open); } - chimmaps.put(file, newList); + } + + /* + * If Chimera doesn't yet have this model, ask it to open it, and retrieve + * the model name(s) added by Chimera. + */ + if (!alreadyOpen) + { + viewer.openModel(file, pe.getId(), ModelType.PDB_MODEL); + List newList = viewer.getModelList(); + // JAL-1728 newList.removeAll(oldList) does not work for (ChimeraModel cm : newList) { - while (mdlToFile.size() < 1 + cm.getModelNumber()) + if (cm.getModelName().equals(pe.getId())) { - mdlToFile.add(new String("")); + modelsToMap.add(cm); } - mdlToFile.set(cm.getModelNumber(), file); } + } - 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); + chimeraMaps.put(file, modelsToMap); - if (ssm != null) + 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" @@ -199,92 +203,64 @@ 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); - */ } + /** + * Start a dedicated HttpServer to listen for Chimera notifications, and tell + * it to start listening + */ + public void startChimeraListener() + { + try + { + chimeraListener = new ChimeraListener(this); + viewer.startListening(chimeraListener.getUri()); + } catch (BindException e) + { + System.err.println("Failed to start Chimera listener: " + + e.getMessage()); + } + } + + /** + * 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); } /** @@ -319,38 +295,40 @@ public abstract class JalviewChimeraBinding extends + ";focus " + cmdstring, false); } - public void closeViewer() + /** + * Close down the Jalview viewer and listener, 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(); + } + if (this.chimeraListener != null) + { + chimeraListener.shutdown(); + chimeraListener = 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",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); } /** @@ -400,7 +378,7 @@ public abstract class JalviewChimeraBinding extends assert (_alignment.length == _refStructure.length && _alignment.length != _hiddenCols.length); 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 @@ -412,7 +390,7 @@ 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; @@ -474,7 +452,7 @@ public abstract class JalviewChimeraBinding extends 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) @@ -482,12 +460,14 @@ public abstract class JalviewChimeraBinding extends 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) { @@ -506,7 +486,7 @@ 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; @@ -540,7 +520,7 @@ public abstract class JalviewChimeraBinding extends + targetC[pdbfnum]; atomSpec[pdbfnum] = asp.getRNA() != null ? PHOSPHORUS : ALPHACARBON; // move on to next pdb file - s = sequence[pdbfnum].length; + s = seqCountForPdbFile; break; } } @@ -647,16 +627,21 @@ public abstract class JalviewChimeraBinding extends // TODO: handle sub-models command.append(selcom[pdbfnum]); command.append("@" + atomSpec[pdbfnum]); + // JAL-1757 exclude alternative CA locations + command.append(NO_ALTLOCS); command.append(" #" + refStructure /* +".1" */); command.append(selcom[refStructure]); command.append("@" + atomSpec[refStructure]); + command.append(NO_ALTLOCS); } if (selectioncom.length() > 0) { - // TODO remove debug output - 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; "); @@ -668,9 +653,12 @@ 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(), true /* false */); } @@ -681,7 +669,7 @@ public abstract class JalviewChimeraBinding extends { if (!viewer.isChimeraLaunched()) { - viewer.launchChimera(csm.getChimeraPaths()); + viewer.launchChimera(StructureManager.getChimeraPaths()); } if (!viewer.isChimeraLaunched()) { @@ -689,34 +677,36 @@ 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() -// { // trim command or it may never find a match in the replyLog!! - lastReply = viewer.sendChimeraCommand(command.trim(), resp); - if (debug && resp) - { - log("Response from command ('" + command + "') was:\n" - + lastReply); - } -// } -// }); - // TODO - use j7/8 thread management -// try -// { -// t.join(); -// } catch (InterruptedException foo) -// { -// } -// ; + lastReply = viewer.sendChimeraCommand(command.trim(), logResponse); + if (debug && logResponse) + { + log("Response from command ('" + command + "') was:\n" + lastReply); + } } viewerCommandHistory(true); lastCommand = command; @@ -734,7 +724,7 @@ public abstract class JalviewChimeraBinding extends { return; } - if (ssm == null) + if (getSsm() == null) { return; } @@ -749,22 +739,44 @@ public abstract class JalviewChimeraBinding extends } AlignmentI alignment = alignmentv.getAlignment(); - for (jalview.structure.StructureMappingcommandSet cpdbbyseq : ChimeraCommands - .getColourBySequenceCommand(ssm, files, sequence, sr, fr, - alignment)) + for (jalview.structure.StructureMappingcommandSet cpdbbyseq : getColourBySequenceCommands( + files, sr, fr, alignment)) { - for (String cbyseq : cpdbbyseq.commands) + for (String command : cpdbbyseq.commands) { - waitForChimera(); - evalStateCommand(cbyseq, false); - waitForChimera(); + executeWhenReady(command); } } } + /** + * @param files + * @param sr + * @param fr + * @param alignment + * @return + */ + protected StructureMappingcommandSet[] getColourBySequenceCommands( + String[] files, SequenceRenderer sr, FeatureRenderer fr, + AlignmentI alignment) + { + return ChimeraCommands.getColourBySequenceCommand(getSsm(), files, + getSequence(), sr, fr, alignment); + } + + /** + * @param command + */ + protected void executeWhenReady(String command) + { + waitForChimera(); + evalStateCommand(command, false); + waitForChimera(); + } + private void waitForChimera() { - while (viewer.isBusy()) + while (viewer != null && viewer.isBusy()) { try { Thread.sleep(15); @@ -773,30 +785,11 @@ public abstract class JalviewChimeraBinding extends } } - public boolean isColourBySequence() - { - return colourBySequence; - } - public void setColourBySequence(boolean colourBySequence) - { - this.colourBySequence = colourBySequence; - } // 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) { @@ -871,8 +864,8 @@ 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()]); } /** @@ -895,294 +888,130 @@ 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)
+   *   ~show #0:43.C;show #0:44.C
+   * Note this removes the highlight 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.stopListening(chimeraListener.getUri()); + viewer.sendChimeraCommand(cmd, false); + viewer.startListening(chimeraListener.getUri()); } - - 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); - } - - private void viewerCommandHistory(boolean enable) - { - log("(Not yet implemented) History " - + ((debug || enable) ? "on" : "off")); - } - - public void loadInline(String string) + /** + * Query Chimera for its current selection, and highlight it on the alignment + */ + public void highlightChimeraSelection() { - 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); - log("cannot load inline in Chimera, yet"); - } + /* + * Ask Chimera for its current selection + */ + List selection = viewer.getSelectedResidueSpecs(); - public void mouseOverStructure(int atomIndex, String strInfo) - { - // function to parse a mouseOver event from Chimera - // - int pdbResNum; - int alocsep = strInfo.indexOf("^"); - int mdlSep = strInfo.indexOf("/"); - int chainSeparator = strInfo.indexOf(":"), chainSeparator1 = -1; - - if (chainSeparator == -1) + /* + * Parse model number, residue and chain for each selected position, + * formatted as #0:123.A or #1.2:87.B (#model.submodel:residue.chain) + */ + List atomSpecs = new ArrayList(); + for (String atomSpec : selection) { - chainSeparator = strInfo.indexOf("."); - if (mdlSep > -1 && mdlSep < chainSeparator) + int colonPos = atomSpec.indexOf(":"); + if (colonPos == -1) { - chainSeparator1 = chainSeparator; - chainSeparator = mdlSep; + continue; // malformed } - } - // 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) - { - chainId = strInfo.substring(strInfo.indexOf(":") + 1, - strInfo.indexOf(".")); - } - else - { - chainId = " "; - } - - String pdbfilename = modelFileNames[frameNo]; // default is first or current - // model - if (mdlSep > -1) - { - if (chainSeparator1 == -1) - { - chainSeparator1 = strInfo.indexOf(".", mdlSep); + + int hashPos = atomSpec.indexOf("#"); + String modelSubmodel = atomSpec.substring(hashPos + 1, colonPos); + int dotPos = modelSubmodel.indexOf("."); + int modelId = 0; + try { + modelId = Integer.valueOf(dotPos == -1 ? modelSubmodel + : modelSubmodel.substring(0, dotPos)); + } catch (NumberFormatException e) { + // ignore, default to model 0 } - String mdlId = (chainSeparator1 > -1) ? strInfo.substring(mdlSep + 1, - chainSeparator1) : strInfo.substring(mdlSep + 1); - try + + String residueChain = atomSpec.substring(colonPos + 1); + dotPos = residueChain.indexOf("."); + int pdbResNum = Integer.parseInt(dotPos == -1 ? residueChain + : residueChain.substring(0, dotPos)); + + String chainId = dotPos == -1 ? "" : residueChain + .substring(dotPos + 1); + + /* + * Work out the pdbfilename from the model number + */ + String pdbfilename = modelFileNames[frameNo]; + findfileloop: for (String pdbfile : this.chimeraMaps.keySet()) { - // recover PDB filename for the model hovered over. - int _mp = _modelFileNameMap.length - 1, mnumber = new Integer(mdlId) - .intValue() - 1; - while (mnumber < _modelFileNameMap[_mp]) - { - _mp--; - } - pdbfilename = modelFileNames[_mp]; - if (pdbfilename == null) + for (ChimeraModel cm : chimeraMaps.get(pdbfile)) { - // pdbfilename = new File(viewer.getModelFileName(mnumber)) - // .getAbsolutePath(); + if (cm.getModelNumber() == modelId) + { + pdbfilename = pdbfile; + break findfileloop; + } } - - } catch (Exception e) - { } - ; - } - if (lastMessage == null || !lastMessage.equals(strInfo)) - { - ssm.mouseOverStructure(pdbResNum, chainId, pdbfilename); + atomSpecs.add(new AtomSpec(pdbfilename, chainId, pdbResNum, 0)); } - lastMessage = strInfo; + /* + * Broadcast the selection (which may be empty, if the user just cleared all + * selections) + */ + getSsm().mouseOverStructure(atomSpecs); } - public void notifyAtomPicked(int atomIndex, String strInfo, String strData) + private void log(String message) { - /** - * this implements the toggle label behaviour copied from the original - * structure viewer, MCView - */ - if (strData != null) - { - System.err.println("Ignoring additional pick data string " + strData); - } - // rewrite these selections for chimera (DNA, RNA and protein) - 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) - { - mdlString += strInfo.substring(p, strInfo.indexOf(" #")); - } - picked = "((" + picked + ".CA" + mdlString + ")|(" + picked + ".P" - + mdlString + "))"; - viewerCommandHistory(false); - - if (!atomsPicked.contains(picked)) - { - viewer.select(picked); - atomsPicked.add(picked); - } - else - { - viewer.select("not " + picked); - atomsPicked.remove(picked); - } - viewerCommandHistory(true); - // TODO: in application this happens - // - // if (scriptWindow != null) - // { - // scriptWindow.sendConsoleMessage(strInfo); - // scriptWindow.sendConsoleMessage("\n"); - // } - + System.err.println("## Chimera log: " + message); } - // incremented every time a load notification is successfully handled - - // lightweight mechanism for other threads to detect when they can start - // referring to new structures. - private long loadNotifiesHandled = 0; - - public long getLoadNotifiesHandled() + private void viewerCommandHistory(boolean enable) { - return loadNotifiesHandled; + // log("(Not yet implemented) History " + // + ((debug || enable) ? "on" : "off")); } - public void notifyFileLoaded(String fullPathName, String fileName2, - String modelName, String errorMsg, int modelParts) + public long getLoadNotifiesHandled() { - if (errorMsg != null) - { - fileLoadingError = errorMsg; - 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. - fileLoadingError = null; - String[] oldmodels = modelFileNames; - modelFileNames = null; - chainNames = new ArrayList(); - chainFile = new HashMap(); - boolean notifyLoaded = false; - String[] modelfilenames = getPdbFile(); - // first check if we've lost any structures - if (oldmodels != null && oldmodels.length > 0) - { - int oldm = 0; - for (int i = 0; i < oldmodels.length; i++) - { - for (int n = 0; n < modelfilenames.length; n++) - { - if (modelfilenames[n] == oldmodels[i]) - { - oldmodels[i] = null; - break; - } - } - if (oldmodels[i] != null) - { - oldm++; - } - } - if (oldm > 0) - { - String[] oldmfn = new String[oldm]; - oldm = 0; - for (int i = 0; i < oldmodels.length; i++) - { - if (oldmodels[i] != null) - { - oldmfn[oldm++] = oldmodels[i]; - } - } - // deregister the Jmol instance for these structures - we'll add - // ourselves again at the end for the current structure set. - ssm.removeStructureViewerListener(this, oldmfn); - } - } - - // register ourselves as a listener and notify the gui that it needs to - // update itself. - ssm.addStructureViewerListener(this); - - if (notifyLoaded) - { - FeatureRenderer fr = getFeatureRenderer(null); - if (fr != null) - { - fr.featuresAdded(); - } - refreshGUI(); - loadNotifiesHandled++; - } - setLoadingFromArchive(false); + return loadNotifiesHandled; } public void setJalviewColourScheme(ColourSchemeI cs) @@ -1194,70 +1023,32 @@ public abstract class JalviewChimeraBinding extends 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()) - { - res = en.nextElement().toString(); - index = ((Integer) ResidueProperties.aa3Hash.get(res)).intValue(); - if (index > 20) - { - continue; - } + StringBuilder command = new StringBuilder(128); - 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() + "];"); + List residueSet = ResidueProperties.getResidues(isNucleotide(), + false); + for (String res : residueSet) + { + Color col = cs.findColour(res.charAt(0)); + 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; @@ -1265,8 +1056,8 @@ 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() { @@ -1284,165 +1075,89 @@ 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 synchronized PDBEntry[] addSequenceAndChain(PDBEntry[] pdbe, - SequenceI[][] seq, String[][] chns) + public String printMapping(String pdbfile) { - List v = new ArrayList(); - List rtn = new ArrayList(); - for (int i = 0; i < pdbentry.length; i++) - { - v.add(pdbentry[i]); - } - for (int i = 0; i < pdbe.length; i++) + return getSsm().printMapping(pdbfile); + } + + /** + * Ask Chimera to save its session to the given file. Returns true if + * successful, else false. + * + * @param filepath + * @return + */ + public boolean saveSession(String filepath) + { + 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.add(new int[] - { v.size(), i }); - v.add(pdbe[i]); + return true; } else { - // just make sure the sequence/chain entries are all up to date - addSequenceAndChain(r, seq[i], chns[i]); - } - } - pdbe = v.toArray(new PDBEntry[v.size()]); - pdbentry = pdbe; - if (rtn.size() > 0) - { - // expand the tied sequence[] 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 = (rtn.get(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]]); + Cache.log + .error("Error saving Chimera session: " + reply.toString()); } } - else - { - pdbe = null; - } - return pdbe; + return false; } /** - * Adds sequences to the pe'th pdbentry's sequence set. + * 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 pe - * @param seq + * @param filepath + * @return */ - public void addSequence(int pe, SequenceI[] seq) + public boolean openSession(String filepath) { - 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(MessageManager.formatMessage( - "error.implementation_error_no_pdbentry_from_index", - new Object[] - { Integer.valueOf(pe).toString() })); - } - final String nullChain = "TheNullChain"; - List s = new ArrayList(); - List c = new ArrayList(); - if (chains == null) - { - chains = new String[pdbentry.length][]; - } - if (sequence[pe] != null) - { - for (int i = 0; i < sequence[pe].length; i++) - { - s.add(sequence[pe][i]); - if (chains[pe] != null) - { - if (i < chains[pe].length) - { - c.add(chains[pe][i]); - } - else - { - c.add(nullChain); - } - } - else - { - if (tchain != null && tchain.length > 0) - { - c.add(nullChain); - } - } - } - } - for (int i = 0; i < seq.length; i++) - { - if (!s.contains(seq[i])) - { - s.add(seq[i]); - if (tchain != null && i < tchain.length) - { - c.add(tchain[i] == null ? nullChain : tchain[i]); - } - } - } - SequenceI[] tmp = s.toArray(new SequenceI[s.size()]); - sequence[pe] = tmp; - if (c.size() > 0) - { - String[] tch = c.toArray(new String[c.size()]); - 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; } }