X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Frbvi%2Fchimera%2FJalviewChimeraBinding.java;h=b05c168c50f1649db40a440e68116dabdd09c8c5;hb=400b50efffaa43ae2c3b4d3f653bf8215c5d1edc;hp=7cd657ae2c8b70ec6fc245c41154ad540ebe1873;hpb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;p=jalview.git diff --git a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java index 7cd657a..b05c168 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 2.9.0b1) - * Copyright (C) 2015 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. * @@ -23,12 +23,14 @@ package jalview.ext.rbvi.chimera; import jalview.api.AlignmentViewPanel; import jalview.api.FeatureRenderer; import jalview.api.SequenceRenderer; +import jalview.api.structures.JalviewStructureDisplayI; import jalview.bin.Cache; import jalview.datamodel.AlignmentI; import jalview.datamodel.ColumnSelection; import jalview.datamodel.PDBEntry; import jalview.datamodel.SequenceI; import jalview.httpserver.AbstractRequestHandler; +import jalview.io.DataSourceType; import jalview.schemes.ColourSchemeI; import jalview.schemes.ResidueProperties; import jalview.structure.AtomSpec; @@ -40,6 +42,7 @@ import jalview.util.MessageManager; import java.awt.Color; import java.net.BindException; import java.util.ArrayList; +import java.util.Hashtable; import java.util.LinkedHashMap; import java.util.List; import java.util.Map; @@ -63,6 +66,10 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel private static final String ALPHACARBON = "CA"; + private List chainNames = new ArrayList(); + + private Hashtable chainFile = new Hashtable(); + /* * Object through which we talk to Chimera */ @@ -86,8 +93,6 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel */ private boolean loadingFinished = true; - public String fileLoadingError; - /* * Map of ChimeraModel objects keyed by PDB full local file name */ @@ -101,16 +106,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel private String lastCommand; - private boolean loadedInline; - - /** - * current set of model filenames loaded - */ - String[] modelFileNames = null; - - String lastMousedOverAtomSpec; - - private List lastReply; + String lastHighlightCommand; /* * incremented every time a load notification is successfully handled - @@ -119,6 +115,8 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel */ private long loadNotifiesHandled = 0; + private Thread chimeraMonitor; + /** * Open a PDB structure file in Chimera and set up mappings from Jalview. * @@ -196,16 +194,44 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel * @param ssm * @param pdbentry * @param sequenceIs - * @param chains * @param protocol */ public JalviewChimeraBinding(StructureSelectionManager ssm, - PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains, - String protocol) + PDBEntry[] pdbentry, SequenceI[][] sequenceIs, DataSourceType protocol) { - super(ssm, pdbentry, sequenceIs, chains, protocol); - viewer = new ChimeraManager( - new ext.edu.ucsf.rbvi.strucviz2.StructureManager(true)); + super(ssm, pdbentry, sequenceIs, protocol); + viewer = new ChimeraManager(new StructureManager(true)); + } + + /** + * Starts a thread that waits for the Chimera process to finish, so that we + * can then close the associated resources. This avoids leaving orphaned + * Chimera viewer panels in Jalview if the user closes Chimera. + */ + protected void startChimeraProcessMonitor() + { + final Process p = viewer.getChimeraProcess(); + chimeraMonitor = new Thread(new Runnable() + { + + @Override + public void run() + { + try + { + p.waitFor(); + JalviewStructureDisplayI display = getViewer(); + if (display != null) + { + display.closeViewer(false); + } + } catch (InterruptedException e) + { + // exit thread if Chimera Viewer is closed in Jalview + } + } + }); + chimeraMonitor.start(); } /** @@ -226,18 +252,6 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel } /** - * Construct a title string for the viewer window based on the data Jalview - * knows about - * - * @param verbose - * @return - */ - public String getViewerTitle(boolean verbose) - { - return getViewerTitle("Chimera", verbose); - } - - /** * Tells Chimera to display only the specified chains * * @param toshow @@ -253,11 +267,14 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel boolean first = true; for (String chain : toshow) { + int modelNumber = getModelNoForChain(chain); + String showChainCmd = modelNumber == -1 ? "" : modelNumber + ":." + + chain.split(":")[1]; if (!first) { cmd.append(","); } - cmd.append(":.").append(chain); + cmd.append(showChainCmd); first = false; } @@ -266,7 +283,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel * window, but it looks more helpful not to (easier to relate chains to the * whole) */ - final String command = "~display #*; ~ribbon #*; ribbon " + final String command = "~display #*; ~ribbon #*; ribbon :" + cmd.toString(); sendChimeraCommand(command, false); } @@ -290,9 +307,14 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel lastCommand = null; viewer = null; + if (chimeraMonitor != null) + { + chimeraMonitor.interrupt(); + } releaseUIResources(); } + @Override public void colourByChain() { colourBySequence = false; @@ -308,6 +330,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel *
  • all others - white
    • * */ + @Override public void colourByCharge() { colourBySequence = false; @@ -329,6 +352,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel * @param _hiddenCols * an array of corresponding hidden columns for each alignment */ + @Override public void superposeStructures(AlignmentI[] _alignment, int[] _refStructure, ColumnSelection[] _hiddenCols) { @@ -570,23 +594,29 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel /** * Launch Chimera, unless an instance linked to this object is already - * running. Returns true if chimera is successfully launched, or already + * running. Returns true if Chimera is successfully launched, or already * running, else false. * * @return */ public boolean launchChimera() { - if (!viewer.isChimeraLaunched()) - { - return viewer.launchChimera(StructureManager.getChimeraPaths()); - } if (viewer.isChimeraLaunched()) { return true; } - log("Failed to launch Chimera!"); - return false; + + boolean launched = viewer.launchChimera(StructureManager + .getChimeraPaths()); + if (launched) + { + startChimeraProcessMonitor(); + } + else + { + log("Failed to launch Chimera!"); + } + return launched; } /** @@ -617,7 +647,8 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel if (lastCommand == null || !lastCommand.equals(command)) { // trim command or it may never find a match in the replyLog!! - lastReply = viewer.sendChimeraCommand(command.trim(), logResponse); + List lastReply = viewer.sendChimeraCommand(command.trim(), + logResponse); if (logResponse && debug) { log("Response from command ('" + command + "') was:\n" + lastReply); @@ -638,34 +669,15 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel String progressMsg); /** - * colour any structures associated with sequences in the given alignment - * using the getFeatureRenderer() and getSequenceRenderer() renderers but only - * if colourBySequence is enabled. + * Sends a set of colour commands to the structure viewer + * + * @param colourBySequenceCommands */ - public void colourBySequence(boolean showFeatures, - jalview.api.AlignmentViewPanel alignmentv) + @Override + protected void colourBySequence( + StructureMappingcommandSet[] colourBySequenceCommands) { - if (!colourBySequence || !loadingFinished) - { - return; - } - if (getSsm() == null) - { - return; - } - String[] files = getPdbFile(); - - SequenceRenderer sr = getSequenceRenderer(alignmentv); - - FeatureRenderer fr = null; - if (showFeatures) - { - fr = getFeatureRenderer(alignmentv); - } - AlignmentI alignment = alignmentv.getAlignment(); - - for (jalview.structure.StructureMappingcommandSet cpdbbyseq : getColourBySequenceCommands( - files, sr, fr, alignment)) + for (StructureMappingcommandSet cpdbbyseq : colourBySequenceCommands) { for (String command : cpdbbyseq.commands) { @@ -681,6 +693,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel * @param alignment * @return */ + @Override protected StructureMappingcommandSet[] getColourBySequenceCommands( String[] files, SequenceRenderer sr, FeatureRenderer fr, AlignmentI alignment) @@ -715,28 +728,6 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel // End StructureListener // ////////////////////////// - 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; - } - - /** - * returns the current featureRenderer that should be used to colour the - * structures - * - * @param alignment - * - * @return - */ - public abstract FeatureRenderer getFeatureRenderer( - AlignmentViewPanel alignment); - /** * instruct the Jalview binding to update the pdbentries vector if necessary * prior to matching the viewer's contents to the list of structure files @@ -744,23 +735,6 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel */ public abstract void refreshPdbEntries(); - private int getModelNum(String modelFileName) - { - String[] mfn = getPdbFile(); - 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 - @@ -777,60 +751,28 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel { return new String[0]; } - // if (modelFileNames == null) - // { - // Collection chimodels = viewer.getChimeraModels(); - // _modelFileNameMap = new int[chimodels.size()]; - // int j = 0; - // for (ChimeraModel chimodel : chimodels) - // { - // String mdlName = chimodel.getModelName(); - // } - // modelFileNames = new String[j]; - // // System.arraycopy(mset, 0, modelFileNames, 0, j); - // } return chimeraMaps.keySet().toArray( modelFileNames = new String[chimeraMaps.size()]); } /** - * map from string to applet - */ - public Map getRegistryInfo() - { - // TODO Auto-generated method stub - return null; - } - - /** - * returns the current sequenceRenderer that should be used to colour the - * structures - * - * @param alignment - * - * @return - */ - public abstract SequenceRenderer getSequenceRenderer( - AlignmentViewPanel alignment); - - /** - * Construct and send a command to highlight zero, one or more atoms. - * - * 
    -   * Done by generating a command like (to 'highlight' position 44)
-   *   show #0:44.C
-   *
    + * Construct and send a command to highlight zero, one or more atoms. We do + * this by sending an "rlabel" command to show the residue label at that + * position. */ @Override public void highlightAtoms(List atoms) { - if (atoms == null) + if (atoms == null || atoms.size() == 0) { return; } - StringBuilder atomSpecs = new StringBuilder(); + + StringBuilder cmd = new StringBuilder(128); boolean first = true; + boolean found = false; + for (AtomSpec atom : atoms) { int pdbResNum = atom.getPdbResNum(); @@ -839,39 +781,46 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel List cms = chimeraMaps.get(pdbfile); if (cms != null && !cms.isEmpty()) { - /* - * Formatting as #0:34.A,#1:33.A doesn't work as desired, so instead we - * concatenate multiple 'show' commands - */ - atomSpecs.append(first ? "" : ";show "); + if (first) + { + cmd.append("rlabel #").append(cms.get(0).getModelNumber()) + .append(":"); + } + else + { + cmd.append(","); + } first = false; - atomSpecs.append("#" + cms.get(0).getModelNumber()); - atomSpecs.append(":" + pdbResNum); + cmd.append(pdbResNum); if (!chain.equals(" ")) { - atomSpecs.append("." + chain); + cmd.append(".").append(chain); } + found = true; } } - String atomSpec = atomSpecs.toString(); + String command = cmd.toString(); /* - * Avoid repeated commands for the same residue + * avoid repeated commands for the same residue */ - if (atomSpec.equals(lastMousedOverAtomSpec)) + if (command.equals(lastHighlightCommand)) { return; } - StringBuilder command = new StringBuilder(32); - viewerCommandHistory(false); - if (atomSpec.length() > 0) + /* + * unshow the label for the previous residue + */ + if (lastHighlightCommand != null) { - command.append("show ").append(atomSpec); - viewer.sendChimeraCommand(command.toString(), false); + viewer.sendChimeraCommand("~" + lastHighlightCommand, false); } - viewerCommandHistory(true); - this.lastMousedOverAtomSpec = atomSpec; + if (found) + { + viewer.sendChimeraCommand(command, false); + } + this.lastHighlightCommand = command; } /** @@ -959,6 +908,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel return loadNotifiesHandled; } + @Override public void setJalviewColourScheme(ColourSchemeI cs) { colourBySequence = false; @@ -975,12 +925,14 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel List residueSet = ResidueProperties.getResidues(isNucleotide(), false); - for (String res : residueSet) + for (String resName : residueSet) { - Color col = cs.findColour(res.charAt(0)); + char res = resName.length() == 3 ? ResidueProperties + .getSingleCharacterCode(resName) : resName.charAt(0); + Color col = cs.findColour(res, 0, null, null, 0f); command.append("color " + col.getRed() / normalise + "," + col.getGreen() / normalise + "," + col.getBlue() - / normalise + " ::" + res + ";"); + / normalise + " ::" + resName + ";"); } sendAsynchronousCommand(command.toString(), COLOURING_CHIMERA); @@ -994,6 +946,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel */ public abstract void refreshGUI(); + @Override public void setLoadingFromArchive(boolean loadingFromArchive) { this.loadingFromArchive = loadingFromArchive; @@ -1004,6 +957,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel * @return true if Chimeral is still restoring state or loading is still going * on (see setFinsihedLoadingFromArchive) */ + @Override public boolean isLoadingFromArchive() { return loadingFromArchive && !loadingFinished; @@ -1015,6 +969,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel * * @param finishedLoading */ + @Override public void setFinishedLoadingFromArchive(boolean finishedLoading) { loadingFinished = finishedLoading; @@ -1028,6 +983,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel * .html * @param col */ + @Override public void setBackgroundColour(Color col) { viewerCommandHistory(false); @@ -1080,39 +1036,65 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel } /** - * Returns a list of chains mapped in this viewer. Note this list is not - * currently scoped per structure. + * Send a 'focus' command to Chimera to recentre the visible display + */ + public void focusView() + { + sendChimeraCommand("focus", false); + } + + /** + * Send a 'show' command for all atoms in the currently selected columns * - * @return + * TODO: pull up to abstract structure viewer interface + * + * @param vp */ - public List getChainNames() + public void highlightSelection(AlignmentViewPanel vp) { - List names = new ArrayList(); - String[][] allNames = getChains(); - if (allNames != null) + List cols = vp.getAlignViewport().getColumnSelection() + .getSelected(); + AlignmentI alignment = vp.getAlignment(); + StructureSelectionManager sm = getSsm(); + for (SequenceI seq : alignment.getSequences()) { - for (String[] chainsForPdb : allNames) + /* + * convert selected columns into sequence positions + */ + int[] positions = new int[cols.size()]; + int i = 0; + for (Integer col : cols) { - if (chainsForPdb != null) - { - for (String chain : chainsForPdb) - { - if (chain != null && !names.contains(chain)) - { - names.add(chain); - } - } - } + positions[i++] = seq.findPosition(col); } + sm.highlightStructure(this, seq, positions); } - return names; } - /** - * Send a 'focus' command to Chimera to recentre the visible display - */ - public void focusView() + + @Override + public List getChainNames() { - sendChimeraCommand("focus", false); + return chainNames; + } + + public Hashtable getChainFile() + { + return chainFile; + } + + public List getChimeraModelByChain(String chain) + { + return chimeraMaps.get(chainFile.get(chain)); + } + + public int getModelNoForChain(String chain) + { + List foundModels = getChimeraModelByChain(chain); + if (foundModels != null && !foundModels.isEmpty()) + { + return foundModels.get(0).getModelNumber(); + } + return -1; } }