X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Frbvi%2Fchimera%2FJalviewChimeraBinding.java;h=327d787a4898aecde131f5d9232d547fa3d71258;hb=260f6abfaaafac067d5bda703e5b21be480bcc8f;hp=1ce0d2b05934599faa99ca8a0b201cda7de5ef19;hpb=f3b39605256b4803fef19117e7e8bd682bb51758;p=jalview.git diff --git a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java index 1ce0d2b..327d787 100644 --- a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java +++ b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java @@ -23,6 +23,7 @@ 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; @@ -40,6 +41,7 @@ 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 +65,10 @@ 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 */ @@ -101,17 +107,8 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel private String lastCommand; - private boolean loadedInline; - - /** - * current set of model filenames loaded - */ - String[] modelFileNames = null; - String lastHighlightCommand; - private List lastReply; - /* * incremented every time a load notification is successfully handled - * lightweight mechanism for other threads to detect when they can start @@ -119,6 +116,8 @@ 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. * @@ -200,12 +199,41 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel * @param protocol */ public JalviewChimeraBinding(StructureSelectionManager ssm, - PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains, - String protocol) + PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String protocol) + { + 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() { - super(ssm, pdbentry, sequenceIs, chains, protocol); - viewer = new ChimeraManager( - new ext.edu.ucsf.rbvi.strucviz2.StructureManager(true)); + 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(); } /** @@ -253,11 +281,14 @@ 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 +297,7 @@ 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); } @@ -290,6 +321,10 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel lastCommand = null; viewer = null; + if (chimeraMonitor != null) + { + chimeraMonitor.interrupt(); + } releaseUIResources(); } @@ -570,23 +605,29 @@ 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 +658,8 @@ 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); @@ -715,17 +757,6 @@ 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 @@ -777,33 +808,12 @@ 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 * @@ -815,20 +825,18 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel AlignmentViewPanel alignment); /** - * Construct and send a command to highlight zero, one or more atoms. - * - * 
-   * Done by generating a command like (to 'highlight' positions 44 and 46)
-   *   show #0:44,46.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 cmd = new StringBuilder(128); boolean first = true; boolean found = false; @@ -843,7 +851,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel { if (first) { - cmd.append("show #").append(cms.get(0).getModelNumber()) + cmd.append("rlabel #").append(cms.get(0).getModelNumber()) .append(":"); } else @@ -851,7 +859,6 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel cmd.append(","); } first = false; - cmd.append(cms.get(0).getModelNumber()).append(":"); cmd.append(pdbResNum); if (!chain.equals(" ")) { @@ -863,19 +870,24 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel String command = cmd.toString(); /* - * Avoid repeated commands for the same residue + * avoid repeated commands for the same residue */ if (command.equals(lastHighlightCommand)) { return; } - viewerCommandHistory(false); + /* + * unshow the label for the previous residue + */ + if (lastHighlightCommand != null) + { + viewer.sendChimeraCommand("~" + lastHighlightCommand, false); + } if (found) { - viewer.sendChimeraCommand(command.toString(), false); + viewer.sendChimeraCommand(command, false); } - viewerCommandHistory(true); this.lastHighlightCommand = command; } @@ -1088,35 +1100,6 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel } /** - * Returns a list of chains mapped in this viewer. Note this list is not - * currently scoped per structure. - * - * @return - */ - public List getChainNames() - { - List names = new ArrayList(); - String[][] allNames = getChains(); - if (allNames != null) - { - for (String[] chainsForPdb : allNames) - { - if (chainsForPdb != null) - { - for (String chain : chainsForPdb) - { - if (chain != null && !names.contains(chain)) - { - names.add(chain); - } - } - } - } - } - return names; - } - - /** * Send a 'focus' command to Chimera to recentre the visible display */ public void focusView() @@ -1151,4 +1134,30 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel sm.highlightStructure(this, seq, positions); } } + + @Override + public List getChainNames() + { + 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; + } }