X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Frbvi%2Fchimera%2FJalviewChimeraBinding.java;h=36562044f1e1106751d9cf47b24585f0cda5173b;hb=fea6f8ed76719fd78b600adfea8891dafb8c9d12;hp=543cad40d7d76de4dbc7bbd3c8077bd7791994c7;hpb=2150df780eddbdf72013d29ee8eabb0f235c7bb4;p=jalview.git diff --git a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java index 543cad4..3656204 100644 --- a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java +++ b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java @@ -20,39 +20,49 @@ */ 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.structures.JalviewStructureDisplayI; import jalview.bin.Cache; import jalview.datamodel.AlignmentI; -import jalview.datamodel.ColumnSelection; +import jalview.datamodel.HiddenColumns; import jalview.datamodel.PDBEntry; +import jalview.datamodel.SearchResultMatchI; +import jalview.datamodel.SearchResultsI; +import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; +import jalview.gui.StructureViewer.ViewerType; import jalview.httpserver.AbstractRequestHandler; -import jalview.schemes.ColourSchemeI; -import jalview.schemes.ResidueProperties; +import jalview.io.DataSourceType; import jalview.structure.AtomSpec; -import jalview.structure.StructureMapping; -import jalview.structure.StructureMappingcommandSet; +import jalview.structure.StructureCommandsI.SuperposeData; import jalview.structure.StructureSelectionManager; import jalview.structures.models.AAStructureBindingModel; -import jalview.util.Comparison; import jalview.util.MessageManager; +import java.io.File; +import java.io.FileOutputStream; +import java.io.IOException; +import java.io.PrintWriter; +import java.net.BindException; +import java.util.ArrayList; +import java.util.BitSet; +import java.util.Collections; +import java.util.Iterator; +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 { + public static final String CHIMERA_FEATURE_GROUP = "Chimera"; + + // Chimera clause to exclude alternate locations in atom selection + private static final String NO_ALTLOCS = "&~@.B-Z&~@.2-9"; private static final boolean debug = false; @@ -60,12 +70,10 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel private static final String ALPHACARBON = "CA"; - private StructureManager csm; - /* * Object through which we talk to Chimera */ - private ChimeraManager viewer; + private ChimeraManager chimeraManager; /* * Object which listens to Chimera notifications @@ -73,67 +81,19 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel 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; - - /* - * 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 Chimera viewer's paint method can be called - */ - private boolean finishedInit = false; - - private List atomsPicked = new ArrayList(); - - private List chainNames; - - private Map chainFile; - - public String fileLoadingError; - - /* * Map of ChimeraModel objects keyed by PDB full local file name */ - private Map> chimeraMaps = new LinkedHashMap>(); - - /* - * the default or current model displayed if the model cannot be identified - * from the selection message - */ - private int frameNo = 0; + protected Map> chimeraMaps = new LinkedHashMap<>(); - private String lastCommand; + String lastHighlightCommand; - private boolean loadedInline; - - /** - * current set of model filenames loaded - */ - String[] modelFileNames = null; - - String lastMousedOverAtomSpec; - - private List lastReply; - - /* - * 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; + private Thread chimeraMonitor; /** * 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. + * 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 @@ -143,8 +103,8 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel String file = pe.getFile(); try { - List modelsToMap = new ArrayList(); - List oldList = viewer.getModelList(); + List modelsToMap = new ArrayList<>(); + List oldList = chimeraManager.getModelList(); boolean alreadyOpen = false; /* @@ -165,16 +125,8 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel */ 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) - { - if (cm.getModelName().equals(pe.getId())) - { - modelsToMap.add(cm); - } - } + chimeraManager.openModel(file, pe.getId(), ModelType.PDB_MODEL); + addChimeraModel(pe, modelsToMap); } chimeraMaps.put(file, modelsToMap); @@ -182,13 +134,6 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel if (getSsm() != null) { getSsm().addStructureViewerListener(this); - // ssm.addSelectionListener(this); - FeatureRenderer fr = getFeatureRenderer(null); - if (fr != null) - { - fr.featuresAdded(); - } - refreshGUI(); } return true; } catch (Exception q) @@ -201,37 +146,27 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel } /** - * Constructor + * Adds the ChimeraModel corresponding to the given PDBEntry, based on model + * name matching PDB id * - * @param ssm - * @param pdbentry - * @param sequenceIs - * @param chains - * @param protocol - */ - public JalviewChimeraBinding(StructureSelectionManager ssm, - PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains, - String protocol) - { - super(ssm, pdbentry, sequenceIs, chains, protocol); - viewer = new ChimeraManager( - csm = new ext.edu.ucsf.rbvi.strucviz2.StructureManager(true)); - } - - /** - * Start a dedicated HttpServer to listen for Chimera notifications, and tell - * it to start listening + * @param pe + * @param modelsToMap */ - public void startChimeraListener() + protected void addChimeraModel(PDBEntry pe, + List modelsToMap) { - try - { - chimeraListener = new ChimeraListener(this); - viewer.startListening(chimeraListener.getUri()); - } catch (BindException e) + /* + * Chimera: query for actual models and find the one with + * matching model name - already set in viewer.openModel() + */ + List newList = chimeraManager.getModelList(); + // JAL-1728 newList.removeAll(oldList) does not work + for (ChimeraModel cm : newList) { - System.err.println("Failed to start Chimera listener: " - + e.getMessage()); + if (cm.getModelName().equals(pe.getId())) + { + modelsToMap.add(cm); + } } } @@ -239,58 +174,72 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel * Constructor * * @param ssm - * @param theViewer + * @param pdbentry + * @param sequenceIs + * @param protocol */ public JalviewChimeraBinding(StructureSelectionManager ssm, - ChimeraManager theViewer) + PDBEntry[] pdbentry, SequenceI[][] sequenceIs, + DataSourceType protocol) { - super(ssm, null); - viewer = theViewer; - csm = viewer.getStructureManager(); + super(ssm, pdbentry, sequenceIs, protocol); + chimeraManager = new ChimeraManager(new StructureManager(true)); + chimeraManager.setChimeraX(ViewerType.CHIMERAX.equals(getViewerType())); + setStructureCommands(new ChimeraCommands()); + } + + @Override + protected ViewerType getViewerType() + { + return ViewerType.CHIMERA; } /** - * Construct a title string for the viewer window based on the data Jalview - * knows about - * - * @param verbose - * @return + * 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. */ - public String getViewerTitle(boolean verbose) + protected void startChimeraProcessMonitor() { - return getViewerTitle("Chimera", verbose); + final Process p = chimeraManager.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(); } /** - * prepare the view for a given set of models/chains. chainList contains - * strings of the form 'pdbfilename:Chaincode' - * - * @param toshow - * list of chains to make visible + * Start a dedicated HttpServer to listen for Chimera notifications, and tell it + * to start listening */ - public void centerViewer(List toshow) + public void startChimeraListener() { - StringBuilder cmd = new StringBuilder(64); - int mlength, p; - for (String lbl : toshow) + try { - mlength = 0; - do - { - p = mlength; - mlength = lbl.indexOf(":", p); - } while (p < mlength && mlength < (lbl.length() - 2)); - // TODO: lookup each pdb id and recover proper model number for it. - cmd.append("#" + getModelNum(chainFile.get(lbl)) + "." - + lbl.substring(mlength + 1) + " or "); - } - if (cmd.length() > 0) + chimeraListener = new ChimeraListener(this); + chimeraManager.startListening(chimeraListener.getUri()); + } catch (BindException e) { - cmd.setLength(cmd.length() - 4); + System.err.println( + "Failed to start Chimera listener: " + e.getMessage()); } - String cmdstring = cmd.toString(); - evalStateCommand("~display #*; ~ribbon #*; ribbon " + cmdstring - + ";focus " + cmdstring, false); } /** @@ -299,309 +248,189 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel */ public void closeViewer(boolean closeChimera) { - getSsm().removeStructureViewerListener(this, this.getPdbFile()); + getSsm().removeStructureViewerListener(this, this.getStructureFiles()); if (closeChimera) { - viewer.exitChimera(); + chimeraManager.exitChimera(); } if (this.chimeraListener != null) { chimeraListener.shutdown(); chimeraListener = null; } - lastCommand = null; - viewer = null; + chimeraManager = null; + if (chimeraMonitor != null) + { + chimeraMonitor.interrupt(); + } releaseUIResources(); } - public void colourByChain() - { - colourBySequence = false; - evalStateCommand("rainbow chain", false); - } - - public void colourByCharge() - { - colourBySequence = false; - evalStateCommand( - "color white;color red ::ASP;color red ::GLU;color blue ::LYS;color blue ::ARG;color yellow ::CYS", - false); - } - /** - * superpose the structures associated with sequences in the alignment - * according to their corresponding positions. + * {@inheritDoc} */ - public void superposeStructures(AlignmentI alignment) + public String superposeStructures(AlignmentI[] _alignment, + int[] _refStructure, HiddenColumns[] _hiddenCols) { - superposeStructures(alignment, -1, null); - } + // TODO delete method + StringBuilder allComs = new StringBuilder(128); + String[] files = getStructureFiles(); - /** - * superpose the structures associated with sequences in the alignment - * according to their corresponding positions. ded) - * - * @param refStructure - * - select which pdb file to use as reference (default is -1 - the - * first structure in the alignment) - */ - public void superposeStructures(AlignmentI alignment, int refStructure) - { - superposeStructures(alignment, refStructure, null); - } - - /** - * superpose the structures associated with sequences in the alignment - * according to their corresponding positions. ded) - * - * @param refStructure - * - select which pdb file to use as reference (default is -1 - the - * first structure in the alignment) - * @param hiddenCols - * TODO - */ - public void superposeStructures(AlignmentI alignment, int refStructure, - ColumnSelection hiddenCols) - { - superposeStructures(new AlignmentI[] - { alignment }, new int[] - { refStructure }, new ColumnSelection[] - { hiddenCols }); - } - - public void superposeStructures(AlignmentI[] _alignment, - int[] _refStructure, ColumnSelection[] _hiddenCols) - { - 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 Chimera files - long starttime = System.currentTimeMillis(); - boolean waiting = true; - do + if (!waitForFileLoad(files)) { - waiting = false; - for (String file : files) - { - try - { - // HACK - in Jalview 2.8 this call may not be threadsafe so we catch - // every possible exception - StructureMapping[] sm = getSsm().getMapping(file); - if (sm == null || sm.length == 0) - { - waiting = true; - } - } catch (Exception x) - { - waiting = true; - } catch (Error q) - { - waiting = true; - } - } - // we wait around for a reasonable time before we give up - } while (waiting - && System.currentTimeMillis() < (10000 + 1000 * files.length + starttime)); - if (waiting) - { - System.err - .println("RUNTIME PROBLEM: Chimera seems to be taking a long time to process all the structures."); - return; + return null; } + refreshPdbEntries(); - StringBuffer selectioncom = new StringBuffer(); + StringBuilder selectioncom = new StringBuilder(256); + boolean chimeraX = chimeraManager.isChimeraX(); for (int a = 0; a < _alignment.length; a++) { int refStructure = _refStructure[a]; AlignmentI alignment = _alignment[a]; - ColumnSelection hiddenCols = _hiddenCols[a]; - if (a > 0 - && selectioncom.length() > 0 - && !selectioncom.substring(selectioncom.length() - 1).equals( - " ")) - { - selectioncom.append(" "); - } - // process this alignment + HiddenColumns hiddenCols = _hiddenCols[a]; + if (refStructure >= files.length) { - System.err.println("Invalid reference structure value " + System.err.println("Ignoring invalid reference structure value " + refStructure); refStructure = -1; } - if (refStructure < -1) + + /* + * 'matched' bit i will be set for visible alignment columns i where + * all sequences have a residue with a mapping to the PDB structure + */ + BitSet matched = new BitSet(); + for (int m = 0; m < alignment.getWidth(); m++) + { + if (hiddenCols == null || hiddenCols.isVisible(m)) + { + matched.set(m); + } + } + + SuperposeData[] structures = new SuperposeData[files.length]; + for (int f = 0; f < files.length; f++) { - refStructure = -1; + structures[f] = new SuperposeData(alignment.getWidth(), f); } - boolean matched[] = new boolean[alignment.getWidth()]; - for (int m = 0; m < matched.length; m++) + /* + * Calculate the superposable alignment columns ('matched'), and the + * corresponding structure residue positions (structures.pdbResNo) + */ + int candidateRefStructure = findSuperposableResidues(alignment, + matched, structures); + if (refStructure < 0) { + /* + * If no reference structure was specified, pick the first one that has + * a mapping in the alignment + */ + refStructure = candidateRefStructure; + } - matched[m] = (hiddenCols != null) ? hiddenCols.isVisible(m) : true; + int nmatched = matched.cardinality(); + if (nmatched < 4) + { + return MessageManager.formatMessage("label.insufficient_residues", + nmatched); } - int commonrpositions[][] = new int[files.length][alignment.getWidth()]; - String isel[] = new String[files.length]; - String[] targetC = new String[files.length]; - String[] chainNames = new String[files.length]; - String[] atomSpec = new String[files.length]; + /* + * Generate select statements to select regions to superimpose structures + */ + String[] selcom = new String[files.length]; for (int pdbfnum = 0; pdbfnum < files.length; 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) + final int modelNo = pdbfnum + (chimeraX ? 1 : 0); + // todo correct resolution to model number + String chainCd = "." + structures[pdbfnum].chain; + int lpos = -1; + boolean run = false; + StringBuilder molsel = new StringBuilder(); + if (chimeraX) { - throw new Error(MessageManager.getString("error.implementation_error_chimera_getting_data")); + molsel.append("/" + structures[pdbfnum].chain + ":"); } - int lastPos = -1; - final int seqCountForPdbFile = getSequence()[pdbfnum].length; - for (int s = 0; s < seqCountForPdbFile; s++) + + int nextColumnMatch = matched.nextSetBit(0); + while (nextColumnMatch != -1) { - for (int sp, m = 0; m < mapping.length; m++) + int pdbResNum = structures[pdbfnum].pdbResNo[nextColumnMatch]; + if (lpos != pdbResNum - 1) { - final SequenceI theSequence = getSequence()[pdbfnum][s]; - if (mapping[m].getSequence() == theSequence - && (sp = alignment.findIndex(theSequence)) > -1) + /* + * discontiguous - append last residue now + */ + if (lpos != -1) { - if (refStructure == -1) + molsel.append(String.valueOf(lpos)); + if (!chimeraX) { - refStructure = pdbfnum; + molsel.append(chainCd); } - SequenceI asp = alignment.getSequenceAt(sp); - for (int r = 0; r < matched.length; r++) - { - if (!matched[r]) - { - continue; - } - matched[r] = false; // assume this is not a good site - if (r >= asp.getLength()) - { - continue; - } - - if (Comparison.isGap(asp.getCharAt(r))) - { - // no mapping to gaps in sequence - continue; - } - int t = asp.findPosition(r); // sequence position - int apos = mapping[m].getAtomNum(t); - int pos = mapping[m].getPDBResNum(t); - - if (pos < 1 || pos == lastPos) - { - // can't align unmapped sequence - continue; - } - matched[r] = true; // this is a good ite - lastPos = pos; - // just record this residue position - commonrpositions[pdbfnum][r] = pos; - } - // create model selection suffix - isel[pdbfnum] = "#" + pdbfnum; - if (mapping[m].getChain() == null - || mapping[m].getChain().trim().length() == 0) - { - targetC[pdbfnum] = ""; - } - else - { - targetC[pdbfnum] = "." + mapping[m].getChain(); - } - chainNames[pdbfnum] = mapping[m].getPdbId() - + targetC[pdbfnum]; - atomSpec[pdbfnum] = asp.getRNA() != null ? PHOSPHORUS : ALPHACARBON; - // move on to next pdb file - s = seqCountForPdbFile; - break; + molsel.append(","); } + run = false; } - } - } - - // TODO: consider bailing if nmatched less than 4 because superposition - // not - // well defined. - // TODO: refactor superposable position search (above) from jmol selection - // construction (below) - - String[] selcom = new String[files.length]; - int nmatched = 0; - String sep = ""; - // generate select statements to select regions to superimpose structures - { - for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) - { - String chainCd = targetC[pdbfnum]; - int lpos = -1; - boolean run = false; - StringBuffer molsel = new StringBuffer(); - for (int r = 0; r < matched.length; r++) + else { - if (matched[r]) + /* + * extending a contiguous run + */ + if (!run) { - if (pdbfnum == 0) - { - nmatched++; - } - if (lpos != commonrpositions[pdbfnum][r] - 1) - { - // discontinuity - if (lpos != -1) - { - molsel.append((run ? "" : ":") + lpos); - molsel.append(chainCd); - molsel.append(","); - } - } - else - { - // continuous run - and lpos >-1 - if (!run) - { - // at the beginning, so add dash - molsel.append(":" + lpos); - molsel.append("-"); - } - run = true; - } - lpos = commonrpositions[pdbfnum][r]; - // molsel.append(lpos); + /* + * start the range selection + */ + molsel.append(String.valueOf(lpos)); + molsel.append("-"); } + run = true; } - // add final selection phrase - if (lpos != -1) + lpos = pdbResNum; + nextColumnMatch = matched.nextSetBit(nextColumnMatch + 1); + } + + /* + * and terminate final selection + */ + if (lpos != -1) + { + molsel.append(String.valueOf(lpos)); + if (!chimeraX) { - molsel.append((run ? "" : ":") + lpos); molsel.append(chainCd); - // molsel.append(""); } - if (molsel.length() > 1) + } + if (molsel.length() > 1) + { + selcom[pdbfnum] = molsel.toString(); + selectioncom.append("#").append(String.valueOf(modelNo)); + if (!chimeraX) { - selcom[pdbfnum] = molsel.toString(); - selectioncom.append("#" + pdbfnum); - selectioncom.append(selcom[pdbfnum]); - selectioncom.append(" "); - if (pdbfnum < files.length - 1) - { - selectioncom.append("| "); - } + selectioncom.append(":"); } - else + selectioncom.append(selcom[pdbfnum]); + // selectioncom.append(" "); + if (pdbfnum < files.length - 1) { - selcom[pdbfnum] = null; + selectioncom.append("|"); } } + else + { + selcom[pdbfnum] = null; + } } + StringBuilder command = new StringBuilder(256); for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) { + final int modelNo = pdbfnum + (chimeraX ? 1 : 0); if (pdbfnum == refStructure || selcom[pdbfnum] == null || selcom[refStructure] == null) { @@ -614,36 +443,71 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel /* * Form Chimera match command, from the 'new' structure to the - * 'reference' structure e.g. (residues 1-91, chain B/A, alphacarbons): + * 'reference' structure e.g. (50 residues, chain B/A, alphacarbons): * - * match #1:1-91.B@CA #0:1-91.A@CA + * match #1:1-30.B,81-100.B@CA #0:21-40.A,61-90.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(chimeraX ? "align " : "match "); + command.append(getModelSpec(modelNo)); + if (!chimeraX) + { + command.append(":"); + } command.append(selcom[pdbfnum]); - command.append("@" + atomSpec[pdbfnum]); - command.append(" #" + refStructure /* +".1" */); + command.append("@").append( + structures[pdbfnum].isRna ? PHOSPHORUS : ALPHACARBON); + // JAL-1757 exclude alternate CA locations - ChimeraX syntax tbd + if (!chimeraX) + { + command.append(NO_ALTLOCS); + } + command.append(chimeraX ? " toAtoms " : " ") + .append(getModelSpec(refStructure + (chimeraX ? 1 : 0))); + if (!chimeraX) + { + command.append(":"); + } command.append(selcom[refStructure]); - command.append("@" + atomSpec[refStructure]); + command.append("@").append( + structures[refStructure].isRna ? PHOSPHORUS : ALPHACARBON); + if (!chimeraX) + { + command.append(NO_ALTLOCS); + } } if (selectioncom.length() > 0) { if (debug) { System.out.println("Select regions:\n" + selectioncom.toString()); - System.out.println("Superimpose command(s):\n" - + command.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; "); + // allComs.append("~display all; "); + // if (chimeraX) + // { + // allComs.append("show ").append(selectioncom.toString()) + // .append(" pbonds"); + // } + // else + // { + // allComs.append("chain @CA|P; ribbon "); + // allComs.append(selectioncom.toString()); + // } + if (allComs.length() > 0) { + allComs.append(";"); + } + allComs.append(command.toString()); } } + + String error = null; if (selectioncom.length() > 0) - {// finally, mark all regions that were superposed. + { + // TODO: visually distinguish regions that were superposed if (selectioncom.substring(selectioncom.length() - 1).equals("|")) { selectioncom.setLength(selectioncom.length() - 1); @@ -652,111 +516,139 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel { System.out.println("Select regions:\n" + selectioncom.toString()); } - allComs.append("; ~display all; chain @CA|P; ribbon " - + selectioncom.toString() + "; focus"); - // evalStateCommand("select *; backbone; select "+selcom.toString()+"; cartoons; center "+selcom.toString()); - evalStateCommand(allComs.toString(), true /* false */); + allComs.append(";~display all; "); + if (chimeraX) + { + allComs.append("show @CA|P pbonds; show ") + .append(selectioncom.toString()).append(" ribbons; view"); + } + else + { + allComs.append("chain @CA|P; ribbon "); + allComs.append(selectioncom.toString()).append("; focus"); + } + // allComs.append("; ~display all; chain @CA|P; ribbon ") + // .append(selectioncom.toString()).append("; focus"); + List chimeraReplies = executeCommand(allComs.toString(), + true); + for (String reply : chimeraReplies) + { + if (reply.toLowerCase().contains("unequal numbers of atoms")) + { + error = reply; + } + } + } + return error; + } + + /** + * Helper method to construct model spec in Chimera format: + *
    + *
  • #0 (#1 etc) for a PDB file with no sub-models
    • + *
  • #0.1 (#1.1 etc) for a PDB file with sub-models
    • + *
      + * Note for now we only ever choose the first of multiple models. This + * corresponds to the hard-coded Jmol equivalent (compare {1.1}). Refactor in + * future if there is a need to select specific sub-models. + * + * @param pdbfnum + * @return + */ + protected String getModelSpec(int pdbfnum) + { + if (pdbfnum < 0 || pdbfnum >= getPdbCount()) + { + return "#" + pdbfnum; // temp hack for ChimeraX } - + + /* + * For now, the test for having sub-models is whether multiple Chimera + * models are mapped for the PDB file; the models are returned as a response + * to the Chimera command 'list models type molecule', see + * ChimeraManager.getModelList(). + */ + List maps = chimeraMaps.get(getStructureFiles()[pdbfnum]); + boolean hasSubModels = maps != null && maps.size() > 1; + return "#" + String.valueOf(pdbfnum) + (hasSubModels ? ".1" : ""); } - private void checkLaunched() + /** + * Launch Chimera, unless an instance linked to this object is already + * running. Returns true if Chimera is successfully launched, or already + * running, else false. + * + * @return + */ + public boolean launchChimera() { - if (!viewer.isChimeraLaunched()) + if (chimeraManager.isChimeraLaunched()) { - viewer.launchChimera(StructureManager.getChimeraPaths()); + return true; + } + + boolean launched = chimeraManager.launchChimera(getChimeraPaths()); + if (launched) + { + startChimeraProcessMonitor(); } - if (!viewer.isChimeraLaunched()) + else { log("Failed to launch Chimera!"); } + return launched; } /** - * Answers true if the Chimera process is still running, false if ended or not - * started. + * Returns a list of candidate paths to the Chimera program executable * * @return */ - public boolean isChimeraRunning() + protected List getChimeraPaths() { - return viewer.isChimeraLaunched(); + return StructureManager.getChimeraPaths(false); } /** - * Send a command to Chimera, launching it first if necessary, and optionally - * log any responses. + * Answers true if the Chimera process is still running, false if ended or not + * started. * - * @param command - * @param logResponse + * @return */ - public void evalStateCommand(final String command, boolean logResponse) + public boolean isChimeraRunning() { - viewerCommandHistory(false); - checkLaunched(); - if (lastCommand == null || !lastCommand.equals(command)) - { - // 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; + return chimeraManager.isChimeraLaunched(); } /** - * colour any structures associated with sequences in the given alignment - * using the getFeatureRenderer() and getSequenceRenderer() renderers but only - * if colourBySequence is enabled. + * Send a command to Chimera, and optionally log and return any responses. + * + * @param command + * @param getResponse */ - public void colourBySequence(boolean showFeatures, - jalview.api.AlignmentViewPanel alignmentv) + @Override + public List executeCommand(final String command, + boolean getResponse) { - if (!colourBySequence || !loadingFinished) + if (chimeraManager == null || command == null) { - return; - } - if (getSsm() == null) - { - return; - } - String[] files = getPdbFile(); - - SequenceRenderer sr = getSequenceRenderer(alignmentv); - - FeatureRenderer fr = null; - if (showFeatures) - { - fr = getFeatureRenderer(alignmentv); + // ? thread running after viewer shut down + return null; } - AlignmentI alignment = alignmentv.getAlignment(); - - for (jalview.structure.StructureMappingcommandSet cpdbbyseq : getColourBySequenceCommands( - files, sr, fr, alignment)) + List reply = null; + // trim command or it may never find a match in the replyLog!! + List lastReply = chimeraManager + .sendChimeraCommand(command.trim(), getResponse); + if (getResponse) { - for (String command : cpdbbyseq.commands) + reply = lastReply; + if (debug) { - executeWhenReady(command); + log("Response from command ('" + command + "') was:\n" + lastReply); } } - } - /** - * @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); + return reply; } /** @@ -765,232 +657,184 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel protected void executeWhenReady(String command) { waitForChimera(); - evalStateCommand(command, false); + executeCommand(command, false); waitForChimera(); } private void waitForChimera() { - while (viewer != null && viewer.isBusy()) + while (chimeraManager != null && chimeraManager.isBusy()) { - try { + try + { Thread.sleep(15); } catch (InterruptedException q) - {} + { + } } } - - - // End StructureListener - // ////////////////////////// - - public Color getColour(int atomIndex, int pdbResNum, String chain, - String pdbfile) + @Override + public synchronized String[] getStructureFiles() { - if (getModelNum(pdbfile) < 0) + if (chimeraManager == null) { - return null; + return new String[0]; } - 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); + return chimeraMaps.keySet() + .toArray(modelFileNames = new String[chimeraMaps.size()]); + } /** - * instruct the Jalview binding to update the pdbentries vector if necessary - * prior to matching the jmol view's contents to the list of structure files - * Jalview knows about. + * 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. */ - public abstract void refreshPdbEntries(); - - private int getModelNum(String modelFileName) + @Override + public void highlightAtoms(List atoms) { - String[] mfn = getPdbFile(); - if (mfn == null) + if (atoms == null || atoms.size() == 0) { - return -1; + return; } - for (int i = 0; i < mfn.length; i++) + + boolean forChimeraX = chimeraManager.isChimeraX(); + StringBuilder cmd = new StringBuilder(128); + boolean first = true; + boolean found = false; + + for (AtomSpec atom : atoms) { - if (mfn[i].equalsIgnoreCase(modelFileName)) + int pdbResNum = atom.getPdbResNum(); + String chain = atom.getChain(); + String pdbfile = atom.getPdbFile(); + List cms = chimeraMaps.get(pdbfile); + if (cms != null && !cms.isEmpty()) { - return i; + if (first) + { + cmd.append(forChimeraX ? "label #" : "rlabel #"); + } + else + { + cmd.append(","); + } + first = false; + if (forChimeraX) + { + cmd.append(cms.get(0).getModelNumber()) + .append("/").append(chain).append(":").append(pdbResNum); + } + else + { + cmd.append(cms.get(0).getModelNumber()) + .append(":").append(pdbResNum); + if (!chain.equals(" ") && !forChimeraX) + { + cmd.append(".").append(chain); + } + } + found = true; } } - return -1; - } + String command = cmd.toString(); - /** - * 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 - - * use getPdbFile to get number of unique models. - */ - private int _modelFileNameMap[]; + /* + * avoid repeated commands for the same residue + */ + if (command.equals(lastHighlightCommand)) + { + return; + } - // //////////////////////////////// - // /StructureListener - public synchronized String[] getPdbFile() - { - if (viewer == null) + /* + * unshow the label for the previous residue + */ + if (lastHighlightCommand != null) { - return new String[0]; + chimeraManager.sendChimeraCommand("~" + lastHighlightCommand, false); } - // 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()]); + if (found) + { + chimeraManager.sendChimeraCommand(command, false); + } + this.lastHighlightCommand = command; } /** - * map from string to applet + * Query Chimera for its current selection, and highlight it on the alignment */ - public Map getRegistryInfo() + public void highlightChimeraSelection() { - // TODO Auto-generated method stub - return null; + /* + * Ask Chimera for its current selection + */ + List selection = chimeraManager.getSelectedResidueSpecs(); + + /* + * 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 = convertStructureResiduesToAlignment( + selection); + + /* + * Broadcast the selection (which may be empty, if the user just cleared all + * selections) + */ + getSsm().mouseOverStructure(atomSpecs); } /** - * returns the current sequenceRenderer that should be used to colour the - * structures - * - * @param alignment + * Converts a list of Chimera atomspecs to a list of AtomSpec representing the + * corresponding residues (if any) in Jalview * + * @param structureSelection * @return */ - public abstract SequenceRenderer getSequenceRenderer( - AlignmentViewPanel alignment); - - /** - * 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) + protected List convertStructureResiduesToAlignment( + List structureSelection) { - List cms = chimeraMaps.get(pdbfile); - if (cms != null) + boolean chimeraX = chimeraManager.isChimeraX(); + List atomSpecs = new ArrayList<>(); + for (String atomSpec : structureSelection) { - StringBuilder sb = new StringBuilder(); - sb.append(" #" + cms.get(0).getModelNumber()); - sb.append(":" + pdbResNum); - if (!chain.equals(" ")) - { - sb.append("." + chain); - } - String atomSpec = sb.toString(); - - StringBuilder command = new StringBuilder(32); - if (lastMousedOverAtomSpec != null) + try { - command.append("~show " + lastMousedOverAtomSpec + ";"); - } - viewerCommandHistory(false); - command.append("show ").append(atomSpec); - String cmd = command.toString(); - if (cmd.length() > 0) + AtomSpec spec = AtomSpec.fromChimeraAtomspec(atomSpec, chimeraX); + String pdbfilename = getPdbFileForModel(spec.getModelNumber()); + spec.setPdbFile(pdbfilename); + atomSpecs.add(spec); + } catch (IllegalArgumentException e) { - viewer.stopListening(chimeraListener.getUri()); - viewer.sendChimeraCommand(cmd, false); - viewer.startListening(chimeraListener.getUri()); + System.err.println("Failed to parse atomspec: " + atomSpec); } - viewerCommandHistory(true); - this.lastMousedOverAtomSpec = atomSpec; } + return atomSpecs; } /** - * Query Chimera for its current selection, and highlight it on the alignment + * @param modelId + * @return */ - public void highlightChimeraSelection() + protected String getPdbFileForModel(int modelId) { /* - * Ask Chimera for its current selection + * Work out the pdbfilename from the model number */ - List selection = viewer.getSelectedResidueSpecs(); - - /* - * 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) + String pdbfilename = modelFileNames[0]; + findfileloop: for (String pdbfile : this.chimeraMaps.keySet()) { - int colonPos = atomSpec.indexOf(":"); - if (colonPos == -1) - { - continue; // malformed - } - - 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 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()) + for (ChimeraModel cm : chimeraMaps.get(pdbfile)) { - for (ChimeraModel cm : chimeraMaps.get(pdbfile)) + if (cm.getModelNumber() == modelId) { - if (cm.getModelNumber() == modelId) - { - pdbfilename = pdbfile; - break findfileloop; - } + pdbfilename = pdbfile; + break findfileloop; } } - atomSpecs.add(new AtomSpec(pdbfilename, chainId, pdbResNum, 0)); } - - /* - * Broadcast the selection (which may be empty, if the user just cleared all - * selections) - */ - getSsm().mouseOverStructure(atomSpecs); + return pdbfilename; } private void log(String message) @@ -998,168 +842,336 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel System.err.println("## Chimera log: " + message); } - private void viewerCommandHistory(boolean enable) - { - // log("(Not yet implemented) History " - // + ((debug || enable) ? "on" : "off")); - } - - public long getLoadNotifiesHandled() - { - return loadNotifiesHandled; - } - - public void setJalviewColourScheme(ColourSchemeI cs) + /** + * Ask Chimera to save its session to the given file. Returns true if + * successful, else false. + * + * @param filepath + * @return + */ + public boolean saveSession(String filepath) { - colourBySequence = false; - - if (cs == null) - { - return; - } - - 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 - StringBuilder command = new StringBuilder(128); - command.append("color white;"); - for (String res : ResidueProperties.aa3Hash.keySet()) + if (isChimeraRunning()) { - index = ResidueProperties.aa3Hash.get(res).intValue(); - if (index > 20) + /* + * Chimera: https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/save.html + * ChimeraX: https://www.cgl.ucsf.edu/chimerax/docs/user/commands/save.html + */ + String command = getCommandGenerator().saveSession(filepath); + List reply = chimeraManager.sendChimeraCommand(command, true); + if (reply.contains("Session written")) { - continue; + return true; + } + else + { + Cache.log + .error("Error saving Chimera session: " + reply.toString()); } - - col = cs.findColour(ResidueProperties.aa[index].charAt(0)); - command.append("color " + col.getRed() / normalise + "," - + col.getGreen() / normalise + "," + col.getBlue() - / normalise + " ::" + res + ";"); } - - evalStateCommand(command.toString(),false); - viewerCommandHistory(true); + return false; } /** - * 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 occurred. + * Ask Chimera to open a session file. Returns true if successful, else false. + * The filename must have a .py (Chimera) or .cxs (ChimeraX) extension for + * this command to work. + * + * @param filepath + * @return */ - public abstract void refreshGUI(); - - public void setLoadingFromArchive(boolean loadingFromArchive) + public boolean openSession(String filepath) { - this.loadingFromArchive = loadingFromArchive; + /* + * Chimera: https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/open.html + * ChimeraX: https://www.cgl.ucsf.edu/chimerax/docs/user/commands/open.html + */ + executeCommand("open " + filepath, true); + // todo: test for failure - how? + return true; } /** + * Send a 'show' command for all atoms in the currently selected columns * - * @return true if Chimeral is still restoring state or loading is still going - * on (see setFinsihedLoadingFromArchive) + * TODO: pull up to abstract structure viewer interface + * + * @param vp */ - public boolean isLoadingFromArchive() + public void highlightSelection(AlignmentViewPanel vp) { - return loadingFromArchive && !loadingFinished; + List cols = vp.getAlignViewport().getColumnSelection() + .getSelected(); + AlignmentI alignment = vp.getAlignment(); + StructureSelectionManager sm = getSsm(); + for (SequenceI seq : alignment.getSequences()) + { + /* + * convert selected columns into sequence positions + */ + int[] positions = new int[cols.size()]; + int i = 0; + for (Integer col : cols) + { + positions[i++] = seq.findPosition(col); + } + sm.highlightStructure(this, seq, positions); + } } /** - * modify flag which controls if sequence colouring events are honoured by the - * binding. Should be true for normal operation + * Constructs and send commands to Chimera to set attributes on residues for + * features visible in Jalview * - * @param finishedLoading + * @param avp + * @return */ - public void setFinishedLoadingFromArchive(boolean finishedLoading) + public int sendFeaturesToViewer(AlignmentViewPanel avp) { - loadingFinished = finishedLoading; + // TODO refactor as required to pull up to an interface + String[] files = getStructureFiles(); + if (files == null) + { + return 0; + } + + String[] commands = getCommandGenerator() + .setAttributesForFeatures(getSsm(), files, getSequence(), avp); + if (commands.length > 10) + { + sendCommandsByFile(commands); + } + else + { + for (String command : commands) + { + sendAsynchronousCommand(command, null); + } + } + return commands.length; } /** - * Send the Chimera 'background solid " command. + * Write commands to a temporary file, and send a command to Chimera to open the + * file as a commands script. For use when sending a large number of separate + * commands would overload the REST interface mechanism. * - * @see https - * ://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/background - * .html - * @param col + * @param commands */ - public void setBackgroundColour(Color col) + protected void sendCommandsByFile(String[] commands) { - viewerCommandHistory(false); - double normalise = 255D; - final String command = "background solid " + col.getRed() / normalise + "," - + col.getGreen() / normalise + "," + col.getBlue() - / normalise + ";"; - viewer.sendChimeraCommand(command, false); - viewerCommandHistory(true); + try + { + File tmp = File.createTempFile("chim", getCommandFileExtension()); + tmp.deleteOnExit(); + PrintWriter out = new PrintWriter(new FileOutputStream(tmp)); + for (String command : commands) + { + out.println(command); + } + out.flush(); + out.close(); + String path = tmp.getAbsolutePath(); + String command = getCommandGenerator().openCommandFile(path); + sendAsynchronousCommand(command, null); + } catch (IOException e) + { + System.err.println("Sending commands to Chimera via file failed with " + + e.getMessage()); + } } /** + * Returns the file extension required for a file of commands to be read by + * the structure viewer + * @return + */ + protected String getCommandFileExtension() + { + return ".com"; + } + + /** + * Get Chimera residues which have the named attribute, find the mapped + * positions in the Jalview sequence(s), and set as sequence features * - * @param pdbfile - * @return text report of alignment between pdbfile and any associated - * alignment sequences + * @param attName + * @param alignmentPanel */ - public String printMapping(String pdbfile) + public void copyStructureAttributesToFeatures(String attName, + AlignmentViewPanel alignmentPanel) { - return getSsm().printMapping(pdbfile); + // todo pull up to AAStructureBindingModel (and interface?) + + /* + * ask Chimera to list residues with the attribute, reporting its value + */ + // this alternative command + // list residues spec ':*/attName' attr attName + // doesn't report 'None' values (which is good), but + // fails for 'average.bfactor' (which is bad): + + String cmd = "list residues attr '" + attName + "'"; + List residues = executeCommand(cmd, true); + + boolean featureAdded = createFeaturesForAttributes(attName, residues); + if (featureAdded) + { + alignmentPanel.getFeatureRenderer().featuresAdded(); + } } /** - * Ask Chimera to save its session to the given file. Returns true if - * successful, else false. + * Create features in Jalview for the given attribute name and structure + * residues. * - * @param filepath + * 
      +   * The residue list should be 0, 1 or more reply lines of the format: 
+   *     residue id #0:5.A isHelix -155.000836316 index 5 
+   * or 
+   *     residue id #0:6.A isHelix None
+   *
      + * + * @param attName + * @param residues * @return */ - public boolean saveSession(String filepath) + protected boolean createFeaturesForAttributes(String attName, + List residues) { - if (isChimeraRunning()) + boolean featureAdded = false; + String featureGroup = getViewerFeatureGroup(); + boolean chimeraX = chimeraManager.isChimeraX(); + + for (String residue : residues) { - List reply = viewer.sendChimeraCommand("save " + filepath, - true); - if (reply.contains("Session written")) + AtomSpec spec = null; + String[] tokens = residue.split(" "); + if (tokens.length < 5) { - return true; + continue; } - else + String atomSpec = tokens[2]; + String attValue = tokens[4]; + + /* + * ignore 'None' (e.g. for phi) or 'False' (e.g. for isHelix) + */ + if ("None".equalsIgnoreCase(attValue) + || "False".equalsIgnoreCase(attValue)) { - Cache.log - .error("Error saving Chimera session: " + reply.toString()); + continue; + } + + try + { + spec = AtomSpec.fromChimeraAtomspec(atomSpec, chimeraX); + } catch (IllegalArgumentException e) + { + System.err.println("Problem parsing atomspec " + atomSpec); + continue; + } + + String chainId = spec.getChain(); + String description = attValue; + float score = Float.NaN; + try + { + score = Float.valueOf(attValue); + description = chainId; + } catch (NumberFormatException e) + { + // was not a float value + } + + String pdbFile = getPdbFileForModel(spec.getModelNumber()); + spec.setPdbFile(pdbFile); + + List atoms = Collections.singletonList(spec); + + /* + * locate the mapped position in the alignment (if any) + */ + SearchResultsI sr = getSsm() + .findAlignmentPositionsForStructurePositions(atoms); + + /* + * expect one matched alignment position, or none + * (if the structure position is not mapped) + */ + for (SearchResultMatchI m : sr.getResults()) + { + SequenceI seq = m.getSequence(); + int start = m.getStart(); + int end = m.getEnd(); + SequenceFeature sf = new SequenceFeature(attName, description, + start, end, score, featureGroup); + // todo: should SequenceFeature have an explicit property for chain? + // note: repeating the action shouldn't duplicate features + featureAdded |= seq.addSequenceFeature(sf); } } - return false; + return featureAdded; } /** - * 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. + * Answers the feature group name to apply to features created in Jalview from + * Chimera attributes * - * @param filepath * @return */ - public boolean openSession(String filepath) + protected String getViewerFeatureGroup() { - evalStateCommand("open " + filepath, true); - // todo: test for failure - how? - return true; + // todo pull up to interface + return CHIMERA_FEATURE_GROUP; } - public boolean isFinishedInit() + @Override + public int getModelNoForFile(String pdbFile) { - return finishedInit; + List foundModels = chimeraMaps.get(pdbFile); + if (foundModels != null && !foundModels.isEmpty()) + { + return foundModels.get(0).getModelNumber(); + } + return -1; } - public void setFinishedInit(boolean finishedInit) + /** + * Answers a (possibly empty) list of attribute names in Chimera[X], excluding + * any which were added from Jalview + * + * @return + */ + public List getChimeraAttributes() { - this.finishedInit = finishedInit; + List atts = chimeraManager.getAttrList(); + Iterator it = atts.iterator(); + while (it.hasNext()) + { + if (it.next().startsWith(ChimeraCommands.NAMESPACE_PREFIX)) + { + /* + * attribute added from Jalview - exclude it + */ + it.remove(); + } + } + return atts; } - public List getChainNames() + /** + * Returns the file extension to use for a saved viewer session file + * + * @return + */ + public String getSessionFileExtension() { - return chainNames; + return ".py"; } + public String getHelpURL() + { + return "https://www.cgl.ucsf.edu/chimera/docs/UsersGuide"; + } }