From 3bc2fbe640abb0d8941aead117c9624dd16773a3 Mon Sep 17 00:00:00 2001 From: gmungoc Date: Fri, 5 Jun 2015 15:15:01 +0100 Subject: [PATCH] JAL-1622 fix bug computing superposition + associated refactorings --- src/jalview/ext/jmol/JalviewJmolBinding.java | 243 +++---- .../ext/rbvi/chimera/JalviewChimeraBinding.java | 665 ++++++++++---------- src/jalview/gui/ChimeraViewFrame.java | 309 +++++---- src/jalview/gui/StructureChooser.java | 34 +- src/jalview/gui/StructureViewer.java | 96 ++- .../structures/models/AAStructureBindingModel.java | 191 +++++- .../ext/rbvi/chimera/JalviewChimeraView.java | 23 +- .../models/AAStructureBindingModelTest.java | 183 ++++++ 8 files changed, 1085 insertions(+), 659 deletions(-) create mode 100644 test/jalview/structures/models/AAStructureBindingModelTest.java diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java index deadbfc..cdd137b 100644 --- a/src/jalview/ext/jmol/JalviewJmolBinding.java +++ b/src/jalview/ext/jmol/JalviewJmolBinding.java @@ -50,11 +50,10 @@ import jalview.datamodel.SequenceI; import jalview.io.AppletFormatAdapter; import jalview.schemes.ColourSchemeI; import jalview.schemes.ResidueProperties; -import jalview.structure.StructureMapping; +import jalview.structure.AtomSpec; import jalview.structure.StructureMappingcommandSet; import jalview.structure.StructureSelectionManager; import jalview.structures.models.AAStructureBindingModel; -import jalview.util.MessageManager; public abstract class JalviewJmolBinding extends AAStructureBindingModel implements JmolStatusListener, JmolSelectionListener, @@ -243,47 +242,31 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel { hiddenCols }); } + /** + * Construct and send a command to align structures against a reference + * structure, based on one or more sequence alignments + * + * @param _alignment + * an array of alignments to process + * @param _refStructure + * an array of corresponding reference structures (index into pdb + * file array); if a negative value is passed, the first PDB file + * mapped to an alignment sequence is used as the reference for + * superposition + * @param _hiddenCols + * an array of corresponding hidden columns for each alignment + */ public void superposeStructures(AlignmentI[] _alignment, int[] _refStructure, ColumnSelection[] _hiddenCols) { - assert (_alignment.length == _refStructure.length && _alignment.length != _hiddenCols.length); - String[] files = getPdbFile(); - // check to see if we are still waiting for Jmol files - long starttime = System.currentTimeMillis(); - boolean waiting = true; - do - { - 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) + + if (!waitForFileLoad(files)) { - System.err - .println("RUNTIME PROBLEM: Jmol seems to be taking a long time to process all the structures."); return; } - StringBuffer selectioncom = new StringBuffer(); + + StringBuilder selectioncom = new StringBuilder(256); // In principle - nSeconds specifies the speed of animation for each // superposition - but is seems to behave weirdly, so we don't specify it. String nSeconds = " "; @@ -319,134 +302,78 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel + refStructure); refStructure = -1; } - if (refStructure < -1) - { - refStructure = -1; - } - StringBuffer command = new StringBuffer(); + /* + * 'matched' array will hold 'true' for visible alignment columns where + * all sequences have a residue with a mapping to the PDB structure + */ boolean matched[] = new boolean[alignment.getWidth()]; for (int m = 0; m < matched.length; m++) { - matched[m] = (hiddenCols != null) ? hiddenCols.isVisible(m) : true; } - int commonrpositions[][] = new int[files.length][alignment.getWidth()]; - String isel[] = new String[files.length]; - // reference structure - all others are superposed in it - String[] targetC = new String[files.length]; - String[] chainNames = new String[files.length]; - for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) + SuperposeData[] structures = new SuperposeData[files.length]; + for (int f = 0; f < files.length; f++) { - StructureMapping[] mapping = getSsm().getMapping(files[pdbfnum]); - // RACE CONDITION - getMapping only returns Jmol loaded filenames once - // Jmol callback has completed. - if (mapping == null || mapping.length < 1) - { - throw new Error(MessageManager.getString("error.implementation_error_jmol_getting_data")); - } - int lastPos = -1; - final int sequenceCountForPdbFile = getSequence()[pdbfnum].length; - for (int s = 0; s < sequenceCountForPdbFile; s++) - { - for (int sp, m = 0; m < mapping.length; m++) - { - if (mapping[m].getSequence() == getSequence()[pdbfnum][s] - && (sp = alignment.findIndex(getSequence()[pdbfnum][s])) > -1) - { - if (refStructure == -1) - { - refStructure = pdbfnum; - } - 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 (jalview.util.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 + 1) + ".1"; - 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]; - // move on to next pdb file - s = getSequence()[pdbfnum].length; - break; - } - } - } + structures[f] = new SuperposeData(alignment.getWidth()); } - // TODO: consider bailing if nmatched less than 4 because superposition - // not - // well defined. - // TODO: refactor superposable position search (above) from jmol selection - // construction (below) + /* + * 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; + } String[] selcom = new String[files.length]; int nmatched = 0; - // generate select statements to select regions to superimpose structures + for (boolean b : matched) + { + if (b) + { + nmatched++; + } + } + if (nmatched < 4) + { + // TODO: bail out here because superposition illdefined? + } + + /* + * generate select statements to select regions to superimpose structures + */ { for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) { - String chainCd = targetC[pdbfnum]; + String chainCd = ":" + structures[pdbfnum].chain; int lpos = -1; boolean run = false; - StringBuffer molsel = new StringBuffer(); + StringBuilder molsel = new StringBuilder(); molsel.append("{"); for (int r = 0; r < matched.length; r++) { if (matched[r]) { - if (pdbfnum == 0) - { - nmatched++; - } - if (lpos != commonrpositions[pdbfnum][r] - 1) + int pdbResNo = structures[pdbfnum].pdbResNo[r]; + if (lpos != pdbResNo - 1) { // discontinuity if (lpos != -1) { molsel.append(lpos); molsel.append(chainCd); - // molsel.append("} {"); molsel.append("|"); } + run = false; } else { @@ -459,11 +386,12 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel } run = true; } - lpos = commonrpositions[pdbfnum][r]; - // molsel.append(lpos); + lpos = pdbResNo; } } - // add final selection phrase + /* + * add final selection phrase + */ if (lpos != -1) { molsel.append(lpos); @@ -490,6 +418,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel } } } + StringBuilder command = new StringBuilder(256); for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) { if (pdbfnum == refStructure || selcom[pdbfnum] == null @@ -499,23 +428,23 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel } command.append("echo "); command.append("\"Superposing ("); - command.append(chainNames[pdbfnum]); + command.append(structures[pdbfnum].pdbId); command.append(") against reference ("); - command.append(chainNames[refStructure]); + command.append(structures[refStructure].pdbId); command.append(")\";\ncompare " + nSeconds); command.append("{"); - command.append(1 + pdbfnum); + command.append(Integer.toString(1 + pdbfnum)); command.append(".1} {"); - command.append(1 + refStructure); + command.append(Integer.toString(1 + refStructure)); // conformation=1 excludes alternate locations for CA (JAL-1757) command.append(".1} SUBSET {(*.CA | *.P) and conformation=1} ATOMS "); - // form the matched pair strings - String sep = ""; - for (int s = 0; s < 2; s++) - { - command.append(selcom[(s == 0 ? pdbfnum : refStructure)]); - } + // for (int s = 0; s < 2; s++) + // { + // command.append(selcom[(s == 0 ? pdbfnum : refStructure)]); + // } + command.append(selcom[pdbfnum]); + command.append(selcom[refStructure]); command.append(" ROTATE TRANSLATE;\n"); } if (selectioncom.length() > 0) @@ -524,10 +453,11 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel evalStateCommand("select *; cartoons off; backbone; select (" + selectioncom.toString() + "); cartoons; "); // selcom.append("; ribbons; "); + String cmdString = command.toString(); System.out - .println("Superimpose command(s):\n" + command.toString()); +.println("Superimpose command(s):\n" + cmdString); - evalStateCommand(command.toString()); + evalStateCommand(cmdString); } } if (selectioncom.length() > 0) @@ -703,6 +633,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel // //////////////////////////////// // /StructureListener + @Override public synchronized String[] getPdbFile() { if (viewer == null) @@ -786,6 +717,22 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel jmolpopup.show(x, y); } + /** + * Highlight zero, one or more atoms on the structure + */ + @Override + public void highlightAtoms(List atoms) + { + if (atoms != null) + { + for (AtomSpec atom : atoms) + { + highlightAtom(atom.getAtomIndex(), atom.getPdbResNum(), + atom.getChain(), atom.getPdbFile()); + } + } + } + // jmol/ssm only public void highlightAtom(int atomIndex, int pdbResNum, String chain, String pdbfile) diff --git a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java index 3c455c2..cee271a 100644 --- a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java +++ b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java @@ -44,11 +44,9 @@ import jalview.httpserver.AbstractRequestHandler; import jalview.schemes.ColourSchemeI; import jalview.schemes.ResidueProperties; import jalview.structure.AtomSpec; -import jalview.structure.StructureMapping; import jalview.structure.StructureMappingcommandSet; import jalview.structure.StructureSelectionManager; import jalview.structures.models.AAStructureBindingModel; -import jalview.util.Comparison; import jalview.util.MessageManager; public abstract class JalviewChimeraBinding extends AAStructureBindingModel @@ -56,14 +54,15 @@ 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"; + private static final String COLOURING_CHIMERA = MessageManager + .getString("status.colouring_chimera"); + 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 */ @@ -92,12 +91,6 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel */ private boolean finishedInit = false; - private List atomsPicked = new ArrayList(); - - private List chainNames; - - private Map chainFile; - public String fileLoadingError; /* @@ -217,7 +210,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel { super(ssm, pdbentry, sequenceIs, chains, protocol); viewer = new ChimeraManager( - csm = new ext.edu.ucsf.rbvi.strucviz2.StructureManager(true)); + new ext.edu.ucsf.rbvi.strucviz2.StructureManager(true)); } /** @@ -238,20 +231,6 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel } /** - * Constructor - * - * @param ssm - * @param theViewer - */ - public JalviewChimeraBinding(StructureSelectionManager ssm, - ChimeraManager theViewer) - { - super(ssm, null); - viewer = theViewer; - csm = viewer.getStructureManager(); - } - - /** * Construct a title string for the viewer window based on the data Jalview * knows about * @@ -264,34 +243,37 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel } /** - * prepare the view for a given set of models/chains. chainList contains - * strings of the form 'pdbfilename:Chaincode' + * Tells Chimera to display only the specified chains * * @param toshow - * list of chains to make visible */ - public void centerViewer(List toshow) + public void showChains(List toshow) { + /* + * Construct a chimera command like + * + * ~display #*;~ribbon #*;ribbon :.A,:.B + */ StringBuilder cmd = new StringBuilder(64); - int mlength, p; - for (String lbl : toshow) + boolean first = true; + for (String chain : toshow) { - mlength = 0; - do + if (!first) { - 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) - { - cmd.setLength(cmd.length() - 4); + cmd.append(","); + } + cmd.append(":.").append(chain); + first = false; } - String cmdstring = cmd.toString(); - evalStateCommand("~display #*; ~ribbon #*; ribbon " + cmdstring, false); + + /* + * could append ";focus" to this command to resize the display to fill the + * window, but it looks more helpful not to (easier to relate chains to the + * whole) + */ + final String command = "~display #*; ~ribbon #*; ribbon " + + cmd.toString(); + sendChimeraCommand(command, false); } /** @@ -319,287 +301,182 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel 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. - */ - public void superposeStructures(AlignmentI alignment) - { - superposeStructures(alignment, -1, null); + sendAsynchronousCommand("rainbow chain", COLOURING_CHIMERA); } /** - * 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) + * Constructs and sends a Chimera command to colour by charge + *
    + *
  • Aspartic acid and Glutamic acid (negative charge) red
    • + *
  • Lysine and Arginine (positive charge) blue
    • + *
  • Cysteine - yellow
    • + *
  • all others - white
    • + *
*/ - public void superposeStructures(AlignmentI alignment, int refStructure) + public void colourByCharge() { - superposeStructures(alignment, refStructure, null); + colourBySequence = false; + String command = "color white;color red ::ASP;color red ::GLU;color blue ::LYS;color blue ::ARG;color yellow ::CYS"; + sendAsynchronousCommand(command, COLOURING_CHIMERA); } /** - * superpose the structures associated with sequences in the alignment - * according to their corresponding positions. ded) + * Construct and send a command to align structures against a reference + * structure, based on one or more sequence alignments * - * @param refStructure - * - select which pdb file to use as reference (default is -1 - the - * first structure in the alignment) - * @param hiddenCols - * TODO + * @param _alignment + * an array of alignments to process + * @param _refStructure + * an array of corresponding reference structures (index into pdb + * file array); if a negative value is passed, the first PDB file + * mapped to an alignment sequence is used as the reference for + * superposition + * @param _hiddenCols + * an array of corresponding hidden columns for each alignment */ - 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 + StringBuilder allComs = new StringBuilder(128); String[] files = getPdbFile(); - // check to see if we are still waiting for Chimera files - long starttime = System.currentTimeMillis(); - boolean waiting = true; - do - { - 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) + + if (!waitForFileLoad(files)) { - System.err - .println("RUNTIME PROBLEM: Chimera seems to be taking a long time to process all the structures."); return; } + refreshPdbEntries(); - StringBuffer selectioncom = new StringBuffer(); + StringBuilder selectioncom = new StringBuilder(256); 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 + 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) - { - refStructure = -1; - } + /* + * 'matched' array will hold 'true' for visible alignment columns where + * all sequences have a residue with a mapping to the PDB structure + */ boolean matched[] = new boolean[alignment.getWidth()]; for (int m = 0; m < matched.length; m++) { - matched[m] = (hiddenCols != null) ? hiddenCols.isVisible(m) : true; } - 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]; - for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) + SuperposeData[] structures = new SuperposeData[files.length]; + for (int f = 0; f < files.length; f++) { - StructureMapping[] mapping = getSsm().getMapping(files[pdbfnum]); - // RACE CONDITION - getMapping only returns Jmol loaded filenames once - // Jmol callback has completed. - if (mapping == null || mapping.length < 1) - { - throw new Error(MessageManager.getString("error.implementation_error_chimera_getting_data")); - } - int lastPos = -1; - final int seqCountForPdbFile = getSequence()[pdbfnum].length; - for (int s = 0; s < seqCountForPdbFile; s++) + structures[f] = new SuperposeData(alignment.getWidth()); + } + + /* + * 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; + } + + int nmatched = 0; + for (boolean b : matched) + { + if (b) { - for (int sp, m = 0; m < mapping.length; m++) - { - final SequenceI theSequence = getSequence()[pdbfnum][s]; - if (mapping[m].getSequence() == theSequence - && (sp = alignment.findIndex(theSequence)) > -1) - { - if (refStructure == -1) - { - refStructure = pdbfnum; - } - 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; - } - } + nmatched++; } } + if (nmatched < 4) + { + // TODO: bail out here because superposition illdefined? + } - // TODO: consider bailing if nmatched less than 4 because superposition - // not - // well defined. - // TODO: refactor superposable position search (above) from jmol selection - // construction (below) - + /* + * Generate select statements to select regions to superimpose structures + */ 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++) { - for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) + String chainCd = "." + structures[pdbfnum].chain; + int lpos = -1; + boolean run = false; + StringBuilder molsel = new StringBuilder(); + for (int r = 0; r < matched.length; r++) { - String chainCd = targetC[pdbfnum]; - int lpos = -1; - boolean run = false; - StringBuffer molsel = new StringBuffer(); - for (int r = 0; r < matched.length; r++) + if (matched[r]) { - if (matched[r]) + int pdbResNum = structures[pdbfnum].pdbResNo[r]; + if (lpos != pdbResNum - 1) { - if (pdbfnum == 0) + /* + * discontiguous - append last residue now + */ + if (lpos != -1) { - nmatched++; + molsel.append(String.valueOf(lpos)); + molsel.append(chainCd); + molsel.append(","); } - 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); + run = false; } - } - // add final selection phrase - if (lpos != -1) - { - molsel.append((run ? "" : ":") + lpos); - molsel.append(chainCd); - // molsel.append(""); - } - if (molsel.length() > 1) - { - selcom[pdbfnum] = molsel.toString(); - selectioncom.append("#" + pdbfnum); - selectioncom.append(selcom[pdbfnum]); - selectioncom.append(" "); - if (pdbfnum < files.length - 1) + else { - selectioncom.append("| "); + /* + * extending a contiguous run + */ + if (!run) + { + /* + * start the range selection + */ + molsel.append(String.valueOf(lpos)); + molsel.append("-"); + } + run = true; } + lpos = pdbResNum; } - else + } + + /* + * and terminate final selection + */ + if (lpos != -1) + { + molsel.append(String.valueOf(lpos)); + molsel.append(chainCd); + } + if (molsel.length() > 1) + { + selcom[pdbfnum] = molsel.toString(); + selectioncom.append("#").append(String.valueOf(pdbfnum)) + .append(":"); + 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++) { @@ -615,22 +492,23 @@ 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("match ").append(getModelSpec(pdbfnum)).append(":"); command.append(selcom[pdbfnum]); - command.append("@" + atomSpec[pdbfnum]); - // JAL-1757 exclude alternative CA locations + command.append("@").append( + structures[pdbfnum].isRna ? PHOSPHORUS : ALPHACARBON); + // JAL-1757 exclude alternate CA locations command.append(NO_ALTLOCS); - command.append(" #" + refStructure /* +".1" */); + command.append(" ").append(getModelSpec(refStructure)).append(":"); command.append(selcom[refStructure]); - command.append("@" + atomSpec[refStructure]); + command.append("@").append( + structures[refStructure].isRna ? PHOSPHORUS : ALPHACARBON); command.append(NO_ALTLOCS); } if (selectioncom.length() > 0) @@ -641,13 +519,14 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel 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; chain @CA|P; ribbon ") + .append(selectioncom.toString()) + .append(";" + command.toString()); } } 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); @@ -656,24 +535,63 @@ 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; chain @CA|P; ribbon ") + .append(selectioncom.toString()).append("; focus"); + sendChimeraCommand(allComs.toString(), false); } - + } - private void checkLaunched() + /** + * 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 (!viewer.isChimeraLaunched()) + if (pdbfnum < 0 || pdbfnum >= getPdbCount()) { - viewer.launchChimera(StructureManager.getChimeraPaths()); + return ""; } + + /* + * 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(getPdbFile()[pdbfnum]); + boolean hasSubModels = maps != null && maps.size() > 1; + return "#" + String.valueOf(pdbfnum) + (hasSubModels ? ".1" : ""); + } + + /** + * 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()) { - log("Failed to launch Chimera!"); + return viewer.launchChimera(StructureManager.getChimeraPaths()); } + if (viewer.isChimeraLaunched()) + { + return true; + } + log("Failed to launch Chimera!"); + return false; } /** @@ -688,21 +606,19 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel } /** - * Send a command to Chimera, launching it first if necessary, and optionally - * log any responses. + * Send a command to Chimera, and optionally log any responses. * * @param command * @param logResponse */ - public void evalStateCommand(final String command, boolean logResponse) + public void sendChimeraCommand(final String command, boolean logResponse) { 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) + if (logResponse && debug) { log("Response from command ('" + command + "') was:\n" + lastReply); } @@ -712,6 +628,16 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel } /** + * Send a Chimera command asynchronously in a new thread. If the progress + * message is not null, display this message while the command is executing. + * + * @param command + * @param progressMsg + */ + protected abstract void sendAsynchronousCommand(String command, + String progressMsg); + + /** * colour any structures associated with sequences in the given alignment * using the getFeatureRenderer() and getSequenceRenderer() renderers but only * if colourBySequence is enabled. @@ -743,7 +669,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel { for (String command : cpdbbyseq.commands) { - executeWhenReady(command); + sendAsynchronousCommand(command, COLOURING_CHIMERA); } } } @@ -769,7 +695,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel protected void executeWhenReady(String command) { waitForChimera(); - evalStateCommand(command, false); + sendChimeraCommand(command, false); waitForChimera(); } @@ -777,15 +703,15 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel { while (viewer != null && viewer.isBusy()) { - try { + try + { Thread.sleep(15); } catch (InterruptedException q) - {} + { + } } } - - // End StructureListener // ////////////////////////// @@ -813,7 +739,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel /** * 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 + * prior to matching the viewer's contents to the list of structure files * Jalview knows about. */ public abstract void refreshPdbEntries(); @@ -844,6 +770,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel // //////////////////////////////// // /StructureListener + @Override public synchronized String[] getPdbFile() { if (viewer == null) @@ -888,46 +815,63 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel AlignmentViewPanel alignment); /** - * Construct and send a command to highlight an atom. + * Construct and send a command to highlight zero, one or more atoms. * * 
          * 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.
+   *   show #0:44.C
    *
      */ - public void highlightAtom(int atomIndex, int pdbResNum, String chain, - String pdbfile) + @Override + public void highlightAtoms(List atoms) { - List cms = chimeraMaps.get(pdbfile); - if (cms != null) + if (atoms == null) + { + return; + } + StringBuilder atomSpecs = new StringBuilder(); + boolean first = true; + for (AtomSpec atom : atoms) { - StringBuilder sb = new StringBuilder(); - sb.append(" #" + cms.get(0).getModelNumber()); - sb.append(":" + pdbResNum); - if (!chain.equals(" ")) + int pdbResNum = atom.getPdbResNum(); + String chain = atom.getChain(); + String pdbfile = atom.getPdbFile(); + List cms = chimeraMaps.get(pdbfile); + if (cms != null && !cms.isEmpty()) { - sb.append("." + chain); + /* + * Formatting as #0:34.A,#1:33.A doesn't work as desired, so instead we + * concatenate multiple 'show' commands + */ + atomSpecs.append(first ? "" : ";show "); + first = false; + atomSpecs.append("#" + cms.get(0).getModelNumber()); + atomSpecs.append(":" + pdbResNum); + if (!chain.equals(" ")) + { + atomSpecs.append("." + chain); + } } - String atomSpec = sb.toString(); + } + String atomSpec = atomSpecs.toString(); - StringBuilder command = new StringBuilder(32); - if (lastMousedOverAtomSpec != null) - { - command.append("~show " + lastMousedOverAtomSpec + ";"); - } - viewerCommandHistory(false); + /* + * Avoid repeated commands for the same residue + */ + if (atomSpec.equals(lastMousedOverAtomSpec)) + { + return; + } + + StringBuilder command = new StringBuilder(32); + viewerCommandHistory(false); + if (atomSpec.length() > 0) + { command.append("show ").append(atomSpec); - String cmd = command.toString(); - if (cmd.length() > 0) - { - viewer.stopListening(chimeraListener.getUri()); - viewer.sendChimeraCommand(cmd, false); - viewer.startListening(chimeraListener.getUri()); - } - viewerCommandHistory(true); - this.lastMousedOverAtomSpec = atomSpec; + viewer.sendChimeraCommand(command.toString(), false); } + viewerCommandHistory(true); + this.lastMousedOverAtomSpec = atomSpec; } /** @@ -952,26 +896,28 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel { continue; // malformed } - + int hashPos = atomSpec.indexOf("#"); String modelSubmodel = atomSpec.substring(hashPos + 1, colonPos); int dotPos = modelSubmodel.indexOf("."); int modelId = 0; - try { + try + { modelId = Integer.valueOf(dotPos == -1 ? modelSubmodel : modelSubmodel.substring(0, dotPos)); - } catch (NumberFormatException e) { + } 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 */ @@ -1037,7 +983,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel / normalise + " ::" + res + ";"); } - evalStateCommand(command.toString(),false); + sendAsynchronousCommand(command.toString(), COLOURING_CHIMERA); viewerCommandHistory(true); } @@ -1077,7 +1023,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel /** * Send the Chimera 'background solid " command. * - * @see https + * @see https * ://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/background * .html * @param col @@ -1086,8 +1032,8 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel { viewerCommandHistory(false); double normalise = 255D; - final String command = "background solid " + col.getRed() / normalise + "," - + col.getGreen() / normalise + "," + col.getBlue() + final String command = "background solid " + col.getRed() / normalise + + "," + col.getGreen() / normalise + "," + col.getBlue() / normalise + ";"; viewer.sendChimeraCommand(command, false); viewerCommandHistory(true); @@ -1128,7 +1074,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel */ public boolean openSession(String filepath) { - evalStateCommand("open " + filepath, true); + sendChimeraCommand("open " + filepath, true); // todo: test for failure - how? return true; } @@ -1143,9 +1089,40 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel this.finishedInit = finishedInit; } + /** + * Returns a list of chains mapped in this viewer. Note this list is not + * currently scoped per structure. + * + * @return + */ public List getChainNames() { - return chainNames; + 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() + { + sendChimeraCommand("focus", false); + } } diff --git a/src/jalview/gui/ChimeraViewFrame.java b/src/jalview/gui/ChimeraViewFrame.java index 7d8d97c..1915936 100644 --- a/src/jalview/gui/ChimeraViewFrame.java +++ b/src/jalview/gui/ChimeraViewFrame.java @@ -32,7 +32,9 @@ import java.io.IOException; import java.io.PrintWriter; import java.util.ArrayList; import java.util.List; +import java.util.Map; import java.util.Random; +import java.util.Set; import java.util.Vector; import javax.swing.JCheckBoxMenuItem; @@ -71,7 +73,7 @@ import jalview.util.Platform; import jalview.ws.dbsources.Pdb; /** - * GUI elements for handlnig an external chimera display + * GUI elements for handling an external chimera display * * @author jprocter * @@ -151,6 +153,8 @@ public class ChimeraViewFrame extends StructureViewerBase } }); viewMenu.add(seqColourBy); + viewMenu.add(fitToWindow); + final ItemListener handler; JMenu alpanels = new ViewSelectionMenu( MessageManager.getString("label.superpose_with"), this, @@ -204,110 +208,161 @@ public class ChimeraViewFrame extends StructureViewerBase String[] chains, final AlignmentPanel ap) { super(); - progressBar = ap.alignFrame; - // //////////////////////////////// - // Is the pdb file already loaded? + + /* + * is the pdb file already loaded? + */ + String pdbId = pdbentry.getId(); String alreadyMapped = ap.getStructureSelectionManager() - .alreadyMappedToFile(pdbentry.getId()); + .alreadyMappedToFile(pdbId); if (alreadyMapped != null) { - int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop, - MessageManager.formatMessage( - "label.pdb_entry_is_already_displayed", new Object[] - { pdbentry.getId() }), MessageManager.formatMessage( - "label.map_sequences_to_visible_window", new Object[] - { pdbentry.getId() }), - JOptionPane.YES_NO_CANCEL_OPTION); - + int option = chooseAddSequencesToViewer(pdbId); if (option == JOptionPane.CANCEL_OPTION) { return; } if (option == JOptionPane.YES_OPTION) { - // TODO : Fix multiple seq to one chain issue here. - ap.getStructureSelectionManager().setMapping(seq, chains, - alreadyMapped, AppletFormatAdapter.FILE); - if (ap.getSeqPanel().seqCanvas.fr != null) - { - ap.getSeqPanel().seqCanvas.fr.featuresAdded(); - ap.paintAlignment(true); - } - - // Now this ChimeraViewFrame is mapped to new sequences. We must add - // them to the existing array - JInternalFrame[] frames = Desktop.instance.getAllFrames(); - - for (JInternalFrame frame : frames) - { - if (frame instanceof ChimeraViewFrame) - { - final ChimeraViewFrame topView = ((ChimeraViewFrame) frame); - // JBPNOTE: this looks like a binding routine, rather than a gui - // routine - for (int pe = 0; pe < topView.jmb.getPdbCount(); pe++) - { - if (topView.jmb.getPdbEntry(pe).getFile() - .equals( - alreadyMapped)) - { - topView.jmb.addSequence(pe, seq); - topView.addAlignmentPanel(ap); - // add it to the set used for colouring - topView.useAlignmentPanelForColourbyseq(ap); - topView.buildActionMenu(); - ap.getStructureSelectionManager() - .sequenceColoursChanged(ap); - break; - } - } - } - } - + addSequenceMappingsToStructure(seq, chains, ap, alreadyMapped); return; } } - // ///////////////////////////////// - // Check if there are other Chimera views involving this alignment - // and prompt user about adding this molecule to one of them + + /* + * Check if there are other Chimera views involving this alignment and give + * user the option to add and align this molecule to one of them + */ List existingViews = getChimeraWindowsFor(ap); - for (ChimeraViewFrame topView : existingViews) + for (ChimeraViewFrame view : existingViews) { - // TODO: highlight topView in view somehow + // TODO: highlight view somehow /* * JAL-1742 exclude view with this structure already mapped (don't offer * to align chain B to chain A of the same structure) */ - if (topView.hasPdbId(pdbentry.getId())) + if (view.hasPdbId(pdbId)) { continue; } - int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop, - MessageManager.formatMessage("label.add_pdbentry_to_view", - new Object[] - { pdbentry.getId(), topView.getTitle() }), - MessageManager - .getString("label.align_to_existing_structure_view"), - JOptionPane.YES_NO_CANCEL_OPTION); + int option = chooseAlignStructureToViewer(pdbId, view); if (option == JOptionPane.CANCEL_OPTION) { return; } if (option == JOptionPane.YES_OPTION) { - topView.useAlignmentPanelForSuperposition(ap); - topView.addStructure(pdbentry, seq, chains, true, ap.alignFrame); + view.useAlignmentPanelForSuperposition(ap); + view.addStructure(pdbentry, seq, chains, true, ap.alignFrame); return; } } - // ///////////////////////////////// + + /* + * If the options above are declined or do not apply, open a new viewer + */ openNewChimera(ap, new PDBEntry[] { pdbentry }, new SequenceI[][] { seq }); } /** + * Presents a dialog with the option to add an align a structure to an + * existing Chimera view + * + * @param pdbId + * @param view + * @return YES, NO or CANCEL JOptionPane code + */ + protected int chooseAlignStructureToViewer(String pdbId, + ChimeraViewFrame view) + { + int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop, + MessageManager.formatMessage("label.add_pdbentry_to_view", + new Object[] + { pdbId, view.getTitle() }), MessageManager + .getString("label.align_to_existing_structure_view"), + JOptionPane.YES_NO_CANCEL_OPTION); + return option; + } + + /** + * Presents a dialog with the option to add sequences to a viewer which + * already has their structure open + * + * @param pdbId + * @return YES, NO or CANCEL JOptionPane code + */ + protected int chooseAddSequencesToViewer(String pdbId) + { + int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop, + MessageManager.formatMessage( + "label.pdb_entry_is_already_displayed", new Object[] + { pdbId }), MessageManager.formatMessage( + "label.map_sequences_to_visible_window", new Object[] + { pdbId }), JOptionPane.YES_NO_CANCEL_OPTION); + return option; + } + + /** + * Adds mappings for the given sequences to an already opened PDB structure, + * and updates any viewers that have the PDB file + * + * @param seq + * @param chains + * @param ap + * @param pdbFilename + */ + protected void addSequenceMappingsToStructure(SequenceI[] seq, + String[] chains, final AlignmentPanel ap, String pdbFilename) + { + // TODO : Fix multiple seq to one chain issue here. + /* + * create the mappings + */ + ap.getStructureSelectionManager().setMapping(seq, chains, pdbFilename, + AppletFormatAdapter.FILE); + + /* + * alert the FeatureRenderer to show new (PDB RESNUM) features + */ + if (ap.getSeqPanel().seqCanvas.fr != null) + { + ap.getSeqPanel().seqCanvas.fr.featuresAdded(); + ap.paintAlignment(true); + } + + /* + * add the sequences to any other Chimera viewers for this pdb file + */ + // JBPNOTE: this looks like a binding routine, rather than a gui routine + for (JInternalFrame frame : Desktop.instance.getAllFrames()) + { + if (frame instanceof ChimeraViewFrame) + { + ChimeraViewFrame chimeraView = ((ChimeraViewFrame) frame); + for (int pe = 0; pe < chimeraView.jmb.getPdbCount(); pe++) + { + if (chimeraView.jmb.getPdbEntry(pe).getFile().equals(pdbFilename)) + { + chimeraView.jmb.addSequence(pe, seq); + chimeraView.addAlignmentPanel(ap); + /* + * add it to the set of alignments used for colouring structure by + * sequence + */ + chimeraView.useAlignmentPanelForColourbyseq(ap); + chimeraView.buildActionMenu(); + ap.getStructureSelectionManager().sequenceColoursChanged(ap); + break; + } + } + } + } + } + + /** * Create a helper to manage progress bar display */ protected void createProgressBar() @@ -327,7 +382,6 @@ public class ChimeraViewFrame extends StructureViewerBase SequenceI[][] seqs) { createProgressBar(); - String[][] chains = extractChains(seqs); jmb = new JalviewChimeraBindingModel(this, ap.getStructureSelectionManager(), pdbentrys, seqs, chains, @@ -390,21 +444,6 @@ public class ChimeraViewFrame extends StructureViewerBase } /** - * create a new viewer containing several structures superimposed using the - * given alignPanel. - * - * @param ap - * @param pe - * @param seqs - */ - public ChimeraViewFrame(AlignmentPanel ap, PDBEntry[] pe, - SequenceI[][] seqs) - { - super(); - openNewChimera(ap, pe, seqs); - } - - /** * Create a new viewer from saved session state data including Chimera session * file. * @@ -439,6 +478,44 @@ public class ChimeraViewFrame extends StructureViewerBase } /** + * create a new viewer containing several structures superimposed using the + * given alignPanel. + * + * @param pe + * @param seqs + * @param ap + */ + public ChimeraViewFrame(PDBEntry[] pe, SequenceI[][] seqs, + AlignmentPanel ap) + { + super(); + openNewChimera(ap, pe, seqs); + } + + public ChimeraViewFrame(Map> toView, + AlignmentPanel alignPanel) + { + super(); + + /* + * Convert the map of sequences per pdb entry into the tied arrays expected + * by openNewChimera + * + * TODO pass the Map down to openNewChimera and its callees instead + */ + final Set pdbEntries = toView.keySet(); + PDBEntry[] pdbs = pdbEntries.toArray(new PDBEntry[pdbEntries.size()]); + SequenceI[][] seqsForPdbs = new SequenceI[pdbEntries.size()][]; + for (int i = 0; i < pdbs.length; i++) + { + final List seqsForPdb = toView.get(pdbs[i]); + seqsForPdbs[i] = seqsForPdb.toArray(new SequenceI[seqsForPdb.size()]); + } + + openNewChimera(alignPanel, pdbs, seqsForPdbs); + } + + /** * add a new structure (with associated sequences and chains) to this viewer, * retrieving it if necessary first. * @@ -489,7 +566,7 @@ public class ChimeraViewFrame extends StructureViewerBase addingStructures = true; _started = false; alignAddedStructures = b; - progressBar = alignFrame; // visual indication happens on caller frame. + // progressBar = alignFrame; // visual indication happens on caller frame. (worker = new Thread(this)).start(); return; } @@ -522,10 +599,7 @@ public class ChimeraViewFrame extends StructureViewerBase jalview.gui.Desktop.addInternalFrame(this, jmb.getViewerTitle("Chimera", true), getBounds().width, getBounds().height); - /* - * Pass an empty 'command' to launch Chimera - */ - jmb.evalStateCommand("", false); + jmb.launchChimera(); if (this.chimeraSessionFile != null) { @@ -542,10 +616,16 @@ public class ChimeraViewFrame extends StructureViewerBase jmb.startChimeraListener(); } + /** + * If the list is not empty, add menu items for 'All' and each individual + * chain to the "View | Show Chain" sub-menu. Multiple selections are allowed. + * + * @param chainNames + */ void setChainMenuItems(List chainNames) { chainMenu.removeAll(); - if (chainNames == null) + if (chainNames == null || chainNames.isEmpty()) { return; } @@ -563,7 +643,7 @@ public class ChimeraViewFrame extends StructureViewerBase ((JCheckBoxMenuItem) chainMenu.getItem(i)).setSelected(true); } } - centerViewer(); + showSelectedChains(); allChainsSelected = false; } }); @@ -579,7 +659,7 @@ public class ChimeraViewFrame extends StructureViewerBase { if (!allChainsSelected) { - centerViewer(); + showSelectedChains(); } } }); @@ -588,7 +668,10 @@ public class ChimeraViewFrame extends StructureViewerBase } } - void centerViewer() + /** + * Show only the selected chain(s) in the viewer + */ + void showSelectedChains() { List toshow = new ArrayList(); for (int i = 0; i < chainMenu.getItemCount(); i++) @@ -602,7 +685,7 @@ public class ChimeraViewFrame extends StructureViewerBase } } } - jmb.centerViewer(toshow); + jmb.showChains(toshow); } /** @@ -760,8 +843,8 @@ public class ChimeraViewFrame extends StructureViewerBase stopProgressBar("", startTime); } // Explicitly map to the filename used by Chimera ; - // TODO: use pe.getId() instead of pe.getFile() ? - jmb.getSsm().setMapping(jmb.getSequence()[pos], null, + jmb.getSsm().setMapping(jmb.getSequence()[pos], + jmb.getChains()[pos], pe.getFile(), protocol); } catch (OutOfMemoryError oomerror) @@ -819,9 +902,19 @@ public class ChimeraViewFrame extends StructureViewerBase Pdb pdbclient = new Pdb(); AlignmentI pdbseq = null; String pdbid = processingEntry.getId(); - long hdl = startProgressBar(MessageManager.formatMessage( - "status.fetching_pdb", new Object[] - { pdbid })); + long handle = System.currentTimeMillis() + + Thread.currentThread().hashCode(); + + /* + * Write 'fetching PDB' progress on AlignFrame as we are not yet visible + */ + String msg = MessageManager.formatMessage("status.fetching_pdb", + new Object[] + { pdbid }); + getAlignmentPanel().alignFrame.setProgressBar(msg, handle); + // long hdl = startProgressBar(MessageManager.formatMessage( + // "status.fetching_pdb", new Object[] + // { pdbid })); try { pdbseq = pdbclient.getSequenceRecords(pdbid); @@ -830,9 +923,10 @@ public class ChimeraViewFrame extends StructureViewerBase new OOMWarning("Retrieving PDB id " + pdbid, oomerror); } finally { - String msg = pdbid + " " + msg = pdbid + " " + MessageManager.getString("label.state_completed"); - stopProgressBar(msg, hdl); + getAlignmentPanel().alignFrame.setProgressBar(msg, handle); + // stopProgressBar(msg, hdl); } /* * If PDB data were saved and are not invalid (empty alignment), return the @@ -867,6 +961,13 @@ public class ChimeraViewFrame extends StructureViewerBase return tm; } + /** + * End the progress bar with the specified handle, leaving a message (if not + * null) on the status bar + * + * @param msg + * @param handle + */ public void stopProgressBar(String msg, long handle) { if (progressBar != null) @@ -1136,12 +1237,12 @@ public class ChimeraViewFrame extends StructureViewerBase { return; } - ; + if (_alignwith.size() == 0) { _alignwith.add(getAlignmentPanel()); } - ; + try { AlignmentI[] als = new Alignment[_alignwith.size()]; @@ -1165,9 +1266,7 @@ public class ChimeraViewFrame extends StructureViewerBase } Cache.log.info("Couldn't align structures with the " + sp.toString() + "associated alignment panels.", e); - } - } public void setJalviewColourScheme(ColourSchemeI ucs) diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java index 2cc5079..2e3b37a 100644 --- a/src/jalview/gui/StructureChooser.java +++ b/src/jalview/gui/StructureChooser.java @@ -22,19 +22,6 @@ package jalview.gui; -import jalview.datamodel.DBRefEntry; -import jalview.datamodel.PDBEntry; -import jalview.datamodel.SequenceI; -import jalview.jbgui.GStructureChooser; -import jalview.jbgui.PDBDocFieldPreferences; -import jalview.structure.StructureSelectionManager; -import jalview.util.MessageManager; -import jalview.ws.dbsources.PDBRestClient; -import jalview.ws.dbsources.PDBRestClient.PDBDocField; -import jalview.ws.uimodel.PDBRestRequest; -import jalview.ws.uimodel.PDBRestResponse; -import jalview.ws.uimodel.PDBRestResponse.PDBResponseSummary; - import java.awt.event.ItemEvent; import java.util.ArrayList; import java.util.Collection; @@ -49,6 +36,19 @@ import javax.swing.JLabel; import javax.swing.JOptionPane; import javax.swing.table.DefaultTableModel; +import jalview.datamodel.DBRefEntry; +import jalview.datamodel.PDBEntry; +import jalview.datamodel.SequenceI; +import jalview.jbgui.GStructureChooser; +import jalview.jbgui.PDBDocFieldPreferences; +import jalview.structure.StructureSelectionManager; +import jalview.util.MessageManager; +import jalview.ws.dbsources.PDBRestClient; +import jalview.ws.dbsources.PDBRestClient.PDBDocField; +import jalview.ws.uimodel.PDBRestRequest; +import jalview.ws.uimodel.PDBRestResponse; +import jalview.ws.uimodel.PDBRestResponse.PDBResponseSummary; + /** * Provides the behaviors for the Structure chooser Panel @@ -746,17 +746,17 @@ public class StructureChooser extends GStructureChooser private void launchStructureViewer(StructureSelectionManager ssm, PDBEntry[] pdbEntriesToView, AlignmentPanel alignPanel, - SequenceI[] selectedSequences) + SequenceI[] sequences) { StructureViewer sViewer = new StructureViewer(ssm); if (pdbEntriesToView.length > 1) { - sViewer.viewStructures(alignPanel, pdbEntriesToView, - alignPanel.av.collateForPDB(pdbEntriesToView)); + sViewer.viewStructures(pdbEntriesToView, alignPanel.av.collateForPDB(pdbEntriesToView), + alignPanel); } else { - sViewer.viewStructures(pdbEntriesToView[0], selectedSequences, null, + sViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel); } } diff --git a/src/jalview/gui/StructureViewer.java b/src/jalview/gui/StructureViewer.java index 7584612..2285765 100644 --- a/src/jalview/gui/StructureViewer.java +++ b/src/jalview/gui/StructureViewer.java @@ -20,6 +20,10 @@ */ package jalview.gui; +import java.awt.Rectangle; +import java.util.ArrayList; +import java.util.List; + import jalview.api.structures.JalviewStructureDisplayI; import jalview.bin.Cache; import jalview.datamodel.PDBEntry; @@ -27,8 +31,6 @@ import jalview.datamodel.SequenceI; import jalview.datamodel.StructureViewerModel; import jalview.structure.StructureSelectionManager; -import java.awt.Rectangle; - /** * proxy for handling structure viewers. * @@ -64,23 +66,85 @@ public class StructureViewer ssm = structureSelectionManager; } - public JalviewStructureDisplayI viewStructures(AlignmentPanel ap, - PDBEntry[] pr, SequenceI[][] collateForPDB) + /** + * View multiple PDB entries, each with associated sequences + * + * @param pdbs + * @param seqsForPdbs + * @param ap + * @return + */ + public JalviewStructureDisplayI viewStructures(PDBEntry[] pdbs, + SequenceI[][] seqsForPdbs, AlignmentPanel ap) { - return viewStructures(getViewerType(), ap, pr, collateForPDB); + JalviewStructureDisplayI viewer = onlyOnePdb(pdbs, seqsForPdbs, ap); + if (viewer != null) + { + return viewer; + } + return viewStructures(getViewerType(), pdbs, seqsForPdbs, ap); } - public JalviewStructureDisplayI viewStructures(ViewerType viewerType, - AlignmentPanel ap, PDBEntry[] pr, SequenceI[][] collateForPDB) + /** + * A strictly temporary method pending JAL-1761 refactoring. Determines if all + * the passed PDB entries are the same (this is the case if selected sequences + * to view structure for are chains of the same structure). If so, calls the + * single-pdb version of viewStructures and returns the viewer, else returns + * null. + * + * @param pdbs + * @param seqsForPdbs + * @param ap + * @return + */ + private JalviewStructureDisplayI onlyOnePdb(PDBEntry[] pdbs, + SequenceI[][] seqsForPdbs, + AlignmentPanel ap) + { + List seqs = new ArrayList(); + if (pdbs == null || pdbs.length == 0) + { + return null; + } + int i = 0; + String firstFile = pdbs[0].getFile(); + for (PDBEntry pdb : pdbs) + { + String pdbFile = pdb.getFile(); + if (pdbFile == null || !pdbFile.equals(firstFile)) + { + return null; + } + SequenceI[] pdbseqs = seqsForPdbs[i++]; + if (pdbseqs != null) + { + for (SequenceI sq : pdbseqs) + { + seqs.add(sq); + } + } + } + return viewStructures(pdbs[0], + seqs.toArray(new SequenceI[seqs.size()]), ap); + } + + public JalviewStructureDisplayI viewStructures(PDBEntry pdb, + SequenceI[] seqsForPdb, AlignmentPanel ap) + { + return viewStructures(getViewerType(), pdb, seqsForPdb, ap); + } + + protected JalviewStructureDisplayI viewStructures(ViewerType viewerType, + PDBEntry[] pdbs, SequenceI[][] seqsForPdbs, AlignmentPanel ap) { JalviewStructureDisplayI sview = null; if (viewerType.equals(ViewerType.JMOL)) { - sview = new AppJmol(ap, pr, ap.av.collateForPDB(pr)); + sview = new AppJmol(ap, pdbs, ap.av.collateForPDB(pdbs)); } else if (viewerType.equals(ViewerType.CHIMERA)) { - sview = new ChimeraViewFrame(ap, pr, ap.av.collateForPDB(pr)); + sview = new ChimeraViewFrame(pdbs, ap.av.collateForPDB(pdbs), ap); } else { @@ -90,17 +154,17 @@ public class StructureViewer return sview; } - public JalviewStructureDisplayI viewStructures(ViewerType viewerType, - AlignmentPanel ap, PDBEntry pr, SequenceI[] collateForPDB) + protected JalviewStructureDisplayI viewStructures(ViewerType viewerType, + PDBEntry pdb, SequenceI[] seqsForPdb, AlignmentPanel ap) { JalviewStructureDisplayI sview = null; if (viewerType.equals(ViewerType.JMOL)) { - sview = new AppJmol(pr, collateForPDB, null, ap); + sview = new AppJmol(pdb, seqsForPdb, null, ap); } else if (viewerType.equals(ViewerType.CHIMERA)) { - sview = new ChimeraViewFrame(pr, collateForPDB, null, ap); + sview = new ChimeraViewFrame(pdb, seqsForPdb, null, ap); } else { @@ -110,12 +174,6 @@ public class StructureViewer return sview; } - public JalviewStructureDisplayI viewStructures(PDBEntry pdb, - SequenceI[] sequenceIs, Object object, AlignmentPanel ap) - { - return viewStructures(getViewerType(), ap, pdb, sequenceIs); - } - /** * Create a new panel controlling a structure viewer. * diff --git a/src/jalview/structures/models/AAStructureBindingModel.java b/src/jalview/structures/models/AAStructureBindingModel.java index 298e82c..86c9a21 100644 --- a/src/jalview/structures/models/AAStructureBindingModel.java +++ b/src/jalview/structures/models/AAStructureBindingModel.java @@ -5,10 +5,12 @@ import java.util.Arrays; import java.util.List; import jalview.api.StructureSelectionManagerProvider; +import jalview.datamodel.AlignmentI; import jalview.datamodel.PDBEntry; import jalview.datamodel.SequenceI; import jalview.structure.AtomSpec; import jalview.structure.StructureListener; +import jalview.structure.StructureMapping; import jalview.structure.StructureSelectionManager; import jalview.util.Comparison; import jalview.util.MessageManager; @@ -51,6 +53,35 @@ public abstract class AAStructureBindingModel extends private boolean nucleotide; /** + * Data bean class to simplify parameterisation in superposeStructures + */ + protected class SuperposeData + { + /** + * Constructor with alignment width argument + * + * @param width + */ + public SuperposeData(int width) + { + pdbResNo = new int[width]; + } + + public String filename; + + public String pdbId; + + public String chain = ""; + + public boolean isRna; + + /* + * The pdb residue number (if any) mapped to each column of the alignment + */ + public int[] pdbResNo; + } + + /** * Constructor * * @param ssm @@ -388,6 +419,14 @@ public abstract class AAStructureBindingModel extends } } + @Override + public abstract void highlightAtoms(List atoms); + + protected boolean isNucleotide() + { + return this.nucleotide; + } + /** * Returns a readable description of all mappings for the wrapped pdbfile to * any mapped sequences @@ -412,24 +451,154 @@ public abstract class AAStructureBindingModel extends return sb.toString(); } - @Override - public void highlightAtoms(List atoms) + /** + * Returns the mapped structure position for a given aligned column of a given + * sequence, or -1 if the column is gapped, beyond the end of the sequence, or + * not mapped to structure. + * + * @param seq + * @param alignedPos + * @param mapping + * @return + */ + protected int getMappedPosition(SequenceI seq, int alignedPos, + StructureMapping mapping) { - if (atoms != null) + if (alignedPos >= seq.getLength()) { - for (AtomSpec atom : atoms) + return -1; + } + + if (Comparison.isGap(seq.getCharAt(alignedPos))) + { + return -1; + } + int seqPos = seq.findPosition(alignedPos); + int pos = mapping.getPDBResNum(seqPos); + return pos; + } + + /** + * Helper method to identify residues that can participate in a structure + * superposition command. For each structure, identify a sequence in the + * alignment which is mapped to the structure. Identify non-gapped columns in + * the sequence which have a mapping to a residue in the structure. Returns + * the index of the first structure that has a mapping to the alignment. + * + * @param alignment + * the sequence alignment which is the basis of structure + * superposition + * @param matched + * an array of booleans, indexed by alignment column, where true + * indicates that every structure has a mapped residue present in the + * column (so the column can participate in structure alignment) + * @param structures + * an array of data beans corresponding to pdb file index + * @return + */ + protected int findSuperposableResidues(AlignmentI alignment, + boolean[] matched, SuperposeData[] structures) + { + int refStructure = -1; + String[] files = getPdbFile(); + for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) + { + StructureMapping[] mappings = getSsm().getMapping(files[pdbfnum]); + int lastPos = -1; + + /* + * Find the first mapped sequence (if any) for this PDB entry which is in + * the alignment + */ + final int seqCountForPdbFile = getSequence()[pdbfnum].length; + for (int s = 0; s < seqCountForPdbFile; s++) { - highlightAtom(atom.getAtomIndex(), atom.getPdbResNum(), - atom.getChain(), atom.getPdbFile()); + for (StructureMapping mapping : mappings) + { + final SequenceI theSequence = getSequence()[pdbfnum][s]; + if (mapping.getSequence() == theSequence + && alignment.findIndex(theSequence) > -1) + { + if (refStructure < 0) + { + refStructure = pdbfnum; + } + for (int r = 0; r < matched.length; r++) + { + if (!matched[r]) + { + continue; + } + int pos = getMappedPosition(theSequence, r, mapping); + if (pos < 1 || pos == lastPos) + { + matched[r] = false; + continue; + } + lastPos = pos; + structures[pdbfnum].pdbResNo[r] = pos; + } + String chain = mapping.getChain(); + if (chain != null && chain.trim().length() > 0) + { + structures[pdbfnum].chain = chain; + } + structures[pdbfnum].pdbId = mapping.getPdbId(); + structures[pdbfnum].isRna = theSequence.getRNA() != null; + // move on to next pdb file + s = seqCountForPdbFile; + break; + } + } } } + return refStructure; } - protected abstract void highlightAtom(int atomIndex, int pdbResNum, - String chain, String pdbFile); - - protected boolean isNucleotide() + /** + * Returns true if the structure viewer has loaded all of the files of + * interest (identified by the file mapping having been set up), or false if + * any are still not loaded after a timeout interval. + * + * @param files + */ + protected boolean waitForFileLoad(String[] files) { - return this.nucleotide; + /* + * give up after 10 secs plus 1 sec per file + */ + long starttime = System.currentTimeMillis(); + long endTime = 10000 + 1000 * files.length + starttime; + String notLoaded = null; + + boolean waiting = true; + while (waiting && System.currentTimeMillis() < endTime) + { + waiting = false; + for (String file : files) + { + notLoaded = file; + try + { + StructureMapping[] sm = getSsm().getMapping(file); + if (sm == null || sm.length == 0) + { + waiting = true; + } + } catch (Throwable x) + { + waiting = true; + } + } + } + + if (waiting) + { + System.err + .println("Timed out waiting for structure viewer to load file " + + notLoaded); + return false; + } + return true; } } \ No newline at end of file diff --git a/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java b/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java index f2535cb..807d7bb 100644 --- a/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java +++ b/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java @@ -7,7 +7,6 @@ import org.junit.BeforeClass; import org.junit.Test; import jalview.api.structures.JalviewStructureDisplayI; -import jalview.datamodel.PDBEntry; import jalview.datamodel.SequenceI; import jalview.gui.AlignFrame; import jalview.gui.StructureViewer; @@ -63,14 +62,11 @@ public class JalviewChimeraView { final StructureViewer structureViewer = new StructureViewer(af .getViewport().getStructureSelectionManager()); - + structureViewer.setViewerType(ViewerType.JMOL); JalviewStructureDisplayI jmolViewer = structureViewer - .viewStructures(ViewerType.JMOL, af.getCurrentView() - .getAlignPanel(), new PDBEntry[] - { (PDBEntry) dsq.getPDBId().elementAt(q) }, - new SequenceI[][] - { new SequenceI[] - { sq } }); + .viewStructures(dsq.getPDBId().elementAt(q), + new SequenceI[] + { sq }, af.getCurrentView().getAlignPanel()); /* * Wait for viewer thread to start */ @@ -110,14 +106,11 @@ public class JalviewChimeraView { final StructureViewer structureViewer = new StructureViewer(af .getViewport().getStructureSelectionManager()); - + structureViewer.setViewerType(ViewerType.CHIMERA); JalviewStructureDisplayI chimeraViewer = structureViewer - .viewStructures(ViewerType.CHIMERA, af.getCurrentView() - .getAlignPanel(), new PDBEntry[] - { (PDBEntry) dsq.getPDBId().elementAt(q) }, - new SequenceI[][] - { new SequenceI[] - { sq } }); + .viewStructures(dsq.getPDBId().elementAt(q), + new SequenceI[] + { sq }, af.getCurrentView().getAlignPanel()); /* * Wait for viewer thread to start */ diff --git a/test/jalview/structures/models/AAStructureBindingModelTest.java b/test/jalview/structures/models/AAStructureBindingModelTest.java new file mode 100644 index 0000000..3db7f23 --- /dev/null +++ b/test/jalview/structures/models/AAStructureBindingModelTest.java @@ -0,0 +1,183 @@ +package jalview.structures.models; + +import static org.junit.Assert.assertEquals; +import static org.junit.Assert.assertFalse; +import static org.junit.Assert.assertTrue; + +import java.util.Arrays; +import java.util.List; + +import org.junit.Before; +import org.junit.Test; + +import jalview.datamodel.Alignment; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.PDBEntry; +import jalview.datamodel.PDBEntry.Type; +import jalview.datamodel.Sequence; +import jalview.datamodel.SequenceI; +import jalview.io.AppletFormatAdapter; +import jalview.structure.AtomSpec; +import jalview.structure.StructureSelectionManager; +import jalview.structures.models.AAStructureBindingModel.SuperposeData; + +/** + * Unit tests for non-abstract methods of abstract base class + * + * @author gmcarstairs + * + */ +public class AAStructureBindingModelTest +{ + private static final String PDB_1 = "HEADER COMPLEX (ANTI-ONCOGENE/ANKYRIN REPEATS) 30-SEP-96 1YCS \n" + + "ATOM 2 CA VAL A 97 24.134 4.926 45.821 1.00 47.43 C \n" + + "ATOM 9 CA PRO A 98 25.135 8.584 46.217 1.00 41.60 C \n" + + "ATOM 16 CA SER A 99 28.243 9.596 44.271 1.00 39.63 C \n" + + "ATOM 22 CA GLN A 100 31.488 10.133 46.156 1.00 35.60 C \n" + + "ATOM 31 CA LYS A 101 33.323 11.587 43.115 1.00 41.69 C \n"; + + private static final String PDB_2 = "HEADER HYDROLASE 09-SEP-09 3A6S \n" + + "ATOM 2 CA MET A 1 15.366 -11.648 24.854 1.00 32.05 C \n" + + "ATOM 10 CA LYS A 2 16.846 -9.215 22.340 1.00 25.68 C \n" + + "ATOM 19 CA LYS A 3 15.412 -6.335 20.343 1.00 19.42 C \n" + + "ATOM 28 CA LEU A 4 15.629 -5.719 16.616 1.00 15.49 C \n" + + "ATOM 36 CA GLN A 5 14.412 -2.295 15.567 1.00 12.19 C \n"; + + private static final String PDB_3 = "HEADER STRUCTURAL GENOMICS 04-MAR-03 1OOT \n" + + "ATOM 2 CA SER A 1 29.427 3.330 -6.578 1.00 32.50 C \n" + + "ATOM 8 CA PRO A 2 29.975 3.340 -2.797 1.00 17.62 C \n" + + "ATOM 16 CA ALYS A 3 26.958 3.024 -0.410 0.50 8.78 C \n" + + "ATOM 33 CA ALA A 4 26.790 4.320 3.172 1.00 11.98 C \n" + + "ATOM 39 CA AVAL A 5 24.424 3.853 6.106 0.50 13.83 C \n"; + + AAStructureBindingModel testee; + + AlignmentI al = null; + + /** + * Set up test conditions with three aligned sequences, + */ + @Before + public void setUp() + { + SequenceI seq1 = new Sequence("1YCS", "-VPSQK"); + SequenceI seq2 = new Sequence("3A6S", "MK-KLQ"); + SequenceI seq3 = new Sequence("1OOT", "SPK-AV"); + al = new Alignment(new SequenceI[] + { seq1, seq2, seq3 }); + al.setDataset(null); + + PDBEntry[] pdbFiles = new PDBEntry[3]; + pdbFiles[0] = new PDBEntry("1YCS", "A", Type.PDB, "1YCS.pdb"); + pdbFiles[1] = new PDBEntry("3A6S", "B", Type.PDB, "3A6S.pdb"); + pdbFiles[2] = new PDBEntry("1OOT", "A", Type.PDB, "1OOT.pdb"); + String[][] chains = new String[3][]; + SequenceI[][] seqs = new SequenceI[3][]; + seqs[0] = new SequenceI[] + { seq1 }; + seqs[1] = new SequenceI[] + { seq2 }; + seqs[2] = new SequenceI[] + { seq3 }; + StructureSelectionManager ssm = new StructureSelectionManager(); + + ssm.setMapping(new SequenceI[] + { seq1 }, null, PDB_1, AppletFormatAdapter.PASTE); + ssm.setMapping(new SequenceI[] + { seq2 }, null, PDB_2, AppletFormatAdapter.PASTE); + ssm.setMapping(new SequenceI[] + { seq3 }, null, PDB_3, AppletFormatAdapter.PASTE); + + testee = new AAStructureBindingModel(ssm, pdbFiles, seqs, chains, null) + { + @Override + public String[] getPdbFile() + { + /* + * fudge 'filenames' to match those generated when PDBFile parses PASTE + * data + */ + return new String[] + { "INLINE1YCS", "INLINE3A6S", "INLINE1OOT" }; + } + @Override + public void updateColours(Object source) + { + } + @Override + public void releaseReferences(Object svl) + { + } + @Override + public void highlightAtoms(List atoms) + { + } + }; + } + + /** + * Verify that the method determines that columns 2, 5 and 6 of the aligment + * are alignable in structure + */ + @Test + public void testFindSuperposableResidues() + { + SuperposeData[] structs = new SuperposeData[al.getHeight()]; + for (int i = 0; i < structs.length; i++) + { + structs[i] = testee.new SuperposeData(al.getWidth()); + } + /* + * initialise array of 'superposable columns' to true (would be false for + * hidden columns) + */ + boolean[] matched = new boolean[al.getWidth()]; + Arrays.fill(matched, true); + + int refStructure = testee + .findSuperposableResidues(al, matched, structs); + + assertEquals(0, refStructure); + + /* + * only ungapped, structure-mapped columns are superposable + */ + assertFalse(matched[0]); // gap in first sequence + assertTrue(matched[1]); + assertFalse(matched[2]); // gap in second sequence + assertFalse(matched[3]); // gap in third sequence + assertTrue(matched[4]); + assertTrue(matched[5]); + } + + @Test + public void testFindSuperposableResidues_hiddenColumn() + { + SuperposeData[] structs = new SuperposeData[al.getHeight()]; + for (int i = 0; i < structs.length; i++) + { + structs[i] = testee.new SuperposeData(al.getWidth()); + } + /* + * initialise array of 'superposable columns' to true (would be false for + * hidden columns) + */ + boolean[] matched = new boolean[al.getWidth()]; + Arrays.fill(matched, true); + // treat column 5 of the alignment as hidden + matched[4] = false; + + int refStructure = testee + .findSuperposableResidues(al, matched, structs); + + assertEquals(0, refStructure); + + // only ungapped, structure-mapped columns are not superposable + assertFalse(matched[0]); + assertTrue(matched[1]); + assertFalse(matched[2]); + assertFalse(matched[3]); + assertFalse(matched[4]); // superposable, but hidden, column + assertTrue(matched[5]); + } +} -- 1.7.10.2