X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructures%2Fmodels%2FAAStructureBindingModel.java;h=44d698dafe9f27282aead9cf00cab8af2be94fce;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=ffd865ff07a2fa8382536182b19a11268a4cf88e;hpb=e5c6af77202c042ed3dfc88c3a0319efb4f8a8c0;p=jalview.git diff --git a/src/jalview/structures/models/AAStructureBindingModel.java b/src/jalview/structures/models/AAStructureBindingModel.java index ffd865f..44d698d 100644 --- a/src/jalview/structures/models/AAStructureBindingModel.java +++ b/src/jalview/structures/models/AAStructureBindingModel.java @@ -20,35 +20,59 @@ */ package jalview.structures.models; +import java.util.Locale; + +import java.awt.Color; +import java.io.File; +import java.io.IOException; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.BitSet; +import java.util.HashMap; +import java.util.LinkedHashMap; +import java.util.List; +import java.util.Map; + +import javax.swing.SwingUtilities; + +import jalview.api.AlignViewportI; import jalview.api.AlignmentViewPanel; +import jalview.api.FeatureRenderer; import jalview.api.SequenceRenderer; import jalview.api.StructureSelectionManagerProvider; import jalview.api.structures.JalviewStructureDisplayI; +import jalview.bin.Console; import jalview.datamodel.AlignmentI; import jalview.datamodel.HiddenColumns; +import jalview.datamodel.MappedFeatures; import jalview.datamodel.PDBEntry; +import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; +import jalview.ext.rbvi.chimera.JalviewChimeraBinding; +import jalview.gui.AlignmentPanel; +import jalview.gui.Desktop; +import jalview.gui.StructureViewer.ViewerType; import jalview.io.DataSourceType; +import jalview.io.StructureFile; +import jalview.renderer.seqfeatures.FeatureColourFinder; import jalview.schemes.ColourSchemeI; +import jalview.schemes.ResidueProperties; import jalview.structure.AtomSpec; +import jalview.structure.AtomSpecModel; +import jalview.structure.StructureCommandI; +import jalview.structure.StructureCommandsI; +import jalview.structure.StructureCommandsI.AtomSpecType; import jalview.structure.StructureListener; import jalview.structure.StructureMapping; -import jalview.structure.StructureMappingcommandSet; import jalview.structure.StructureSelectionManager; import jalview.util.Comparison; import jalview.util.MessageManager; -import java.awt.Color; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.BitSet; -import java.util.List; - /** * - * A base class to hold common function for protein structure model binding. - * Initial version created by refactoring JMol and Chimera binding models, but - * other structure viewers could in principle be accommodated in future. + * A base class to hold common function for 3D structure model binding. Initial + * version created by refactoring JMol and Chimera binding models, but other + * structure viewers could in principle be accommodated in future. * * @author gmcarstairs * @@ -57,10 +81,74 @@ public abstract class AAStructureBindingModel extends SequenceStructureBindingModel implements StructureListener, StructureSelectionManagerProvider { + /** + * Data bean class to simplify parameterisation in superposeStructures + */ + public static class SuperposeData + { + public String filename; + + public String pdbId; + + public String chain = ""; + + /** + * is the mapped sequence not protein ? + */ + public boolean isRna; + + /* + * The pdb residue number (if any) mapped to columns of the alignment + */ + public int[] pdbResNo; // or use SparseIntArray? + + public String modelId; + + /** + * Constructor + * + * @param width + * width of alignment (number of columns that may potentially + * participate in superposition) + * @param model + * structure viewer model number + */ + public SuperposeData(int width, String model) + { + pdbResNo = new int[width]; + modelId = model; + } + } + + private static final int MIN_POS_TO_SUPERPOSE = 4; + + private static final String COLOURING_STRUCTURES = MessageManager + .getString("status.colouring_structures"); + + /* + * the Jalview panel through which the user interacts + * with the structure viewer + */ + private JalviewStructureDisplayI viewer; + + /* + * helper that generates command syntax + */ + private StructureCommandsI commandGenerator; private StructureSelectionManager ssm; /* + * modelled chains, formatted as "pdbid:chainCode" + */ + private List chainNames; + + /* + * lookup of pdb file name by key "pdbid:chainCode" + */ + private Map chainFile; + + /* * distinct PDB entries (pdb files) associated * with sequences */ @@ -83,45 +171,21 @@ public abstract class AAStructureBindingModel protected boolean colourBySequence = true; + /** + * true if all sequences appear to be nucleotide + */ private boolean nucleotide; private boolean finishedInit = false; /** - * current set of model filenames loaded in the Jmol instance + * current set of model filenames loaded in the viewer */ protected String[] modelFileNames = null; public String fileLoadingError; - /** - * 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; - } + protected Thread externalViewerMonitor; /** * Constructor @@ -134,6 +198,8 @@ public abstract class AAStructureBindingModel { this.ssm = ssm; this.sequence = seqs; + chainNames = new ArrayList<>(); + chainFile = new HashMap<>(); } /** @@ -148,8 +214,7 @@ public abstract class AAStructureBindingModel PDBEntry[] pdbentry, SequenceI[][] sequenceIs, DataSourceType protocol) { - this.ssm = ssm; - this.sequence = sequenceIs; + this(ssm, sequenceIs); this.nucleotide = Comparison.isNucleotide(sequenceIs); this.pdbEntry = pdbentry; this.protocol = protocol; @@ -178,7 +243,8 @@ public abstract class AAStructureBindingModel String chain = (chains != null && chains[pe] != null) ? chains[pe][se] : null; - SequenceI sq = asq.getDatasetSequence(); + SequenceI sq = (asq.getDatasetSequence() == null) ? asq + : asq.getDatasetSequence(); if (sq.getAllPDBEntries() != null) { for (PDBEntry pdbentry : sq.getAllPDBEntries()) @@ -206,6 +272,7 @@ public abstract class AAStructureBindingModel chains = newchains; return chainmaps > 0; } + public StructureSelectionManager getSsm() { return ssm; @@ -330,7 +397,11 @@ public abstract class AAStructureBindingModel */ protected void releaseUIResources() { + } + @Override + public void releaseReferences(Object svl) + { } public boolean isColourBySequence() @@ -338,6 +409,25 @@ public abstract class AAStructureBindingModel return colourBySequence; } + /** + * Called when the binding thinks the UI needs to be refreshed after a + * structure viewer state change. This could be because structures were + * loaded, or because an error has occurred. Default does nothing, override as + * required. + */ + public void refreshGUI() + { + } + + /** + * 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. By default does nothing, override as required. + */ + public void refreshPdbEntries() + { + } + public void setColourBySequence(boolean colourBySequence) { this.colourBySequence = colourBySequence; @@ -354,8 +444,8 @@ public abstract class AAStructureBindingModel { Integer.valueOf(pe).toString() })); } final String nullChain = "TheNullChain"; - List s = new ArrayList(); - List c = new ArrayList(); + List s = new ArrayList<>(); + List c = new ArrayList<>(); if (getChains() == null) { setChains(new String[getPdbCount()][]); @@ -424,8 +514,8 @@ public abstract class AAStructureBindingModel public synchronized PDBEntry[] addSequenceAndChain(PDBEntry[] pdbe, SequenceI[][] seq, String[][] chns) { - List v = new ArrayList(); - List rtn = new ArrayList(); + List v = new ArrayList<>(); + List rtn = new ArrayList<>(); for (int i = 0; i < getPdbCount(); i++) { v.add(getPdbEntry(i)); @@ -580,7 +670,8 @@ public abstract class AAStructureBindingModel * @return */ protected int findSuperposableResidues(AlignmentI alignment, - BitSet matched, SuperposeData[] structures) + BitSet matched, + AAStructureBindingModel.SuperposeData[] structures) { int refStructure = -1; String[] files = getStructureFiles(); @@ -631,14 +722,14 @@ public abstract class AAStructureBindingModel structures[pdbfnum].chain = chain; } structures[pdbfnum].pdbId = mapping.getPdbId(); - structures[pdbfnum].isRna = theSequence.getRNA() != null; + structures[pdbfnum].isRna = !theSequence.isProtein(); /* * move on to next pdb file (ignore sequences for other chains * for the same structure) */ s = seqCountForPdbFile; - break; + break; // fixme break out of two loops here! } } } @@ -731,11 +822,15 @@ public abstract class AAStructureBindingModel } /** - * Returns a list of chains mapped in this viewer. + * Returns a list of chains mapped in this viewer, formatted as + * "pdbid:chainCode" * * @return */ - public abstract List getChainNames(); + public List getChainNames() + { + return chainNames; + } /** * Returns the Jalview panel hosting the structure viewer (if any) @@ -744,34 +839,138 @@ public abstract class AAStructureBindingModel */ public JalviewStructureDisplayI getViewer() { - return null; + return viewer; } - public abstract void setJalviewColourScheme(ColourSchemeI cs); + public void setViewer(JalviewStructureDisplayI v) + { + viewer = v; + } /** * Constructs and sends a command to align structures against a reference * structure, based on one or more sequence alignments. May optionally return - * an error or warning message for the alignment command. - * - * @param alignments - * an array of alignments to process - * @param structureIndices - * 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 + * an error or warning message for the alignment command(s). + * + * @param alignWith + * an array of one or more alignment views to process * @return */ - public abstract String superposeStructures(AlignmentI[] alignments, - int[] structureIndices, HiddenColumns[] hiddenCols); + public String superposeStructures(List alignWith) + { + String error = ""; + String[] files = getStructureFiles(); + + if (!waitForFileLoad(files)) + { + return null; + } + refreshPdbEntries(); + + for (AlignmentViewPanel view : alignWith) + { + AlignmentI alignment = view.getAlignment(); + HiddenColumns hiddenCols = alignment.getHiddenColumns(); + + /* + * 'matched' bit i will be set for visible alignment columns i where + * all sequences have a residue with a mapping to their PDB structure + */ + BitSet matched = new BitSet(); + final int width = alignment.getWidth(); + for (int m = 0; m < width; m++) + { + if (hiddenCols == null || hiddenCols.isVisible(m)) + { + matched.set(m); + } + } + + AAStructureBindingModel.SuperposeData[] structures = new AAStructureBindingModel.SuperposeData[files.length]; + for (int f = 0; f < files.length; f++) + { + structures[f] = new AAStructureBindingModel.SuperposeData(width, + getModelIdForFile(files[f])); + } + + /* + * Calculate the superposable alignment columns ('matched'), and the + * corresponding structure residue positions (structures.pdbResNo) + */ + int refStructure = findSuperposableResidues(alignment, matched, + structures); + + /* + * require at least 4 positions to be able to execute superposition + */ + int nmatched = matched.cardinality(); + if (nmatched < MIN_POS_TO_SUPERPOSE) + { + String msg = MessageManager + .formatMessage("label.insufficient_residues", nmatched); + error += view.getViewName() + ": " + msg + "; "; + continue; + } + + /* + * get a model of the superposable residues in the reference structure + */ + AtomSpecModel refAtoms = getAtomSpec(structures[refStructure], + matched); + + /* + * Show all as backbone before doing superposition(s) + * (residues used for matching will be shown as ribbon) + */ + // todo better way to ensure synchronous than setting getReply true!! + executeCommands(commandGenerator.showBackbone(), true, null); + + AtomSpecType backbone = structures[refStructure].isRna + ? AtomSpecType.PHOSPHATE + : AtomSpecType.ALPHA; + /* + * superpose each (other) structure to the reference in turn + */ + for (int i = 0; i < structures.length; i++) + { + if (i != refStructure) + { + AtomSpecModel atomSpec = getAtomSpec(structures[i], matched); + List commands = commandGenerator + .superposeStructures(refAtoms, atomSpec, backbone); + List replies = executeCommands(commands, true, null); + for (String reply : replies) + { + // return this error (Chimera only) to the user + if (reply.toLowerCase(Locale.ROOT) + .contains("unequal numbers of atoms")) + { + error += "; " + reply; + } + } + } + } + } - public abstract void setBackgroundColour(Color col); + return error; + } + + private AtomSpecModel getAtomSpec( + AAStructureBindingModel.SuperposeData superposeData, + BitSet matched) + { + AtomSpecModel model = new AtomSpecModel(); + int nextColumnMatch = matched.nextSetBit(0); + while (nextColumnMatch != -1) + { + int pdbResNum = superposeData.pdbResNo[nextColumnMatch]; + model.addRange(superposeData.modelId, pdbResNum, pdbResNum, + superposeData.chain); + nextColumnMatch = matched.nextSetBit(nextColumnMatch + 1); + } - protected abstract StructureMappingcommandSet[] getColourBySequenceCommands( - String[] files, SequenceRenderer sr, AlignmentViewPanel avp); + return model; + } /** * returns the current sequenceRenderer that should be used to colour the @@ -784,42 +983,977 @@ public abstract class AAStructureBindingModel public abstract SequenceRenderer getSequenceRenderer( AlignmentViewPanel alignment); - protected abstract void colourBySequence( - StructureMappingcommandSet[] colourBySequenceCommands); + /** + * Sends a command to the structure viewer to colour each chain with a + * distinct colour (to the extent supported by the viewer) + */ + public void colourByChain() + { + colourBySequence = false; - public abstract void colourByChain(); + // TODO: JAL-628 colour chains distinctly across all visible models - public abstract void colourByCharge(); + executeCommand(false, COLOURING_STRUCTURES, + commandGenerator.colourByChain()); + } /** - * colour any structures associated with sequences in the given alignment - * using the getFeatureRenderer() and getSequenceRenderer() renderers but only - * if colourBySequence is enabled. + * Sends a command to the structure viewer to colour each chain with a + * distinct colour (to the extent supported by the viewer) */ - public void colourBySequence(AlignmentViewPanel alignmentv) + public void colourByCharge() + { + colourBySequence = false; + + executeCommands(commandGenerator.colourByCharge(), false, + COLOURING_STRUCTURES); + } + + /** + * Sends a command to the structure to apply a colour scheme (defined in + * Jalview but not necessarily applied to the alignment), which defines a + * colour per residue letter. More complex schemes (e.g. that depend on + * consensus) cannot be used here and are ignored. + * + * @param cs + */ + public void colourByJalviewColourScheme(ColourSchemeI cs) { - if (!colourBySequence || !isLoadingFinished()) + colourBySequence = false; + + if (cs == null || !cs.isSimple()) { return; } - if (getSsm() == null) + + /* + * build a map of {Residue3LetterCode, Color} + */ + Map colours = new HashMap<>(); + List residues = ResidueProperties.getResidues(isNucleotide(), + false); + for (String resName : residues) + { + char res = resName.length() == 3 + ? ResidueProperties.getSingleCharacterCode(resName) + : resName.charAt(0); + Color colour = cs.findColour(res, 0, null, null, 0f); + colours.put(resName, colour); + } + + /* + * pass to the command constructor, and send the command + */ + List cmd = commandGenerator + .colourByResidues(colours); + executeCommands(cmd, false, COLOURING_STRUCTURES); + } + + public void setBackgroundColour(Color col) + { + StructureCommandI cmd = commandGenerator.setBackgroundColour(col); + executeCommand(false, null, cmd); + } + + /** + * Execute one structure viewer command. If {@code getReply} is true, may + * optionally return one or more reply messages, else returns null. + * + * @param cmd + * @param getReply + */ + protected abstract List executeCommand(StructureCommandI cmd, + boolean getReply); + + /** + * Executes one or more structure viewer commands + * + * @param commands + * @param getReply + * @param msg + */ + protected List executeCommands(List commands, + boolean getReply, String msg) + { + return executeCommand(getReply, msg, + commands.toArray(new StructureCommandI[commands.size()])); + } + + /** + * Executes one or more structure viewer commands, optionally returning the + * reply, and optionally showing a status message while the command is being + * executed. + *

+ * If a reply is wanted, the execution is done synchronously (waits), + * otherwise it is done in a separate thread (doesn't wait). WARNING: if you + * are sending commands that need to execute before later calls to + * executeCommand (e.g. mouseovers, which clean up after previous ones) then + * set getReply true to ensure that commands are not executed out of order. + * + * @param getReply + * @param msg + * @param cmds + * @return + */ + protected List executeCommand(boolean getReply, String msg, + StructureCommandI... cmds) + { + JalviewStructureDisplayI theViewer = getViewer(); + final long handle = msg == null ? 0 : theViewer.startProgressBar(msg); + + if (getReply) + { + /* + * execute and wait for reply + */ + List response = new ArrayList<>(); + try + { + for (StructureCommandI cmd : cmds) + { + List replies = executeCommand(cmd, true); + if (replies != null) + { + response.addAll(replies); + } + } + return response; + } finally + { + if (msg != null) + { + theViewer.stopProgressBar(null, handle); + } + } + } + + /* + * fire and forget + */ + String threadName = msg == null ? "StructureCommand" : msg; + new Thread(new Runnable() + { + @Override + public void run() + { + try + { + for (StructureCommandI cmd : cmds) + { + executeCommand(cmd, false); + } + } finally + { + if (msg != null) + { + SwingUtilities.invokeLater(new Runnable() + { + @Override + public void run() + { + theViewer.stopProgressBar(null, handle); + } + }); + } + } + } + }, threadName).start(); + return null; + } + + /** + * Colours any structures associated with sequences in the given alignment as + * coloured in the alignment view, provided colourBySequence is enabled + */ + public void colourBySequence(AlignmentViewPanel alignmentv) + { + if (!colourBySequence || !isLoadingFinished() || getSsm() == null) { return; } - String[] files = getStructureFiles(); + Map colourMap = buildColoursMap(ssm, sequence, + alignmentv); + + List colourBySequenceCommands = commandGenerator + .colourBySequence(colourMap); + executeCommands(colourBySequenceCommands, false, COLOURING_STRUCTURES); + } - SequenceRenderer sr = getSequenceRenderer(alignmentv); + /** + * Centre the display in the structure viewer + */ + public void focusView() + { + executeCommand(false, null, commandGenerator.focusView()); + } + + /** + * Generates and executes a command to show only specified chains in the + * structure viewer. The list of chains to show should contain entries + * formatted as "pdbid:chaincode". + * + * @param toShow + */ + public void showChains(List toShow) + { + // todo or reformat toShow list entries as modelNo:pdbId:chainCode ? - StructureMappingcommandSet[] colourBySequenceCommands = getColourBySequenceCommands( - files, sr, alignmentv); - colourBySequence(colourBySequenceCommands); + /* + * Reformat the pdbid:chainCode values as modelNo:chainCode + * since this is what is needed to construct the viewer command + * todo: find a less messy way to do this + */ + List showThese = new ArrayList<>(); + for (String chainId : toShow) + { + String[] tokens = chainId.split("\\:"); + if (tokens.length == 2) + { + String pdbFile = getFileForChain(chainId); + String model = getModelIdForFile(pdbFile); + showThese.add(model + ":" + tokens[1]); + } + } + executeCommands(commandGenerator.showChains(showThese), false, null); } + /** + * Answers the structure viewer's model id given a PDB file name. Returns an + * empty string if model id is not found. + * + * @param chainId + * @return + */ + protected abstract String getModelIdForFile(String chainId); + public boolean hasFileLoadingError() { return fileLoadingError != null && fileLoadingError.length() > 0; } - public abstract jalview.api.FeatureRenderer getFeatureRenderer( - AlignmentViewPanel alignment); + /** + * Returns the FeatureRenderer for the given alignment view + * + * @param avp + * @return + */ + public FeatureRenderer getFeatureRenderer(AlignmentViewPanel avp) + { + AlignmentViewPanel ap = (avp == null) ? getViewer().getAlignmentPanel() + : avp; + if (ap == null) + { + return null; + } + return ap.getFeatureRenderer(); + } + + protected void setStructureCommands(StructureCommandsI cmd) + { + commandGenerator = cmd; + } + + /** + * Records association of one chain id (formatted as "pdbid:chainCode") with + * the corresponding PDB file name + * + * @param chainId + * @param fileName + */ + public void addChainFile(String chainId, String fileName) + { + chainFile.put(chainId, fileName); + } + + /** + * Returns the PDB filename for the given chain id (formatted as + * "pdbid:chainCode"), or null if not found + * + * @param chainId + * @return + */ + protected String getFileForChain(String chainId) + { + return chainFile.get(chainId); + } + + @Override + public void updateColours(Object source) + { + AlignmentViewPanel ap = (AlignmentViewPanel) source; + // ignore events from panels not used to colour this view + if (!getViewer().isUsedForColourBy(ap)) + { + return; + } + if (!isLoadingFromArchive()) + { + colourBySequence(ap); + } + } + + public StructureCommandsI getCommandGenerator() + { + return commandGenerator; + } + + protected abstract ViewerType getViewerType(); + + /** + * Builds a data structure which records mapped structure residues for each + * colour. From this we can easily generate the viewer commands for colour by + * sequence. Constructs and returns a map of {@code Color} to + * {@code AtomSpecModel}, where the atomspec model holds + * + * 

+   *   Model ids
+   *     Chains
+   *       Residue positions
+   *
+ * + * Ordering is by order of addition (for colours), natural ordering (for + * models and chains) + * + * @param ssm + * @param sequence + * @param viewPanel + * @return + */ + protected Map buildColoursMap( + StructureSelectionManager ssm, SequenceI[][] sequence, + AlignmentViewPanel viewPanel) + { + String[] files = getStructureFiles(); + SequenceRenderer sr = getSequenceRenderer(viewPanel); + FeatureRenderer fr = viewPanel.getFeatureRenderer(); + FeatureColourFinder finder = new FeatureColourFinder(fr); + AlignViewportI viewport = viewPanel.getAlignViewport(); + HiddenColumns cs = viewport.getAlignment().getHiddenColumns(); + AlignmentI al = viewport.getAlignment(); + Map colourMap = new LinkedHashMap<>(); + Color lastColour = null; + + for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) + { + final String modelId = getModelIdForFile(files[pdbfnum]); + StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]); + + if (mapping == null || mapping.length < 1) + { + continue; + } + + int startPos = -1, lastPos = -1; + String lastChain = ""; + for (int s = 0; s < sequence[pdbfnum].length; s++) + { + for (int sp, m = 0; m < mapping.length; m++) + { + final SequenceI seq = sequence[pdbfnum][s]; + if (mapping[m].getSequence() == seq + && (sp = al.findIndex(seq)) > -1) + { + SequenceI asp = al.getSequenceAt(sp); + for (int r = 0; r < asp.getLength(); r++) + { + // no mapping to gaps in sequence + if (Comparison.isGap(asp.getCharAt(r))) + { + continue; + } + int pos = mapping[m].getPDBResNum(asp.findPosition(r)); + + if (pos < 1 || pos == lastPos) + { + continue; + } + + Color colour = sr.getResidueColour(seq, r, finder); + + /* + * darker colour for hidden regions + */ + if (!cs.isVisible(r)) + { + colour = Color.GRAY; + } + + final String chain = mapping[m].getChain(); + + /* + * Just keep incrementing the end position for this colour range + * _unless_ colour, PDB model or chain has changed, or there is a + * gap in the mapped residue sequence + */ + final boolean newColour = !colour.equals(lastColour); + final boolean nonContig = lastPos + 1 != pos; + final boolean newChain = !chain.equals(lastChain); + if (newColour || nonContig || newChain) + { + if (startPos != -1) + { + addAtomSpecRange(colourMap, lastColour, modelId, startPos, + lastPos, lastChain); + } + startPos = pos; + } + lastColour = colour; + lastPos = pos; + lastChain = chain; + } + // final colour range + if (lastColour != null) + { + addAtomSpecRange(colourMap, lastColour, modelId, startPos, + lastPos, lastChain); + } + // break; + } + } + } + } + return colourMap; + } + + /** + * todo better refactoring (map lookup or similar to get viewer structure id) + * + * @param pdbfnum + * @param file + * @return + */ + protected String getModelId(int pdbfnum, String file) + { + return String.valueOf(pdbfnum); + } + + /** + * Saves chains, formatted as "pdbId:chainCode", and lookups from this to the + * full PDB file path + * + * @param pdb + * @param file + */ + public void stashFoundChains(StructureFile pdb, String file) + { + for (int i = 0; i < pdb.getChains().size(); i++) + { + String chid = pdb.getId() + ":" + pdb.getChains().elementAt(i).id; + addChainFile(chid, file); + getChainNames().add(chid); + } + } + + /** + * Helper method to add one contiguous range to the AtomSpec model for the + * given value (creating the model if necessary). As used by Jalview, + * {@code value} is + *
    + *
  • a colour, when building a 'colour structure by sequence' command
    • + *
  • a feature value, when building a 'set Chimera attributes from features' + * command
    • + *
+ * + * @param map + * @param value + * @param model + * @param startPos + * @param endPos + * @param chain + */ + public static final void addAtomSpecRange(Map map, + Object value, String model, int startPos, int endPos, + String chain) + { + /* + * Get/initialize map of data for the colour + */ + AtomSpecModel atomSpec = map.get(value); + if (atomSpec == null) + { + atomSpec = new AtomSpecModel(); + map.put(value, atomSpec); + } + + atomSpec.addRange(model, startPos, endPos, chain); + } + + /** + * Returns the file extension (including '.' separator) to use for a saved + * viewer session file. Default is to return null (not supported), override as + * required. + * + * @return + */ + public String getSessionFileExtension() + { + return null; + } + + /** + * If supported, saves the state of the structure viewer to a temporary file + * and returns the file. Returns null and logs an error on any failure. + * + * @return + */ + public File saveSession() + { + String prefix = getViewerType().toString(); + String suffix = getSessionFileExtension(); + File f = null; + try + { + f = File.createTempFile(prefix, suffix); + saveSession(f); + } catch (IOException e) + { + Console.error(String.format("Error saving %s session: %s", prefix, + e.toString())); + } + + return f; + } + + /** + * Saves the structure viewer session to the given file + * + * @param f + */ + protected void saveSession(File f) + { + StructureCommandI cmd = commandGenerator.saveSession(f.getPath()); + if (cmd != null) + { + executeCommand(cmd, false); + } + } + + /** + * Returns true if the viewer is an external structure viewer for which the + * process is still alive, else false (for Jmol, or an external viewer which + * the user has independently closed) + * + * @return + */ + public boolean isViewerRunning() + { + return false; + } + + /** + * Closes Jalview's structure viewer panel and releases associated resources. + * If it is managing an external viewer program, and {@code forceClose} is + * true, also asks that program to close. + * + * @param forceClose + */ + public void closeViewer(boolean forceClose) + { + getSsm().removeStructureViewerListener(this, this.getStructureFiles()); + releaseUIResources(); + + /* + * end the thread that closes this panel if the external viewer closes + */ + if (externalViewerMonitor != null) + { + externalViewerMonitor.interrupt(); + externalViewerMonitor = null; + } + + stopListening(); + + if (forceClose) + { + StructureCommandI cmd = getCommandGenerator().closeViewer(); + if (cmd != null) + { + executeCommand(cmd, false); + } + } + } + + /** + * Returns the URL of a help page for the structure viewer, or null if none is + * known + * + * @return + */ + public String getHelpURL() + { + return null; + } + + /** + * 
+   * Helper method to build a map of 
+   *   { featureType, { feature value, AtomSpecModel } }
+   *
+ * + * @param viewPanel + * @return + */ + protected Map> buildFeaturesMap( + AlignmentViewPanel viewPanel) + { + Map> theMap = new LinkedHashMap<>(); + String[] files = getStructureFiles(); + if (files == null) + { + return theMap; + } + + FeatureRenderer fr = viewPanel.getFeatureRenderer(); + if (fr == null) + { + return theMap; + } + + AlignViewportI viewport = viewPanel.getAlignViewport(); + List visibleFeatures = fr.getDisplayedFeatureTypes(); + + /* + * if alignment is showing features from complement, we also transfer + * these features to the corresponding mapped structure residues + */ + boolean showLinkedFeatures = viewport.isShowComplementFeatures(); + List complementFeatures = new ArrayList<>(); + FeatureRenderer complementRenderer = null; + if (showLinkedFeatures) + { + AlignViewportI comp = fr.getViewport().getCodingComplement(); + if (comp != null) + { + complementRenderer = Desktop.getAlignFrameFor(comp) + .getFeatureRenderer(); + complementFeatures = complementRenderer.getDisplayedFeatureTypes(); + } + } + if (visibleFeatures.isEmpty() && complementFeatures.isEmpty()) + { + return theMap; + } + + AlignmentI alignment = viewPanel.getAlignment(); + SequenceI[][] seqs = getSequence(); + + for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) + { + String modelId = getModelIdForFile(files[pdbfnum]); + StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]); + + if (mapping == null || mapping.length < 1) + { + continue; + } + + for (int seqNo = 0; seqNo < seqs[pdbfnum].length; seqNo++) + { + for (int m = 0; m < mapping.length; m++) + { + final SequenceI seq = seqs[pdbfnum][seqNo]; + int sp = alignment.findIndex(seq); + StructureMapping structureMapping = mapping[m]; + if (structureMapping.getSequence() == seq && sp > -1) + { + /* + * found a sequence with a mapping to a structure; + * now scan its features + */ + if (!visibleFeatures.isEmpty()) + { + scanSequenceFeatures(visibleFeatures, structureMapping, seq, + theMap, modelId); + } + if (showLinkedFeatures) + { + scanComplementFeatures(complementRenderer, structureMapping, + seq, theMap, modelId); + } + } + } + } + } + return theMap; + } + + /** + * Ask the structure viewer to open a session file. Returns true if + * successful, else false (or not supported). + * + * @param filepath + * @return + */ + public boolean openSession(String filepath) + { + StructureCommandI cmd = getCommandGenerator().openSession(filepath); + if (cmd == null) + { + return false; + } + executeCommand(cmd, true); + // todo: test for failure - how? + return true; + } + + /** + * Scans visible features in mapped positions of the CDS/peptide complement, + * and adds any found to the map of attribute values/structure positions + * + * @param complementRenderer + * @param structureMapping + * @param seq + * @param theMap + * @param modelNumber + */ + protected static void scanComplementFeatures( + FeatureRenderer complementRenderer, + StructureMapping structureMapping, SequenceI seq, + Map> theMap, + String modelNumber) + { + /* + * for each sequence residue mapped to a structure position... + */ + for (int seqPos : structureMapping.getMapping().keySet()) + { + /* + * find visible complementary features at mapped position(s) + */ + MappedFeatures mf = complementRenderer + .findComplementFeaturesAtResidue(seq, seqPos); + if (mf != null) + { + for (SequenceFeature sf : mf.features) + { + String type = sf.getType(); + + /* + * Don't copy features which originated from Chimera + */ + if (JalviewChimeraBinding.CHIMERA_FEATURE_GROUP + .equals(sf.getFeatureGroup())) + { + continue; + } + + /* + * record feature 'value' (score/description/type) as at the + * corresponding structure position + */ + List mappedRanges = structureMapping + .getPDBResNumRanges(seqPos, seqPos); + + if (!mappedRanges.isEmpty()) + { + String value = sf.getDescription(); + if (value == null || value.length() == 0) + { + value = type; + } + float score = sf.getScore(); + if (score != 0f && !Float.isNaN(score)) + { + value = Float.toString(score); + } + Map featureValues = theMap.get(type); + if (featureValues == null) + { + featureValues = new HashMap<>(); + theMap.put(type, featureValues); + } + for (int[] range : mappedRanges) + { + addAtomSpecRange(featureValues, value, modelNumber, range[0], + range[1], structureMapping.getChain()); + } + } + } + } + } + } + + /** + * Inspect features on the sequence; for each feature that is visible, + * determine its mapped ranges in the structure (if any) according to the + * given mapping, and add them to the map. + * + * @param visibleFeatures + * @param mapping + * @param seq + * @param theMap + * @param modelId + */ + protected static void scanSequenceFeatures(List visibleFeatures, + StructureMapping mapping, SequenceI seq, + Map> theMap, String modelId) + { + List sfs = seq.getFeatures().getPositionalFeatures( + visibleFeatures.toArray(new String[visibleFeatures.size()])); + for (SequenceFeature sf : sfs) + { + String type = sf.getType(); + + /* + * Don't copy features which originated from Chimera + */ + if (JalviewChimeraBinding.CHIMERA_FEATURE_GROUP + .equals(sf.getFeatureGroup())) + { + continue; + } + + List mappedRanges = mapping.getPDBResNumRanges(sf.getBegin(), + sf.getEnd()); + + if (!mappedRanges.isEmpty()) + { + String value = sf.getDescription(); + if (value == null || value.length() == 0) + { + value = type; + } + float score = sf.getScore(); + if (score != 0f && !Float.isNaN(score)) + { + value = Float.toString(score); + } + Map featureValues = theMap.get(type); + if (featureValues == null) + { + featureValues = new HashMap<>(); + theMap.put(type, featureValues); + } + for (int[] range : mappedRanges) + { + addAtomSpecRange(featureValues, value, modelId, range[0], + range[1], mapping.getChain()); + } + } + } + } + + /** + * Returns the number of structure files in the structure viewer and mapped to + * Jalview. This may be zero if the files are still in the process of loading + * in the viewer. + * + * @return + */ + public int getMappedStructureCount() + { + String[] files = getStructureFiles(); + return files == null ? 0 : files.length; + } + + /** + * Starts a thread that waits for the external viewer program process to + * finish, so that we can then close the associated resources. This avoids + * leaving orphaned viewer panels in Jalview if the user closes the external + * viewer. + * + * @param p + */ + protected void startExternalViewerMonitor(Process p) + { + externalViewerMonitor = 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 + } + } + }); + externalViewerMonitor.start(); + } + + /** + * If supported by the external structure viewer, sends it commands to notify + * model or selection changes to the specified URL (where Jalview has started + * a listener) + * + * @param uri + */ + protected void startListening(String uri) + { + List commands = getCommandGenerator() + .startNotifications(uri); + if (commands != null) + { + executeCommands(commands, false, null); + } + } + + /** + * If supported by the external structure viewer, sends it commands to stop + * notifying model or selection changes + */ + protected void stopListening() + { + List commands = getCommandGenerator() + .stopNotifications(); + if (commands != null) + { + executeCommands(commands, false, null); + } + } + + /** + * If supported by the structure viewer, queries it for all residue attributes + * with the given attribute name, and creates features on corresponding + * residues of the alignment. Returns the number of features added. + * + * @param attName + * @param alignmentPanel + * @return + */ + public int copyStructureAttributesToFeatures(String attName, + AlignmentPanel alignmentPanel) + { + StructureCommandI cmd = getCommandGenerator() + .getResidueAttributes(attName); + if (cmd == null) + { + return 0; + } + List residueAttributes = executeCommand(cmd, true); + + int featuresAdded = createFeaturesForAttributes(attName, + residueAttributes); + if (featuresAdded > 0) + { + alignmentPanel.getFeatureRenderer().featuresAdded(); + } + return featuresAdded; + } + + /** + * Parses {@code residueAttributes} and creates sequence features on any + * mapped alignment residues. Returns the number of features created. + *

+ * {@code residueAttributes} is the reply from the structure viewer to a + * command to list any residue attributes for the given attribute name. Syntax + * and parsing of this is viewer-specific. + * + * @param attName + * @param residueAttributes + * @return + */ + protected int createFeaturesForAttributes(String attName, + List residueAttributes) + { + return 0; + } }