X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructures%2Fmodels%2FAAStructureBindingModel.java;h=5a7b4484cd728b78f51d21b0a6ef9dd7e735dcb0;hb=a395b6d73484b2827f3e80295631e69dd8841c47;hp=8c2dc46e46f30727e8c55223aab84e21516ca89a;hpb=2ab7b9b152018bb808693218ad88dc3778166492;p=jalview.git diff --git a/src/jalview/structures/models/AAStructureBindingModel.java b/src/jalview/structures/models/AAStructureBindingModel.java index 8c2dc46..5a7b448 100644 --- a/src/jalview/structures/models/AAStructureBindingModel.java +++ b/src/jalview/structures/models/AAStructureBindingModel.java @@ -20,19 +20,44 @@ */ package jalview.structures.models; +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.Cache; 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.StructureListener; import jalview.structure.StructureMapping; @@ -40,16 +65,6 @@ 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.HashMap; -import java.util.List; -import java.util.Map; - -import javax.swing.SwingUtilities; - /** * * A base class to hold common function for protein structure model binding. @@ -63,6 +78,44 @@ 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 = ""; + + 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"); @@ -117,40 +170,13 @@ public abstract class AAStructureBindingModel 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 @@ -237,6 +263,7 @@ public abstract class AAStructureBindingModel chains = newchains; return chainmaps > 0; } + public StructureSelectionManager getSsm() { return ssm; @@ -361,7 +388,11 @@ public abstract class AAStructureBindingModel */ protected void releaseUIResources() { + } + @Override + public void releaseReferences(Object svl) + { } public boolean isColourBySequence() @@ -369,6 +400,25 @@ 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; @@ -611,7 +661,8 @@ 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(); @@ -669,7 +720,7 @@ public abstract class AAStructureBindingModel * for the same structure) */ s = seqCountForPdbFile; - break; + break; // fixme break out of two loops here! } } } @@ -790,21 +841,123 @@ public abstract class AAStructureBindingModel /** * 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. + * an error or warning message for the alignment command(s). * - * @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 + * @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); + + /* + * 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); + List replies = executeCommands(commands, true, null); + for (String reply : replies) + { + // return this error (Chimera only) to the user + if (reply.toLowerCase().contains("unequal numbers of atoms")) + { + error += "; " + reply; + } + } + } + } + } + + 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); + } + + return model; + } /** * returns the current sequenceRenderer that should be used to colour the @@ -827,8 +980,8 @@ public abstract class AAStructureBindingModel // TODO: JAL-628 colour chains distinctly across all visible models - executeCommand(commandGenerator.colourByChain(), false, - COLOURING_STRUCTURES); + executeCommand(false, COLOURING_STRUCTURES, + commandGenerator.colourByChain()); } /** @@ -839,7 +992,7 @@ public abstract class AAStructureBindingModel { colourBySequence = false; - executeCommand(commandGenerator.colourByCharge(), false, + executeCommands(commandGenerator.colourByCharge(), false, COLOURING_STRUCTURES); } @@ -859,7 +1012,7 @@ public abstract class AAStructureBindingModel { return; } - + /* * build a map of {Residue3LetterCode, Color} */ @@ -878,137 +1031,136 @@ public abstract class AAStructureBindingModel /* * pass to the command constructor, and send the command */ - String cmd = commandGenerator.colourByResidues(colours); - executeCommand(cmd, false, COLOURING_STRUCTURES); + List cmd = commandGenerator + .colourByResidues(colours); + executeCommands(cmd, false, COLOURING_STRUCTURES); } public void setBackgroundColour(Color col) { - String cmd = commandGenerator.setBackgroundColour(col); - executeCommand(cmd, false, null); + StructureCommandI cmd = commandGenerator.setBackgroundColour(col); + executeCommand(false, null, cmd); } /** - * Sends one command to the structure viewer. If {@code getReply} is true, the - * command is sent synchronously, otherwise in a deferred thread. - *

- * If a progress message is supplied, this is displayed before command - * execution, and removed afterwards. + * 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 - * @return */ - private List executeCommand(String cmd, boolean getReply, - String msg) + protected List executeCommands(List commands, + boolean getReply, String msg) { - if (getReply) - { - return executeSynchronous(cmd, msg, getReply); - } - else - { - executeAsynchronous(cmd, msg); - return null; - } + return executeCommand(getReply, msg, + commands.toArray(new StructureCommandI[commands.size()])); } /** - * Sends the command in the current thread. If a message is supplied, this is - * shown before the thread is started, and removed when it completes. May - * return a reply to the command if requested. + * 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). * - * @param cmd - * @param msg * @param getReply + * @param msg + * @param cmds * @return */ - private List executeSynchronous(String cmd, String msg, boolean getReply) + protected List executeCommand(boolean getReply, String msg, + StructureCommandI... cmds) { - final JalviewStructureDisplayI theViewer = getViewer(); + JalviewStructureDisplayI theViewer = getViewer(); final long handle = msg == null ? 0 : theViewer.startProgressBar(msg); - try - { - return executeCommand(cmd, getReply); - } finally + + if (getReply) { - if (msg != null) + /* + * 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 { - theViewer.stopProgressBar(null, handle); + if (msg != null) + { + theViewer.stopProgressBar(null, handle); + } } } - } - - /** - * Sends the command in a separate thread. If a message is supplied, this is - * shown before the thread is started, and removed when it completes. No value - * is returned. - * - * @param cmd - * @param msg - */ - private void executeAsynchronous(String cmd, String msg) - { - final JalviewStructureDisplayI theViewer = getViewer(); - final long handle = msg == null ? 0 : theViewer.startProgressBar(msg); - SwingUtilities.invokeLater(new Runnable() + /* + * fire and forget + */ + String threadName = msg == null ? "StructureCommand" : msg; + new Thread(new Runnable() { @Override public void run() { try { - executeCommand(cmd, false); + for (StructureCommandI cmd : cmds) + { + executeCommand(cmd, false); + } } finally { if (msg != null) { - theViewer.stopProgressBar(null, handle); + SwingUtilities.invokeLater(new Runnable() + { + @Override + public void run() + { + theViewer.stopProgressBar(null, handle); + } + }); } } } - }); - } - - protected abstract List executeCommand(String command, - boolean getReply); - - protected List executeCommands(boolean getReply, - String... commands) - { - List response = null; - for (String cmd : commands) - { - response = executeCommand(cmd, getReply); - } - return response; + }, threadName).start(); + return null; } /** - * colour any structures associated with sequences in the given alignment - * using the getFeatureRenderer() and getSequenceRenderer() renderers but only - * if colourBySequence is enabled. + * 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()) - { - return; - } - if (getSsm() == null) + if (!colourBySequence || !isLoadingFinished() || getSsm() == null) { return; } - String[] files = getStructureFiles(); + Map colourMap = buildColoursMap(ssm, sequence, + alignmentv); - SequenceRenderer sr = getSequenceRenderer(alignmentv); - - String[] colourBySequenceCommands = commandGenerator - .colourBySequence(getSsm(), files, getSequence(), sr, - alignmentv); - executeCommands(false, colourBySequenceCommands); + List colourBySequenceCommands = commandGenerator + .colourBySequence(colourMap); + executeCommands(colourBySequenceCommands, false, COLOURING_STRUCTURES); } /** @@ -1016,7 +1168,7 @@ public abstract class AAStructureBindingModel */ public void focusView() { - executeCommand(commandGenerator.focusView(), false); + executeCommand(false, null, commandGenerator.focusView()); } /** @@ -1042,22 +1194,21 @@ public abstract class AAStructureBindingModel if (tokens.length == 2) { String pdbFile = getFileForChain(chainId); - int modelNo = getModelNoForFile(pdbFile); - String model = modelNo == -1 ? "" : String.valueOf(modelNo); + String model = getModelIdForFile(pdbFile); showThese.add(model + ":" + tokens[1]); } } - executeCommand(commandGenerator.showChains(showThese), false); + executeCommands(commandGenerator.showChains(showThese), false, null); } /** - * Answers the structure viewer's model number given a PDB file name. Returns - * -1 if model number is not found. + * 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 int getModelNoForFile(String chainId); + protected abstract String getModelIdForFile(String chainId); public boolean hasFileLoadingError() { @@ -1065,8 +1216,7 @@ public abstract class AAStructureBindingModel } /** - * Returns the FeatureRenderer for the given alignment view, or null if - * feature display is turned off in the view. + * Returns the FeatureRenderer for the given alignment view * * @param avp * @return @@ -1075,9 +1225,11 @@ public abstract class AAStructureBindingModel { AlignmentViewPanel ap = (avp == null) ? getViewer().getAlignmentPanel() : avp; - return ap.getAlignViewport().isShowSequenceFeatures() - ? ap.getFeatureRenderer() - : null; + if (ap == null) + { + return null; + } + return ap.getFeatureRenderer(); } protected void setStructureCommands(StructureCommandsI cmd) @@ -1108,4 +1260,684 @@ public abstract class AAStructureBindingModel { 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) + { + Cache.log.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; + } }