X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructures%2Fmodels%2FAAStructureBindingModel.java;h=9ecf630b571a4b54639c3378e8308a16f1d561a8;hb=8286731258d314669ee6facb627947fe159ac1eb;hp=f69a423b5c9ec962a5ee35d68247476173dab8a1;hpb=4994aa94fd62af0058f2db96f0ea6c4ca1abe80b;p=jalview.git diff --git a/src/jalview/structures/models/AAStructureBindingModel.java b/src/jalview/structures/models/AAStructureBindingModel.java index f69a423..9ecf630 100644 --- a/src/jalview/structures/models/AAStructureBindingModel.java +++ b/src/jalview/structures/models/AAStructureBindingModel.java @@ -20,6 +20,8 @@ */ package jalview.structures.models; +import java.util.Locale; + import java.awt.Color; import java.io.File; import java.io.IOException; @@ -39,7 +41,7 @@ import jalview.api.FeatureRenderer; import jalview.api.SequenceRenderer; import jalview.api.StructureSelectionManagerProvider; import jalview.api.structures.JalviewStructureDisplayI; -import jalview.bin.Cache; +import jalview.bin.Console; import jalview.datamodel.AlignmentI; import jalview.datamodel.HiddenColumns; import jalview.datamodel.MappedFeatures; @@ -47,6 +49,7 @@ 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; @@ -58,6 +61,7 @@ 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.StructureSelectionManager; @@ -66,7 +70,7 @@ import jalview.util.MessageManager; /** * - * A base class to hold common function for protein structure model binding. + * 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. * @@ -83,20 +87,23 @@ public abstract class AAStructureBindingModel 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 * @@ -164,6 +171,9 @@ public abstract class AAStructureBindingModel protected boolean colourBySequence = true; + /** + * true if all sequences appear to be nucleotide + */ private boolean nucleotide; private boolean finishedInit = false; @@ -262,6 +272,7 @@ public abstract class AAStructureBindingModel chains = newchains; return chainmaps > 0; } + public StructureSelectionManager getSsm() { return ssm; @@ -580,6 +591,7 @@ public abstract class AAStructureBindingModel } } } + @Override public abstract void highlightAtoms(List atoms); @@ -659,7 +671,8 @@ public abstract class AAStructureBindingModel * @return */ protected int findSuperposableResidues(AlignmentI alignment, - BitSet matched, AAStructureBindingModel.SuperposeData[] structures) + BitSet matched, + AAStructureBindingModel.SuperposeData[] structures) { int refStructure = -1; String[] files = getStructureFiles(); @@ -710,7 +723,7 @@ 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 @@ -885,8 +898,8 @@ public abstract class AAStructureBindingModel * Calculate the superposable alignment columns ('matched'), and the * corresponding structure residue positions (structures.pdbResNo) */ - int refStructure = findSuperposableResidues(alignment, - matched, structures); + int refStructure = findSuperposableResidues(alignment, matched, + structures); /* * require at least 4 positions to be able to execute superposition @@ -894,8 +907,8 @@ public abstract class AAStructureBindingModel int nmatched = matched.cardinality(); if (nmatched < MIN_POS_TO_SUPERPOSE) { - String msg = MessageManager.formatMessage("label.insufficient_residues", - nmatched); + String msg = MessageManager + .formatMessage("label.insufficient_residues", nmatched); error += view.getViewName() + ": " + msg + "; "; continue; } @@ -912,7 +925,8 @@ public abstract class AAStructureBindingModel */ // 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 */ @@ -922,12 +936,12 @@ public abstract class AAStructureBindingModel { AtomSpecModel atomSpec = getAtomSpec(structures[i], matched); List commands = commandGenerator - .superposeStructures(refAtoms, atomSpec); + .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().contains("unequal numbers of atoms")) + if (reply.toLowerCase(Locale.ROOT).contains("unequal numbers of atoms")) { error += "; " + reply; } @@ -939,7 +953,8 @@ public abstract class AAStructureBindingModel return error; } - private AtomSpecModel getAtomSpec(AAStructureBindingModel.SuperposeData superposeData, + private AtomSpecModel getAtomSpec( + AAStructureBindingModel.SuperposeData superposeData, BitSet matched) { AtomSpecModel model = new AtomSpecModel(); @@ -976,8 +991,8 @@ 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()); } /** @@ -1008,7 +1023,7 @@ public abstract class AAStructureBindingModel { return; } - + /* * build a map of {Residue3LetterCode, Color} */ @@ -1035,34 +1050,72 @@ public abstract class AAStructureBindingModel public void setBackgroundColour(Color col) { StructureCommandI cmd = commandGenerator.setBackgroundColour(col); - executeCommand(cmd, false, null); + 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(StructureCommandI cmd, + 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) { /* - * synchronous (same thread) execution so reply can be returned + * execute and wait for reply */ - final JalviewStructureDisplayI theViewer = getViewer(); - final long handle = msg == null ? 0 : theViewer.startProgressBar(msg); + List response = new ArrayList<>(); try { - return executeCommand(cmd, getReply); + for (StructureCommandI cmd : cmds) + { + List replies = executeCommand(cmd, true); + if (replies != null) + { + response.addAll(replies); + } + } + return response; } finally { if (msg != null) @@ -1071,81 +1124,39 @@ public abstract class AAStructureBindingModel } } } - else + + /* + * fire and forget + */ + String threadName = msg == null ? "StructureCommand" : msg; + new Thread(new Runnable() { - /* - * asynchronous (new thread) execution if no reply needed - */ - final JalviewStructureDisplayI theViewer = getViewer(); - final long handle = msg == null ? 0 : theViewer.startProgressBar(msg); - - SwingUtilities.invokeLater(new Runnable() + @Override + public void run() { - @Override - public void run() + try { - try + for (StructureCommandI cmd : cmds) { executeCommand(cmd, false); - } finally + } + } finally + { + if (msg != null) { - if (msg != null) + SwingUtilities.invokeLater(new Runnable() { - theViewer.stopProgressBar(null, handle); - } + @Override + public void run() + { + theViewer.stopProgressBar(null, handle); + } + }); } } - }); - return null; - } - } - - /** - * 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. If a progress message is - * provided, it is shown first, and removed after all commands have been run. - * - * @param commands - * @param getReply - * @param msg - */ - protected List executeCommands(List commands, - boolean getReply, String msg) - { - /* - * show progress message if specified - */ - final JalviewStructureDisplayI theViewer = getViewer(); - final long handle = msg == null ? 0 : theViewer.startProgressBar(msg); - - List response = getReply ? new ArrayList<>() : null; - try - { - for (StructureCommandI cmd : commands) - { - List replies = executeCommand(cmd, getReply, null); - if (getReply && replies != null) - { - response.addAll(replies); - } - } - return response; - } finally - { - if (msg != null) - { - theViewer.stopProgressBar(null, handle); } - } + }, threadName).start(); + return null; } /** @@ -1163,7 +1174,7 @@ public abstract class AAStructureBindingModel List colourBySequenceCommands = commandGenerator .colourBySequence(colourMap); - executeCommands(colourBySequenceCommands, false, null); + executeCommands(colourBySequenceCommands, false, COLOURING_STRUCTURES); } /** @@ -1171,7 +1182,7 @@ public abstract class AAStructureBindingModel */ public void focusView() { - executeCommand(commandGenerator.focusView(), false, null); + executeCommand(false, null, commandGenerator.focusView()); } /** @@ -1219,8 +1230,7 @@ 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 @@ -1233,9 +1243,7 @@ public abstract class AAStructureBindingModel { return null; } - return ap.getAlignViewport().isShowSequenceFeatures() - ? ap.getFeatureRenderer() - : null; + return ap.getFeatureRenderer(); } protected void setStructureCommands(StructureCommandsI cmd) @@ -1290,40 +1298,6 @@ public abstract class AAStructureBindingModel protected abstract ViewerType getViewerType(); /** - * Send a structure viewer 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 void sendAsynchronousCommand(StructureCommandI command, - String progressMsg) - { - final JalviewStructureDisplayI theViewer = getViewer(); - final long handle = progressMsg == null ? 0 - : theViewer.startProgressBar(progressMsg); - SwingUtilities.invokeLater(new Runnable() - { - @Override - public void run() - { - try - { - executeCommand(command, false, null); - } finally - { - if (progressMsg != null) - { - theViewer.stopProgressBar(null, handle); - } - } - } - }); - - } - - /** * 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 @@ -1356,17 +1330,17 @@ public abstract class AAStructureBindingModel 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++) @@ -1386,14 +1360,14 @@ public abstract class AAStructureBindingModel 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 */ @@ -1401,9 +1375,9 @@ public abstract class AAStructureBindingModel { 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 @@ -1416,8 +1390,8 @@ public abstract class AAStructureBindingModel { if (startPos != -1) { - addAtomSpecRange(colourMap, lastColour, modelId, - startPos, lastPos, lastChain); + addAtomSpecRange(colourMap, lastColour, modelId, startPos, + lastPos, lastChain); } startPos = pos; } @@ -1469,8 +1443,9 @@ public abstract class AAStructureBindingModel } /** - * 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 + * 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' @@ -1485,8 +1460,8 @@ public abstract class AAStructureBindingModel * @param chain */ public static final void addAtomSpecRange(Map map, - Object value, - String model, int startPos, int endPos, String chain) + Object value, String model, int startPos, int endPos, + String chain) { /* * Get/initialize map of data for the colour @@ -1497,7 +1472,7 @@ public abstract class AAStructureBindingModel atomSpec = new AtomSpecModel(); map.put(value, atomSpec); } - + atomSpec.addRange(model, startPos, endPos, chain); } @@ -1530,8 +1505,8 @@ public abstract class AAStructureBindingModel saveSession(f); } catch (IOException e) { - Cache.log.error(String.format("Error saving %s session: %s", - prefix, e.toString())); + Console.error(String.format("Error saving %s session: %s", prefix, + e.toString())); } return f; @@ -1544,8 +1519,7 @@ public abstract class AAStructureBindingModel */ protected void saveSession(File f) { - StructureCommandI cmd = commandGenerator - .saveSession(f.getPath()); + StructureCommandI cmd = commandGenerator.saveSession(f.getPath()); if (cmd != null) { executeCommand(cmd, false); @@ -1586,7 +1560,7 @@ public abstract class AAStructureBindingModel } stopListening(); - + if (forceClose) { StructureCommandI cmd = getCommandGenerator().closeViewer(); @@ -1632,10 +1606,10 @@ public abstract class AAStructureBindingModel { 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 @@ -1657,7 +1631,7 @@ public abstract class AAStructureBindingModel { return theMap; } - + AlignmentI alignment = viewPanel.getAlignment(); SequenceI[][] seqs = getSequence(); @@ -1665,12 +1639,12 @@ public abstract class AAStructureBindingModel { 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++) @@ -1721,8 +1695,8 @@ public abstract class AAStructureBindingModel } /** - * Scans visible features in mapped positions of the CDS/peptide complement, and - * adds any found to the map of attribute values/structure positions + * 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 @@ -1751,7 +1725,7 @@ public abstract class AAStructureBindingModel for (SequenceFeature sf : mf.features) { String type = sf.getType(); - + /* * Don't copy features which originated from Chimera */ @@ -1760,14 +1734,14 @@ public abstract class AAStructureBindingModel { 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(); @@ -1817,7 +1791,7 @@ public abstract class AAStructureBindingModel for (SequenceFeature sf : sfs) { String type = sf.getType(); - + /* * Don't copy features which originated from Chimera */ @@ -1826,10 +1800,10 @@ public abstract class AAStructureBindingModel { continue; } - + List mappedRanges = mapping.getPDBResNumRanges(sf.getBegin(), sf.getEnd()); - + if (!mappedRanges.isEmpty()) { String value = sf.getDescription(); @@ -1882,7 +1856,7 @@ public abstract class AAStructureBindingModel { externalViewerMonitor = new Thread(new Runnable() { - + @Override public void run() { @@ -1933,4 +1907,51 @@ public abstract class AAStructureBindingModel 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; + } }