X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructures%2Fmodels%2FAAStructureBindingModel.java;h=6e926df87a475774acbbf2ff05bea75c8b3766fd;hb=d85a2741994c169e1b81db8f9166f5214ff1f561;hp=92b00c77cc01bbf6e92362f4a0abb03cbfcf0015;hpb=6cb920bb7a7f285a165cd34b3429dabba71f7518;p=jalview.git diff --git a/src/jalview/structures/models/AAStructureBindingModel.java b/src/jalview/structures/models/AAStructureBindingModel.java index 92b00c7..6e926df 100644 --- a/src/jalview/structures/models/AAStructureBindingModel.java +++ b/src/jalview/structures/models/AAStructureBindingModel.java @@ -20,19 +20,39 @@ */ 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.PDBEntry; import jalview.datamodel.SequenceI; +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 +60,6 @@ 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 +73,44 @@ 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"); @@ -117,42 +165,13 @@ 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; - } - - /** * Constructor * * @param ssm @@ -634,7 +653,7 @@ 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(); @@ -692,7 +711,7 @@ public abstract class AAStructureBindingModel * for the same structure) */ s = seqCountForPdbFile; - break; + break; // fixme break out of two loops here! } } } @@ -813,21 +832,122 @@ 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 @@ -862,7 +982,7 @@ public abstract class AAStructureBindingModel { colourBySequence = false; - executeCommand(commandGenerator.colourByCharge(), false, + executeCommands(commandGenerator.colourByCharge(), false, COLOURING_STRUCTURES); } @@ -901,13 +1021,14 @@ 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); + StructureCommandI cmd = commandGenerator.setBackgroundColour(col); executeCommand(cmd, false, null); } @@ -923,90 +1044,119 @@ public abstract class AAStructureBindingModel * @param msg * @return */ - private List executeCommand(String cmd, boolean getReply, - String msg) + private List executeCommand(StructureCommandI cmd, + boolean getReply, String msg) { if (getReply) { - return executeSynchronous(cmd, msg, getReply); + /* + * synchronous (same thread) execution so reply can be returned + */ + final JalviewStructureDisplayI theViewer = getViewer(); + final long handle = msg == null ? 0 : theViewer.startProgressBar(msg); + try + { + return executeCommand(cmd, getReply); + } finally + { + if (msg != null) + { + theViewer.stopProgressBar(null, handle); + } + } } else { - executeAsynchronous(cmd, msg); + /* + * 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() + { + try + { + executeCommand(cmd, false); + } finally + { + if (msg != null) + { + theViewer.stopProgressBar(null, handle); + } + } + } + }); return null; } } /** - * 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. + * Execute one structure viewer command. If {@code getReply} is true, may + * optionally return one or more reply messages, else returns null. * * @param cmd - * @param msg * @param getReply - * @return */ - private List executeSynchronous(String cmd, String msg, boolean getReply) + protected abstract List executeCommand(StructureCommandI cmd, + boolean getReply); + + /** + * A helper method that converts list of commands to a vararg array + * + * @param commands + * @param getReply + * @param msg + */ + private List executeCommands(List commands, + boolean getReply, String msg) { - final JalviewStructureDisplayI theViewer = getViewer(); - final long handle = msg == null ? 0 : theViewer.startProgressBar(msg); - try - { - return executeCommand(cmd, getReply); - } finally - { - if (msg != null) - { - theViewer.stopProgressBar(null, handle); - } - } + return executeCommands(getReply, msg, + commands.toArray(new StructureCommandI[commands.size()])); } /** - * 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. + * 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 cmd + * @param getReply * @param msg + * @param commands + * @return */ - private void executeAsynchronous(String cmd, String msg) + protected List executeCommands(boolean getReply, String msg, + StructureCommandI[] commands) { + // todo: tidy this up + + /* + * show progress message if specified + */ final JalviewStructureDisplayI theViewer = getViewer(); final long handle = msg == null ? 0 : theViewer.startProgressBar(msg); - SwingUtilities.invokeLater(new Runnable() + List response = getReply ? new ArrayList<>() : null; + try { - @Override - public void run() + for (StructureCommandI cmd : commands) { - try - { - executeCommand(cmd, false); - } finally + List replies = executeCommand(cmd, getReply, null); + if (getReply && replies != null) { - if (msg != null) - { - theViewer.stopProgressBar(null, handle); - } + response.addAll(replies); } } - }); - } - - protected abstract List executeCommand(String command, - boolean getReply); - - protected List executeCommands(boolean getReply, - String... commands) - { - List response = null; - for (String cmd : commands) + return response; + } finally { - response = executeCommand(cmd, getReply); + if (msg != null) + { + theViewer.stopProgressBar(null, handle); + } } - return response; } /** @@ -1027,11 +1177,12 @@ public abstract class AAStructureBindingModel String[] files = getStructureFiles(); SequenceRenderer sr = getSequenceRenderer(alignmentv); + Map colourMap = buildColoursMap(ssm, files, + sequence, sr, alignmentv); - String[] colourBySequenceCommands = commandGenerator - .colourBySequence(getSsm(), files, getSequence(), sr, - alignmentv); - executeCommands(false, colourBySequenceCommands); + List colourBySequenceCommands = commandGenerator + .colourBySequence(colourMap); + executeCommands(colourBySequenceCommands, false, null); } /** @@ -1039,7 +1190,7 @@ public abstract class AAStructureBindingModel */ public void focusView() { - executeCommand(commandGenerator.focusView(), false); + executeCommand(commandGenerator.focusView(), false, null); } /** @@ -1065,22 +1216,21 @@ 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() { @@ -1151,4 +1301,297 @@ public abstract class AAStructureBindingModel { return commandGenerator; } + + 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 + * {@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 files + * @param sequence + * @param sr + * @param viewPanel + * @return + */ + protected Map buildColoursMap( + StructureSelectionManager ssm, String[] files, + SequenceI[][] sequence, SequenceRenderer sr, AlignmentViewPanel 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 shuts down that program. + * + * @param forceClose + */ + public void closeViewer(boolean forceClose) + { + getSsm().removeStructureViewerListener(this, this.getStructureFiles()); + releaseUIResources(); + + // add external viewer shutdown in overrides + // todo - or can maybe pull up to here + } }