X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructures%2Fmodels%2FAAStructureBindingModel.java;h=8c2dc46e46f30727e8c55223aab84e21516ca89a;hb=2ab7b9b152018bb808693218ad88dc3778166492;hp=82ba2d7bf4d63eb9a8de8869a2a68b693179c53a;hpb=2888e7307e1f7c8239234941498cb86e8c65ab36;p=jalview.git diff --git a/src/jalview/structures/models/AAStructureBindingModel.java b/src/jalview/structures/models/AAStructureBindingModel.java index 82ba2d7..8c2dc46 100644 --- a/src/jalview/structures/models/AAStructureBindingModel.java +++ b/src/jalview/structures/models/AAStructureBindingModel.java @@ -21,19 +21,21 @@ package jalview.structures.models; import jalview.api.AlignmentViewPanel; +import jalview.api.FeatureRenderer; import jalview.api.SequenceRenderer; import jalview.api.StructureSelectionManagerProvider; import jalview.api.structures.JalviewStructureDisplayI; import jalview.datamodel.AlignmentI; -import jalview.datamodel.ColumnSelection; +import jalview.datamodel.HiddenColumns; import jalview.datamodel.PDBEntry; import jalview.datamodel.SequenceI; import jalview.io.DataSourceType; import jalview.schemes.ColourSchemeI; +import jalview.schemes.ResidueProperties; import jalview.structure.AtomSpec; +import jalview.structure.StructureCommandsI; import jalview.structure.StructureListener; import jalview.structure.StructureMapping; -import jalview.structure.StructureMappingcommandSet; import jalview.structure.StructureSelectionManager; import jalview.util.Comparison; import jalview.util.MessageManager; @@ -42,7 +44,11 @@ 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; /** * @@ -53,14 +59,37 @@ import java.util.List; * @author gmcarstairs * */ -public abstract class AAStructureBindingModel extends - SequenceStructureBindingModel implements StructureListener, - StructureSelectionManagerProvider +public abstract class AAStructureBindingModel + extends SequenceStructureBindingModel + implements StructureListener, StructureSelectionManagerProvider { + 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 */ @@ -134,6 +163,8 @@ public abstract class AAStructureBindingModel extends { this.ssm = ssm; this.sequence = seqs; + chainNames = new ArrayList<>(); + chainFile = new HashMap<>(); } /** @@ -142,20 +173,70 @@ public abstract class AAStructureBindingModel extends * @param ssm * @param pdbentry * @param sequenceIs - * @param chains * @param protocol */ public AAStructureBindingModel(StructureSelectionManager ssm, 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; + resolveChains(); } + private boolean resolveChains() + { + /** + * final count of chain mappings discovered + */ + int chainmaps = 0; + // JBPNote: JAL-2693 - this should be a list of chain mappings per + // [pdbentry][sequence] + String[][] newchains = new String[pdbEntry.length][]; + int pe = 0; + for (PDBEntry pdb : pdbEntry) + { + SequenceI[] seqsForPdb = sequence[pe]; + if (seqsForPdb != null) + { + newchains[pe] = new String[seqsForPdb.length]; + int se = 0; + for (SequenceI asq : seqsForPdb) + { + String chain = (chains != null && chains[pe] != null) + ? chains[pe][se] + : null; + SequenceI sq = (asq.getDatasetSequence() == null) ? asq + : asq.getDatasetSequence(); + if (sq.getAllPDBEntries() != null) + { + for (PDBEntry pdbentry : sq.getAllPDBEntries()) + { + if (pdb.getFile() != null && pdbentry.getFile() != null + && pdb.getFile().equals(pdbentry.getFile())) + { + String chaincode = pdbentry.getChainCode(); + if (chaincode != null && chaincode.length() > 0) + { + chain = chaincode; + chainmaps++; + break; + } + } + } + } + newchains[pe][se] = chain; + se++; + } + pe++; + } + } + + chains = newchains; + return chainmaps > 0; + } public StructureSelectionManager getSsm() { return ssm; @@ -300,11 +381,12 @@ public abstract class AAStructureBindingModel extends { throw new Error(MessageManager.formatMessage( "error.implementation_error_no_pdbentry_from_index", - new Object[] { Integer.valueOf(pe).toString() })); + new Object[] + { 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()][]); @@ -373,8 +455,8 @@ public abstract class AAStructureBindingModel extends 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)); @@ -532,7 +614,7 @@ public abstract class AAStructureBindingModel extends BitSet matched, SuperposeData[] structures) { int refStructure = -1; - String[] files = getPdbFile(); + String[] files = getStructureFiles(); if (files == null) { return -1; @@ -638,8 +720,8 @@ public abstract class AAStructureBindingModel extends if (waiting) { - System.err - .println("Timed out waiting for structure viewer to load file " + System.err.println( + "Timed out waiting for structure viewer to load file " + notLoaded); return false; } @@ -657,10 +739,8 @@ public abstract class AAStructureBindingModel extends { for (SequenceI s : seqs) { - if (s == seq - || (s.getDatasetSequence() != null && s - .getDatasetSequence() == seq - .getDatasetSequence())) + if (s == seq || (s.getDatasetSequence() != null + && s.getDatasetSequence() == seq.getDatasetSequence())) { return true; } @@ -682,11 +762,15 @@ public abstract class AAStructureBindingModel extends } /** - * 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) @@ -695,10 +779,13 @@ public abstract class AAStructureBindingModel extends */ 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 @@ -716,13 +803,8 @@ public abstract class AAStructureBindingModel extends * an array of corresponding hidden columns for each alignment * @return */ - public abstract String superposeStructures(AlignmentI[] alignments, int[] structureIndices, - ColumnSelection[] hiddenCols); - - public abstract void setBackgroundColour(Color col); - - protected abstract StructureMappingcommandSet[] getColourBySequenceCommands( - String[] files, SequenceRenderer sr, AlignmentViewPanel avp); + public abstract String superposeStructures(AlignmentI[] alignments, + int[] structureIndices, HiddenColumns[] hiddenCols); /** * returns the current sequenceRenderer that should be used to colour the @@ -732,14 +814,177 @@ public abstract class AAStructureBindingModel extends * * @return */ - public abstract SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment); + public abstract SequenceRenderer getSequenceRenderer( + AlignmentViewPanel alignment); + + /** + * 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; + + // TODO: JAL-628 colour chains distinctly across all visible models + + executeCommand(commandGenerator.colourByChain(), false, + COLOURING_STRUCTURES); + } + + /** + * Sends a command to the structure viewer to colour each chain with a + * distinct colour (to the extent supported by the viewer) + */ + public void colourByCharge() + { + colourBySequence = false; + + executeCommand(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) + { + colourBySequence = false; + + if (cs == null || !cs.isSimple()) + { + return; + } + + /* + * 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 + */ + String cmd = commandGenerator.colourByResidues(colours); + executeCommand(cmd, false, COLOURING_STRUCTURES); + } + + public void setBackgroundColour(Color col) + { + String cmd = commandGenerator.setBackgroundColour(col); + executeCommand(cmd, false, null); + } + + /** + * 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. + * + * @param cmd + * @param getReply + * @param msg + * @return + */ + private List executeCommand(String cmd, boolean getReply, + String msg) + { + if (getReply) + { + return executeSynchronous(cmd, msg, getReply); + } + else + { + executeAsynchronous(cmd, msg); + 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. + * + * @param cmd + * @param msg + * @param getReply + * @return + */ + private List executeSynchronous(String cmd, String msg, boolean getReply) + { + 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); + } + } + } - protected abstract void colourBySequence( - StructureMappingcommandSet[] colourBySequenceCommands); + /** + * 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); - public abstract void colourByChain(); + SwingUtilities.invokeLater(new Runnable() + { + @Override + public void run() + { + try + { + executeCommand(cmd, false); + } finally + { + if (msg != null) + { + theViewer.stopProgressBar(null, handle); + } + } + } + }); + } + + protected abstract List executeCommand(String command, + boolean getReply); - public abstract void colourByCharge(); + protected List executeCommands(boolean getReply, + String... commands) + { + List response = null; + for (String cmd : commands) + { + response = executeCommand(cmd, getReply); + } + return response; + } /** * colour any structures associated with sequences in the given alignment @@ -756,20 +1001,111 @@ public abstract class AAStructureBindingModel extends { return; } - String[] files = getPdbFile(); - + String[] files = getStructureFiles(); + SequenceRenderer sr = getSequenceRenderer(alignmentv); - - StructureMappingcommandSet[] colourBySequenceCommands = getColourBySequenceCommands( - files, sr, alignmentv); - colourBySequence(colourBySequenceCommands); + + String[] colourBySequenceCommands = commandGenerator + .colourBySequence(getSsm(), files, getSequence(), sr, + alignmentv); + executeCommands(false, colourBySequenceCommands); + } + + /** + * Centre the display in the structure viewer + */ + public void focusView() + { + executeCommand(commandGenerator.focusView(), false); } + /** + * 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 ? + + /* + * 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); + int modelNo = getModelNoForFile(pdbFile); + String model = modelNo == -1 ? "" : String.valueOf(modelNo); + showThese.add(model + ":" + tokens[1]); + } + } + executeCommand(commandGenerator.showChains(showThese), false); + } + + /** + * Answers the structure viewer's model number given a PDB file name. Returns + * -1 if model number is not found. + * + * @param chainId + * @return + */ + protected abstract int getModelNoForFile(String chainId); + public boolean hasFileLoadingError() { return fileLoadingError != null && fileLoadingError.length() > 0; } - protected abstract jalview.api.FeatureRenderer getFeatureRenderer( - AlignmentViewPanel alignment); + /** + * Returns the FeatureRenderer for the given alignment view, or null if + * feature display is turned off in the view. + * + * @param avp + * @return + */ + public FeatureRenderer getFeatureRenderer(AlignmentViewPanel avp) + { + AlignmentViewPanel ap = (avp == null) ? getViewer().getAlignmentPanel() + : avp; + return ap.getAlignViewport().isShowSequenceFeatures() + ? ap.getFeatureRenderer() + : null; + } + + 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); + } }