X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructures%2Fmodels%2FAAStructureBindingModel.java;h=8c2dc46e46f30727e8c55223aab84e21516ca89a;hb=2ab7b9b152018bb808693218ad88dc3778166492;hp=dc423158a27a1776209443cd9c9478c074694364;hpb=0293d494ae19bbd5b5e92ade0cde30292b109f81;p=jalview.git diff --git a/src/jalview/structures/models/AAStructureBindingModel.java b/src/jalview/structures/models/AAStructureBindingModel.java index dc42315..8c2dc46 100644 --- a/src/jalview/structures/models/AAStructureBindingModel.java +++ b/src/jalview/structures/models/AAStructureBindingModel.java @@ -20,20 +20,35 @@ */ 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.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.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; /** * @@ -44,13 +59,40 @@ 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 + */ private PDBEntry[] pdbEntry; /* @@ -66,7 +108,7 @@ public abstract class AAStructureBindingModel extends /* * datasource protocol for access to PDBEntrylatest */ - String protocol = null; + DataSourceType protocol = null; protected boolean colourBySequence = true; @@ -75,6 +117,13 @@ public abstract class AAStructureBindingModel extends private boolean finishedInit = false; /** + * current set of model filenames loaded in the Jmol instance + */ + protected String[] modelFileNames = null; + + public String fileLoadingError; + + /** * Data bean class to simplify parameterisation in superposeStructures */ protected class SuperposeData @@ -114,6 +163,8 @@ public abstract class AAStructureBindingModel extends { this.ssm = ssm; this.sequence = seqs; + chainNames = new ArrayList<>(); + chainFile = new HashMap<>(); } /** @@ -122,25 +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, String[][] chains, - String protocol) + PDBEntry[] pdbentry, SequenceI[][] sequenceIs, + DataSourceType protocol) { - this.ssm = ssm; - this.sequence = sequenceIs; + this(ssm, sequenceIs); this.nucleotide = Comparison.isNucleotide(sequenceIs); - this.chains = chains; this.pdbEntry = pdbentry; this.protocol = protocol; - if (chains == null) + 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) { - this.chains = new String[pdbentry.length][]; + 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; @@ -198,7 +294,7 @@ public abstract class AAStructureBindingModel extends return chains; } - public String getProtocol() + public DataSourceType getProtocol() { return protocol; } @@ -239,24 +335,21 @@ public abstract class AAStructureBindingModel extends // TODO: give a more informative title when multiple structures are // displayed. StringBuilder title = new StringBuilder(64); - final PDBEntry pdbEntry = getPdbEntry(0); + final PDBEntry pdbe = getPdbEntry(0); title.append(viewerName + " view for " + getSequence()[0][0].getName() - + ":" + pdbEntry.getId()); + + ":" + pdbe.getId()); if (verbose) { - if (pdbEntry.getProperty() != null) + String method = (String) pdbe.getProperty("method"); + if (method != null) { - if (pdbEntry.getProperty().get("method") != null) - { - title.append(" Method: "); - title.append(pdbEntry.getProperty().get("method")); - } - if (pdbEntry.getProperty().get("chains") != null) - { - title.append(" Chain:"); - title.append(pdbEntry.getProperty().get("chains")); - } + title.append(" Method: ").append(method); + } + String chain = (String) pdbe.getProperty("chains"); + if (chain != null) + { + title.append(" Chain:").append(chain); } } return title.toString(); @@ -288,11 +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()][]); @@ -361,8 +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)); @@ -509,18 +603,22 @@ public abstract class AAStructureBindingModel extends * the sequence alignment which is the basis of structure * superposition * @param matched - * an array of booleans, indexed by alignment column, where true - * indicates that every structure has a mapped residue present in the - * column (so the column can participate in structure alignment) + * a BitSet, where bit j is set to indicate that every structure has + * a mapped residue present in column j (so the column can + * participate in structure alignment) * @param structures * an array of data beans corresponding to pdb file index * @return */ protected int findSuperposableResidues(AlignmentI alignment, - boolean[] matched, SuperposeData[] structures) + BitSet matched, SuperposeData[] structures) { int refStructure = -1; - String[] files = getPdbFile(); + String[] files = getStructureFiles(); + if (files == null) + { + return -1; + } for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) { StructureMapping[] mappings = getSsm().getMapping(files[pdbfnum]); @@ -543,16 +641,16 @@ public abstract class AAStructureBindingModel extends { refStructure = pdbfnum; } - for (int r = 0; r < matched.length; r++) + for (int r = 0; r < alignment.getWidth(); r++) { - if (!matched[r]) + if (!matched.get(r)) { continue; } int pos = getMappedPosition(theSequence, r, mapping); if (pos < 1 || pos == lastPos) { - matched[r] = false; + matched.clear(r); continue; } lastPos = pos; @@ -565,7 +663,11 @@ public abstract class AAStructureBindingModel extends } structures[pdbfnum].pdbId = mapping.getPdbId(); structures[pdbfnum].isRna = theSequence.getRNA() != null; - // move on to next pdb file + + /* + * move on to next pdb file (ignore sequences for other chains + * for the same structure) + */ s = seqCountForPdbFile; break; } @@ -618,8 +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; } @@ -637,10 +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; } @@ -660,4 +760,352 @@ public abstract class AAStructureBindingModel extends { this.finishedInit = fi; } + + /** + * Returns a list of chains mapped in this viewer, formatted as + * "pdbid:chainCode" + * + * @return + */ + public List getChainNames() + { + return chainNames; + } + + /** + * Returns the Jalview panel hosting the structure viewer (if any) + * + * @return + */ + public JalviewStructureDisplayI getViewer() + { + return viewer; + } + + public void setViewer(JalviewStructureDisplayI v) + { + viewer = v; + } + + /** + * Constructs and sends a command to align structures against a reference + * structure, based on one or more sequence alignments. May optionally return + * an error or warning message for the alignment command. + * + * @param alignments + * an array of alignments to process + * @param structureIndices + * an array of corresponding reference structures (index into pdb + * file array); if a negative value is passed, the first PDB file + * mapped to an alignment sequence is used as the reference for + * superposition + * @param hiddenCols + * an array of corresponding hidden columns for each alignment + * @return + */ + public abstract String superposeStructures(AlignmentI[] alignments, + int[] structureIndices, HiddenColumns[] hiddenCols); + + /** + * returns the current sequenceRenderer that should be used to colour the + * structures + * + * @param alignment + * + * @return + */ + 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); + } + } + } + + /** + * 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() + { + @Override + public void run() + { + try + { + executeCommand(cmd, false); + } finally + { + if (msg != null) + { + 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; + } + + /** + * colour any structures associated with sequences in the given alignment + * using the getFeatureRenderer() and getSequenceRenderer() renderers but only + * if colourBySequence is enabled. + */ + public void colourBySequence(AlignmentViewPanel alignmentv) + { + if (!colourBySequence || !isLoadingFinished()) + { + return; + } + if (getSsm() == null) + { + return; + } + String[] files = getStructureFiles(); + + SequenceRenderer sr = getSequenceRenderer(alignmentv); + + 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; + } + + /** + * 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); + } }