X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructures%2Fmodels%2FAAStructureBindingModel.java;h=92b00c77cc01bbf6e92362f4a0abb03cbfcf0015;hb=6cb920bb7a7f285a165cd34b3429dabba71f7518;hp=ffd865ff07a2fa8382536182b19a11268a4cf88e;hpb=e5c6af77202c042ed3dfc88c3a0319efb4f8a8c0;p=jalview.git diff --git a/src/jalview/structures/models/AAStructureBindingModel.java b/src/jalview/structures/models/AAStructureBindingModel.java index ffd865f..92b00c7 100644 --- a/src/jalview/structures/models/AAStructureBindingModel.java +++ b/src/jalview/structures/models/AAStructureBindingModel.java @@ -21,6 +21,7 @@ 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; @@ -30,10 +31,11 @@ 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; /** * @@ -57,10 +63,33 @@ 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 { this.ssm = ssm; this.sequence = seqs; + chainNames = new ArrayList<>(); + chainFile = new HashMap<>(); } /** @@ -148,8 +179,7 @@ public abstract class AAStructureBindingModel 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; @@ -178,7 +208,8 @@ public abstract class AAStructureBindingModel String chain = (chains != null && chains[pe] != null) ? chains[pe][se] : null; - SequenceI sq = asq.getDatasetSequence(); + SequenceI sq = (asq.getDatasetSequence() == null) ? asq + : asq.getDatasetSequence(); if (sq.getAllPDBEntries() != null) { for (PDBEntry pdbentry : sq.getAllPDBEntries()) @@ -330,7 +361,11 @@ public abstract class AAStructureBindingModel */ protected void releaseUIResources() { + } + @Override + public void releaseReferences(Object svl) + { } public boolean isColourBySequence() @@ -338,6 +373,25 @@ 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; @@ -354,8 +408,8 @@ public abstract class AAStructureBindingModel { 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()][]); @@ -424,8 +478,8 @@ public abstract class AAStructureBindingModel 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)); @@ -731,11 +785,15 @@ public abstract class AAStructureBindingModel } /** - * 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) @@ -744,10 +802,13 @@ public abstract class AAStructureBindingModel */ 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 @@ -768,11 +829,6 @@ public abstract class AAStructureBindingModel public abstract String superposeStructures(AlignmentI[] alignments, int[] structureIndices, HiddenColumns[] hiddenCols); - public abstract void setBackgroundColour(Color col); - - protected abstract StructureMappingcommandSet[] getColourBySequenceCommands( - String[] files, SequenceRenderer sr, AlignmentViewPanel avp); - /** * returns the current sequenceRenderer that should be used to colour the * structures @@ -784,12 +840,174 @@ public abstract class AAStructureBindingModel public abstract SequenceRenderer getSequenceRenderer( AlignmentViewPanel alignment); - protected abstract void colourBySequence( - StructureMappingcommandSet[] colourBySequenceCommands); + /** + * 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); + } - public abstract void colourByChain(); + /** + * 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); + } - public abstract void colourByCharge(); + /** + * 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 @@ -810,16 +1028,127 @@ public abstract class AAStructureBindingModel 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; } - public 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); + } + + @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; + } }