X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructures%2Fmodels%2FAAStructureBindingModel.java;h=6e926df87a475774acbbf2ff05bea75c8b3766fd;hb=d85a2741994c169e1b81db8f9166f5214ff1f561;hp=b00f1bc11a0736a207ab554e2d5a651dc6108775;hpb=f40e44c9db0a689f2df188cf07801b035096c1b1;p=jalview.git diff --git a/src/jalview/structures/models/AAStructureBindingModel.java b/src/jalview/structures/models/AAStructureBindingModel.java index b00f1bc..6e926df 100644 --- a/src/jalview/structures/models/AAStructureBindingModel.java +++ b/src/jalview/structures/models/AAStructureBindingModel.java @@ -20,21 +20,46 @@ */ 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; import jalview.structure.StructureSelectionManager; import jalview.util.Comparison; import jalview.util.MessageManager; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.List; - /** * * A base class to hold common function for protein structure model binding. @@ -44,14 +69,75 @@ import java.util.List; * @author gmcarstairs * */ -public abstract class AAStructureBindingModel extends - SequenceStructureBindingModel implements StructureListener, - StructureSelectionManagerProvider +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"); + + /* + * 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 */ @@ -70,7 +156,7 @@ public abstract class AAStructureBindingModel extends /* * datasource protocol for access to PDBEntrylatest */ - String protocol = null; + DataSourceType protocol = null; protected boolean colourBySequence = true; @@ -79,38 +165,11 @@ public abstract class AAStructureBindingModel extends 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; - /** - * 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; - } + public String fileLoadingError; /** * Constructor @@ -123,6 +182,8 @@ public abstract class AAStructureBindingModel extends { this.ssm = ssm; this.sequence = seqs; + chainNames = new ArrayList<>(); + chainFile = new HashMap<>(); } /** @@ -131,25 +192,70 @@ 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; @@ -207,7 +313,7 @@ public abstract class AAStructureBindingModel extends return chains; } - public String getProtocol() + public DataSourceType getProtocol() { return protocol; } @@ -274,7 +380,11 @@ public abstract class AAStructureBindingModel extends */ protected void releaseUIResources() { + } + @Override + public void releaseReferences(Object svl) + { } public boolean isColourBySequence() @@ -282,6 +392,25 @@ public abstract class AAStructureBindingModel extends 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; @@ -294,11 +423,12 @@ 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()][]); @@ -367,8 +497,8 @@ 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)); @@ -515,18 +645,18 @@ 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, AAStructureBindingModel.SuperposeData[] structures) { int refStructure = -1; - String[] files = getPdbFile(); + String[] files = getStructureFiles(); if (files == null) { return -1; @@ -553,16 +683,16 @@ 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; @@ -581,7 +711,7 @@ public abstract class AAStructureBindingModel extends * for the same structure) */ s = seqCountForPdbFile; - break; + break; // fixme break out of two loops here! } } } @@ -632,8 +762,8 @@ 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; } @@ -651,10 +781,8 @@ 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; } @@ -674,4 +802,796 @@ 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(s). + * + * @param alignWith + * an array of one or more alignment views to process + * @return + */ + 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 + * 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; + + executeCommands(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 + */ + List cmd = commandGenerator + .colourByResidues(colours); + executeCommands(cmd, false, COLOURING_STRUCTURES); + } + + public void setBackgroundColour(Color col) + { + StructureCommandI 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(StructureCommandI cmd, + boolean getReply, String msg) + { + if (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 + { + /* + * 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; + } + } + + /** + * 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); + + /** + * 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) + { + return executeCommands(getReply, msg, + commands.toArray(new StructureCommandI[commands.size()])); + } + + /** + * 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 getReply + * @param msg + * @param commands + * @return + */ + 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); + + 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); + } + } + } + + /** + * 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); + Map colourMap = buildColoursMap(ssm, files, + sequence, sr, alignmentv); + + List colourBySequenceCommands = commandGenerator + .colourBySequence(colourMap); + executeCommands(colourBySequenceCommands, false, null); + } + + /** + * Centre the display in the structure viewer + */ + public void focusView() + { + executeCommand(commandGenerator.focusView(), false, null); + } + + /** + * 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); + String model = getModelIdForFile(pdbFile); + showThese.add(model + ":" + tokens[1]); + } + } + executeCommands(commandGenerator.showChains(showThese), false, null); + } + + /** + * 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 String getModelIdForFile(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); + } + + @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; + } + + 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 + } }