X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructures%2Fmodels%2FAAStructureBindingModel.java;h=b55885d0cead719ee305e5de7edb27c0390fcb4a;hb=8f0f304ea24d01bc052089dde29a22934c73b326;hp=7d578869b93fb697a661df4320095243ae040553;hpb=799c26111d6936a2e70cb5f1fd7d7312311e6db9;p=jalview.git diff --git a/src/jalview/structures/models/AAStructureBindingModel.java b/src/jalview/structures/models/AAStructureBindingModel.java index 7d57886..b55885d 100644 --- a/src/jalview/structures/models/AAStructureBindingModel.java +++ b/src/jalview/structures/models/AAStructureBindingModel.java @@ -27,15 +27,17 @@ 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.ext.rbvi.chimera.AtomSpecModel; +import jalview.ext.rbvi.chimera.ChimeraCommands; import jalview.io.DataSourceType; +import jalview.renderer.seqfeatures.FeatureColourFinder; import jalview.schemes.ColourSchemeI; import jalview.structure.AtomSpec; import jalview.structure.StructureListener; import jalview.structure.StructureMapping; -import jalview.structure.StructureMappingcommandSet; import jalview.structure.StructureSelectionManager; import jalview.util.Comparison; import jalview.util.MessageManager; @@ -44,7 +46,11 @@ import java.awt.Color; import java.util.ArrayList; import java.util.Arrays; import java.util.BitSet; +import java.util.Collections; +import java.util.Iterator; +import java.util.LinkedHashMap; import java.util.List; +import java.util.Map; /** * @@ -55,9 +61,9 @@ 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 StructureSelectionManager ssm; @@ -96,6 +102,19 @@ public abstract class AAStructureBindingModel extends public String fileLoadingError; + private boolean showAlignmentOnly; + + /* + * a list of chains "pdbid:chainid" to show in the viewer; + * empty means show all + */ + // TODO make private once deprecated JalviewJmolBinding.centerViewer removed + protected List chainsToShow; + + private boolean hideHiddenRegions; + + protected List chainNames = new ArrayList<>(); + /** * Data bean class to simplify parameterisation in superposeStructures */ @@ -136,6 +155,7 @@ public abstract class AAStructureBindingModel extends { this.ssm = ssm; this.sequence = seqs; + chainsToShow = new ArrayList<>(); } /** @@ -144,7 +164,6 @@ public abstract class AAStructureBindingModel extends * @param ssm * @param pdbentry * @param sequenceIs - * @param chains * @param protocol */ public AAStructureBindingModel(StructureSelectionManager ssm, @@ -156,8 +175,62 @@ public abstract class AAStructureBindingModel extends this.nucleotide = Comparison.isNucleotide(sequenceIs); this.pdbEntry = pdbentry; this.protocol = protocol; + chainsToShow = new ArrayList<>(); + + 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; @@ -302,11 +375,12 @@ 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()][]); @@ -375,8 +449,8 @@ 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)); @@ -534,7 +608,7 @@ public abstract class AAStructureBindingModel extends BitSet matched, SuperposeData[] structures) { int refStructure = -1; - String[] files = getPdbFile(); + String[] files = getStructureFiles(); if (files == null) { return -1; @@ -640,8 +714,8 @@ 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; } @@ -659,10 +733,8 @@ 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; } @@ -684,13 +756,6 @@ public abstract class AAStructureBindingModel extends } /** - * Returns a list of chains mapped in this viewer. - * - * @return - */ - public abstract List getChainNames(); - - /** * Returns the Jalview panel hosting the structure viewer (if any) * * @return @@ -718,24 +783,13 @@ 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 String superposeStructures(AlignmentI[] alignments, + int[] structureIndices, HiddenColumns[] hiddenCols); public abstract void setBackgroundColour(Color col); - protected abstract StructureMappingcommandSet[] getColourBySequenceCommands( - String[] files, SequenceRenderer sr, FeatureRenderer fr, - AlignViewportI alignViewportI); - - /** - * returns the current featureRenderer that should be used to colour the - * structures - * - * @param alignment - * - * @return - */ - public abstract FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment); + protected abstract String[] getColourBySequenceCommands( + String[] files, AlignmentViewPanel avp); /** * returns the current sequenceRenderer that should be used to colour the @@ -745,49 +799,386 @@ public abstract class AAStructureBindingModel extends * * @return */ - public abstract SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment); + public abstract SequenceRenderer getSequenceRenderer( + AlignmentViewPanel alignment); protected abstract void colourBySequence( - StructureMappingcommandSet[] colourBySequenceCommands); + String[] colourBySequenceCommands); public abstract void colourByChain(); public abstract void colourByCharge(); /** - * colour any structures associated with sequences in the given alignment - * using the getFeatureRenderer() and getSequenceRenderer() renderers but only - * if colourBySequence is enabled. + * Recolours the displayed structures, if they are coloured by sequence, or + * 'show only visible alignment' is selected. This supports updating structure + * colours on either change of alignment colours, or change to the visible + * region of the alignment. */ - public void colourBySequence(AlignmentViewPanel alignmentv) + public void updateStructureColours(AlignmentViewPanel alignmentv) { - if (!colourBySequence || !isLoadingFinished()) + if (!isLoadingFinished()) + { + return; + } + + /* + * if structure is not coloured by sequence, but restricted to the alignment, + * then redraw it (but don't recolour it) in case hidden regions have changed + * (todo: specific messaging for change of hidden region only) + */ + if (!colourBySequence) { + if (isShowAlignmentOnly()) + { + showStructures(alignmentv.getAlignViewport(), false); + } return; } if (getSsm() == null) { return; } - String[] files = getPdbFile(); + String[] files = getStructureFiles(); + + String[] colourBySequenceCommands = getColourBySequenceCommands( + files, alignmentv); + colourBySequence(colourBySequenceCommands); + } + + public boolean hasFileLoadingError() + { + return fileLoadingError != null && fileLoadingError.length() > 0; + } + + public abstract jalview.api.FeatureRenderer getFeatureRenderer( + AlignmentViewPanel alignment); + + /** + * Sets the flag for whether only mapped visible residues in the alignment + * should be visible in the structure viewer + * + * @param b + */ + public void setShowAlignmentOnly(boolean b) + { + showAlignmentOnly = b; + } + + /** + * Answers true if only residues mapped to the alignment should be shown in the + * structure viewer, else false + * + * @return + */ + public boolean isShowAlignmentOnly() + { + return showAlignmentOnly; + } + + /** + * Sets the flag for hiding regions of structure which are hidden in the + * alignment (only applies when the structure viewer is restricted to the + * alignment only) + * + * @param b + */ + public void setHideHiddenRegions(boolean b) + { + hideHiddenRegions = b; + } + + /** + * Answers true if regions hidden in the alignment should also be hidden in the + * structure viewer, else false (only applies when the structure viewer is + * restricted to the alignment only) + * + * @return + */ + public boolean isHideHiddenRegions() + { + return hideHiddenRegions; + } + + /** + * Shows the structures in the viewer, without changing their colouring. This is + * to support toggling of whether the whole structure is shown, or only residues + * mapped to visible regions of the alignment. + * + * @param alignViewportI + * @param refocus + * if true, refit the display to the viewer + */ + public void showStructures(AlignViewportI alignViewportI, boolean refocus) + { + // override with implementation + } + + @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()) + { + updateStructureColours(ap); + } + } + + /** + * Sets the list of chains to display (as "pdbid:chain"), where an empty list + * means show all + * + * @param chains + */ + public void setChainsToShow(List chains) + { + chainsToShow = chains; + } + + /** + * Answers true if the specified structure and chain are selected to be shown in + * the viewer, else false + * + * @param pdbId + * @param chainId + * @return + */ + protected boolean isShowChain(String pdbId, String chainId) + { + if (chainsToShow.isEmpty()) + { + return true; + } + return chainsToShow.contains(pdbId + ":" + chainId); + } + + @Override + public abstract String[] getStructureFiles(); + + /** + * Builds a model of residues mapped from sequences to show on structure, taking + * into account user choices of + *
    + *
  • which chains are shown
    • + *
  • whether all structure is shown, or only that mapped to the alignment
    • + *
  • whether hidden regions of the alignment are hidden (excluded) or grayed + * out (included)
    • + *
+ * + * @param av + * @return + */ + protected AtomSpecModel getShownResidues(AlignViewportI av) + { + AlignmentI alignment = av.getAlignment(); + final int width = alignment.getWidth(); + + String[] files = getStructureFiles(); - SequenceRenderer sr = getSequenceRenderer(alignmentv); + AtomSpecModel model = new AtomSpecModel(); - FeatureRenderer fr = null; - boolean showFeatures = alignmentv.getAlignViewport() - .isShowSequenceFeatures(); - if (showFeatures) + for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) { - fr = getFeatureRenderer(alignmentv); + StructureMapping[] mappings = getSsm().getMapping(files[pdbfnum]); + + /* + * Find the first mapped sequence (if any) for this PDB entry which is in + * the alignment + */ + final int seqCountForPdbFile = getSequence()[pdbfnum].length; + for (int s = 0; s < seqCountForPdbFile; s++) + { + for (StructureMapping mapping : mappings) + { + final SequenceI theSequence = getSequence()[pdbfnum][s]; + if (mapping.getSequence() == theSequence + && alignment.findIndex(theSequence) > -1) + { + String chainCd = mapping.getChain(); + if (!isShowChain(mapping.getPdbId(), chainCd)) + { + continue; + } + Iterator visible; + if (isShowAlignmentOnly() && isHideHiddenRegions()) + { + visible = alignment.getHiddenColumns() + .getVisContigsIterator(0, width, true); + } + else + { + visible = Collections.singletonList(new int[] { 0, width }) + .iterator(); + } + while (visible.hasNext()) + { + int[] visibleRegion = visible.next(); + int seqStartPos = theSequence.findPosition(visibleRegion[0]); + int seqEndPos = theSequence.findPosition(visibleRegion[1]); + List residueRanges = mapping + .getPDBResNumRanges(seqStartPos, seqEndPos); + if (!residueRanges.isEmpty()) + { + for (int[] range : residueRanges) + { + model.addRange(pdbfnum, range[0], range[1], chainCd); + } + } + } + } + } + } } - StructureMappingcommandSet[] colourBySequenceCommands = getColourBySequenceCommands( - files, sr, fr, alignmentv.getAlignViewport()); - colourBySequence(colourBySequenceCommands); + return model; } - public boolean hasFileLoadingError() + /** + * Answers a default structure model specification which is simply the string + * form of the model number. Override if needed to specify submodels. + * + * @param model + * @return + */ + public String getModelSpec(int model) { - return fileLoadingError != null && fileLoadingError.length() > 0; + return String.valueOf(model); + } + + /** + * Build a data structure which records contiguous subsequences for each colour. + * From this we can easily generate the Chimera command for colour by sequence. + * + * 
+   * Color
+   *     Model number
+   *         Chain
+   *             list of start/end ranges
+   *
+ * + * Ordering is by order of addition (for colours and positions), natural + * ordering (for models and chains) + * + * @param viewPanel + * @return + */ + public Map buildColoursMap( + AlignmentViewPanel viewPanel) + { + FeatureRenderer fr = viewPanel.getFeatureRenderer(); + FeatureColourFinder finder = new FeatureColourFinder(fr); + AlignViewportI viewport = viewPanel.getAlignViewport(); + HiddenColumns cs = viewport.getAlignment().getHiddenColumns(); + AlignmentI al = viewport.getAlignment(); + SequenceRenderer sr = getSequenceRenderer(viewPanel); + String[] files = getStructureFiles(); + + Map colourMap = new LinkedHashMap<>(); + Color lastColour = null; + + for (int pdbfnum = 0; pdbfnum < files.length; 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); + + /* + * hidden regions are shown gray or, optionally, ignored + */ + if (!cs.isVisible(r)) + { + if (hideHiddenRegions) + { + continue; + } + else + { + 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) + { + ChimeraCommands.addAtomSpecRange(colourMap, lastColour, + pdbfnum, startPos, + lastPos, lastChain); + } + startPos = pos; + } + lastColour = colour; + lastPos = pos; + lastChain = chain; + } + // final colour range + if (lastColour != null) + { + ChimeraCommands.addAtomSpecRange(colourMap, lastColour, + pdbfnum, + startPos, lastPos, lastChain); + } + // break; + } + } + } + } + return colourMap; + } + + /** + * Returns a list of chains mapped in this viewer. Note this list is not + * currently scoped per structure. + * + * @return + */ + public List getChainNames() + { + return chainNames; } }