X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Frbvi%2Fchimera%2FChimeraCommands.java;h=3caaac3532367e30f3f2d11003cbdb23c9560437;hb=refs%2Fheads%2FJAL-3253-applet-SwingJS-omnibus;hp=b9957a6fad602d3702ff9a0c479e08a840d23a2c;hpb=ab43013b7e357b84b4abade0dba949668dfb2a0e;p=jalview.git diff --git a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java index b9957a6..3caaac3 100644 --- a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java +++ b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -20,19 +20,29 @@ */ package jalview.ext.rbvi.chimera; +import jalview.api.AlignViewportI; +import jalview.api.AlignmentViewPanel; import jalview.api.FeatureRenderer; import jalview.api.SequenceRenderer; -import jalview.api.structures.JalviewStructureDisplayI; import jalview.datamodel.AlignmentI; +import jalview.datamodel.HiddenColumns; +import jalview.datamodel.MappedFeatures; +import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; +import jalview.gui.Desktop; +import jalview.renderer.seqfeatures.FeatureColourFinder; import jalview.structure.StructureMapping; import jalview.structure.StructureMappingcommandSet; import jalview.structure.StructureSelectionManager; -import jalview.util.Format; +import jalview.util.ColorUtils; +import jalview.util.Comparison; import java.awt.Color; import java.util.ArrayList; -import java.util.Hashtable; +import java.util.HashMap; +import java.util.LinkedHashMap; +import java.util.List; +import java.util.Map; /** * Routines for generating Chimera commands for Jalview/Chimera binding @@ -43,116 +53,603 @@ import java.util.Hashtable; public class ChimeraCommands { + public static final String NAMESPACE_PREFIX = "jv_"; + /** - * utility to construct the commands to colour chains by the given alignment - * for passing to Chimera - * - * @returns Object[] { Object[] { , + * Constructs Chimera commands to colour residues as per the Jalview alignment * + * @param ssm + * @param files + * @param sequence + * @param sr + * @param fr + * @param viewPanel + * @return */ public static StructureMappingcommandSet[] getColourBySequenceCommand( StructureSelectionManager ssm, String[] files, - SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr, - AlignmentI alignment) + SequenceI[][] sequence, SequenceRenderer sr, + AlignmentViewPanel viewPanel) + { + Map colourMap = buildColoursMap(ssm, files, + sequence, sr, viewPanel); + + List colourCommands = buildColourCommands(colourMap); + + StructureMappingcommandSet cs = new StructureMappingcommandSet( + ChimeraCommands.class, null, + colourCommands.toArray(new String[colourCommands.size()])); + + return new StructureMappingcommandSet[] { cs }; + } + + /** + * Traverse the map of colours/models/chains/positions to construct a list of + * 'color' commands (one per distinct colour used). The format of each command + * is + * + * 
+   * 
 
+   * color colorname #modelnumber:range.chain 
+   * e.g. color #00ff00 #0:2.B,4.B,9-12.B|#1:1.A,2-6.A,...
+   * 

+   *
+ * + * @param colourMap + * @return + */ + protected static List buildColourCommands( + Map colourMap) + { + /* + * This version concatenates all commands into a single String (semi-colon + * delimited). If length limit issues arise, refactor to return one color + * command per colour. + */ + List commands = new ArrayList<>(); + StringBuilder sb = new StringBuilder(256); + boolean firstColour = true; + for (Object key : colourMap.keySet()) + { + Color colour = (Color) key; + String colourCode = ColorUtils.toTkCode(colour); + if (!firstColour) + { + sb.append("; "); + } + sb.append("color ").append(colourCode).append(" "); + firstColour = false; + final AtomSpecModel colourData = colourMap.get(colour); + sb.append(colourData.getAtomSpec()); + } + commands.add(sb.toString()); + return commands; + } + + /** + * Traverses a map of { modelNumber, {chain, {list of from-to ranges} } } and + * builds a Chimera format atom spec + * + * @param modelAndChainRanges + */ + protected static String getAtomSpec( + Map>> modelAndChainRanges) + { + StringBuilder sb = new StringBuilder(128); + boolean firstModelForColour = true; + for (Integer model : modelAndChainRanges.keySet()) + { + boolean firstPositionForModel = true; + if (!firstModelForColour) + { + sb.append("|"); + } + firstModelForColour = false; + sb.append("#").append(model).append(":"); + + final Map> modelData = modelAndChainRanges + .get(model); + for (String chain : modelData.keySet()) + { + boolean hasChain = !"".equals(chain.trim()); + for (int[] range : modelData.get(chain)) + { + if (!firstPositionForModel) + { + sb.append(","); + } + if (range[0] == range[1]) + { + sb.append(range[0]); + } + else + { + sb.append(range[0]).append("-").append(range[1]); + } + if (hasChain) + { + sb.append(".").append(chain); + } + firstPositionForModel = false; + } + } + } + return sb.toString(); + } + + /** + * 
+   * 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)
+   *
+ */ + protected static 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; - ArrayList cset = new ArrayList(); - Hashtable colranges=new Hashtable(); for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) { - float cols[] = new float[4]; StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]); - StringBuffer command = new StringBuffer(); - StructureMappingcommandSet smc; - ArrayList str = new ArrayList(); if (mapping == null || mapping.length < 1) + { continue; + } - int startPos = -1, lastPos = -1, startModel = -1, lastModel = -1; - String startChain = "", lastChain = ""; - Color lastCol = null; + 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++) { - if (mapping[m].getSequence() == sequence[pdbfnum][s] - && (sp = alignment.findIndex(sequence[pdbfnum][s])) > -1) + final SequenceI seq = sequence[pdbfnum][s]; + if (mapping[m].getSequence() == seq + && (sp = al.findIndex(seq)) > -1) { - SequenceI asp = alignment.getSequenceAt(sp); + SequenceI asp = al.getSequenceAt(sp); for (int r = 0; r < asp.getLength(); r++) { // no mapping to gaps in sequence - if (jalview.util.Comparison.isGap(asp.getCharAt(r))) + 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; + } - Color col = sr.getResidueBoxColour(sequence[pdbfnum][s], r); + final String chain = mapping[m].getChain(); - if (fr != null) - col = fr.findFeatureColour(col, sequence[pdbfnum][s], r); - if (lastCol != col || lastPos + 1 != pos - || pdbfnum != lastModel - || !mapping[m].getChain().equals(lastChain)) + /* + * 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 (lastCol != null) + if (startPos != -1) { - addColourRange(colranges, lastCol,startModel,startPos,lastPos,lastChain); + addAtomSpecRange(colourMap, lastColour, pdbfnum, startPos, + lastPos, lastChain); } - lastCol = null; startPos = pos; - startModel = pdbfnum; - startChain = mapping[m].getChain(); } - lastCol = col; + lastColour = colour; lastPos = pos; - lastModel = pdbfnum; - lastChain = mapping[m].getChain(); + lastChain = chain; } // final colour range - if (lastCol != null) + if (lastColour != null) + { + addAtomSpecRange(colourMap, lastColour, pdbfnum, startPos, + lastPos, lastChain); + } + // break; + } + } + } + } + return colourMap; + } + + /** + * 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 + */ + protected static void addAtomSpecRange(Map map, + Object value, int 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); + } + + /** + * Constructs and returns Chimera commands to set attributes on residues + * corresponding to features in Jalview. Attribute names are the Jalview + * feature type, with a "jv_" prefix. + * + * @param ssm + * @param files + * @param seqs + * @param viewPanel + * @return + */ + public static StructureMappingcommandSet getSetAttributeCommandsForFeatures( + StructureSelectionManager ssm, String[] files, SequenceI[][] seqs, + AlignmentViewPanel viewPanel) + { + Map> featureMap = buildFeaturesMap( + ssm, files, seqs, viewPanel); + + List commands = buildSetAttributeCommands(featureMap); + + StructureMappingcommandSet cs = new StructureMappingcommandSet( + ChimeraCommands.class, null, + commands.toArray(new String[commands.size()])); + + return cs; + } + + /** + * 
+   * Helper method to build a map of 
+   *   { featureType, { feature value, AtomSpecModel } }
+   *
+ * + * @param ssm + * @param files + * @param seqs + * @param viewPanel + * @return + */ + protected static Map> buildFeaturesMap( + StructureSelectionManager ssm, String[] files, SequenceI[][] seqs, + AlignmentViewPanel viewPanel) + { + Map> theMap = new LinkedHashMap<>(); + + FeatureRenderer fr = viewPanel.getFeatureRenderer(); + if (fr == null) + { + return theMap; + } + + AlignViewportI viewport = viewPanel.getAlignViewport(); + List visibleFeatures = fr.getDisplayedFeatureTypes(); + + /* + * if alignment is showing features from complement, we also transfer + * these features to the corresponding mapped structure residues + */ + boolean showLinkedFeatures = viewport.isShowComplementFeatures(); + List complementFeatures = new ArrayList<>(); + FeatureRenderer complementRenderer = null; + if (showLinkedFeatures) + { + AlignViewportI comp = fr.getViewport().getCodingComplement(); + if (comp != null) + { + complementRenderer = Desktop.getAlignFrameFor(comp) + .getFeatureRenderer(); + complementFeatures = complementRenderer.getDisplayedFeatureTypes(); + } + } + if (visibleFeatures.isEmpty() && complementFeatures.isEmpty()) + { + return theMap; + } + + AlignmentI alignment = viewPanel.getAlignment(); + for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) + { + StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]); + + if (mapping == null || mapping.length < 1) + { + continue; + } + + for (int seqNo = 0; seqNo < seqs[pdbfnum].length; seqNo++) + { + for (int m = 0; m < mapping.length; m++) + { + final SequenceI seq = seqs[pdbfnum][seqNo]; + int sp = alignment.findIndex(seq); + StructureMapping structureMapping = mapping[m]; + if (structureMapping.getSequence() == seq && sp > -1) + { + /* + * found a sequence with a mapping to a structure; + * now scan its features + */ + if (!visibleFeatures.isEmpty()) + { + scanSequenceFeatures(visibleFeatures, structureMapping, seq, + theMap, pdbfnum); + } + if (showLinkedFeatures) + { + scanComplementFeatures(complementRenderer, structureMapping, + seq, theMap, pdbfnum); + } + } + } + } + } + return theMap; + } + + /** + * Scans visible features in mapped positions of the CDS/peptide complement, and + * adds any found to the map of attribute values/structure positions + * + * @param complementRenderer + * @param structureMapping + * @param seq + * @param theMap + * @param modelNumber + */ + protected static void scanComplementFeatures( + FeatureRenderer complementRenderer, + StructureMapping structureMapping, SequenceI seq, + Map> theMap, int modelNumber) + { + /* + * for each sequence residue mapped to a structure position... + */ + for (int seqPos : structureMapping.getMapping().keySet()) + { + /* + * find visible complementary features at mapped position(s) + */ + MappedFeatures mf = complementRenderer + .findComplementFeaturesAtResidue(seq, seqPos); + if (mf != null) + { + for (SequenceFeature sf : mf.features) + { + String type = sf.getType(); + + /* + * Don't copy features which originated from Chimera + */ + if (JalviewChimeraBinding.CHIMERA_FEATURE_GROUP + .equals(sf.getFeatureGroup())) + { + continue; + } + + /* + * record feature 'value' (score/description/type) as at the + * corresponding structure position + */ + List mappedRanges = structureMapping + .getPDBResNumRanges(seqPos, seqPos); + + if (!mappedRanges.isEmpty()) + { + String value = sf.getDescription(); + if (value == null || value.length() == 0) + { + value = type; + } + float score = sf.getScore(); + if (score != 0f && !Float.isNaN(score)) + { + value = Float.toString(score); + } + Map featureValues = theMap.get(type); + if (featureValues == null) + { + featureValues = new HashMap<>(); + theMap.put(type, featureValues); + } + for (int[] range : mappedRanges) { - addColourRange(colranges, lastCol,startModel,startPos,lastPos,lastChain); + addAtomSpecRange(featureValues, value, modelNumber, range[0], + range[1], structureMapping.getChain()); } - break; } } } - // Finally, add the command set ready to be returned. - StringBuffer coms=new StringBuffer(); - for (String cr:colranges.keySet()) + } + } + + /** + * Inspect features on the sequence; for each feature that is visible, determine + * its mapped ranges in the structure (if any) according to the given mapping, + * and add them to the map. + * + * @param visibleFeatures + * @param mapping + * @param seq + * @param theMap + * @param modelNumber + */ + protected static void scanSequenceFeatures(List visibleFeatures, + StructureMapping mapping, SequenceI seq, + Map> theMap, int modelNumber) + { + List sfs = seq.getFeatures().getPositionalFeatures( + visibleFeatures.toArray(new String[visibleFeatures.size()])); + for (SequenceFeature sf : sfs) + { + String type = sf.getType(); + + /* + * Don't copy features which originated from Chimera + */ + if (JalviewChimeraBinding.CHIMERA_FEATURE_GROUP + .equals(sf.getFeatureGroup())) { - coms.append("color #"+cr+" "+colranges.get(cr)+";"); + continue; + } + + List mappedRanges = mapping.getPDBResNumRanges(sf.getBegin(), + sf.getEnd()); + + if (!mappedRanges.isEmpty()) + { + String value = sf.getDescription(); + if (value == null || value.length() == 0) + { + value = type; + } + float score = sf.getScore(); + if (score != 0f && !Float.isNaN(score)) + { + value = Float.toString(score); + } + Map featureValues = theMap.get(type); + if (featureValues == null) + { + featureValues = new HashMap<>(); + theMap.put(type, featureValues); + } + for (int[] range : mappedRanges) + { + addAtomSpecRange(featureValues, value, modelNumber, range[0], + range[1], mapping.getChain()); + } } - cset.add(new StructureMappingcommandSet(ChimeraCommands.class, - files[pdbfnum], new String[] { coms.toString() })); } - return cset.toArray(new StructureMappingcommandSet[cset.size()]); } - private static void addColourRange(Hashtable colranges, Color lastCol, int startModel, - int startPos, int lastPos, String lastChain) + /** + * Traverse the map of features/values/models/chains/positions to construct a + * list of 'setattr' commands (one per distinct feature type and value). + *

+ * The format of each command is + * + * 

+   * 
 setattr r  " " #modelnumber:range.chain 
+   * e.g. setattr r jv:chain  #0:2.B,4.B,9-12.B|#1:1.A,2-6.A,...
+   * 

+   *
+ * + * @param featureMap + * @return + */ + protected static List buildSetAttributeCommands( + Map> featureMap) + { + List commands = new ArrayList<>(); + for (String featureType : featureMap.keySet()) + { + String attributeName = makeAttributeName(featureType); + + /* + * clear down existing attributes for this feature + */ + // 'problem' - sets attribute to None on all residues - overkill? + // commands.add("~setattr r " + attributeName + " :*"); + + Map values = featureMap.get(featureType); + for (Object value : values.keySet()) + { + /* + * for each distinct value recorded for this feature type, + * add a command to set the attribute on the mapped residues + * Put values in single quotes, encoding any embedded single quotes + */ + StringBuilder sb = new StringBuilder(128); + String featureValue = value.toString(); + featureValue = featureValue.replaceAll("\\'", "'"); + sb.append("setattr r ").append(attributeName).append(" '") + .append(featureValue).append("' "); + sb.append(values.get(value).getAtomSpec()); + commands.add(sb.toString()); + } + } + + return commands; + } + + /** + * Makes a prefixed and valid Chimera attribute name. A jv_ prefix is applied + * for a 'Jalview' namespace, and any non-alphanumeric character is converted + * to an underscore. + * + * @param featureType + * @return + * + * 
+   * @see https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/setattr.html
+   *
+ */ + protected static String makeAttributeName(String featureType) { - - String colstring = ((lastCol.getRed()< 16) ? "0":"")+Integer.toHexString(lastCol.getRed()) - + ((lastCol.getGreen()< 16) ? "0":"")+Integer.toHexString(lastCol.getGreen()) - + ((lastCol.getBlue()< 16) ? "0":"")+Integer.toHexString(lastCol.getBlue()); - StringBuffer currange = colranges.get(colstring); - if (currange==null) + StringBuilder sb = new StringBuilder(); + if (featureType != null) { - colranges.put(colstring,currange = new StringBuffer()); + for (char c : featureType.toCharArray()) + { + sb.append(Character.isLetterOrDigit(c) ? c : '_'); + } } - if (currange.length()>0) + String attName = NAMESPACE_PREFIX + sb.toString(); + + /* + * Chimera treats an attribute name ending in 'color' as colour-valued; + * Jalview doesn't, so prevent this by appending an underscore + */ + if (attName.toUpperCase().endsWith("COLOR")) { - currange.append("|"); + attName += "_"; } - currange.append("#" + startModel + ":" + ((startPos==lastPos) ? startPos : startPos + "-" - + lastPos) + "." + lastChain); + + return attName; } }