X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Frbvi%2Fchimera%2FChimeraCommands.java;h=45b22f73c18c0d9b48aed09fd4c49dfbf76be4c9;hb=5c6564f903f75960af960720a8635ab8709afc37;hp=3c47ed1a3e4befa31041491ddb95ea757e8ed454;hpb=81316c6cc11e29c893d55e87ebd16d9ecd09c1f3;p=jalview.git diff --git a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java index 3c47ed1..45b22f7 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 2.8.2) - * 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. * @@ -20,20 +20,30 @@ */ package jalview.ext.rbvi.chimera; +import jalview.api.AlignViewportI; +import jalview.api.AlignmentViewPanel; import jalview.api.FeatureRenderer; import jalview.api.SequenceRenderer; 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.structures.models.AAStructureBindingModel; +import jalview.util.ColorUtils; import jalview.util.Comparison; +import jalview.util.IntRangeComparator; import java.awt.Color; -import java.io.File; -import java.io.FileOutputStream; -import java.io.IOException; import java.util.ArrayList; +import java.util.Collections; +import java.util.HashMap; +import java.util.Iterator; import java.util.LinkedHashMap; import java.util.List; import java.util.Map; @@ -46,44 +56,109 @@ import java.util.Map; */ public class ChimeraCommands { + public static final String NAMESPACE_PREFIX = "jv_"; + + /* + * colour for residues shown in structure but hidden in alignment + */ + private static final String COLOR_GRAY_HEX = "color " + + ColorUtils.toTkCode(Color.GRAY); /** - * utility to construct the commands to colour chains by the given alignment - * for passing to Chimera + * Constructs Chimera commands to colour residues as per the Jalview alignment * - * @returns Object[] { Object[] { , + * @param colourMap + * @param binding + * @return + */ + public static String[] getColourBySequenceCommand( + Map colourMap, + AAStructureBindingModel binding) + { + List colourCommands = buildColourCommands(colourMap, binding); + + return colourCommands.toArray(new String[colourCommands.size()]); + } + + /** + * 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 + * @param binding + * @return */ - public static StructureMappingcommandSet[] getColourBySequenceCommand( - StructureSelectionManager ssm, String[] files, - SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr, - AlignmentI alignment) + protected static List buildColourCommands( + Map colourMap, + AAStructureBindingModel binding) { - String defAttrPath = null; - FileOutputStream fos = null; - try - { - File outFile = File.createTempFile("jalviewdefattr", ".xml"); - outFile.deleteOnExit(); - defAttrPath = outFile.getPath(); - fos = new FileOutputStream(outFile); - fos.write("attribute: jalviewclr\n".getBytes()); - } catch (IOException e1) + /* + * 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); + sb.append(COLOR_GRAY_HEX); + + for (Object key : colourMap.keySet()) { - e1.printStackTrace(); + Color colour = (Color) key; + String colourCode = ColorUtils.toTkCode(colour); + sb.append("; "); + sb.append("color ").append(colourCode).append(" "); + final AtomSpecModel colourData = colourMap.get(colour); + sb.append(getAtomSpec(colourData, binding)); } - List cset = new ArrayList(); + commands.add(sb.toString()); + return commands; + } + + /** + * 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 ssm + * @param files + * @param sequence + * @param sr + * @param hideHiddenRegions + * @param viewPanel + * @return + */ + protected static Map buildColoursMap( + StructureSelectionManager ssm, String[] files, + SequenceI[][] sequence, SequenceRenderer sr, + boolean hideHiddenRegions, 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; - /* - * Map of { colour, positionSpecs} - */ - Map colranges = new LinkedHashMap(); - StringBuilder setAttributes = new StringBuilder(256); - String lastColour = "none"; - Color lastCol = null; for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) { - boolean startModel = true; StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]); if (mapping == null || mapping.length < 1) @@ -99,9 +174,9 @@ public class ChimeraCommands { final SequenceI seq = sequence[pdbfnum][s]; if (mapping[m].getSequence() == seq - && (sp = alignment.findIndex(seq)) > -1) + && (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 @@ -116,200 +191,541 @@ public class ChimeraCommands continue; } - Color col = getResidueColour(seq, r, sr, fr); + 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 = !col.equals(lastCol); + final boolean newColour = !colour.equals(lastColour); final boolean nonContig = lastPos + 1 != pos; - final boolean newChain = !mapping[m].getChain().equals(lastChain); - if (newColour || nonContig || startModel || newChain) + final boolean newChain = !chain.equals(lastChain); + if (newColour || nonContig || newChain) { - if (/* lastCol != null */startPos != -1) + if (startPos != -1) { - addColourRange(colranges, lastCol, pdbfnum, startPos, - lastPos, lastChain, startModel); - startModel = false; + addAtomSpecRange(colourMap, lastColour, pdbfnum, startPos, + lastPos, lastChain); } - // lastCol = null; startPos = pos; } - lastCol = col; + lastColour = colour; lastPos = pos; - // lastModel = pdbfnum; - lastChain = mapping[m].getChain(); + lastChain = chain; } // final colour range - if (lastCol != null) + if (lastColour != null) { - addColourRange(colranges, lastCol, pdbfnum, startPos, - lastPos, lastChain, false); + addAtomSpecRange(colourMap, lastColour, pdbfnum, startPos, + lastPos, lastChain); } - break; + // break; } } } } - try - { - lastColour = buildColourCommands(cset, colranges, - fos, setAttributes); - } catch (IOException e) - { - e.printStackTrace(); - } + return colourMap; + } - try + /** + * 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 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) { - fos.close(); - } catch (IOException e) + 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 + * @param binding + * @return + */ + public static StructureMappingcommandSet getSetAttributeCommandsForFeatures( + AlignmentViewPanel viewPanel, AAStructureBindingModel binding) + { + StructureSelectionManager ssm = binding.getSsm(); + String[] files = binding.getStructureFiles(); + SequenceI[][] seqs = binding.getSequence(); + + Map> featureMap = buildFeaturesMap( + ssm, files, seqs, viewPanel); + + List commands = buildSetAttributeCommands(featureMap, binding); + + 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) { - e.printStackTrace(); + return theMap; } + AlignViewportI viewport = viewPanel.getAlignViewport(); + List visibleFeatures = fr.getDisplayedFeatureTypes(); + /* - * Send a rangeColor command, preceded by either defattr or setattr, - * whichever we end up preferring! - * - * rangecolor requires a minimum of two attribute values to operate on + * if alignment is showing features from complement, we also transfer + * these features to the corresponding mapped structure residues */ - StringBuilder rangeColor = new StringBuilder(256); - rangeColor.append("rangecolor jalviewclr"); - int colourId = 0; - for (String colour : colranges.keySet()) + 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()) { - colourId++; - rangeColor.append(" " + colourId + " " + colour); + return theMap; } - String rangeColorCommand = rangeColor.toString(); - if (rangeColorCommand.split(" ").length < 5) + + AlignmentI alignment = viewPanel.getAlignment(); + for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) { - rangeColorCommand += " max " + lastColour; + 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); + } + } + } + } } - final String defAttrCommand = "defattr " + defAttrPath - + " raiseTool false"; - final String setAttrCommand = setAttributes.toString(); - final String attrCommand = false ? defAttrCommand : setAttrCommand; - cset.add(new StructureMappingcommandSet(ChimeraCommands.class, null, - new String[] - { attrCommand /* , rangeColorCommand */})); - - return cset.toArray(new StructureMappingcommandSet[cset.size()]); + return theMap; } /** - * Get the residue colour at the given sequence position - as determined by - * the sequence group colour (if any), else the colour scheme, possibly - * overridden by a feature colour. + * 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 position - * @param sr - * @param fr - * @return + * @param theMap + * @param modelNumber */ - protected static Color getResidueColour(final SequenceI seq, - int position, SequenceRenderer sr, FeatureRenderer fr) + protected static void scanComplementFeatures( + FeatureRenderer complementRenderer, + StructureMapping structureMapping, SequenceI seq, + Map> theMap, int modelNumber) { - Color col = sr.getResidueBoxColour(seq, position); + /* + * 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) + { + addAtomSpecRange(featureValues, value, modelNumber, range[0], + range[1], structureMapping.getChain()); + } + } + } + } + } + } - if (fr != null) + /** + * 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) { - col = fr.findFeatureColour(col, seq, position); + String type = sf.getType(); + + /* + * Don't copy features which originated from Chimera + */ + if (JalviewChimeraBinding.CHIMERA_FEATURE_GROUP + .equals(sf.getFeatureGroup())) + { + 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()); + } + } } - return col; } /** - * Helper method to build the colour commands for one PDBfile. + * 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 * - * @param cset - * the list of commands to be added to - * @param colranges - * the map of colours to residue positions already determined - * @param fos - * file to write 'defattr' commands to - * @param setAttributes - * @throws IOException + * 

+   * 
 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 + * @param binding + * @return */ - protected static String buildColourCommands( - List cset, - Map colranges, - FileOutputStream fos, StringBuilder setAttributes) - throws IOException + protected static List buildSetAttributeCommands( + Map> featureMap, + AAStructureBindingModel binding) { - int colourId = 0; - String lastColour = null; - for (String colour : colranges.keySet()) + List commands = new ArrayList<>(); + for (String featureType : featureMap.keySet()) { - lastColour = colour; - colourId++; + String attributeName = makeAttributeName(featureType); + /* - * Using color command directly is slow for larger structures. - * setAttributes.append("color #" + colour + " " + colranges.get(colour)+ - * ";"); + * clear down existing attributes for this feature */ - setAttributes.append("color " + colour + " " + colranges.get(colour) - + ";"); - final String atomSpec = new String(colranges.get(colour)); - // setAttributes.append("setattr r jalviewclr " + colourId + " " - // + atomSpec + ";"); - fos.write(("\t" + atomSpec + "\t" + colourId + "\n").getBytes()); + // '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(getAtomSpec(values.get(value), binding)); + commands.add(sb.toString()); + } } - return lastColour; + + return commands; } /** - * Helper method to record a range of positions of the same colour. + * 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 colranges - * @param colour - * @param model - * @param startPos - * @param endPos - * @param chain - * @param changeModel + * @param featureType + * @return + * + * 
+   * @see https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/setattr.html
+   *
*/ - private static void addColourRange(Map colranges, - Color colour, int model, int startPos, int endPos, String chain, - boolean startModel) + protected static String makeAttributeName(String featureType) { - String colstring = "#" + ((colour.getRed() < 16) ? "0" : "") - + Integer.toHexString(colour.getRed()) - + ((colour.getGreen()< 16) ? "0":"")+Integer.toHexString(colour.getGreen()) - + ((colour.getBlue()< 16) ? "0":"")+Integer.toHexString(colour.getBlue()); - StringBuilder currange = colranges.get(colstring); - if (currange == null) + StringBuilder sb = new StringBuilder(); + if (featureType != null) { - colranges.put(colstring, currange = new StringBuilder(256)); + for (char c : featureType.toCharArray()) + { + sb.append(Character.isLetterOrDigit(c) ? c : '_'); + } } + String attName = NAMESPACE_PREFIX + sb.toString(); + /* - * Format as (e.g.) #0:1-3.A,5.A,7-10.A,...#1:1-4.B,..etc + * Chimera treats an attribute name ending in 'color' as colour-valued; + * Jalview doesn't, so prevent this by appending an underscore */ - // if (currange.length() > 0) - // { - // currange.append("|"); - // } - // currange.append("#" + model + ":" + ((startPos==endPos) ? startPos : - // startPos + "-" - // + endPos) + "." + chain); - if (currange.length() == 0) + if (attName.toUpperCase().endsWith("COLOR")) { - currange.append("#" + model + ":"); + attName += "_"; } - else if (startModel) + + return attName; + } + + /** + * Returns the range(s) formatted as a Chimera atomspec + * + * @return + */ + public static String getAtomSpec(AtomSpecModel atomSpec, + AAStructureBindingModel binding) + { + StringBuilder sb = new StringBuilder(128); + boolean firstModel = true; + for (Integer model : atomSpec.getModels()) { - currange.append(",#" + model + ":"); + if (!firstModel) + { + sb.append("|"); + } + firstModel = false; + // todo use JalviewChimeraBinding.getModelSpec(model) + // which means this cannot be static + sb.append(binding.getModelSpec(model)).append(":"); + + boolean firstPositionForModel = true; + + for (String chain : atomSpec.getChains(model)) + { + chain = " ".equals(chain) ? chain : chain.trim(); + + List rangeList = atomSpec.getRanges(model, chain); + + /* + * sort ranges into ascending start position order + */ + Collections.sort(rangeList, IntRangeComparator.ASCENDING); + + int start = rangeList.isEmpty() ? 0 : rangeList.get(0)[0]; + int end = rangeList.isEmpty() ? 0 : rangeList.get(0)[1]; + + Iterator iterator = rangeList.iterator(); + while (iterator.hasNext()) + { + int[] range = iterator.next(); + if (range[0] <= end + 1) + { + /* + * range overlaps or is contiguous with the last one + * - so just extend the end position, and carry on + * (unless this is the last in the list) + */ + end = Math.max(end, range[1]); + } + else + { + /* + * we have a break so append the last range + */ + appendRange(sb, start, end, chain, firstPositionForModel); + firstPositionForModel = false; + start = range[0]; + end = range[1]; + } + } + + /* + * and append the last range + */ + if (!rangeList.isEmpty()) + { + appendRange(sb, start, end, chain, firstPositionForModel); + firstPositionForModel = false; + } + } + } + return sb.toString(); + } + + /** + * A helper method that appends one start-end range to a Chimera atomspec + * + * @param sb + * @param start + * @param end + * @param chain + * @param firstPositionForModel + */ + static void appendRange(StringBuilder sb, int start, int end, + String chain, boolean firstPositionForModel) + { + if (!firstPositionForModel) + { + sb.append(","); + } + if (end == start) + { + sb.append(start); } else { - currange.append(","); + sb.append(start).append("-").append(end); + } + + sb.append("."); + if (!" ".equals(chain)) + { + sb.append(chain); } - final String rangeSpec = (startPos == endPos) ? Integer - .toString(startPos) : (startPos + "-" + endPos); - currange.append(rangeSpec + "." + chain); } }