X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Frbvi%2Fchimera%2FChimeraCommands.java;h=c52b9a217412d522dfa1cf8b641789bd51bfc033;hb=2d62933ef95beb94c1ec2444bcced4a3a7ec42c0;hp=ec94e7da18598d676ad88723854281ccebaa7d4f;hpb=defb4c1d5b4edbd8fbd490f25c15ef1f1de6fe37;p=jalview.git diff --git a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java index ec94e7d..c52b9a2 100644 --- a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java +++ b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java @@ -32,12 +32,16 @@ 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.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; @@ -52,29 +56,34 @@ 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); /** * Constructs Chimera commands to colour residues as per the Jalview alignment * - * @param ssm * @param files - * @param sequence - * @param sr - * @param fr * @param viewPanel + * @param binding * @return */ public static StructureMappingcommandSet[] getColourBySequenceCommand( - StructureSelectionManager ssm, String[] files, - SequenceI[][] sequence, SequenceRenderer sr, - AlignmentViewPanel viewPanel) + String[] files, AlignmentViewPanel viewPanel, + AAStructureBindingModel binding) { + StructureSelectionManager ssm = binding.getSsm(); + SequenceRenderer sr = binding.getSequenceRenderer(viewPanel); + SequenceI[][] sequence = binding.getSequence(); + boolean hideHiddenRegions = binding.isShowAlignmentOnly() + && binding.isHideHiddenRegions(); + Map colourMap = buildColoursMap(ssm, files, - sequence, sr, viewPanel); + sequence, sr, hideHiddenRegions, viewPanel); - List colourCommands = buildColourCommands(colourMap); + List colourCommands = buildColourCommands(colourMap, binding); StructureMappingcommandSet cs = new StructureMappingcommandSet( ChimeraCommands.class, null, @@ -96,10 +105,12 @@ public class ChimeraCommands * * * @param colourMap + * @param binding * @return */ protected static List buildColourCommands( - Map colourMap) + Map colourMap, + AAStructureBindingModel binding) { /* * This version concatenates all commands into a single String (semi-colon @@ -117,78 +128,38 @@ public class ChimeraCommands sb.append("; "); sb.append("color ").append(colourCode).append(" "); final AtomSpecModel colourData = colourMap.get(colour); - sb.append(colourData.getAtomSpec()); + sb.append(getAtomSpec(colourData, binding)); } commands.add(sb.toString()); return commands; } /** - * Traverses a map of { modelNumber, {chain, {list of from-to ranges} } } and - * builds a Chimera format atom spec + * Build a data structure which records contiguous subsequences for each colour. + * From this we can easily generate the Chimera command for colour by sequence. * - * @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)
    *
+ * + * 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, - AlignmentViewPanel viewPanel) + boolean hideHiddenRegions, AlignmentViewPanel viewPanel) { FeatureRenderer fr = viewPanel.getFeatureRenderer(); FeatureColourFinder finder = new FeatureColourFinder(fr); @@ -235,12 +206,18 @@ public class ChimeraCommands Color colour = sr.getResidueColour(seq, r, finder); /* - * hidden regions are shown gray - * todo: iterate over visible columns only + * hidden regions are shown gray or, optionally, ignored */ if (!cs.isVisible(r)) { - continue; // colour = Color.GRAY; + if (hideHiddenRegions) + { + continue; + } + else + { + colour = Color.GRAY; + } } final String chain = mapping[m].getChain(); @@ -308,23 +285,27 @@ public class ChimeraCommands /** * 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. + * 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( - StructureSelectionManager ssm, String[] files, SequenceI[][] seqs, - AlignmentViewPanel viewPanel) + 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); + List commands = buildSetAttributeCommands(featureMap, binding); StructureMappingcommandSet cs = new StructureMappingcommandSet( ChimeraCommands.class, null, @@ -470,10 +451,12 @@ public class ChimeraCommands * * * @param featureMap + * @param binding * @return */ protected static List buildSetAttributeCommands( - Map> featureMap) + Map> featureMap, + AAStructureBindingModel binding) { List commands = new ArrayList<>(); for (String featureType : featureMap.keySet()) @@ -499,7 +482,7 @@ public class ChimeraCommands featureValue = featureValue.replaceAll("\\'", "'"); sb.append("setattr r ").append(attributeName).append(" '") .append(featureValue).append("' "); - sb.append(values.get(value).getAtomSpec()); + sb.append(getAtomSpec(values.get(value), binding)); commands.add(sb.toString()); } } @@ -543,4 +526,111 @@ public class ChimeraCommands 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()) + { + 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 + { + sb.append(start).append("-").append(end); + } + + sb.append("."); + if (!" ".equals(chain)) + { + sb.append(chain); + } + } + }