- * 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
- */
- @Override
- public List<StructureCommandI> setAttributesForFeatures(
- StructureSelectionManager ssm, String[] files, SequenceI[][] seqs,
- AlignmentViewPanel viewPanel)
- {
- Map<String, Map<Object, AtomSpecModel>> featureMap = buildFeaturesMap(
- ssm, files, seqs, viewPanel);
-
- return setAttributes(featureMap);
- }
-
- /**
- * <pre>
- * Helper method to build a map of
- * { featureType, { feature value, AtomSpecModel } }
- * </pre>
- *
- * @param ssm
- * @param files
- * @param seqs
- * @param viewPanel
- * @return
- */
- protected Map<String, Map<Object, AtomSpecModel>> buildFeaturesMap(
- StructureSelectionManager ssm, String[] files, SequenceI[][] seqs,
- AlignmentViewPanel viewPanel)
- {
- Map<String, Map<Object, AtomSpecModel>> theMap = new LinkedHashMap<>();
-
- FeatureRenderer fr = viewPanel.getFeatureRenderer();
- if (fr == null)
- {
- return theMap;
- }
-
- AlignViewportI viewport = viewPanel.getAlignViewport();
- List<String> 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<String> 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++)
- {
- final int modelNumber = pdbfnum + getModelStartNo();
- String modelId = String.valueOf(modelNumber);
- 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, modelId);
- }
- if (showLinkedFeatures)
- {
- scanComplementFeatures(complementRenderer, structureMapping,
- seq, theMap, modelId);
- }
- }
- }
- }
- }
- 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<String, Map<Object, AtomSpecModel>> theMap,
- String 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<int[]> 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<Object, AtomSpecModel> 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());
- }
- }
- }
- }
- }
- }
-
- /**
- * 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 modelId
- */
- protected static void scanSequenceFeatures(List<String> visibleFeatures,
- StructureMapping mapping, SequenceI seq,
- Map<String, Map<Object, AtomSpecModel>> theMap, String modelId)
- {
- List<SequenceFeature> 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()))
- {
- continue;
- }
-
- List<int[]> 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<Object, AtomSpecModel> featureValues = theMap.get(type);
- if (featureValues == null)
- {
- featureValues = new HashMap<>();
- theMap.put(type, featureValues);
- }
- for (int[] range : mappedRanges)
- {
- addAtomSpecRange(featureValues, value, modelId, range[0],
- range[1], mapping.getChain());
- }
- }
- }
- }
-
- /**