X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignmentUtils.java;h=aacd92dfb50de2224b4d01ee2d94ceb1bc3d1bbb;hb=b5667f39acdf309cd92881b73edfda591e0acaf4;hp=bdc5fc16373ad8465ac7d3611ad0d1b04844bdd3;hpb=6a99631de459c9ba52894900d08be0a2d6500488;p=jalview.git diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java index bdc5fc1..aacd92d 100644 --- a/src/jalview/analysis/AlignmentUtils.java +++ b/src/jalview/analysis/AlignmentUtils.java @@ -74,12 +74,15 @@ import java.util.TreeMap; */ public class AlignmentUtils { - private static final int CODON_LENGTH = 3; private static final String SEQUENCE_VARIANT = "sequence_variant:"; - private static final String ID = "ID"; + /* + * the 'id' attribute is provided for variant features fetched from + * Ensembl using its REST service with JSON format + */ + public static final String VARIANT_ID = "id"; /** * A data model to hold the 'normal' base value at a position, and an optional @@ -1461,28 +1464,31 @@ public class AlignmentUtils final List result = new ArrayList<>(); for (AlignmentAnnotation dsann : datasetAnnotations) { - /* - * Find matching annotations on the alignment. If none is found, then - * add this annotation to the list of 'addable' annotations for this - * sequence. - */ - final Iterable matchedAlignmentAnnotations = al - .findAnnotations(seq, dsann.getCalcId(), dsann.label); - if (!matchedAlignmentAnnotations.iterator().hasNext()) + if (dsann.annotations != null) // ignore non-positional annotation { - result.add(dsann); - if (labelForCalcId != null) + /* + * Find matching annotations on the alignment. If none is found, then + * add this annotation to the list of 'addable' annotations for this + * sequence. + */ + final Iterable matchedAlignmentAnnotations = al + .findAnnotations(seq, dsann.getCalcId(), dsann.label); + if (!matchedAlignmentAnnotations.iterator().hasNext()) { - labelForCalcId.put(dsann.getCalcId(), dsann.label); + result.add(dsann); + if (labelForCalcId != null) + { + labelForCalcId.put(dsann.getCalcId(), dsann.label); + } } } - } - /* - * Save any addable annotations for this sequence - */ - if (!result.isEmpty()) - { - candidates.put(seq, result); + /* + * Save any addable annotations for this sequence + */ + if (!result.isEmpty()) + { + candidates.put(seq, result); + } } } } @@ -1888,7 +1894,7 @@ public class AlignmentUtils * @param seqMappings * the set of mappings involving dnaSeq * @param aMapping - * an initial candidate from seqMappings + * a transcript-to-peptide mapping * @return */ static SequenceI findCdsForProtein(List mappings, @@ -1913,7 +1919,15 @@ public class AlignmentUtils if (mappedFromLength == dnaLength || mappedFromLength == dnaLength - CODON_LENGTH) { - return seqDss; + /* + * if sequence has CDS features, this is a transcript with no UTR + * - do not take this as the CDS sequence! (JAL-2789) + */ + if (seqDss.getFeatures().getFeaturesByOntology(SequenceOntologyI.CDS) + .isEmpty()) + { + return seqDss; + } } /* @@ -1938,10 +1952,12 @@ public class AlignmentUtils { /* * found a 3:1 mapping to the protein product which covers - * the whole dna sequence i.e. is from CDS; finally check it - * is from the dna start sequence + * the whole dna sequence i.e. is from CDS; finally check the CDS + * is mapped from the given dna start sequence */ SequenceI cdsSeq = map.getFromSeq(); + // todo this test is weak if seqMappings contains multiple mappings; + // we get away with it if transcript:cds relationship is 1:1 List dnaToCdsMaps = MappingUtils .findMappingsForSequence(cdsSeq, seqMappings); if (!dnaToCdsMaps.isEmpty()) @@ -2056,9 +2072,11 @@ public class AlignmentUtils protected static List propagateDBRefsToCDS(SequenceI cdsSeq, SequenceI contig, SequenceI proteinProduct, Mapping mapping) { + // gather direct refs from contig congruent with mapping List direct = new ArrayList<>(); HashSet directSources = new HashSet<>(); + if (contig.getDBRefs() != null) { for (DBRefEntry dbr : contig.getDBRefs()) @@ -2235,12 +2253,13 @@ public class AlignmentUtils int mappedDnaLength = MappingUtils.getLength(ranges); /* - * if not a whole number of codons, something is wrong, - * abort mapping + * if not a whole number of codons, truncate mapping */ - if (mappedDnaLength % CODON_LENGTH > 0) + int codonRemainder = mappedDnaLength % CODON_LENGTH; + if (codonRemainder > 0) { - return null; + mappedDnaLength -= codonRemainder; + MappingUtils.removeEndPositions(codonRemainder, ranges); } int proteinLength = proteinSeq.getLength(); @@ -2430,11 +2449,14 @@ public class AlignmentUtils { for (String base : alleles.split(",")) { - if (!base1.equals(base)) + if (!base1.equalsIgnoreCase(base)) { - String codon = base + base2 + base3; + String codon = base.toUpperCase() + base2.toLowerCase() + + base3.toLowerCase(); + String canonical = base1.toUpperCase() + base2.toLowerCase() + + base3.toLowerCase(); if (addPeptideVariant(peptide, peptidePos, residue, var, - codon)) + codon, canonical)) { count++; } @@ -2456,11 +2478,14 @@ public class AlignmentUtils { for (String base : alleles.split(",")) { - if (!base2.equals(base)) + if (!base2.equalsIgnoreCase(base)) { - String codon = base1 + base + base3; + String codon = base1.toLowerCase() + base.toUpperCase() + + base3.toLowerCase(); + String canonical = base1.toLowerCase() + base2.toUpperCase() + + base3.toLowerCase(); if (addPeptideVariant(peptide, peptidePos, residue, var, - codon)) + codon, canonical)) { count++; } @@ -2482,11 +2507,14 @@ public class AlignmentUtils { for (String base : alleles.split(",")) { - if (!base3.equals(base)) + if (!base3.equalsIgnoreCase(base)) { - String codon = base1 + base2 + base; + String codon = base1.toLowerCase() + base2.toLowerCase() + + base.toUpperCase(); + String canonical = base1.toLowerCase() + base2.toLowerCase() + + base3.toUpperCase(); if (addPeptideVariant(peptide, peptidePos, residue, var, - codon)) + codon, canonical)) { count++; } @@ -2500,20 +2528,22 @@ public class AlignmentUtils } /** - * Helper method that adds a peptide variant feature, provided the given codon - * translates to a value different to the current residue (is a non-synonymous - * variant). ID and clinical_significance attributes of the dna variant (if - * present) are copied to the new feature. + * Helper method that adds a peptide variant feature. ID and + * clinical_significance attributes of the dna variant (if present) are copied + * to the new feature. * * @param peptide * @param peptidePos * @param residue * @param var * @param codon + * the variant codon e.g. aCg + * @param canonical + * the 'normal' codon e.g. aTg * @return true if a feature was added, else false */ static boolean addPeptideVariant(SequenceI peptide, int peptidePos, - String residue, DnaVariant var, String codon) + String residue, DnaVariant var, String codon, String canonical) { /* * get peptide translation of codon e.g. GAT -> D @@ -2528,7 +2558,7 @@ public class AlignmentUtils { return false; } - String desc = codon; + String desc = canonical + "/" + codon; String featureType = ""; if (trans.equals(residue)) { @@ -2551,15 +2581,15 @@ public class AlignmentUtils peptidePos, var.getSource()); StringBuilder attributes = new StringBuilder(32); - String id = (String) var.variant.getValue(ID); + String id = (String) var.variant.getValue(VARIANT_ID); if (id != null) { if (id.startsWith(SEQUENCE_VARIANT)) { id = id.substring(SEQUENCE_VARIANT.length()); } - sf.setValue(ID, id); - attributes.append(ID).append("=").append(id); + sf.setValue(VARIANT_ID, id); + attributes.append(VARIANT_ID).append("=").append(id); // TODO handle other species variants JAL-2064 StringBuilder link = new StringBuilder(32); try