X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignmentUtils.java;h=a1a7fefc70565e4ad216f15ef84b5b7fb5482635;hb=ac3fe94f6d237a0a2032474844217d542040776c;hp=f95ff73a4900373d7c34302a95b9e88bfe909c04;hpb=27aed96d1aeae689818bd0a0028553186e3c3839;p=jalview.git diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java index f95ff73..a1a7fef 100644 --- a/src/jalview/analysis/AlignmentUtils.java +++ b/src/jalview/analysis/AlignmentUtils.java @@ -20,8 +20,6 @@ */ package jalview.analysis; -import java.util.Locale; - import java.util.ArrayList; import java.util.Arrays; import java.util.Collection; @@ -31,6 +29,7 @@ import java.util.HashSet; import java.util.Iterator; import java.util.LinkedHashMap; import java.util.List; +import java.util.Locale; import java.util.Map; import java.util.Map.Entry; import java.util.NoSuchElementException; @@ -38,7 +37,7 @@ import java.util.Set; import java.util.SortedMap; import java.util.TreeMap; -import jalview.bin.Cache; +import jalview.bin.Console; import jalview.commands.RemoveGapColCommand; import jalview.datamodel.AlignedCodon; import jalview.datamodel.AlignedCodonFrame; @@ -46,6 +45,7 @@ import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; +import jalview.datamodel.ContactMatrixI; import jalview.datamodel.DBRefEntry; import jalview.datamodel.GeneLociI; import jalview.datamodel.IncompleteCodonException; @@ -186,8 +186,8 @@ public class AlignmentUtils .getSequence(s.getStart() - 1 - ustream_ds, s.getStart() - 1)) .toLowerCase(Locale.ROOT).toCharArray(); char[] downstream = new String( - ds.getSequence(s_end - 1, s_end + dstream_ds)).toLowerCase(Locale.ROOT) - .toCharArray(); + ds.getSequence(s_end - 1, s_end + dstream_ds)) + .toLowerCase(Locale.ROOT).toCharArray(); char[] coreseq = s.getSequence(); char[] nseq = new char[offset + upstream.length + downstream.length + coreseq.length]; @@ -465,7 +465,8 @@ public class AlignmentUtils if (cdnaLength != mappedLength && cdnaLength > 2) { String lastCodon = String.valueOf(cdnaSeqChars, - cdnaLength - CODON_LENGTH, CODON_LENGTH).toUpperCase(Locale.ROOT); + cdnaLength - CODON_LENGTH, CODON_LENGTH) + .toUpperCase(Locale.ROOT); for (String stop : ResidueProperties.STOP_CODONS) { if (lastCodon.equals(stop)) @@ -482,7 +483,8 @@ public class AlignmentUtils */ int startOffset = 0; if (cdnaLength != mappedLength && cdnaLength > 2 - && String.valueOf(cdnaSeqChars, 0, CODON_LENGTH).toUpperCase(Locale.ROOT) + && String.valueOf(cdnaSeqChars, 0, CODON_LENGTH) + .toUpperCase(Locale.ROOT) .equals(ResidueProperties.START)) { startOffset += CODON_LENGTH; @@ -976,8 +978,8 @@ public class AlignmentUtils mapList = mapList.getInverse(); } final int cdsLength = cdsDss.getLength(); - int mappedFromLength = MappingUtils.getLength(mapList - .getFromRanges()); + int mappedFromLength = MappingUtils + .getLength(mapList.getFromRanges()); int mappedToLength = MappingUtils .getLength(mapList.getToRanges()); boolean addStopCodon = (cdsLength == mappedFromLength @@ -1469,7 +1471,8 @@ public class AlignmentUtils */ final Iterable matchedAlignmentAnnotations = al .findAnnotations(seq, dsann.getCalcId(), dsann.label); - if (!matchedAlignmentAnnotations.iterator().hasNext()) + if (matchedAlignmentAnnotations == null + || !matchedAlignmentAnnotations.iterator().hasNext()) { result.add(dsann); if (labelForCalcId != null) @@ -1515,7 +1518,7 @@ public class AlignmentUtils startRes = selectionGroup.getStartRes(); endRes = selectionGroup.getEndRes(); } - copyAnn.restrict(startRes, endRes); + copyAnn.restrict(startRes, endRes + 0); /* * Add to the sequence (sets copyAnn.datasetSequence), unless the @@ -1523,6 +1526,12 @@ public class AlignmentUtils */ if (!seq.hasAnnotation(ann)) { + ContactMatrixI cm = seq.getDatasetSequence() + .getContactMatrixFor(ann); + if (cm != null) + { + seq.addContactListFor(copyAnn, cm); + } seq.addAlignmentAnnotation(copyAnn); } // adjust for gaps @@ -1532,6 +1541,7 @@ public class AlignmentUtils copyAnn.visible = true; } } + } /** @@ -1651,8 +1661,8 @@ public class AlignmentUtils productSeqs = new HashSet<>(); for (SequenceI seq : products) { - productSeqs.add(seq.getDatasetSequence() == null ? seq : seq - .getDatasetSequence()); + productSeqs.add(seq.getDatasetSequence() == null ? seq + : seq.getDatasetSequence()); } } @@ -1756,7 +1766,7 @@ public class AlignmentUtils dataset.addSequence(cdsSeqDss); AlignedCodonFrame cdsToProteinMapping = new AlignedCodonFrame(); cdsToProteinMapping.addMap(cdsSeqDss, proteinProduct, - cdsToProteinMap); + cdsToProteinMap); /* * guard against duplicating the mapping if repeating this action @@ -1809,20 +1819,21 @@ public class AlignmentUtils List primrefs = dnaDss.getPrimaryDBRefs(); for (int ip = 0, np = primrefs.size(); ip < np; ip++) { - DBRefEntry primRef = primrefs.get(ip); + DBRefEntry primRef = primrefs.get(ip); /* * create a cross-reference from CDS to the source sequence's * primary reference and vice versa */ String source = primRef.getSource(); String version = primRef.getVersion(); - DBRefEntry cdsCrossRef = new DBRefEntry(source, source + ":" - + version, primRef.getAccessionId()); - cdsCrossRef.setMap(new Mapping(dnaDss, new MapList(cdsToDnaMap))); + DBRefEntry cdsCrossRef = new DBRefEntry(source, + source + ":" + version, primRef.getAccessionId()); + cdsCrossRef + .setMap(new Mapping(dnaDss, new MapList(cdsToDnaMap))); cdsSeqDss.addDBRef(cdsCrossRef); - dnaSeq.addDBRef(new DBRefEntry(source, version, cdsSeq - .getName(), new Mapping(cdsSeqDss, dnaToCdsMap))); + dnaSeq.addDBRef(new DBRefEntry(source, version, + cdsSeq.getName(), new Mapping(cdsSeqDss, dnaToCdsMap))); // problem here is that the cross-reference is synthesized - // cdsSeq.getName() may be like 'CDS|dnaaccession' or // 'CDS|emblcdsacc' @@ -1831,8 +1842,8 @@ public class AlignmentUtils DBRefEntry proteinToCdsRef = new DBRefEntry(source, version, cdsSeq.getName()); // - proteinToCdsRef.setMap(new Mapping(cdsSeqDss, cdsToProteinMap - .getInverse())); + proteinToCdsRef.setMap( + new Mapping(cdsSeqDss, cdsToProteinMap.getInverse())); proteinProduct.addDBRef(proteinToCdsRef); } /* @@ -1844,8 +1855,8 @@ public class AlignmentUtils } } - AlignmentI cds = new Alignment(cdsSeqs.toArray(new SequenceI[cdsSeqs - .size()])); + AlignmentI cds = new Alignment( + cdsSeqs.toArray(new SequenceI[cdsSeqs.size()])); cds.setDataset(dataset); return cds; @@ -2056,8 +2067,9 @@ public class AlignmentUtils } else { - Cache.log.error( - "JAL-2154 regression: warning - found (and ignored) a duplicate CDS sequence:" + mtch.toString()); + Console.error( + "JAL-2154 regression: warning - found (and ignored) a duplicate CDS sequence:" + + mtch.toString()); } } } @@ -2181,9 +2193,9 @@ public class AlignmentUtils /* * get features, optionally restricted by an ontology term */ - List sfs = select == null ? fromSeq.getFeatures() - .getPositionalFeatures() : fromSeq.getFeatures() - .getFeaturesByOntology(select); + List sfs = select == null + ? fromSeq.getFeatures().getPositionalFeatures() + : fromSeq.getFeatures().getFeaturesByOntology(select); int count = 0; for (SequenceFeature sf : sfs) @@ -2328,8 +2340,8 @@ public class AlignmentUtils { List result = new ArrayList<>(); - List sfs = dnaSeq.getFeatures().getFeaturesByOntology( - SequenceOntologyI.CDS); + List sfs = dnaSeq.getFeatures() + .getFeaturesByOntology(SequenceOntologyI.CDS); if (sfs.isEmpty()) { return result; @@ -2341,11 +2353,11 @@ public class AlignmentUtils int phase = 0; try { - String s = sf.getPhase(); - if (s != null) - { - phase = Integer.parseInt(s); - } + String s = sf.getPhase(); + if (s != null) + { + phase = Integer.parseInt(s); + } } catch (NumberFormatException e) { // leave as zero @@ -2401,11 +2413,11 @@ public class AlignmentUtils SequenceIdMatcher matcher = new SequenceIdMatcher(seqs); if (xrefs != null) { - // BH 2019.01.25 recoded to remove iterators - + // BH 2019.01.25 recoded to remove iterators + for (int ix = 0, nx = xrefs.length; ix < nx; ix++) { - SequenceI xref = xrefs[ix]; + SequenceI xref = xrefs[ix]; List dbrefs = xref.getDBRefs(); if (dbrefs != null) { @@ -2520,10 +2532,10 @@ public class AlignmentUtils * true; else returns false * * @param unaligned - * - sequences to be aligned based on aligned + * - sequences to be aligned based on aligned * @param aligned - * - 'guide' alignment containing sequences derived from same - * dataset as unaligned + * - 'guide' alignment containing sequences derived from same dataset + * as unaligned * @return */ static boolean alignAsSameSequences(AlignmentI unaligned, @@ -2559,8 +2571,7 @@ public class AlignmentUtils { return false; } - SequenceI alignedSeq = alignedDatasets.get(ds) - .get(0); + SequenceI alignedSeq = alignedDatasets.get(ds).get(0); int startCol = alignedSeq.findIndex(seq.getStart()); // 1.. leftmost = Math.min(leftmost, startCol); }