X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignmentUtils.java;h=fdc74e2fed6f1f8cf4ba65a040c99374255163c0;hb=7723baa88fa4f365c01e9f0ee9551e278219d2e5;hp=9a63eb177b83205ab771e590de3e9e7bdbeeb537;hpb=c604058f0c3be7bd38baa8ac01cff87989deecd5;p=jalview.git diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java index 9a63eb1..fdc74e2 100644 --- a/src/jalview/analysis/AlignmentUtils.java +++ b/src/jalview/analysis/AlignmentUtils.java @@ -20,6 +20,8 @@ */ package jalview.analysis; +import java.util.Locale; + import java.util.ArrayList; import java.util.Arrays; import java.util.Collection; @@ -36,7 +38,7 @@ 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; @@ -182,10 +184,10 @@ public class AlignmentUtils // TODO use Character.toLowerCase to avoid creating String objects? char[] upstream = new String(ds .getSequence(s.getStart() - 1 - ustream_ds, s.getStart() - 1)) - .toLowerCase().toCharArray(); + .toLowerCase(Locale.ROOT).toCharArray(); char[] downstream = new String( - ds.getSequence(s_end - 1, s_end + dstream_ds)).toLowerCase() - .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]; @@ -463,7 +465,8 @@ public class AlignmentUtils if (cdnaLength != mappedLength && cdnaLength > 2) { String lastCodon = String.valueOf(cdnaSeqChars, - cdnaLength - CODON_LENGTH, CODON_LENGTH).toUpperCase(); + cdnaLength - CODON_LENGTH, CODON_LENGTH) + .toUpperCase(Locale.ROOT); for (String stop : ResidueProperties.STOP_CODONS) { if (lastCodon.equals(stop)) @@ -480,7 +483,8 @@ public class AlignmentUtils */ int startOffset = 0; if (cdnaLength != mappedLength && cdnaLength > 2 - && String.valueOf(cdnaSeqChars, 0, CODON_LENGTH).toUpperCase() + && String.valueOf(cdnaSeqChars, 0, CODON_LENGTH) + .toUpperCase(Locale.ROOT) .equals(ResidueProperties.START)) { startOffset += CODON_LENGTH; @@ -974,8 +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 @@ -1649,8 +1653,8 @@ 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()); } } @@ -1754,7 +1758,7 @@ 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 @@ -1807,20 +1811,21 @@ 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' @@ -1829,8 +1834,8 @@ 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); } /* @@ -1842,8 +1847,8 @@ 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; @@ -2054,8 +2059,9 @@ 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()); } } } @@ -2179,9 +2185,9 @@ 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) @@ -2326,8 +2332,8 @@ 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; @@ -2339,11 +2345,11 @@ 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 @@ -2399,11 +2405,11 @@ 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) { @@ -2518,10 +2524,10 @@ 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, @@ -2557,8 +2563,7 @@ 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); }