From ee336f6b257b8c732425a9ab2cc657e80f73f976 Mon Sep 17 00:00:00 2001 From: gmungoc Date: Fri, 9 Feb 2018 12:07:56 +0000 Subject: [PATCH] JAL-2789 code format changes only (before functional fixes) --- src/jalview/analysis/AlignmentUtils.java | 54 +++++++++++++++--------------- 1 file changed, 27 insertions(+), 27 deletions(-) diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java index 90d9197..dfb185a 100644 --- a/src/jalview/analysis/AlignmentUtils.java +++ b/src/jalview/analysis/AlignmentUtils.java @@ -117,7 +117,7 @@ public class AlignmentUtils */ public static AlignmentI expandContext(AlignmentI core, int flankSize) { - List sq = new ArrayList(); + List sq = new ArrayList<>(); int maxoffset = 0; for (SequenceI s : core.getSequences()) { @@ -247,7 +247,7 @@ public class AlignmentUtils public static Map> getSequencesByName( AlignmentI al) { - Map> theMap = new LinkedHashMap>(); + Map> theMap = new LinkedHashMap<>(); for (SequenceI seq : al.getSequences()) { String name = seq.getName(); @@ -256,7 +256,7 @@ public class AlignmentUtils List seqs = theMap.get(name); if (seqs == null) { - seqs = new ArrayList(); + seqs = new ArrayList<>(); theMap.put(name, seqs); } seqs.add(seq); @@ -283,8 +283,8 @@ public class AlignmentUtils return false; } - Set mappedDna = new HashSet(); - Set mappedProtein = new HashSet(); + Set mappedDna = new HashSet<>(); + Set mappedProtein = new HashSet<>(); /* * First pass - map sequences where cross-references exist. This include @@ -870,7 +870,7 @@ public class AlignmentUtils System.err.println("Wrong alignment type in alignProteinAsDna"); return 0; } - List unmappedProtein = new ArrayList(); + List unmappedProtein = new ArrayList<>(); Map> alignedCodons = buildCodonColumnsMap( protein, dna, unmappedProtein); return alignProteinAs(protein, alignedCodons, unmappedProtein); @@ -1081,7 +1081,7 @@ public class AlignmentUtils * {dnaSequence, {proteinSequence, codonProduct}} at that position. The * comparator keeps the codon positions ordered. */ - Map> alignedCodons = new TreeMap>( + Map> alignedCodons = new TreeMap<>( new CodonComparator()); for (SequenceI dnaSeq : dna.getSequences()) @@ -1127,9 +1127,9 @@ public class AlignmentUtils // TODO delete this ugly hack once JAL-2022 is resolved // i.e. we can model startPhase > 0 (incomplete start codon) - List sequencesChecked = new ArrayList(); + List sequencesChecked = new ArrayList<>(); AlignedCodon lastCodon = null; - Map toAdd = new HashMap(); + Map toAdd = new HashMap<>(); for (Entry> entry : alignedCodons .entrySet()) @@ -1308,7 +1308,7 @@ public class AlignmentUtils Map seqProduct = alignedCodons.get(codon); if (seqProduct == null) { - seqProduct = new HashMap(); + seqProduct = new HashMap<>(); alignedCodons.put(codon, seqProduct); } seqProduct.put(protein, codon); @@ -1445,7 +1445,7 @@ public class AlignmentUtils { continue; } - final List result = new ArrayList(); + final List result = new ArrayList<>(); for (AlignmentAnnotation dsann : datasetAnnotations) { /* @@ -1627,13 +1627,13 @@ public class AlignmentUtils throw new IllegalArgumentException( "IMPLEMENTATION ERROR: dataset.getDataset() must be null!"); } - List foundSeqs = new ArrayList(); - List cdsSeqs = new ArrayList(); + List foundSeqs = new ArrayList<>(); + List cdsSeqs = new ArrayList<>(); List mappings = dataset.getCodonFrames(); HashSet productSeqs = null; if (products != null) { - productSeqs = new HashSet(); + productSeqs = new HashSet<>(); for (SequenceI seq : products) { productSeqs.add(seq.getDatasetSequence() == null ? seq @@ -2002,8 +2002,8 @@ public class AlignmentUtils { // gather direct refs from contig congrent with mapping - List direct = new ArrayList(); - HashSet directSources = new HashSet(); + List direct = new ArrayList<>(); + HashSet directSources = new HashSet<>(); if (contig.getDBRefs() != null) { for (DBRefEntry dbr : contig.getDBRefs()) @@ -2023,7 +2023,7 @@ public class AlignmentUtils DBRefEntry[] onSource = DBRefUtils.selectRefs( proteinProduct.getDBRefs(), directSources.toArray(new String[0])); - List propagated = new ArrayList(); + List propagated = new ArrayList<>(); // and generate appropriate mappings for (DBRefEntry cdsref : direct) @@ -2202,7 +2202,7 @@ public class AlignmentUtils proteinStart++; proteinLength--; } - List proteinRange = new ArrayList(); + List proteinRange = new ArrayList<>(); /* * dna length should map to protein (or protein plus stop codon) @@ -2237,7 +2237,7 @@ public class AlignmentUtils */ public static List findCdsPositions(SequenceI dnaSeq) { - List result = new ArrayList(); + List result = new ArrayList<>(); List sfs = dnaSeq.getFeatures().getFeaturesByOntology( SequenceOntologyI.CDS); @@ -2523,7 +2523,7 @@ public class AlignmentUtils * map from peptide position to all variants of the codon which codes for it * LinkedHashMap ensures we keep the peptide features in sequence order */ - LinkedHashMap[]> variants = new LinkedHashMap[]>(); + LinkedHashMap[]> variants = new LinkedHashMap<>(); List dnaFeatures = dnaSeq.getFeatures() .getFeaturesByOntology(SequenceOntologyI.SEQUENCE_VARIANT); @@ -2558,9 +2558,9 @@ public class AlignmentUtils if (codonVariants == null) { codonVariants = new ArrayList[CODON_LENGTH]; - codonVariants[0] = new ArrayList(); - codonVariants[1] = new ArrayList(); - codonVariants[2] = new ArrayList(); + codonVariants[0] = new ArrayList<>(); + codonVariants[1] = new ArrayList<>(); + codonVariants[2] = new ArrayList<>(); variants.put(peptidePosition, codonVariants); } @@ -2699,7 +2699,7 @@ public class AlignmentUtils /* * fancy case - aligning via mappings between sequences */ - List unmapped = new ArrayList(); + List unmapped = new ArrayList<>(); Map> columnMap = buildMappedColumnsMap( unaligned, aligned, unmapped); int width = columnMap.size(); @@ -2774,7 +2774,7 @@ public class AlignmentUtils } // map from dataset sequence to alignment sequence(s) - Map> alignedDatasets = new HashMap>(); + Map> alignedDatasets = new HashMap<>(); for (SequenceI seq : aligned.getSequences()) { SequenceI ds = seq.getDatasetSequence(); @@ -2837,7 +2837,7 @@ public class AlignmentUtils * {unalignedSequence, characterPerSequence} at that position. * TreeMap keeps the entries in ascending column order. */ - SortedMap> map = new TreeMap>(); + SortedMap> map = new TreeMap<>(); /* * record any sequences that have no mapping so can't be realigned @@ -2942,7 +2942,7 @@ public class AlignmentUtils Map seqsMap = map.get(fromCol); if (seqsMap == null) { - seqsMap = new HashMap(); + seqsMap = new HashMap<>(); map.put(fromCol, seqsMap); } seqsMap.put(seq, seq.getCharAt(mappedCharPos - toStart)); -- 1.7.10.2