JAL-2789 code format changes only (before functional fixes)

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index 90d9197..dfb185a 100644 (file)
--- 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<SequenceI> sq = new ArrayList<SequenceI>();
+    List<SequenceI> sq = new ArrayList<>();
     int maxoffset = 0;
     for (SequenceI s : core.getSequences())
     {
@@ -247,7 +247,7 @@ public class AlignmentUtils
   public static Map<String, List<SequenceI>> getSequencesByName(
           AlignmentI al)
   {
-    Map<String, List<SequenceI>> theMap = new LinkedHashMap<String, List<SequenceI>>();
+    Map<String, List<SequenceI>> theMap = new LinkedHashMap<>();
     for (SequenceI seq : al.getSequences())
     {
       String name = seq.getName();
@@ -256,7 +256,7 @@ public class AlignmentUtils
         List<SequenceI> seqs = theMap.get(name);
         if (seqs == null)
         {
-          seqs = new ArrayList<SequenceI>();
+          seqs = new ArrayList<>();
           theMap.put(name, seqs);
         }
         seqs.add(seq);
@@ -283,8 +283,8 @@ public class AlignmentUtils
       return false;
     }
 
-    Set<SequenceI> mappedDna = new HashSet<SequenceI>();
-    Set<SequenceI> mappedProtein = new HashSet<SequenceI>();
+    Set<SequenceI> mappedDna = new HashSet<>();
+    Set<SequenceI> 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<SequenceI> unmappedProtein = new ArrayList<SequenceI>();
+    List<SequenceI> unmappedProtein = new ArrayList<>();
     Map<AlignedCodon, Map<SequenceI, AlignedCodon>> 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<AlignedCodon, Map<SequenceI, AlignedCodon>> alignedCodons = new TreeMap<AlignedCodon, Map<SequenceI, AlignedCodon>>(
+    Map<AlignedCodon, Map<SequenceI, AlignedCodon>> 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<SequenceI> sequencesChecked = new ArrayList<SequenceI>();
+    List<SequenceI> sequencesChecked = new ArrayList<>();
     AlignedCodon lastCodon = null;
-    Map<SequenceI, AlignedCodon> toAdd = new HashMap<SequenceI, AlignedCodon>();
+    Map<SequenceI, AlignedCodon> toAdd = new HashMap<>();
 
     for (Entry<AlignedCodon, Map<SequenceI, AlignedCodon>> entry : alignedCodons
             .entrySet())
@@ -1308,7 +1308,7 @@ public class AlignmentUtils
     Map<SequenceI, AlignedCodon> seqProduct = alignedCodons.get(codon);
     if (seqProduct == null)
     {
-      seqProduct = new HashMap<SequenceI, AlignedCodon>();
+      seqProduct = new HashMap<>();
       alignedCodons.put(codon, seqProduct);
     }
     seqProduct.put(protein, codon);
@@ -1445,7 +1445,7 @@ public class AlignmentUtils
       {
         continue;
       }
-      final List<AlignmentAnnotation> result = new ArrayList<AlignmentAnnotation>();
+      final List<AlignmentAnnotation> 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<SequenceI> foundSeqs = new ArrayList<SequenceI>();
-    List<SequenceI> cdsSeqs = new ArrayList<SequenceI>();
+    List<SequenceI> foundSeqs = new ArrayList<>();
+    List<SequenceI> cdsSeqs = new ArrayList<>();
     List<AlignedCodonFrame> mappings = dataset.getCodonFrames();
     HashSet<SequenceI> productSeqs = null;
     if (products != null)
     {
-      productSeqs = new HashSet<SequenceI>();
+      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<DBRefEntry> direct = new ArrayList<DBRefEntry>();
-    HashSet<String> directSources = new HashSet<String>();
+    List<DBRefEntry> direct = new ArrayList<>();
+    HashSet<String> 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<DBRefEntry> propagated = new ArrayList<DBRefEntry>();
+    List<DBRefEntry> propagated = new ArrayList<>();
 
     // and generate appropriate mappings
     for (DBRefEntry cdsref : direct)
@@ -2202,7 +2202,7 @@ public class AlignmentUtils
       proteinStart++;
       proteinLength--;
     }
-    List<int[]> proteinRange = new ArrayList<int[]>();
+    List<int[]> proteinRange = new ArrayList<>();
 
     /*
      * dna length should map to protein (or protein plus stop codon)
@@ -2237,7 +2237,7 @@ public class AlignmentUtils
    */
   public static List<int[]> findCdsPositions(SequenceI dnaSeq)
   {
-    List<int[]> result = new ArrayList<int[]>();
+    List<int[]> result = new ArrayList<>();
 
     List<SequenceFeature> 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<Integer, List<DnaVariant>[]> variants = new LinkedHashMap<Integer, List<DnaVariant>[]>();
+    LinkedHashMap<Integer, List<DnaVariant>[]> variants = new LinkedHashMap<>();
 
     List<SequenceFeature> 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<DnaVariant>();
-        codonVariants[1] = new ArrayList<DnaVariant>();
-        codonVariants[2] = new ArrayList<DnaVariant>();
+        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<SequenceI> unmapped = new ArrayList<SequenceI>();
+    List<SequenceI> unmapped = new ArrayList<>();
     Map<Integer, Map<SequenceI, Character>> 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<SequenceI, List<SequenceI>> alignedDatasets = new HashMap<SequenceI, List<SequenceI>>();
+    Map<SequenceI, List<SequenceI>> 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<Integer, Map<SequenceI, Character>> map = new TreeMap<Integer, Map<SequenceI, Character>>();
+    SortedMap<Integer, Map<SequenceI, Character>> map = new TreeMap<>();
 
     /*
      * record any sequences that have no mapping so can't be realigned
@@ -2942,7 +2942,7 @@ public class AlignmentUtils
             Map<SequenceI, Character> seqsMap = map.get(fromCol);
             if (seqsMap == null)
             {
-              seqsMap = new HashMap<SequenceI, Character>();
+              seqsMap = new HashMap<>();
               map.put(fromCol, seqsMap);
             }
             seqsMap.put(seq, seq.getCharAt(mappedCharPos - toStart));