Merge branch 'develop' into feature/JAL-3390hideUnmappedStructure

[jalview.git] / src / jalview / datamodel / AlignedCodonFrame.java

diff --git a/src/jalview/datamodel/AlignedCodonFrame.java b/src/jalview/datamodel/AlignedCodonFrame.java
index 83eeb3d..fffa137 100644 (file)
--- a/src/jalview/datamodel/AlignedCodonFrame.java
+++ b/src/jalview/datamodel/AlignedCodonFrame.java
@@ -116,7 +116,7 @@ public class AlignedCodonFrame
    */
   public AlignedCodonFrame()
   {
-    mappings = new ArrayList<SequenceToSequenceMapping>();
+    mappings = new ArrayList<>();
   }
 
   /**
@@ -179,7 +179,7 @@ public class AlignedCodonFrame
   {
     // TODO return a list instead?
     // return dnaSeqs;
-    List<SequenceI> seqs = new ArrayList<SequenceI>();
+    List<SequenceI> seqs = new ArrayList<>();
     for (SequenceToSequenceMapping ssm : mappings)
     {
       seqs.add(ssm.fromSeq);
@@ -190,7 +190,7 @@ public class AlignedCodonFrame
   public SequenceI[] getAaSeqs()
   {
     // TODO not used - remove?
-    List<SequenceI> seqs = new ArrayList<SequenceI>();
+    List<SequenceI> seqs = new ArrayList<>();
     for (SequenceToSequenceMapping ssm : mappings)
     {
       seqs.add(ssm.mapping.to);
@@ -200,7 +200,7 @@ public class AlignedCodonFrame
 
   public MapList[] getdnaToProt()
   {
-    List<MapList> maps = new ArrayList<MapList>();
+    List<MapList> maps = new ArrayList<>();
     for (SequenceToSequenceMapping ssm : mappings)
     {
       maps.add(ssm.mapping.map);
@@ -210,7 +210,7 @@ public class AlignedCodonFrame
 
   public Mapping[] getProtMappings()
   {
-    List<Mapping> maps = new ArrayList<Mapping>();
+    List<Mapping> maps = new ArrayList<>();
     for (SequenceToSequenceMapping ssm : mappings)
     {
       maps.add(ssm.mapping);
@@ -220,7 +220,7 @@ public class AlignedCodonFrame
 
   /**
    * Returns the first mapping found which is to or from the given sequence, or
-   * null.
+   * null if none is found
    * 
    * @param seq
    * @return
@@ -485,7 +485,7 @@ public class AlignedCodonFrame
   {
     MapList ml = null;
     SequenceI dnaSeq = null;
-    List<char[]> result = new ArrayList<char[]>();
+    List<char[]> result = new ArrayList<>();
 
     for (SequenceToSequenceMapping ssm : mappings)
     {
@@ -505,12 +505,11 @@ public class AlignedCodonFrame
          * Read off the mapped nucleotides (converting to position base 0)
          */
         codonPos = MappingUtils.flattenRanges(codonPos);
-        char[] dna = dnaSeq.getSequence();
         int start = dnaSeq.getStart();
-        result.add(
-                new char[]
-                { dna[codonPos[0] - start], dna[codonPos[1] - start],
-                    dna[codonPos[2] - start] });
+        char c1 = dnaSeq.getCharAt(codonPos[0] - start);
+        char c2 = dnaSeq.getCharAt(codonPos[1] - start);
+        char c3 = dnaSeq.getCharAt(codonPos[2] - start);
+        result.add(new char[] { c1, c2, c3 });
       }
     }
     return result.isEmpty() ? null : result;
@@ -525,8 +524,8 @@ public class AlignedCodonFrame
    */
   public List<Mapping> getMappingsFromSequence(SequenceI seq)
   {
-    List<Mapping> result = new ArrayList<Mapping>();
-    List<SequenceI> related = new ArrayList<SequenceI>();
+    List<Mapping> result = new ArrayList<>();
+    List<SequenceI> related = new ArrayList<>();
     SequenceI seqDs = seq.getDatasetSequence();
     seqDs = seqDs != null ? seqDs : seq;