X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignedCodonFrame.java;fp=src%2Fjalview%2Fdatamodel%2FAlignedCodonFrame.java;h=26f6e2a9b503b63648968c3a0e9b2b088e28eecb;hb=3740241b6d0dfa109dc81847afe58f17497c39e8;hp=ec11fc13b73dfb193fedb4cddee7821fd88731be;hpb=de32fd704f78dafa5bed5eb64f9f96fab320971f;p=jalview.git

diff --git a/src/jalview/datamodel/AlignedCodonFrame.java b/src/jalview/datamodel/AlignedCodonFrame.java
index ec11fc1..26f6e2a 100644
--- 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);
@@ -225,7 +225,7 @@ public class AlignedCodonFrame
    * @param seq
    * @return
    */
-  public Mapping getMappingForSequence(SequenceI seq)
+  public Mapping getMappingForSequence(SequenceI seq, boolean cdsOnly)
   {
     SequenceI seqDs = seq.getDatasetSequence();
     seqDs = seqDs != null ? seqDs : seq;
@@ -234,7 +234,11 @@ public class AlignedCodonFrame
     {
       if (ssm.fromSeq == seqDs || ssm.mapping.to == seqDs)
       {
-        return ssm.mapping;
+        if (!cdsOnly || ssm.fromSeq.getName().startsWith("CDS")
+                || ssm.mapping.to.getName().startsWith("CDS"))
+        {
+          return ssm.mapping;
+        }
       }
     }
     return null;
@@ -485,7 +489,7 @@ public class AlignedCodonFrame
   {
     MapList ml = null;
     SequenceI dnaSeq = null;
-    List<char[]> result = new ArrayList<char[]>();
+    List<char[]> result = new ArrayList<>();
 
     for (SequenceToSequenceMapping ssm : mappings)
     {
@@ -524,8 +528,8 @@ 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;