X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignedCodonFrame.java;h=f5154ec1da1d151cebd4e240ff86d20914c90c1e;hb=282aa9129a74235dc8d6c22b123d51eb1abd2f55;hp=b376c80f96b82eab60d359352198e79ad84b1309;hpb=4d71acba1cc4999e8e4061ec3e9ae55e1b37084e;p=jalview.git

diff --git a/src/jalview/datamodel/AlignedCodonFrame.java b/src/jalview/datamodel/AlignedCodonFrame.java
index b376c80..f5154ec 100644
--- a/src/jalview/datamodel/AlignedCodonFrame.java
+++ b/src/jalview/datamodel/AlignedCodonFrame.java
@@ -118,44 +118,50 @@ public class AlignedCodonFrame
      */
     public boolean covers(SequenceI seq)
     {
-      return covers(seq,false,false);
+      return covers(seq, false, false);
     }
+
     /**
      * 
      * @param seq
-     * @param localCover - when true - compare extent of seq's dataset sequence rather than the local extent
-     * @param either - when true coverage is required for either seq or the mapped sequence 
-     * @return true if mapping covers full length of given sequence (or the other if either==true)
+     * @param localCover
+     *          - when true - compare extent of seq's dataset sequence rather
+     *          than the local extent
+     * @param either
+     *          - when true coverage is required for either seq or the mapped
+     *          sequence
+     * @return true if mapping covers full length of given sequence (or the
+     *         other if either==true)
      */
-    public boolean covers(SequenceI seq, boolean localCover,boolean either)
+    public boolean covers(SequenceI seq, boolean localCover, boolean either)
     {
-      List<int[]> mappedRanges = null,otherRanges=null;
+      List<int[]> mappedRanges = null, otherRanges = null;
       MapList mapList = mapping.getMap();
-      int mstart=seq.getStart(),mend=seq.getEnd(),ostart,oend;
-              ;
+      int mstart = seq.getStart(), mend = seq.getEnd(), ostart, oend;
+      ;
       if (fromSeq == seq || fromSeq == seq.getDatasetSequence())
       {
-        if (localCover && fromSeq !=seq)
+        if (localCover && fromSeq != seq)
         {
-          mstart=fromSeq.getStart();
-          mend=fromSeq.getEnd();
+          mstart = fromSeq.getStart();
+          mend = fromSeq.getEnd();
         }
         mappedRanges = mapList.getFromRanges();
-        otherRanges=mapList.getToRanges();
-        ostart=mapping.to.getStart();
-        oend=mapping.to.getEnd();
+        otherRanges = mapList.getToRanges();
+        ostart = mapping.to.getStart();
+        oend = mapping.to.getEnd();
       }
       else if (mapping.to == seq || mapping.to == seq.getDatasetSequence())
       {
-        if (localCover && mapping.to !=seq)
+        if (localCover && mapping.to != seq)
         {
-          mstart=mapping.to.getStart();
-          mend=mapping.to.getEnd();
+          mstart = mapping.to.getStart();
+          mend = mapping.to.getEnd();
         }
         mappedRanges = mapList.getToRanges();
-        otherRanges=mapList.getFromRanges();
-        ostart=fromSeq.getStart();
-        oend=fromSeq.getEnd();
+        otherRanges = mapList.getFromRanges();
+        ostart = fromSeq.getStart();
+        oend = fromSeq.getEnd();
       }
       else
       {
@@ -167,7 +173,7 @@ public class AlignedCodonFrame
        * (necessary for circular CDS - example EMBL:J03321:AAA91567)
        * and mapped length covers (at least) sequence length
        */
-      int length = countRange(mappedRanges,mstart,mend);
+      int length = countRange(mappedRanges, mstart, mend);
 
       if (length != -1)
       {
@@ -191,9 +197,10 @@ public class AlignedCodonFrame
       }
       return false;
     }
-    private int countRange(List<int[]> mappedRanges,int mstart,int mend)
+
+    private int countRange(List<int[]> mappedRanges, int mstart, int mend)
     {
-      int length=0;
+      int length = 0;
       for (int[] range : mappedRanges)
       {
         int from = Math.min(range[0], range[1]);
@@ -209,8 +216,9 @@ public class AlignedCodonFrame
 
     /**
      * Adds any regions mapped to or from position {@code pos} in sequence
-     * {@code seq} to the given search results
-     * Note: recommend first using the .covers(,true,true) to ensure mapping covers both sequences
+     * {@code seq} to the given search results Note: recommend first using the
+     * .covers(,true,true) to ensure mapping covers both sequences
+     * 
      * @param seq
      * @param pos
      * @param sr
@@ -224,7 +232,7 @@ public class AlignedCodonFrame
       {
         ds = seq;
       }
-      
+
       if (this.fromSeq == seq || this.fromSeq == ds)
       {
         codon = this.mapping.map.locateInTo(pos, pos);
@@ -452,7 +460,8 @@ public class AlignedCodonFrame
     }
     for (SequenceToSequenceMapping ssm : mappings)
     {
-      if (ssm.covers(seq,true,true)) {
+      if (ssm.covers(seq, true, true))
+      {
         ssm.markMappedRegion(ds, index, results);
       }
     }