X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FDna.java;h=2939e3c88284c7fe68beffd3b5454fe13520062a;hb=8a693367d8a0f6113d21248993ca4e0355b32659;hp=5696838739ac6044e11ef26fdceaedae83542fa2;hpb=4099019578bbeb81b76154922851ada38fb0017d;p=jalview.git

diff --git a/src/jalview/analysis/Dna.java b/src/jalview/analysis/Dna.java
index 5696838..2939e3c 100644
--- a/src/jalview/analysis/Dna.java
+++ b/src/jalview/analysis/Dna.java
@@ -208,14 +208,13 @@ public class Dna
     for (int gd = 0; gd < selection.length; gd++)
     {
       SequenceI dna = selection[gd];
-      DBRefEntry[] dnarefs = DBRefUtils
-              .selectRefs(dna.getDBRef(),
-                      jalview.datamodel.DBRefSource.DNACODINGDBS);
+      DBRefEntry[] dnarefs = DBRefUtils.selectRefs(dna.getDBRefs(),
+              jalview.datamodel.DBRefSource.DNACODINGDBS);
       if (dnarefs != null)
       {
         // intersect with pep
         List<DBRefEntry> mappedrefs = new ArrayList<DBRefEntry>();
-        DBRefEntry[] refs = dna.getDBRef();
+        DBRefEntry[] refs = dna.getDBRefs();
         for (int d = 0; d < refs.length; d++)
         {
           if (refs[d].getMap() != null && refs[d].getMap().getMap() != null
@@ -300,8 +299,7 @@ public class Dna
         aa.graphHeight = annotation.graphHeight;
         if (annotation.getThreshold() != null)
         {
-          aa.setThreshold(new GraphLine(annotation
-                  .getThreshold()));
+          aa.setThreshold(new GraphLine(annotation.getThreshold()));
         }
         if (annotation.hasScore)
         {
@@ -446,8 +444,10 @@ public class Dna
           aa = gapString;
           if (skipint == null)
           {
-            skipint = new int[]
-            { alignedCodon.pos1, alignedCodon.pos3 /* cdp[0], cdp[2] */};
+            skipint = new int[] { alignedCodon.pos1, alignedCodon.pos3 /*
+                                                                        * cdp[0],
+                                                                        * cdp[2]
+                                                                        */};
           }
           skipint[1] = alignedCodon.pos3; // cdp[2];
         }
@@ -683,8 +683,7 @@ public class Dna
          * range iv[0] = skipint[1]; } else { } } } else if (iv[0]<skipint[0]) {
          * iv = (int[]) narange.elementAt(vc+1); } } while (iv[0]) } }
          */
-        MapList map = new MapList(scontigs, new int[]
-        { 1, resSize }, 3, 1);
+        MapList map = new MapList(scontigs, new int[] { 1, resSize }, 3, 1);
 
         transferCodedFeatures(selection, newseq, map, null, null);
 
@@ -714,8 +713,7 @@ public class Dna
    * @param proteinSeqs
    * @return
    */
-  protected void insertAAGap(int pos,
-          List<SequenceI> proteinSeqs)
+  protected void insertAAGap(int pos, List<SequenceI> proteinSeqs)
   {
     aaWidth++;
     for (SequenceI seq : proteinSeqs)
@@ -775,7 +773,7 @@ public class Dna
   {
     SequenceFeature[] sfs = dna.getSequenceFeatures();
     Boolean fgstate;
-    DBRefEntry[] dnarefs = DBRefUtils.selectRefs(dna.getDBRef(),
+    DBRefEntry[] dnarefs = DBRefUtils.selectRefs(dna.getDBRefs(),
             DBRefSource.DNACODINGDBS);
     if (dnarefs != null)
     {