Merge branch 'alpha/JAL-3362_Jalview_212_alpha' into alpha/merge_212_JalviewJS_2112

[jalview.git] / src / jalview / analysis / Dna.java

diff --git a/src/jalview/analysis/Dna.java b/src/jalview/analysis/Dna.java
index 9611a4c..4cc5697 100644 (file)
--- a/src/jalview/analysis/Dna.java
+++ b/src/jalview/analysis/Dna.java
@@ -28,7 +28,6 @@ import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.DBRefSource;
 import jalview.datamodel.FeatureProperties;
 import jalview.datamodel.GraphLine;
 import jalview.datamodel.Mapping;
@@ -253,29 +252,30 @@ public class Dna
     for (int gd = 0; gd < selection.length; gd++)
     {
       SequenceI dna = selection[gd];
-      DBRefEntry[] dnarefs = DBRefUtils.selectRefs(dna.getDBRefs(),
+      List<DBRefEntry> dnarefs = DBRefUtils.selectRefs(dna.getDBRefs(),
               jalview.datamodel.DBRefSource.DNACODINGDBS);
       if (dnarefs != null)
       {
         // intersect with pep
         List<DBRefEntry> mappedrefs = new ArrayList<>();
-        DBRefEntry[] refs = dna.getDBRefs();
-        for (int d = 0; d < refs.length; d++)
+        List<DBRefEntry> refs = dna.getDBRefs();
+        for (int d = 0, nd = refs.size(); d < nd; d++)
         {
-          if (refs[d].getMap() != null && refs[d].getMap().getMap() != null
-                  && refs[d].getMap().getMap().getFromRatio() == 3
-                  && refs[d].getMap().getMap().getToRatio() == 1)
+          DBRefEntry ref = refs.get(d);
+          if (ref.getMap() != null && ref.getMap().getMap() != null
+                  && ref.getMap().getMap().getFromRatio() == 3
+                  && ref.getMap().getMap().getToRatio() == 1)
           {
-            mappedrefs.add(refs[d]); // add translated protein maps
+            mappedrefs.add(ref); // add translated protein maps
           }
         }
-        dnarefs = mappedrefs.toArray(new DBRefEntry[mappedrefs.size()]);
-        for (int d = 0; d < dnarefs.length; d++)
+        dnarefs = mappedrefs;//.toArray(new DBRefEntry[mappedrefs.size()]);
+        for (int d = 0, nd = dnarefs.size(); d < nd; d++)
         {
-          Mapping mp = dnarefs[d].getMap();
+          Mapping mp = dnarefs.get(d).getMap();
           if (mp != null)
           {
-            for (int vc = 0; vc < viscontigs.length; vc += 2)
+            for (int vc = 0, nv = viscontigs.length; vc < nv; vc += 2)
             {
               int[] mpr = mp.locateMappedRange(viscontigs[vc],
                       viscontigs[vc + 1]);
@@ -797,19 +797,20 @@ public class Dna
   private static void transferCodedFeatures(SequenceI dna, SequenceI pep,
           MapList map)
   {
-    DBRefEntry[] dnarefs = DBRefUtils.selectRefs(dna.getDBRefs(),
-            DBRefSource.DNACODINGDBS);
-    if (dnarefs != null)
-    {
-      // intersect with pep
-      for (int d = 0; d < dnarefs.length; d++)
-      {
-        Mapping mp = dnarefs[d].getMap();
-        if (mp != null)
-        {
-        }
-      }
-    }
+       //  BH 2019.01.25 nop?
+//    List<DBRefEntry> dnarefs = DBRefUtils.selectRefs(dna.getDBRefs(),
+//            DBRefSource.DNACODINGDBS);
+//    if (dnarefs != null)
+//    {
+//      // intersect with pep
+//      for (int d = 0, nd = dnarefs.size(); d < nd; d++)
+//      {
+//        Mapping mp = dnarefs.get(d).getMap();
+//        if (mp != null)
+//        {
+//        }
+//      }
+//    }
     for (SequenceFeature sf : dna.getFeatures().getAllFeatures())
     {
         if (FeatureProperties.isCodingFeature(null, sf.getType()))