JAL-1665 refactored Sequence.getSequenceFeatures

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

diff --git a/src/jalview/analysis/Dna.java b/src/jalview/analysis/Dna.java
index 2e56e67..b639e36 100644 (file)
--- a/src/jalview/analysis/Dna.java
+++ b/src/jalview/analysis/Dna.java
@@ -20,10 +20,6 @@
  */
 package jalview.analysis;
 
-import java.util.ArrayList;
-import java.util.Hashtable;
-import java.util.Vector;
-
 import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
@@ -39,6 +35,10 @@ import jalview.schemes.ResidueProperties;
 import jalview.util.MapList;
 import jalview.util.ShiftList;
 
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.Vector;
+
 public class Dna
 {
   /**
@@ -52,9 +52,13 @@ public class Dna
   {
     if (cdp2 == null
             || (cdp1[0] == cdp2[0] && cdp1[1] == cdp2[1] && cdp1[2] == cdp2[2]))
+    {
       return 0;
+    }
     if (cdp1[0] < cdp2[0] || cdp1[1] < cdp2[1] || cdp1[2] < cdp2[2])
+     {
       return -1; // one base in cdp1 precedes the corresponding base in the
+    }
     // other codon
     return 1; // one base in cdp1 appears after the corresponding base in the
     // other codon.
@@ -146,7 +150,9 @@ public class Dna
       }
     }
     if (codons.aaWidth == 0)
+    {
       return null;
+    }
     SequenceI[] newseqs = new SequenceI[pepseqs.size()];
     pepseqs.copyInto(newseqs);
     AlignmentI al = new Alignment(newseqs);
@@ -264,7 +270,9 @@ public class Dna
             // generate seqstring for this sequence based on mapping
 
             if (sqstr.length() > alwidth)
+            {
               alwidth = sqstr.length();
+            }
             cdnasqs.addElement(sqstr.toString());
             cdnasqi.addElement(dna);
             cdnaprod.addElement(intersect);
@@ -407,7 +415,7 @@ public class Dna
     }
     if (contrib > 1)
     {
-      annot.value /= (float) contrib;
+      annot.value /= contrib;
     }
     return annot;
   }
@@ -429,6 +437,7 @@ public class Dna
    *             {@link #translateCodingRegion(SequenceI,String,int[],AlignedCodonFrame,char,DBRefEntry,boolean)}
    *             instead
    */
+  @Deprecated
   public static SequenceI translateCodingRegion(SequenceI selection,
           String seqstring, int[] viscontigs, AlignedCodonFrame codons,
           char gapCharacter, DBRefEntry product)
@@ -694,7 +703,9 @@ public class Dna
           scontigs = t;
         }
         if (vc <= 0)
+        {
           scontigs = null;
+        }
       }
       if (scontigs != null)
       {
@@ -705,7 +716,9 @@ public class Dna
           scontigs[vc] = selection.findPosition(scontigs[vc]); // not from 1!
           scontigs[vc + 1] = selection.findPosition(scontigs[vc + 1]); // exclusive
           if (scontigs[vc + 1] == selection.getEnd())
+          {
             break;
+          }
         }
         // trim trailing empty intervals.
         if ((vc + 2) < scontigs.length)
@@ -778,8 +791,7 @@ public class Dna
   private static void transferCodedFeatures(SequenceI dna, SequenceI pep,
           MapList map, Hashtable featureTypes, Hashtable featureGroups)
   {
-    SequenceFeature[] sf = (dna.getDatasetSequence() != null ? dna
-            .getDatasetSequence() : dna).getSequenceFeatures();
+    SequenceFeature[] sf = dna.getSequenceFeatures();
     Boolean fgstate;
     jalview.datamodel.DBRefEntry[] dnarefs = jalview.util.DBRefUtils
             .selectRefs(dna.getDBRef(),