JAL-2089 patch broken merge to master for Release 2.10.0b1

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

diff --git a/src/jalview/analysis/Dna.java b/src/jalview/analysis/Dna.java
index f8bb9f9..799a8ed 100644 (file)
--- a/src/jalview/analysis/Dna.java
+++ b/src/jalview/analysis/Dna.java
@@ -69,7 +69,7 @@ public class Dna
 
   final private int dnaWidth;
 
-  final private Alignment dataset;
+  final private AlignmentI dataset;
 
   /*
    * Working variables for the translation.
@@ -208,13 +208,13 @@ public class Dna
     for (int gd = 0; gd < selection.length; gd++)
     {
       SequenceI dna = selection[gd];
-      DBRefEntry[] dnarefs = DBRefUtils.selectRefs(dna.getDBRef(),
+      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
@@ -773,7 +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)
     {
@@ -852,13 +852,18 @@ public class Dna
     char[] originalSequence = sequence.toCharArray();
     int length = originalSequence.length;
     char[] reversedSequence = new char[length];
-
+    int bases = 0;
     for (int i = 0; i < length; i++)
     {
-      reversedSequence[length - i - 1] = complement ? getComplement(originalSequence[i])
+      char c = complement ? getComplement(originalSequence[i])
               : originalSequence[i];
+      reversedSequence[length - i - 1] = c;
+      if (!Comparison.isGap(c))
+      {
+        bases++;
+      }
     }
-    SequenceI reversed = new Sequence(newName, reversedSequence, 1, length);
+    SequenceI reversed = new Sequence(newName, reversedSequence, 1, bases);
     return reversed;
   }
 
@@ -873,7 +878,12 @@ public class Dna
   public static char getComplement(char c)
   {
     char result = c;
-    switch (c) {
+    switch (c)
+    {
+    case '-':
+    case '.':
+    case ' ':
+      break;
     case 'a':
       result = 't';
       break;