Merge branch 'bug/JAL-3760_protsTreatedAsNucleotides' into releases/Release_2_11_1_Branch

diff --git a/src/jalview/util/Comparison.java b/src/jalview/util/Comparison.java
index d4fc233..286bfb2 100644 (file)
--- a/src/jalview/util/Comparison.java
+++ b/src/jalview/util/Comparison.java
@@ -268,7 +268,38 @@ public class Comparison
    */
   public static final boolean isNucleotide(SequenceI seq)
   {
-    return isNucleotide(new SequenceI[] { seq });
+    if (seq==null)
+    {
+      return false;
+    }
+    long ntCount = 0;
+    long aaCount = 0;
+
+    int len = seq.getLength();
+    for (int i = 0; i < len; i++)
+    {
+      char c = seq.getCharAt(i);
+      if (isNucleotide(c))
+      {
+        ntCount++;
+      }
+      else if (!isGap(c))
+      {
+        aaCount++;
+      }
+    }
+    /*
+     * Check for nucleotide count > 85% of total count (in a form that evades
+     * int / float conversion or divide by zero).
+     */
+    if (ntCount * 100 > EIGHTY_FIVE * (ntCount + aaCount))
+    {
+      return true;
+    }
+    else
+    {
+      return false;
+    }
   }
 
   /**
@@ -285,45 +316,23 @@ public class Comparison
     {
       return false;
     }
-
-    int ntCount = 0;
-    int aaCount = 0;
+    // true if we have seen a nucleotide sequence
+    boolean na=false;
     for (SequenceI seq : seqs)
     {
       if (seq == null)
       {
         continue;
       }
+      na=true;
       // TODO could possibly make an informed guess just from the first sequence
       // to save a lengthy calculation
-      int len = seq.getLength();
-      for (int i = 0; i < len; i++)
-      {
-        char c = seq.getCharAt(i);
-        if (isNucleotide(c))
-        {
-          ntCount++;
-        }
-        else if (!isGap(c))
-        {
-          aaCount++;
-        }
+      if (seq.isProtein()) {
+        // if even one looks like protein, the alignment is protein
+        return false;
       }
     }
-
-    /*
-     * Check for nucleotide count > 85% of total count (in a form that evades
-     * int / float conversion or divide by zero).
-     */
-    if (ntCount * 100 > EIGHTY_FIVE * (ntCount + aaCount))
-    {
-      return true;
-    }
-    else
-    {
-      return false;
-    }
-
+    return na;
   }
 
   /**

diff --git a/test/jalview/util/ComparisonTest.java b/test/jalview/util/ComparisonTest.java
index 6f6841d..2e646f5 100644 (file)
--- a/test/jalview/util/ComparisonTest.java
+++ b/test/jalview/util/ComparisonTest.java
@@ -85,15 +85,15 @@ public class ComparisonTest
     seq = new Sequence("DNA", "ACTugGCCAG");
     SequenceI seq2 = new Sequence("Protein", "FLIMVSPTYW");
     /*
-     * 90% DNA:
+     * 90% DNA but one protein sequence - expect false
      */
-    assertTrue(Comparison.isNucleotide(new SequenceI[] { seq, seq, seq,
+    assertFalse(Comparison.isNucleotide(new SequenceI[] { seq, seq, seq,
         seq, seq, seq, seq, seq, seq, seq2 }));
-    assertTrue(Comparison.isNucleotide(new SequenceI[][] {
+    assertFalse(Comparison.isNucleotide(new SequenceI[][] {
         new SequenceI[] { seq }, new SequenceI[] { seq, seq, seq },
         new SequenceI[] { seq, seq, seq, seq, seq, seq2 } }));
     /*
-     * 80% DNA:
+     * 80% DNA but one protein sequence - Expect false
      */
     assertFalse(Comparison.isNucleotide(new SequenceI[] { seq, seq, seq,
         seq, seq, seq, seq, seq, seq2, seq2 }));