JAL-1619 don't copy hidden or RNA SS annotations to protein translation

diff --git a/src/jalview/analysis/Dna.java b/src/jalview/analysis/Dna.java
index 675a44a..172a910 100644 (file)
--- a/src/jalview/analysis/Dna.java
+++ b/src/jalview/analysis/Dna.java
@@ -27,16 +27,19 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.FeatureProperties;
+import jalview.datamodel.GraphLine;
 import jalview.datamodel.Mapping;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.schemes.ResidueProperties;
+import jalview.util.Comparison;
 import jalview.util.MapList;
 import jalview.util.ShiftList;
 
 import java.util.ArrayList;
 import java.util.Hashtable;
+import java.util.List;
 import java.util.Vector;
 
 public class Dna
@@ -292,7 +295,7 @@ public class Dna
   }
 
   /**
-   * translate na alignment annotations onto translated amino acid alignment al
+   * Translate na alignment annotations onto translated amino acid alignment al
    * using codon mapping codons
    * 
    * @param annotations
@@ -303,76 +306,71 @@ public class Dna
           AlignmentAnnotation[] annotations, AlignmentI al,
           AlignedCodonFrame codons)
   {
-    // //////////////////////////////
-    // Copy annotations across
-    //
     // Can only do this for columns with consecutive codons, or where
     // annotation is sequence associated.
 
-    int pos, a, aSize;
     if (annotations != null)
     {
-      for (int i = 0; i < annotations.length; i++)
+      for (AlignmentAnnotation annotation : annotations)
       {
-        // Skip any autogenerated annotation
-        if (annotations[i].autoCalculated)
-        {
-          continue;
-        }
-
-        // skip hidden sequence annotations
-        final SequenceI seqRef = annotations[i].sequenceRef;
-        if (seqRef != null && !annotations[i].visible)
+        /*
+         * Skip hidden or autogenerated annotation. Also (for now), RNA
+         * secondary structure annotation. If we want to show this against
+         * protein we need a smarter way to 'translate' without generating
+         * invalid (unbalanced) structure annotation.
+         */
+        if (annotation.autoCalculated || !annotation.visible
+                || annotation.isRNA())
         {
           continue;
         }
 
-        aSize = codons.getaaWidth(); // aa alignment width.
-        jalview.datamodel.Annotation[] anots = (annotations[i].annotations == null) ? null
-                : new jalview.datamodel.Annotation[aSize];
+        int aSize = codons.getaaWidth(); // aa alignment width.
+        Annotation[] anots = (annotation.annotations == null) ? null
+                : new Annotation[aSize];
         if (anots != null)
         {
-          for (a = 0; a < aSize; a++)
+          for (int a = 0; a < aSize; a++)
           {
             // process through codon map.
             if (a < codons.codons.length && codons.codons[a] != null
                     && codons.codons[a][0] == (codons.codons[a][2] - 2))
             {
               anots[a] = getCodonAnnotation(codons.codons[a],
-                      annotations[i].annotations);
+                      annotation.annotations);
             }
           }
         }
 
-        jalview.datamodel.AlignmentAnnotation aa = new jalview.datamodel.AlignmentAnnotation(
-                annotations[i].label, annotations[i].description, anots);
-        aa.graph = annotations[i].graph;
-        aa.graphGroup = annotations[i].graphGroup;
-        aa.graphHeight = annotations[i].graphHeight;
-        if (annotations[i].getThreshold() != null)
+        AlignmentAnnotation aa = new AlignmentAnnotation(annotation.label,
+                annotation.description, anots);
+        aa.graph = annotation.graph;
+        aa.graphGroup = annotation.graphGroup;
+        aa.graphHeight = annotation.graphHeight;
+        if (annotation.getThreshold() != null)
         {
-          aa.setThreshold(new jalview.datamodel.GraphLine(annotations[i]
+          aa.setThreshold(new GraphLine(annotation
                   .getThreshold()));
         }
-        if (annotations[i].hasScore)
+        if (annotation.hasScore)
         {
-          aa.setScore(annotations[i].getScore());
+          aa.setScore(annotation.getScore());
         }
+
+        final SequenceI seqRef = annotation.sequenceRef;
         if (seqRef != null)
         {
-          SequenceI aaSeq = codons
-                  .getAaForDnaSeq(seqRef);
+          SequenceI aaSeq = codons.getAaForDnaSeq(seqRef);
           if (aaSeq != null)
           {
             // aa.compactAnnotationArray(); // throw away alignment annotation
             // positioning
             aa.setSequenceRef(aaSeq);
-            aa.createSequenceMapping(aaSeq, aaSeq.getStart(), true); // rebuild
-            // mapping
+            // rebuild mapping
+            aa.createSequenceMapping(aaSeq, aaSeq.getStart(), true);
             aa.adjustForAlignment();
             aaSeq.addAlignmentAnnotation(aa);
           }
-
         }
         al.addAnnotation(aa);
       }
@@ -473,7 +471,7 @@ public class Dna
           String seqstring, int[] viscontigs, AlignedCodonFrame codons,
           char gapCharacter, DBRefEntry product, final boolean starForStop)
   {
-    java.util.List skip = new ArrayList();
+    List<int[]> skip = new ArrayList<int[]>();
     int skipint[] = null;
     ShiftList vismapping = new ShiftList(); // map from viscontigs to seqstring
     // intervals
@@ -494,7 +492,8 @@ public class Dna
       scontigs[vc + 1] = viscontigs[vc + 1];
     }
 
-    StringBuffer protein = new StringBuffer();
+    // allocate a roughly sized buffer for the protein sequence
+    StringBuilder protein = new StringBuilder(seqstring.length() / 2);
     String seq = seqstring.replace('U', 'T');
     char codon[] = new char[3];
     int cdp[] = new int[3], rf = 0, lastnpos = 0, nend;
@@ -502,14 +501,16 @@ public class Dna
     int resSize = 0;
     for (npos = 0, nend = seq.length(); npos < nend; npos++)
     {
-      if (!jalview.util.Comparison.isGap(seq.charAt(npos)))
+      if (!Comparison.isGap(seq.charAt(npos)))
       {
         cdp[rf] = npos; // store position
         codon[rf++] = seq.charAt(npos); // store base
       }
-      // filled an RF yet ?
       if (rf == 3)
       {
+        /*
+         * Filled up a reading frame...
+         */
         String aa = ResidueProperties.codonTranslate(new String(codon));
         rf = 0;
         if (aa == null)