X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FDna.java;h=5dcf212299933186ca544d7d23777cbbfeff9d9f;hb=4b7d3640209c4434d569c746672cf9eed4250ace;hp=2ad8487bcdec37ef0e84d4e83d68f1e573663155;hpb=948bd3bcbacc509da0cefaae3eedd97300a6ccce;p=jalview.git

diff --git a/src/jalview/analysis/Dna.java b/src/jalview/analysis/Dna.java
index 2ad8487..5dcf212 100644
--- a/src/jalview/analysis/Dna.java
+++ b/src/jalview/analysis/Dna.java
@@ -163,7 +163,8 @@ public class Dna
    * @param ac2
    * @return
    */
-  public static final int compareCodonPos(AlignedCodon ac1, AlignedCodon ac2)
+  public static final int compareCodonPos(AlignedCodon ac1,
+          AlignedCodon ac2)
   {
     return comparator.compare(ac1, ac2);
     // return jalview_2_8_2compare(ac1, ac2);
@@ -194,10 +195,11 @@ public class Dna
   }
 
   /**
+   * Translates cDNA using the specified code table
    * 
    * @return
    */
-  public AlignmentI translateCdna()
+  public AlignmentI translateCdna(GeneticCodeI codeTable)
   {
     AlignedCodonFrame acf = new AlignedCodonFrame();
 
@@ -209,7 +211,7 @@ public class Dna
     for (s = 0; s < sSize; s++)
     {
       SequenceI newseq = translateCodingRegion(selection.get(s),
-              seqstring[s], acf, pepseqs);
+              seqstring[s], acf, pepseqs, codeTable);
 
       if (newseq != null)
       {
@@ -252,29 +254,30 @@ 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]);
@@ -429,11 +432,12 @@ public class Dna
    * @param acf
    *          Definition of global ORF alignment reference frame
    * @param proteinSeqs
+   * @param codeTable
    * @return sequence ready to be added to alignment.
    */
   protected SequenceI translateCodingRegion(SequenceI selection,
           String seqstring, AlignedCodonFrame acf,
-          List<SequenceI> proteinSeqs)
+          List<SequenceI> proteinSeqs, GeneticCodeI codeTable)
   {
     List<int[]> skip = new ArrayList<>();
     int[] skipint = null;
@@ -468,7 +472,7 @@ public class Dna
          */
         AlignedCodon alignedCodon = new AlignedCodon(cdp[0], cdp[1],
                 cdp[2]);
-        String aa = ResidueProperties.codonTranslate(new String(codon));
+        String aa = codeTable.translate(new String(codon));
         rf = 0;
         final String gapString = String.valueOf(gapChar);
         if (aa == null)
@@ -796,28 +800,29 @@ 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()))
+      if (FeatureProperties.isCodingFeature(null, sf.getType()))
+      {
+        // if (map.intersectsFrom(sf[f].begin, sf[f].end))
         {
-          // if (map.intersectsFrom(sf[f].begin, sf[f].end))
-          {
 
-          }
         }
+      }
     }
   }