X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FDna.java;h=8bf0c24e61fa6a125863353afcf9f70a91ea8b46;hb=8ef4f0d1832bd4cf56c33eff8f822b233e84f3f1;hp=d534c8f52e1592cc5d5e9b8ae059358540814844;hpb=8213e48c6973494f7a6e22e1a97290520a461d1b;p=jalview.git

diff --git a/src/jalview/analysis/Dna.java b/src/jalview/analysis/Dna.java
index d534c8f..8bf0c24 100644
--- a/src/jalview/analysis/Dna.java
+++ b/src/jalview/analysis/Dna.java
@@ -194,10 +194,11 @@ 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 +210,7 @@ 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 +253,30 @@ 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]);
@@ -429,14 +431,16 @@ 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;
+
     int npos = 0;
     int vc = 0;
 
@@ -465,9 +469,8 @@ public class Dna
         /*
          * Filled up a reading frame...
          */
-        AlignedCodon alignedCodon = new AlignedCodon(cdp[0], cdp[1],
-                cdp[2]);
-        String aa = ResidueProperties.codonTranslate(new String(codon));
+        AlignedCodon alignedCodon = new AlignedCodon(cdp[0], cdp[1], cdp[2]);
+        String aa = codeTable.translate(new String(codon));
         rf = 0;
         final String gapString = String.valueOf(gapChar);
         if (aa == null)
@@ -574,7 +577,7 @@ public class Dna
             skip.add(skipint);
             skipint = null;
           }
-          if (aa.equals("STOP"))
+          if (aa.equals(ResidueProperties.STOP))
           {
             aa = STOP_ASTERIX;
           }
@@ -795,19 +798,20 @@ 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()))
@@ -881,6 +885,23 @@ public class Dna
   }
 
   /**
+   * Answers the reverse complement of the input string
+   * 
+   * @see #getComplement(char)
+   * @param s
+   * @return
+   */
+  public static String reverseComplement(String s)
+  {
+    StringBuilder sb = new StringBuilder(s.length());
+    for (int i = s.length() - 1; i >= 0; i--)
+    {
+      sb.append(Dna.getComplement(s.charAt(i)));
+    }
+    return sb.toString();
+  }
+
+  /**
    * Returns dna complement (preserving case) for aAcCgGtTuU. Ambiguity codes
    * are treated as on http://reverse-complement.com/. Anything else is left
    * unchanged.