X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FDna.java;h=9f3a8d020b14342fac880beada644f5938ba91e5;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=836c39ef2f9a96462ce454a7d7ed4efec1af9785;hpb=4484ac6bdcc92f0e0e430f64d3587f026fafb476;p=jalview.git

diff --git a/src/jalview/analysis/Dna.java b/src/jalview/analysis/Dna.java
index 836c39e..9f3a8d0 100644
--- a/src/jalview/analysis/Dna.java
+++ b/src/jalview/analysis/Dna.java
@@ -1,227 +1,716 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * 
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ */
 package jalview.analysis;
 
+import java.util.Enumeration;
 import java.util.Hashtable;
 import java.util.Vector;
 
+import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.FeatureProperties;
+import jalview.datamodel.Mapping;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.schemes.ResidueProperties;
 import jalview.util.MapList;
+import jalview.util.ShiftList;
 
-public class Dna {
+public class Dna
+{
   /**
    * 
    * @param cdp1
    * @param cdp2
-   * @return -1 if cdp1 aligns before cdp2, 0 if in the same column or cdp2 is null, +1 if after cdp2
+   * @return -1 if cdp1 aligns before cdp2, 0 if in the same column or cdp2 is
+   *         null, +1 if after cdp2
    */
-  private static int compare_codonpos(int[] cdp1, int[] cdp2) {
-    if (cdp2==null || (cdp1[0]==cdp2[0] && cdp1[1] == cdp2[1] && cdp1[2] == cdp2[2]))
+  private static int compare_codonpos(int[] cdp1, int[] cdp2)
+  {
+    if (cdp2 == null
+            || (cdp1[0] == cdp2[0] && cdp1[1] == cdp2[1] && cdp1[2] == cdp2[2]))
       return 0;
-    if (cdp1[0]<cdp2[0] || cdp1[1]<cdp2[1] || cdp1[2]<cdp2[2])
-      return -1; // one base in cdp1 precedes the corresponding base in the other codon
-    return 1; // one base in cdp1 appears after the corresponding base in the other codon.
+    if (cdp1[0] < cdp2[0] || cdp1[1] < cdp2[1] || cdp1[2] < cdp2[2])
+      return -1; // one base in cdp1 precedes the corresponding base in the
+    // other codon
+    return 1; // one base in cdp1 appears after the corresponding base in the
+    // other codon.
   }
+
+  /**
+   * DNA->mapped protein sequence alignment translation given set of sequences
+   * 1. id distinct coding regions within selected region for each sequence 2.
+   * generate peptides based on inframe (or given) translation or (optionally
+   * and where specified) out of frame translations (annotated appropriately) 3.
+   * align peptides based on codon alignment
+   */
   /**
-   * create a new alignment of protein sequences
-   * by an inframe translation of the provided NA sequences
+   * id potential products from dna 1. search for distinct products within
+   * selected region for each selected sequence 2. group by associated DB type.
+   * 3. return as form for input into above function
+   */
+  /**
+   * 
+   */
+  /**
+   * create a new alignment of protein sequences by an inframe translation of
+   * the provided NA sequences
+   * 
    * @param selection
    * @param seqstring
    * @param viscontigs
    * @param gapCharacter
    * @param annotations
    * @param aWidth
+   * @param dataset
+   *          destination dataset for translated sequences and mappings
    * @return
    */
-  public static AlignmentI CdnaTranslate(SequenceI[] selection, String[] seqstring, int viscontigs[], char gapCharacter, 
-      AlignmentAnnotation[] annotations, int aWidth) {
-    int s, sSize = selection.length;
-    SequenceI [] newSeq = new SequenceI[sSize];
-    int res, resSize;
-    StringBuffer protein;
-    String seq;
-
-    int[][] codons = new int[aWidth][]; // stores hash of subsequent positions for each codon start position in alignment
+  public static AlignmentI CdnaTranslate(SequenceI[] selection,
+          String[] seqstring, int viscontigs[], char gapCharacter,
+          AlignmentAnnotation[] annotations, int aWidth, Alignment dataset)
+  {
+    return CdnaTranslate(selection, seqstring, null, viscontigs,
+            gapCharacter, annotations, aWidth, dataset);
+  }
 
-    for (res=0;res<aWidth;res++)
-      codons[res]=null;
-    int aslen=0; // final width of aligned translated aa sequences
-    for(s=0; s<sSize; s++)
+  /**
+   * 
+   * @param selection
+   * @param seqstring
+   * @param product
+   *          - array of DbRefEntry objects from which exon map in seqstring is
+   *          derived
+   * @param viscontigs
+   * @param gapCharacter
+   * @param annotations
+   * @param aWidth
+   * @param dataset
+   * @return
+   */
+  public static AlignmentI CdnaTranslate(SequenceI[] selection,
+          String[] seqstring, DBRefEntry[] product, int viscontigs[],
+          char gapCharacter, AlignmentAnnotation[] annotations, int aWidth,
+          Alignment dataset)
+  {
+    AlignedCodonFrame codons = new AlignedCodonFrame(aWidth); // stores hash of
+    // subsequent
+    // positions for
+    // each codon
+    // start position
+    // in alignment
+    int s, sSize = selection.length;
+    Vector pepseqs = new Vector();
+    for (s = 0; s < sSize; s++)
     {
-      int vc,scontigs[]=new int[viscontigs.length];
-
-      for (vc=0;vc<scontigs.length; vc+=2)
+      SequenceI newseq = translateCodingRegion(selection[s], seqstring[s],
+              viscontigs, codons, gapCharacter,
+              (product != null) ? product[s] : null); // possibly anonymous
+      // product
+      if (newseq != null)
       {
-        scontigs[vc]=selection[s].findPosition(viscontigs[vc]); // not from 1!
-        scontigs[vc+1]=selection[s].findPosition(viscontigs[vc+1]-1); // exclusive
-        if (scontigs[vc+1]==selection[s].getEnd())
-          break;
-      }
-      if ((vc+2)<scontigs.length) {
-        int t[] = new int[vc+2];
-        System.arraycopy(scontigs, 0, t, 0, vc+2);
-        scontigs = t;
+        pepseqs.addElement(newseq);
+        SequenceI ds = newseq;
+        while (ds.getDatasetSequence() != null)
+        {
+          ds = ds.getDatasetSequence();
+        }
+        dataset.addSequence(ds);
       }
-      protein = new StringBuffer();
-      seq = seqstring[s].replace('U', 'T');
-      char codon[]=new char[3];
-      int cdp[]=new int[3],rf=0,gf=0,nend,npos;
-      int aspos=0;
-      resSize=0;
-      for (npos=0,nend=seq.length(); npos<nend; npos++) {
-        if (!jalview.util.Comparison.isGap(seq.charAt(npos))) { 
-          cdp[rf] = npos; // store position
-          codon[rf++]=seq.charAt(npos); // store base
-        }
-        // filled an RF yet ?
-        if (rf==3) {
-          String aa = ResidueProperties.codonTranslate(new String(codon));
-          rf=0;
-          if(aa==null)
-            aa=String.valueOf(gapCharacter);
-          else {
-            if(aa.equals("STOP"))
-            {
-              aa="X";
-            }
-            resSize++;
-          }
-          // insert/delete gaps prior to this codon - if necessary
-          boolean findpos=true;
-          while (findpos) 
-          {
-            // first ensure that the codons array is long enough.
-            if (codons.length<=aslen+1) {
-              // probably never have to do this ?
-              int[][] c = new int[codons.length+10][];
-              for (int i=0; i<codons.length; i++) {
-                c[i] = codons[i];
-                codons[i]=null;
-              }
-              codons = c;
-            }
-            // now check to see if we place the aa at the current aspos in the protein alignment
-            switch (Dna.compare_codonpos(cdp, codons[aspos])) 
+    }
+    if (codons.aaWidth == 0)
+      return null;
+    SequenceI[] newseqs = new SequenceI[pepseqs.size()];
+    pepseqs.copyInto(newseqs);
+    AlignmentI al = new Alignment(newseqs);
+    al.padGaps(); // ensure we look aligned.
+    al.setDataset(dataset);
+    translateAlignedAnnotations(annotations, al, codons);
+    al.addCodonFrame(codons);
+    return al;
+  }
+
+  /**
+   * fake the collection of DbRefs with associated exon mappings to identify if
+   * a translation would generate distinct product in the currently selected
+   * region.
+   * 
+   * @param selection
+   * @param viscontigs
+   * @return
+   */
+  public static boolean canTranslate(SequenceI[] selection,
+          int viscontigs[])
+  {
+    for (int gd = 0; gd < selection.length; gd++)
+    {
+      SequenceI dna = selection[gd];
+      jalview.datamodel.DBRefEntry[] dnarefs = jalview.util.DBRefUtils
+              .selectRefs(dna.getDBRef(),
+                      jalview.datamodel.DBRefSource.DNACODINGDBS);
+      if (dnarefs != null)
+      {
+        // intersect with pep
+        // intersect with pep
+        Vector mappedrefs = new Vector();
+        DBRefEntry[] refs = dna.getDBRef();
+        for (int d = 0; d < refs.length; d++)
+        {
+          if (refs[d].getMap() != null && refs[d].getMap().getMap() != null
+                  && refs[d].getMap().getMap().getFromRatio() == 3
+                  && refs[d].getMap().getMap().getToRatio() == 1)
+          {
+            mappedrefs.addElement(refs[d]); // add translated protein maps
+          }
+        }
+        dnarefs = new DBRefEntry[mappedrefs.size()];
+        mappedrefs.copyInto(dnarefs);
+        for (int d = 0; d < dnarefs.length; d++)
+        {
+          Mapping mp = dnarefs[d].getMap();
+          if (mp != null)
+          {
+            for (int vc = 0; vc < viscontigs.length; vc += 2)
             {
-            case -1:
-              // this aa appears before the aligned codons at aspos - so shift them.
-              aslen++;
-              for (int sq=0;sq<s; sq++) {
-                newSeq[sq].insertCharAt(aspos, gapCharacter);
+              int[] mpr = mp.locateMappedRange(viscontigs[vc],
+                      viscontigs[vc + 1]);
+              if (mpr != null)
+              {
+                return true;
               }
-              System.arraycopy(codons, aspos, codons, aspos+1, aslen-aspos);
-              findpos=false;
-              break;
-            case +1:
-              // this aa appears after the aligned codons at aspos, so prefix it with a gap
-              aa = ""+gapCharacter+aa;
-              aspos++;
-              if (aspos>=aslen)
-                aslen=aspos+1;
-              break; // check the next position for alignment
-            case 0:
-              // codon aligns at aspos position.
-              findpos = false;
             }
           }
-          // codon aligns with all other sequence residues found at aspos
-          protein.append(aa);
-          if (codons[aspos]==null) 
-          {
-            // mark this column as aligning to this aligned reading frame 
-            codons[aspos] = new int[] { cdp[0], cdp[1], cdp[2] };
-          }
-          aspos++;
-          if (aspos>=aslen)
-            aslen=aspos+1;
         }
       }
-      if (resSize>0) 
+    }
+    return false;
+  }
+
+  /**
+   * generate a set of translated protein products from annotated sequenceI
+   * 
+   * @param selection
+   * @param viscontigs
+   * @param gapCharacter
+   * @param dataset
+   *          destination dataset for translated sequences
+   * @param annotations
+   * @param aWidth
+   * @return
+   */
+  public static AlignmentI CdnaTranslate(SequenceI[] selection,
+          int viscontigs[], char gapCharacter, Alignment dataset)
+  {
+    int alwidth = 0;
+    Vector cdnasqs = new Vector();
+    Vector cdnasqi = new Vector();
+    Vector cdnaprod = new Vector();
+    for (int gd = 0; gd < selection.length; gd++)
+    {
+      SequenceI dna = selection[gd];
+      jalview.datamodel.DBRefEntry[] dnarefs = jalview.util.DBRefUtils
+              .selectRefs(dna.getDBRef(),
+                      jalview.datamodel.DBRefSource.DNACODINGDBS);
+      if (dnarefs != null)
       {
-        newSeq[s] = new Sequence(selection[s].getName(),
-            protein.toString());
-        if (rf!=0) 
-        {
-          jalview.bin.Cache.log.debug("trimming contigs for incomplete terminal codon.");
-          // trim contigs
-          vc=scontigs.length-1;
-          nend-=rf;
-          // incomplete ORF could be broken over one or two visible contig intervals.
-          while (vc>0 && scontigs[vc]>nend)
-          {
-            if (scontigs[vc-1]>nend) 
-            {
-              vc-=2;
-            } else {
-              // correct last interval in list.
-              scontigs[vc]=nend;
-            }
+        // intersect with pep
+        Vector mappedrefs = new Vector();
+        DBRefEntry[] refs = dna.getDBRef();
+        for (int d = 0; d < refs.length; d++)
+        {
+          if (refs[d].getMap() != null && refs[d].getMap().getMap() != null
+                  && refs[d].getMap().getMap().getFromRatio() == 3
+                  && refs[d].getMap().getMap().getToRatio() == 1)
+          {
+            mappedrefs.addElement(refs[d]); // add translated protein maps
           }
-          if ((vc+2)<scontigs.length) {
-            // truncate map list
-            int t[] = new int[vc+1];
-            System.arraycopy(scontigs,0,t,0,vc+1);
-            scontigs=t;
+        }
+        dnarefs = new DBRefEntry[mappedrefs.size()];
+        mappedrefs.copyInto(dnarefs);
+        for (int d = 0; d < dnarefs.length; d++)
+        {
+          Mapping mp = dnarefs[d].getMap();
+          StringBuffer sqstr = new StringBuffer();
+          if (mp != null)
+          {
+            Mapping intersect = mp.intersectVisContigs(viscontigs);
+            // generate seqstring for this sequence based on mapping
+
+            if (sqstr.length() > alwidth)
+              alwidth = sqstr.length();
+            cdnasqs.addElement(sqstr.toString());
+            cdnasqi.addElement(dna);
+            cdnaprod.addElement(intersect);
           }
         }
-        MapList map = new MapList(scontigs, new int[] { 1, resSize },3,1); // TODO: store mapping on newSeq for linked DNA/Protein viewing.
       }
-      // register the mapping somehow
-      // 
+      SequenceI[] cdna = new SequenceI[cdnasqs.size()];
+      DBRefEntry[] prods = new DBRefEntry[cdnaprod.size()];
+      String[] xons = new String[cdnasqs.size()];
+      cdnasqs.copyInto(xons);
+      cdnaprod.copyInto(prods);
+      cdnasqi.copyInto(cdna);
+      return CdnaTranslate(cdna, xons, prods, viscontigs, gapCharacter,
+              null, alwidth, dataset);
     }
-    if (aslen==0)
-      return null;
-    AlignmentI al = new Alignment(newSeq);
-    al.padGaps();  // ensure we look aligned.
-    al.setDataset(null);
-
+    return null;
+  }
 
-    ////////////////////////////////
+  /**
+   * translate na alignment annotations onto translated amino acid alignment al
+   * using codon mapping codons
+   * 
+   * @param annotations
+   * @param al
+   * @param codons
+   */
+  public static void translateAlignedAnnotations(
+          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)
+
+    int pos, a, aSize;
+    if (annotations != null)
     {
       for (int i = 0; i < annotations.length; i++)
       {
         // Skip any autogenerated annotation
-        if (annotations[i].autoCalculated) {
+        if (annotations[i].autoCalculated)
+        {
           continue;
         }
 
-        aSize = aslen; // aa alignment width.
-        jalview.datamodel.Annotation[] anots =
-          new jalview.datamodel.Annotation[aSize];
-        
-        for (a = 0; a < aSize; a++)
+        aSize = codons.getaaWidth(); // aa alignment width.
+        jalview.datamodel.Annotation[] anots = (annotations[i].annotations == null) ? null
+                : new jalview.datamodel.Annotation[aSize];
+        if (anots != null)
         {
-          // process through codon map.
-          if (codons[a]!=null && codons[a][0]==(codons[a][2]-2))
+          for (a = 0; a < aSize; a++)
           {
-            pos = codons[a][0];
-            if (annotations[i].annotations[pos] == null
-                || annotations[i].annotations[pos] == null)
-              continue;
-            
-            anots[a] = new Annotation(annotations[i].annotations[pos]);
+            // process through codon map.
+            if (codons.codons[a] != null
+                    && codons.codons[a][0] == (codons.codons[a][2] - 2))
+            {
+              anots[a] = getCodonAnnotation(codons.codons[a],
+                      annotations[i].annotations);
+            }
           }
         }
 
-        jalview.datamodel.AlignmentAnnotation aa
-        = new jalview.datamodel.AlignmentAnnotation(annotations[i].label,
-            annotations[i].description, anots);
+        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)
+        {
+          aa.setThreshold(new jalview.datamodel.GraphLine(annotations[i]
+                  .getThreshold()));
+        }
+        if (annotations[i].hasScore)
+        {
+          aa.setScore(annotations[i].getScore());
+        }
+        if (annotations[i].sequenceRef != null)
+        {
+          SequenceI aaSeq = codons
+                  .getAaForDnaSeq(annotations[i].sequenceRef);
+          if (aaSeq != null)
+          {
+            // aa.compactAnnotationArray(); // throw away alignment annotation
+            // positioning
+            aa.setSequenceRef(aaSeq);
+            aa.createSequenceMapping(aaSeq, aaSeq.getStart(), true); // rebuild
+            // mapping
+            aa.adjustForAlignment();
+            aaSeq.addAlignmentAnnotation(aa);
+          }
+
+        }
         al.addAnnotation(aa);
       }
     }
-    return al;
+  }
+
+  private static Annotation getCodonAnnotation(int[] is,
+          Annotation[] annotations)
+  {
+    // Have a look at all the codon positions for annotation and put the first
+    // one found into the translated annotation pos.
+    int contrib = 0;
+    Annotation annot = null;
+    for (int p = 0; p < 3; p++)
+    {
+      if (annotations[is[p]] != null)
+      {
+        if (annot == null)
+        {
+          annot = new Annotation(annotations[is[p]]);
+          contrib = 1;
+        }
+        else
+        {
+          // merge with last
+          Annotation cpy = new Annotation(annotations[is[p]]);
+          if (annot.colour == null)
+          {
+            annot.colour = cpy.colour;
+          }
+          if (annot.description == null || annot.description.length() == 0)
+          {
+            annot.description = cpy.description;
+          }
+          if (annot.displayCharacter == null)
+          {
+            annot.displayCharacter = cpy.displayCharacter;
+          }
+          if (annot.secondaryStructure == 0)
+          {
+            annot.secondaryStructure = cpy.secondaryStructure;
+          }
+          annot.value += cpy.value;
+          contrib++;
+        }
+      }
+    }
+    if (contrib > 1)
+    {
+      annot.value /= (float) contrib;
+    }
+    return annot;
+  }
+
+  /**
+   * Translate a na sequence
+   * 
+   * @param selection
+   *          sequence displayed under viscontigs visible columns
+   * @param seqstring
+   *          ORF read in some global alignment reference frame
+   * @param viscontigs
+   *          mapping from global reference frame to visible seqstring ORF read
+   * @param codons
+   *          Definition of global ORF alignment reference frame
+   * @param gapCharacter
+   * @param newSeq
+   * @return sequence ready to be added to alignment.
+   */
+  public static SequenceI translateCodingRegion(SequenceI selection,
+          String seqstring, int[] viscontigs, AlignedCodonFrame codons,
+          char gapCharacter, DBRefEntry product)
+  {
+    Vector skip = new Vector();
+    int skipint[] = null;
+    ShiftList vismapping = new ShiftList(); // map from viscontigs to seqstring
+    // intervals
+    int vc, scontigs[] = new int[viscontigs.length];
+    int npos = 0;
+    for (vc = 0; vc < viscontigs.length; vc += 2)
+    {
+      if (vc == 0)
+      {
+        vismapping.addShift(npos, viscontigs[vc]);
+      }
+      else
+      {
+        // hidden region
+        vismapping.addShift(npos, viscontigs[vc] - viscontigs[vc - 1] + 1);
+      }
+      scontigs[vc] = viscontigs[vc];
+      scontigs[vc + 1] = viscontigs[vc + 1];
+    }
+
+    StringBuffer protein = new StringBuffer();
+    String seq = seqstring.replace('U', 'T');
+    char codon[] = new char[3];
+    int cdp[] = new int[3], rf = 0, lastnpos = 0, nend;
+    int aspos = 0;
+    int resSize = 0;
+    for (npos = 0, nend = seq.length(); npos < nend; npos++)
+    {
+      if (!jalview.util.Comparison.isGap(seq.charAt(npos)))
+      {
+        cdp[rf] = npos; // store position
+        codon[rf++] = seq.charAt(npos); // store base
+      }
+      // filled an RF yet ?
+      if (rf == 3)
+      {
+        String aa = ResidueProperties.codonTranslate(new String(codon));
+        rf = 0;
+        if (aa == null)
+        {
+          aa = String.valueOf(gapCharacter);
+          if (skipint == null)
+          {
+            skipint = new int[]
+            { cdp[0], cdp[2] };
+          }
+          skipint[1] = cdp[2];
+        }
+        else
+        {
+          if (skipint != null)
+          {
+            // edit scontigs
+            skipint[0] = vismapping.shift(skipint[0]);
+            skipint[1] = vismapping.shift(skipint[1]);
+            for (vc = 0; vc < scontigs.length; vc += 2)
+            {
+              if (scontigs[vc + 1] < skipint[0])
+              {
+                continue;
+              }
+              if (scontigs[vc] <= skipint[0])
+              {
+                if (skipint[0] == scontigs[vc])
+                {
+
+                }
+                else
+                {
+                  int[] t = new int[scontigs.length + 2];
+                  System.arraycopy(scontigs, 0, t, 0, vc - 1);
+                  // scontigs[vc]; //
+                }
+              }
+            }
+            skip.addElement(skipint);
+            skipint = null;
+          }
+          if (aa.equals("STOP"))
+          {
+            aa = "X";
+          }
+          resSize++;
+        }
+        // insert/delete gaps prior to this codon - if necessary
+        boolean findpos = true;
+        while (findpos)
+        {
+          // first ensure that the codons array is long enough.
+          codons.checkCodonFrameWidth(aspos);
+          // now check to see if we place the aa at the current aspos in the
+          // protein alignment
+          switch (Dna.compare_codonpos(cdp, codons.codons[aspos]))
+          {
+          case -1:
+            codons.insertAAGap(aspos, gapCharacter);
+            findpos = false;
+            break;
+          case +1:
+            // this aa appears after the aligned codons at aspos, so prefix it
+            // with a gap
+            aa = "" + gapCharacter + aa;
+            aspos++;
+            // if (aspos >= codons.aaWidth)
+            // codons.aaWidth = aspos + 1;
+            break; // check the next position for alignment
+          case 0:
+            // codon aligns at aspos position.
+            findpos = false;
+          }
+        }
+        // codon aligns with all other sequence residues found at aspos
+        protein.append(aa);
+        lastnpos = npos;
+        if (codons.codons[aspos] == null)
+        {
+          // mark this column as aligning to this aligned reading frame
+          codons.codons[aspos] = new int[]
+          { cdp[0], cdp[1], cdp[2] };
+        }
+        if (aspos >= codons.aaWidth)
+        {
+          // update maximum alignment width
+          // (we can do this without calling checkCodonFrameWidth because it was
+          // already done above)
+          codons.setAaWidth(aspos);
+        }
+        // ready for next translated reading frame alignment position (if any)
+        aspos++;
+      }
+    }
+    if (resSize > 0)
+    {
+      SequenceI newseq = new Sequence(selection.getName(),
+              protein.toString());
+      if (rf != 0)
+      {
+        jalview.bin.Cache.log
+                .debug("trimming contigs for incomplete terminal codon.");
+        // map and trim contigs to ORF region
+        vc = scontigs.length - 1;
+        lastnpos = vismapping.shift(lastnpos); // place npos in context of
+        // whole dna alignment (rather
+        // than visible contigs)
+        // incomplete ORF could be broken over one or two visible contig
+        // intervals.
+        while (vc >= 0 && scontigs[vc] > lastnpos)
+        {
+          if (vc > 0 && scontigs[vc - 1] > lastnpos)
+          {
+            vc -= 2;
+          }
+          else
+          {
+            // correct last interval in list.
+            scontigs[vc] = lastnpos;
+          }
+        }
+
+        if (vc > 0 && (vc + 1) < scontigs.length)
+        {
+          // truncate map list to just vc elements
+          int t[] = new int[vc + 1];
+          System.arraycopy(scontigs, 0, t, 0, vc + 1);
+          scontigs = t;
+        }
+        if (vc <= 0)
+          scontigs = null;
+      }
+      if (scontigs != null)
+      {
+        npos = 0;
+        // map scontigs to actual sequence positions on selection
+        for (vc = 0; vc < scontigs.length; vc += 2)
+        {
+          scontigs[vc] = selection.findPosition(scontigs[vc]); // not from 1!
+          scontigs[vc + 1] = selection.findPosition(scontigs[vc + 1]); // exclusive
+          if (scontigs[vc + 1] == selection.getEnd())
+            break;
+        }
+        // trim trailing empty intervals.
+        if ((vc + 2) < scontigs.length)
+        {
+          int t[] = new int[vc + 2];
+          System.arraycopy(scontigs, 0, t, 0, vc + 2);
+          scontigs = t;
+        }
+        /*
+         * delete intervals in scontigs which are not translated. 1. map skip
+         * into sequence position intervals 2. truncate existing ranges and add
+         * new ranges to exclude untranslated regions. if (skip.size()>0) {
+         * Vector narange = new Vector(); for (vc=0; vc<scontigs.length; vc++) {
+         * narange.addElement(new int[] {scontigs[vc]}); } int sint=0,iv[]; vc =
+         * 0; while (sint<skip.size()) { skipint = (int[]) skip.elementAt(sint);
+         * do { iv = (int[]) narange.elementAt(vc); if (iv[0]>=skipint[0] &&
+         * iv[0]<=skipint[1]) { if (iv[0]==skipint[0]) { // delete beginning of
+         * range } else { // truncate range and create new one if necessary iv =
+         * (int[]) narange.elementAt(vc+1); if (iv[0]<=skipint[1]) { // truncate
+         * range iv[0] = skipint[1]; } else { } } } else if (iv[0]<skipint[0]) {
+         * iv = (int[]) narange.elementAt(vc+1); } } while (iv[0]) } }
+         */
+        MapList map = new MapList(scontigs, new int[]
+        { 1, resSize }, 3, 1);
+
+        // update newseq as if it was generated as mapping from product
+
+        if (product != null)
+        {
+          newseq.setName(product.getSource() + "|"
+                  + product.getAccessionId());
+          if (product.getMap() != null)
+          {
+            // Mapping mp = product.getMap();
+            // newseq.setStart(mp.getPosition(scontigs[0]));
+            // newseq.setEnd(mp
+            // .getPosition(scontigs[scontigs.length - 1]));
+          }
+        }
+        transferCodedFeatures(selection, newseq, map, null, null);
+        SequenceI rseq = newseq.deriveSequence(); // construct a dataset
+        // sequence for our new
+        // peptide, regardless.
+        // store a mapping (this actually stores a mapping between the dataset
+        // sequences for the two sequences
+        codons.addMap(selection, rseq, map);
+        return rseq;
+      }
+    }
+    // register the mapping somehow
+    //
+    return null;
+  }
+
+  /**
+   * Given a peptide newly translated from a dna sequence, copy over and set any
+   * features on the peptide from the DNA. If featureTypes is null, all features
+   * on the dna sequence are searched (rather than just the displayed ones), and
+   * similarly for featureGroups.
+   * 
+   * @param dna
+   * @param pep
+   * @param map
+   * @param featureTypes
+   *          hash who's keys are the displayed feature type strings
+   * @param featureGroups
+   *          hash where keys are feature groups and values are Boolean objects
+   *          indicating if they are displayed.
+   */
+  private static void transferCodedFeatures(SequenceI dna, SequenceI pep,
+          MapList map, Hashtable featureTypes, Hashtable featureGroups)
+  {
+    SequenceFeature[] sf = dna.getDatasetSequence().getSequenceFeatures();
+    Boolean fgstate;
+    jalview.datamodel.DBRefEntry[] dnarefs = jalview.util.DBRefUtils
+            .selectRefs(dna.getDBRef(),
+                    jalview.datamodel.DBRefSource.DNACODINGDBS);
+    if (dnarefs != null)
+    {
+      // intersect with pep
+      for (int d = 0; d < dnarefs.length; d++)
+      {
+        Mapping mp = dnarefs[d].getMap();
+        if (mp != null)
+        {
+        }
+      }
+    }
+    if (sf != null)
+    {
+      for (int f = 0; f < sf.length; f++)
+      {
+        fgstate = (featureGroups == null) ? null : ((Boolean) featureGroups
+                .get(sf[f].featureGroup));
+        if ((featureTypes == null || featureTypes.containsKey(sf[f]
+                .getType())) && (fgstate == null || fgstate.booleanValue()))
+        {
+          if (FeatureProperties.isCodingFeature(null, sf[f].getType()))
+          {
+            // if (map.intersectsFrom(sf[f].begin, sf[f].end))
+            {
+
+            }
+          }
+        }
+      }
+    }
   }
 }