JAL-1705 include stop codon in mapped CDS range so it is included in the

generated CDS sequence

diff --git a/src/jalview/datamodel/xdb/embl/EmblEntry.java b/src/jalview/datamodel/xdb/embl/EmblEntry.java
index fda042e..691a4c9 100644 (file)
--- a/src/jalview/datamodel/xdb/embl/EmblEntry.java
+++ b/src/jalview/datamodel/xdb/embl/EmblEntry.java
@@ -33,6 +33,7 @@ import jalview.util.MapList;
 import jalview.util.MappingUtils;
 import jalview.util.StringUtils;
 
+import java.util.Arrays;
 import java.util.Hashtable;
 import java.util.List;
 import java.util.Map;
@@ -400,7 +401,6 @@ public class EmblEntry
       }
     }
 
-    // SequenceI product = null;
     DBRefEntry protEMBLCDS = null;
     exon = MappingUtils.removeStartPositions(codonStart - 1, exon);
     boolean noProteinDbref = true;
@@ -436,7 +436,8 @@ public class EmblEntry
                   .println("Not allowing for additional stop codon at end of cDNA fragment... !");
           // this might occur for CDS sequences where no features are
           // marked.
-          exon = new int[] { dna.getStart() + (codonStart - 1), dna.getEnd() };
+          exon = new int[] { dna.getStart() + (codonStart - 1),
+              dna.getEnd() };
           map = new Mapping(product, exon, new int[] { 1, prseq.length() },
                   3, 1);
         }
@@ -469,9 +470,9 @@ public class EmblEntry
           // TODO should from range include stop codon even if not in protein
           // in order to include stop codon in CDS sequence (as done for
           // Ensembl)?
-          int[] cdsRanges = adjustForProteinLength(prseq.length(),
-                  exon);
-          map = new Mapping(product, cdsRanges, new int[] { 1, prseq.length() }, 3, 1);
+          int[] cdsRanges = adjustForProteinLength(prseq.length(), exon);
+          map = new Mapping(product, cdsRanges, new int[] { 1,
+              prseq.length() }, 3, 1);
           // reconstruct the EMBLCDS entry
           // TODO: this is only necessary when there codon annotation is
           // complete (I think JBPNote)
@@ -536,8 +537,7 @@ public class EmblEntry
             if (proteinSeq == null)
             {
               proteinSeq = new Sequence(proteinSeqName,
-                      product
-                      .getSequenceAsString());
+                      product.getSequenceAsString());
               matcher.add(proteinSeq);
               peptides.add(proteinSeq);
             }
@@ -623,11 +623,11 @@ public class EmblEntry
     SequenceFeature sf = new SequenceFeature();
     sf.setBegin(Math.min(exons[exonStartIndex], exons[exonStartIndex + 1]));
     sf.setEnd(Math.max(exons[exonStartIndex], exons[exonStartIndex + 1]));
-    sf.setDescription(String.format(
-            "Exon %d for protein '%s' EMBLCDS:%s", exonNumber, proteinName,
-            proteinAccessionId));
+    sf.setDescription(String.format("Exon %d for protein '%s' EMBLCDS:%s",
+            exonNumber, proteinName, proteinAccessionId));
     sf.setPhase(String.valueOf(codonStart - 1));
-    sf.setStrand(exons[exonStartIndex] <= exons[exonStartIndex + 1] ? "+" : "-");
+    sf.setStrand(exons[exonStartIndex] <= exons[exonStartIndex + 1] ? "+"
+            : "-");
     sf.setValue(FeatureProperties.EXONPOS, exonNumber);
     sf.setValue(FeatureProperties.EXONPRODUCT, proteinName);
     if (!vals.isEmpty())
@@ -689,45 +689,69 @@ public class EmblEntry
    * @param exon
    * @return new exon
    */
-  private int[] adjustForProteinLength(int prlength, int[] exon)
+  static int[] adjustForProteinLength(int prlength, int[] exon)
   {
+    if (prlength <= 0 || exon == null)
+    {
+      return exon;
+    }
+    int desiredCdsLength = prlength * 3;
+    int exonLength = MappingUtils.getLength(Arrays.asList(exon));
+
+    /*
+     * assuming here exon might include stop codon in addition to protein codons
+     */
+    if (desiredCdsLength == exonLength
+            || desiredCdsLength == exonLength - 3)
+    {
+      return exon;
+    }
 
-    int origxon[], sxpos = -1, endxon = 0, cdslength = prlength * 3;
-    // first adjust range for codon start attribute
-    if (prlength >= 1 && exon != null)
+    int origxon[];
+    int sxpos = -1;
+    int endxon = 0;
+    origxon = new int[exon.length];
+    System.arraycopy(exon, 0, origxon, 0, exon.length);
+    int cdspos = 0;
+    for (int x = 0; x < exon.length; x += 2)
     {
-      origxon = new int[exon.length];
-      System.arraycopy(exon, 0, origxon, 0, exon.length);
-      int cdspos = 0;
-      for (int x = 0; x < exon.length && sxpos == -1; x += 2)
+      cdspos += Math.abs(exon[x + 1] - exon[x]) + 1;
+      if (desiredCdsLength <= cdspos)
       {
-        cdspos += Math.abs(exon[x + 1] - exon[x]) + 1;
-        if (cdslength <= cdspos)
+        // advanced beyond last codon.
+        sxpos = x;
+        if (desiredCdsLength != cdspos)
         {
-          // advanced beyond last codon.
-          sxpos = x;
-          if (cdslength != cdspos)
-          {
-            // System.err
-            // .println("Truncating final exon interval on region by "
-            // + (cdspos - cdslength));
-          }
-          // locate the new end boundary of final exon as endxon
-          endxon = exon[x + 1] - cdspos + cdslength;
-          break;
+          // System.err
+          // .println("Truncating final exon interval on region by "
+          // + (cdspos - cdslength));
         }
-      }
 
-      if (sxpos != -1)
-      {
-        // and trim the exon interval set if necessary
-        int[] nxon = new int[sxpos + 2];
-        System.arraycopy(exon, 0, nxon, 0, sxpos + 2);
-        nxon[sxpos + 1] = endxon; // update the end boundary for the new exon
-                                  // set
-        exon = nxon;
+        /*
+         * shrink the final exon - reduce end position if forward
+         * strand, increase it if reverse
+         */
+        if (exon[x + 1] >= exon[x])
+        {
+          endxon = exon[x + 1] - cdspos + desiredCdsLength;
+        }
+        else
+        {
+          endxon = exon[x + 1] + cdspos - desiredCdsLength;
+        }
+        break;
       }
     }
+
+    if (sxpos != -1)
+    {
+      // and trim the exon interval set if necessary
+      int[] nxon = new int[sxpos + 2];
+      System.arraycopy(exon, 0, nxon, 0, sxpos + 2);
+      nxon[sxpos + 1] = endxon; // update the end boundary for the new exon
+                                // set
+      exon = nxon;
+    }
     return exon;
   }
 }