fix to cope with EMBL records containing a CDS fragment (proper start/end codon posit...

diff --git a/src/jalview/datamodel/xdb/embl/EmblEntry.java b/src/jalview/datamodel/xdb/embl/EmblEntry.java
index 763e64a..2ee1fb2 100644 (file)
--- a/src/jalview/datamodel/xdb/embl/EmblEntry.java
+++ b/src/jalview/datamodel/xdb/embl/EmblEntry.java
@@ -580,35 +580,8 @@ public class EmblEntry
       }
     }
     Sequence product = null;
-    int origxon[], sxpos = -1, sxstart, sxstop;
-    // first adjust range for codon start attribute
-    if (prstart > 1)
-    {
-      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 += exon[x + 1] - exon[x] + 1;
-        if (prstart <= cdspos)
-        {
-          sxpos = x;
-          sxstart = exon[x];
-          sxstop = exon[x + 1];
-          // and adjust start boundary of first exon.
-          exon[x] = exon[x + 1] - cdspos + prstart;
-          break;
-        }
-      }
-
-      if (sxpos > 0)
-      {
-        int[] nxon = new int[exon.length - sxpos];
-        System.arraycopy(exon, sxpos, nxon, 0, exon.length - sxpos);
-        exon = nxon;
-      }
-    }
-
+    exon = adjustForPrStart(prstart, exon);
+    
     if (prseq != null && prname != null && prid != null)
     {
       // extract proteins.
@@ -617,7 +590,6 @@ public class EmblEntry
               .setDescription(((prname.length() == 0) ? "Protein Product from "
                       + sourceDb
                       : prname));
-
       if (!noPeptide)
       {
         // Protein is also added to vector of sequences returned
@@ -653,6 +625,9 @@ public class EmblEntry
       }
       else
       {
+        // Trim the exon mapping if necessary - the given product may only be a fragment of a larger protein. (EMBL:AY043181 is an example)
+        
+        
         if (isEmblCdna)
         {
           // TODO: Add a DbRef back to the parent EMBL sequence with the exon
@@ -663,9 +638,12 @@ public class EmblEntry
         }
         else
         {
-          map = new jalview.datamodel.Mapping(product, exon, new int[]
+          // final product length trunctation check
+          
+          map = new jalview.datamodel.Mapping(product, adjustForProteinLength(prseq.length(),exon), 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)
           DBRefEntry pcdnaref = new DBRefEntry();
           pcdnaref.setAccessionId(prid);
           pcdnaref.setSource(DBRefSource.EMBLCDS);
@@ -757,4 +735,85 @@ public class EmblEntry
       }
     }
   }
+
+  private int[] adjustForPrStart(int prstart, int[] exon)
+  {
+
+    int origxon[], sxpos = -1;
+    int sxstart, sxstop; // unnecessary variables used for debugging
+    // first adjust range for codon start attribute
+    if (prstart > 1)
+    {
+      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 += exon[x + 1] - exon[x] + 1;
+        if (prstart <= cdspos)
+        {
+          sxpos = x;
+          sxstart = exon[x];
+          sxstop = exon[x + 1];
+          // and adjust start boundary of first exon.
+          exon[x] = exon[x + 1] - cdspos + prstart;
+          break;
+        }
+      }
+
+      if (sxpos > 0)
+      {
+        int[] nxon = new int[exon.length - sxpos];
+        System.arraycopy(exon, sxpos, nxon, 0, exon.length - sxpos);
+        exon = nxon;
+      }
+    }
+    return exon;
+  }
+  /**
+   * truncate the last exon interval to the prlength'th codon 
+   * @param prlength
+   * @param exon
+   * @return new exon
+   */
+  private int[] adjustForProteinLength(int prlength, int[] exon)
+  {
+
+    int origxon[], sxpos = -1,endxon=0,cdslength=prlength*3;
+    int sxstart, sxstop; // unnecessary variables used for debugging
+    // first adjust range for codon start attribute
+    if (prlength >= 1 && exon!=null)
+    {
+      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 += exon[x + 1] - exon[x] + 1;
+        if (cdslength <= cdspos)
+        {
+          // advanced beyond last codon.
+          sxpos = x;
+          sxstart = exon[x];
+          sxstop = exon[x + 1];
+          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;
+        }
+      }
+
+      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;
+  }
 }