X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2Fxdb%2Fembl%2FEmblEntry.java;h=87e2789ae94db5f2e51556cb3281eb1edd03d537;hb=4d7f98a6dd54d9863ba449ec79dcd95d25ed863d;hp=59320f76e088e29412deb9c0dcd2dc1774362082;hpb=3dbf3b87899897f71f5d10f103fe5cd59cc329f7;p=jalview.git

diff --git a/src/jalview/datamodel/xdb/embl/EmblEntry.java b/src/jalview/datamodel/xdb/embl/EmblEntry.java
index 59320f7..87e2789 100644
--- a/src/jalview/datamodel/xdb/embl/EmblEntry.java
+++ b/src/jalview/datamodel/xdb/embl/EmblEntry.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.datamodel.xdb.embl;
 
 import jalview.datamodel.DBRefEntry;
@@ -8,11 +28,18 @@ import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 
-import java.util.Enumeration;
 import java.util.Hashtable;
-import java.util.Iterator;
+import java.util.Map.Entry;
 import java.util.Vector;
 
+/**
+ * Data model for one entry returned from an EMBL query, as marshalled by a
+ * Castor binding file
+ * 
+ * For example: http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/embl/x53828/emblxml
+ * 
+ * @see embl_mapping.xml
+ */
 public class EmblEntry
 {
   String accession;
@@ -29,13 +56,11 @@ public class EmblEntry
 
   String lastUpdated;
 
-  Vector keywords;
+  Vector<String> keywords;
 
-  Vector refs;
+  Vector<DBRefEntry> dbRefs;
 
-  Vector dbRefs;
-
-  Vector features;
+  Vector<EmblFeature> features;
 
   EmblSequence sequence;
 
@@ -59,7 +84,7 @@ public class EmblEntry
   /**
    * @return the dbRefs
    */
-  public Vector getDbRefs()
+  public Vector<DBRefEntry> getDbRefs()
   {
     return dbRefs;
   }
@@ -68,7 +93,7 @@ public class EmblEntry
    * @param dbRefs
    *          the dbRefs to set
    */
-  public void setDbRefs(Vector dbRefs)
+  public void setDbRefs(Vector<DBRefEntry> dbRefs)
   {
     this.dbRefs = dbRefs;
   }
@@ -93,7 +118,7 @@ public class EmblEntry
   /**
    * @return the features
    */
-  public Vector getFeatures()
+  public Vector<EmblFeature> getFeatures()
   {
     return features;
   }
@@ -102,7 +127,7 @@ public class EmblEntry
    * @param features
    *          the features to set
    */
-  public void setFeatures(Vector features)
+  public void setFeatures(Vector<EmblFeature> features)
   {
     this.features = features;
   }
@@ -110,7 +135,7 @@ public class EmblEntry
   /**
    * @return the keywords
    */
-  public Vector getKeywords()
+  public Vector<String> getKeywords()
   {
     return keywords;
   }
@@ -119,7 +144,7 @@ public class EmblEntry
    * @param keywords
    *          the keywords to set
    */
-  public void setKeywords(Vector keywords)
+  public void setKeywords(Vector<String> keywords)
   {
     this.keywords = keywords;
   }
@@ -142,23 +167,6 @@ public class EmblEntry
   }
 
   /**
-   * @return the refs
-   */
-  public Vector getRefs()
-  {
-    return refs;
-  }
-
-  /**
-   * @param refs
-   *          the refs to set
-   */
-  public void setRefs(Vector refs)
-  {
-    this.refs = refs;
-  }
-
-  /**
    * @return the releaseCreated
    */
   public String getRCreated()
@@ -170,7 +178,7 @@ public class EmblEntry
    * @param releaseCreated
    *          the releaseCreated to set
    */
-  public void setRcreated(String releaseCreated)
+  public void setRCreated(String releaseCreated)
   {
     this.rCreated = releaseCreated;
   }
@@ -247,8 +255,8 @@ public class EmblEntry
    * EMBL Feature support is limited. The text below is included for the benefit
    * of any developer working on improving EMBL feature import in Jalview.
    * Extract from EMBL feature specification see
-   * http://www.embl-ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
-   * 3.5 Location 3.5.1 Purpose
+   * http://www.embl-ebi.ac.uk/embl/Documentation
+   * /FT_definitions/feature_table.html 3.5 Location 3.5.1 Purpose
    * 
    * The location indicates the region of the presented sequence which
    * corresponds to a feature.
@@ -372,7 +380,6 @@ public class EmblEntry
    * 
    * join(1..100,J00194.1:100..202) Joins region 1..100 of the existing entry
    * with the region 100..202 of remote entry J00194
-   * 
    */
   /**
    * Recover annotated sequences from EMBL file
@@ -387,34 +394,44 @@ public class EmblEntry
    */
   public jalview.datamodel.SequenceI[] getSequences(boolean noNa,
           boolean noPeptide, String sourceDb)
-  { //TODO: ensure emblEntry.getSequences behaves correctly for returning all cases of noNa and noPeptide
-    Vector seqs = new Vector();
+  { // TODO: ensure emblEntry.getSequences behaves correctly for returning all
+    // cases of noNa and noPeptide
+    Vector<SequenceI> seqs = new Vector<SequenceI>();
     Sequence dna = null;
     if (!noNa)
     {
-      // In theory we still need to create this if noNa is set to avoid a null pointer exception
+      // In theory we still need to create this if noNa is set to avoid a null
+      // pointer exception
       dna = new Sequence(sourceDb + "|" + accession, sequence.getSequence());
       dna.setDescription(desc);
-      dna.addDBRef(new DBRefEntry(sourceDb, version, accession));
-      // TODO: add mapping for parentAccession attribute
+      DBRefEntry retrievedref = new DBRefEntry(sourceDb, version, accession);
+      dna.addDBRef(retrievedref);
+      // add map to indicate the sequence is a valid coordinate frame for the
+      // dbref
+      retrievedref.setMap(new Mapping(null,
+              new int[] { 1, dna.getLength() }, new int[] { 1,
+                  dna.getLength() }, 1, 1));
       // TODO: transform EMBL Database refs to canonical form
       if (dbRefs != null)
-        for (Iterator i = dbRefs.iterator(); i.hasNext(); dna
-        .addDBRef((DBRefEntry) i.next()))
-        ;
+      {
+        for (DBRefEntry dbref : dbRefs)
+        {
+          dna.addDBRef(dbref);
+        }
+      }
     }
     try
     {
-      for (Iterator i = features.iterator(); i.hasNext();)
+      for (EmblFeature feature : features)
       {
-        EmblFeature feature = (EmblFeature) i.next();
         if (!noNa)
         {
-          if (feature.dbRefs != null && feature.dbRefs.size() > 0)
+          if (feature.dbRefs != null)
           {
-            for (Iterator dbr = feature.dbRefs.iterator(); dbr.hasNext(); dna
-                    .addDBRef((DBRefEntry) dbr.next()))
-              ;
+            for (DBRefEntry dbref : feature.dbRefs)
+            {
+              dna.addDBRef(dbref);
+            }
           }
         }
         if (FeatureProperties.isCodingFeature(sourceDb, feature.getName()))
@@ -424,19 +441,20 @@ public class EmblEntry
         else
         {
           // General feature type.
+          // TODO this is just duplicated code ??
           if (!noNa)
           {
-            if (feature.dbRefs != null && feature.dbRefs.size() > 0)
+            if (feature.dbRefs != null)
             {
-              for (Iterator dbr = feature.dbRefs.iterator(); dbr.hasNext(); dna
-                      .addDBRef((DBRefEntry) dbr.next()))
-                ;
+              for (DBRefEntry dbref : feature.dbRefs)
+              {
+                dna.addDBRef(dbref);
+              }
             }
           }
         }
       }
-    } 
-    catch (Exception e)
+    } catch (Exception e)
     {
       System.err.println("EMBL Record Features parsing error!");
       System.err
@@ -452,33 +470,38 @@ public class EmblEntry
     SequenceI[] sqs = new SequenceI[seqs.size()];
     for (int i = 0, j = seqs.size(); i < j; i++)
     {
-      sqs[i] = (SequenceI) seqs.elementAt(i);
+      sqs[i] = seqs.elementAt(i);
       seqs.set(i, null);
     }
     return sqs;
   }
 
   /**
-   * attempt to extract coding region and product from a feature and properly decorate it with annotations.
-   * @param feature coding feature
-   * @param sourceDb source database for the EMBLXML
-   * @param seqs place where sequences go
-   * @param dna parent dna sequence for this record
-   * @param noPeptide flag for generation of Peptide sequence objects
+   * attempt to extract coding region and product from a feature and properly
+   * decorate it with annotations.
+   * 
+   * @param feature
+   *          coding feature
+   * @param sourceDb
+   *          source database for the EMBLXML
+   * @param seqs
+   *          place where sequences go
+   * @param dna
+   *          parent dna sequence for this record
+   * @param noPeptide
+   *          flag for generation of Peptide sequence objects
    */
-  private void parseCodingFeature(EmblFeature feature, String sourceDb, Vector seqs, Sequence dna, boolean noPeptide)
+  private void parseCodingFeature(EmblFeature feature, String sourceDb,
+          Vector<SequenceI> seqs, Sequence dna, boolean noPeptide)
   {
     boolean isEmblCdna = sourceDb.equals(DBRefSource.EMBLCDS);
     // extract coding region(s)
     jalview.datamodel.Mapping map = null;
     int[] exon = null;
-    if (feature.locations != null && feature.locations.size() > 0)
+    if (feature.locations != null)
     {
-      for (Enumeration locs = feature.locations.elements(); locs
-              .hasMoreElements();)
+      for (EmblFeatureLocations loc : feature.locations)
       {
-        EmblFeatureLocations loc = (EmblFeatureLocations) locs
-                .nextElement();
         int[] se = loc.getElementRanges(accession);
         if (exon == null)
         {
@@ -496,19 +519,17 @@ public class EmblEntry
     String prseq = null;
     String prname = new String();
     String prid = null;
-    Hashtable vals = new Hashtable();
+    Hashtable<String, String> vals = new Hashtable<String, String>();
     int prstart = 1;
     // get qualifiers
-    if (feature.getQualifiers() != null
-            && feature.getQualifiers().size() > 0)
+    if (feature.getQualifiers() != null)
     {
-      for (Iterator quals = feature.getQualifiers().iterator(); quals
-              .hasNext();)
+      for (Qualifier q : feature.getQualifiers())
       {
-        Qualifier q = (Qualifier) quals.next();
-        if (q.getName().equals("translation"))
+        String qname = q.getName();
+        if (qname.equals("translation"))
         {
-          StringBuffer prsq = new StringBuffer(q.getValues()[0]);
+          StringBuilder prsq = new StringBuilder(q.getValues()[0]);
           int p = prsq.indexOf(" ");
           while (p > -1)
           {
@@ -519,44 +540,47 @@ public class EmblEntry
           prsq = null;
 
         }
-        else if (q.getName().equals("protein_id"))
+        else if (qname.equals("protein_id"))
         {
           prid = q.getValues()[0];
         }
-        else if (q.getName().equals("codon_start"))
+        else if (qname.equals("codon_start"))
         {
           prstart = Integer.parseInt(q.getValues()[0]);
         }
-        else if (q.getName().equals("product"))
+        else if (qname.equals("product"))
         {
           prname = q.getValues()[0];
         }
         else
         {
           // throw anything else into the additional properties hash
-          String[] s= q.getValues();
-          StringBuffer sb = new StringBuffer();
-          if (s!=null)
+          String[] s = q.getValues();
+          StringBuilder sb = new StringBuilder();
+          if (s != null)
           {
-            for (int i=0; i<s.length; i++)
+            for (int i = 0; i < s.length; i++)
             {
               sb.append(s[i]);
               sb.append("\n");
             }
           }
-          vals.put(q.getName(), sb.toString());
+          vals.put(qname, sb.toString());
         }
       }
     }
     Sequence product = null;
+    DBRefEntry protEMBLCDS = null;
+    exon = adjustForPrStart(prstart, exon);
+    boolean noProteinDbref = true;
+
     if (prseq != null && prname != null && prid != null)
     {
       // extract proteins.
-      product = new Sequence(prid
-              , prseq, prstart, prstart
-              + prseq.length() - 1);
-      product.setDescription(((prname.length()==0) ? "Protein Product from " + sourceDb : prname));
-      
+      product = new Sequence(prid, prseq, 1, prseq.length());
+      product.setDescription(((prname.length() == 0) ? "Protein Product from "
+              + sourceDb
+              : prname));
       if (!noPeptide)
       {
         // Protein is also added to vector of sequences returned
@@ -569,50 +593,69 @@ public class EmblEntry
         System.err
                 .println("Implementation Notice: EMBLCDS records not properly supported yet - Making up the CDNA region of this sequence... may be incorrect ("
                         + sourceDb + ":" + getAccession() + ")");
-        if (prseq.length() * 3 == dna.getSequence().length)
+        if (prseq.length() * 3 == (1 - prstart + dna.getSequence().length))
         {
+          System.err
+                  .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(), dna.getEnd() };
-          map = new jalview.datamodel.Mapping(product, exon,
-                  new int[]
-                  { prstart, prstart + prseq.length() - 1 }, 3, 1);
+          exon = new int[] { dna.getStart() + (prstart - 1), dna.getEnd() };
+          map = new jalview.datamodel.Mapping(product, exon, new int[] { 1,
+              prseq.length() }, 3, 1);
         }
-        if ((prseq.length() + 1) * 3 == dna.getSequence().length)
+        if ((prseq.length() + 1) * 3 == (1 - prstart + dna.getSequence().length))
         {
-          exon = new int[]
-          { dna.getStart(), dna.getEnd() - 3 };
-          map = new jalview.datamodel.Mapping(product, exon,
-                  new int[]
-                  { prstart, prstart + prseq.length() - 1 }, 3, 1);
+          System.err
+                  .println("Allowing for additional stop codon at end of cDNA fragment... will probably cause an error in VAMSAs!");
+          exon = new int[] { dna.getStart() + (prstart - 1),
+              dna.getEnd() - 3 };
+          map = new jalview.datamodel.Mapping(product, exon, new int[] { 1,
+              prseq.length() }, 3, 1);
         }
       }
       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
           // map
-          // if given a dataset reference, search dataset for parent EMBL sequence if it exists and set its map
+          // if given a dataset reference, search dataset for parent EMBL
+          // sequence if it exists and set its map
           // make a new feature annotating the coding contig
         }
         else
         {
-          map = new jalview.datamodel.Mapping(product, exon,
-                  new int[]
-                  { prstart, prstart + prseq.length() - 1 }, 3, 1);
+          // 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);
           pcdnaref.setVersion(getVersion()); // same as parent EMBL version.
-          jalview.util.MapList mp = new jalview.util.MapList(new int[]
-          { 1+(prstart-1)*3, 1+(prstart-1)*3 + (prseq.length()-1)*3 }, new int[] { prstart, prstart+prseq.length() - 1 }, 3, 1);
+          jalview.util.MapList mp = new jalview.util.MapList(new int[] { 1,
+              prseq.length() }, new int[] { 1 + (prstart - 1),
+              (prstart - 1) + 3 * prseq.length() }, 1, 3);
+          // { 1 + (prstart - 1) * 3,
+          // 1 + (prstart - 1) * 3 + prseq.length() * 3 - 1 }, new int[]
+          // { 1prstart, prstart + prseq.length() - 1 }, 3, 1);
           pcdnaref.setMap(new Mapping(mp));
-          if (product!=null)
+          if (product != null)
+          {
             product.addDBRef(pcdnaref);
-          
+            protEMBLCDS = new DBRefEntry(pcdnaref);
+            protEMBLCDS.setSource(DBRefSource.EMBLCDSProduct);
+            product.addDBRef(protEMBLCDS);
+
+          }
+
         }
       }
       // add cds feature to dna seq - this may include the stop codon
@@ -623,59 +666,59 @@ public class EmblEntry
         sf.setEnd(exon[xint + 1]);
         sf.setType(feature.getName());
         sf.setFeatureGroup(sourceDb);
-        sf.setDescription("Exon " + (1 + xint) + " for protein '"
+        sf.setDescription("Exon " + (1 + xint / 2) + " for protein '"
                 + prname + "' EMBLCDS:" + prid);
         sf.setValue(FeatureProperties.EXONPOS, new Integer(1 + xint));
         sf.setValue(FeatureProperties.EXONPRODUCT, prname);
-        if (vals != null && vals.size() > 0)
+        if (vals != null)
         {
-          Enumeration kv = vals.elements();
-          while (kv.hasMoreElements())
+          for (Entry<String, String> val : vals.entrySet())
           {
-            Object key = kv.nextElement();
-            if (key != null)
-              sf.setValue(key.toString(), vals.get(key));
+            sf.setValue(val.getKey(), val.getValue());
           }
         }
         dna.addSequenceFeature(sf);
       }
     }
     // add dbRefs to sequence
-    if (feature.dbRefs != null && feature.dbRefs.size() > 0)
+    if (feature.dbRefs != null)
     {
-      for (Iterator dbr = feature.dbRefs.iterator(); dbr.hasNext();)
+      for (DBRefEntry ref : feature.dbRefs)
       {
-        DBRefEntry ref = (DBRefEntry) dbr.next();
         ref.setSource(jalview.util.DBRefUtils.getCanonicalName(ref
                 .getSource()));
         // Hard code the kind of protein product accessions that EMBL cite
-        if (ref.getSource().equals(
-                jalview.datamodel.DBRefSource.UNIPROT))
+        if (ref.getSource().equals(jalview.datamodel.DBRefSource.UNIPROT))
         {
           ref.setMap(map);
-          if (map!=null && map.getTo()!=null)
+          if (map != null && map.getTo() != null)
           {
-            map.getTo().addDBRef(new DBRefEntry(ref.getSource(), ref.getVersion(), ref.getAccessionId())); // don't copy map over.
-            if (map.getTo().getName().indexOf(prid)==0)
+            map.getTo().addDBRef(
+                    new DBRefEntry(ref.getSource(), ref.getVersion(), ref
+                            .getAccessionId())); // don't copy map over.
+            if (map.getTo().getName().indexOf(prid) == 0)
             {
-              map.getTo().setName(jalview.datamodel.DBRefSource.UNIPROT+"|"+ref.getAccessionId());
+              map.getTo().setName(
+                      jalview.datamodel.DBRefSource.UNIPROT + "|"
+                              + ref.getAccessionId());
             }
           }
+          noProteinDbref = false;
         }
         if (product != null)
         {
-          DBRefEntry pref = new DBRefEntry(ref.getSource(), ref
-                .getVersion(), ref.getAccessionId());
+          DBRefEntry pref = new DBRefEntry(ref.getSource(),
+                  ref.getVersion(), ref.getAccessionId());
           pref.setMap(null); // reference is direct
           product.addDBRef(pref);
           // Add converse mapping reference
           if (map != null)
           {
             Mapping pmap = new Mapping(dna, map.getMap().getInverse());
-            pref = new DBRefEntry(sourceDb, getVersion(), this
-                    .getAccession());
+            pref = new DBRefEntry(sourceDb, getVersion(),
+                    this.getAccession());
             pref.setMap(pmap);
-            if (map.getTo()!=null)
+            if (map.getTo() != null)
             {
               map.getTo().addDBRef(pref);
             }
@@ -683,6 +726,120 @@ public class EmblEntry
         }
         dna.addDBRef(ref);
       }
+      if (noProteinDbref && product != null)
+      {
+        // add protein coding reference to dna sequence so xref matches
+        if (protEMBLCDS == null)
+        {
+          protEMBLCDS = new DBRefEntry();
+          protEMBLCDS.setAccessionId(prid);
+          protEMBLCDS.setSource(DBRefSource.EMBLCDSProduct);
+          protEMBLCDS.setVersion(getVersion());
+          protEMBLCDS
+                  .setMap(new Mapping(product, map.getMap().getInverse()));
+        }
+        product.addDBRef(protEMBLCDS);
+
+        // Add converse mapping reference
+        if (map != null)
+        {
+          Mapping pmap = new Mapping(product, protEMBLCDS.getMap().getMap()
+                  .getInverse());
+          DBRefEntry ncMap = new DBRefEntry(protEMBLCDS);
+          ncMap.setMap(pmap);
+          if (map.getTo() != null)
+          {
+            dna.addDBRef(ncMap);
+          }
+        }
+      }
+    }
+  }
+
+  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;
   }
 }