X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2Fxdb%2Fembl%2FEmblEntry.java;h=2ee1fb2f6f2906cb44d3f170b22979e4b9ac2a66;hb=4e892da7333869ad8b26d75b25f2c87352ca8c7e;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..2ee1fb2 100644
--- a/src/jalview/datamodel/xdb/embl/EmblEntry.java
+++ b/src/jalview/datamodel/xdb/embl/EmblEntry.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
+ * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program 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 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program 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 this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.datamodel.xdb.embl;
 
 import jalview.datamodel.DBRefEntry;
@@ -247,8 +265,8 @@ 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 +390,6 @@ 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
@@ -387,21 +404,28 @@ 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
+  { // TODO: ensure emblEntry.getSequences behaves correctly for returning all
+    // cases of noNa and noPeptide
     Vector seqs = new Vector();
     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()))
-        ;
+                .addDBRef((DBRefEntry) i.next()))
+          ;
     }
     try
     {
@@ -435,8 +459,7 @@ public class EmblEntry
           }
         }
       }
-    } 
-    catch (Exception e)
+    } catch (Exception e)
     {
       System.err.println("EMBL Record Features parsing error!");
       System.err
@@ -459,14 +482,22 @@ public class EmblEntry
   }
 
   /**
-   * 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 seqs, Sequence dna, boolean noPeptide)
   {
     boolean isEmblCdna = sourceDb.equals(DBRefSource.EMBLCDS);
     // extract coding region(s)
@@ -534,11 +565,11 @@ public class EmblEntry
         else
         {
           // throw anything else into the additional properties hash
-          String[] s= q.getValues();
+          String[] s = q.getValues();
           StringBuffer sb = new StringBuffer();
-          if (s!=null)
+          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");
@@ -549,14 +580,16 @@ public class EmblEntry
       }
     }
     Sequence product = null;
+    exon = adjustForPrStart(prstart, exon);
+    
     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 +602,64 @@ 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);
+          { 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))
         {
+          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(), dna.getEnd() - 3 };
-          map = new jalview.datamodel.Mapping(product, exon,
-                  new int[]
-                  { prstart, prstart + prseq.length() - 1 }, 3, 1);
+          { 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);
+          { 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);
-          
+
         }
       }
       // add cds feature to dna seq - this may include the stop codon
@@ -623,8 +670,8 @@ public class EmblEntry
         sf.setEnd(exon[xint + 1]);
         sf.setType(feature.getName());
         sf.setFeatureGroup(sourceDb);
-        sf.setDescription("Exon " + (1 + xint) + " for protein '"
-                + prname + "' EMBLCDS:" + prid);
+        sf.setDescription("Exon " + (1 + (int) (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)
@@ -649,23 +696,26 @@ public class EmblEntry
         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());
             }
           }
         }
         if (product != null)
         {
           DBRefEntry pref = new DBRefEntry(ref.getSource(), ref
-                .getVersion(), ref.getAccessionId());
+                  .getVersion(), ref.getAccessionId());
           pref.setMap(null); // reference is direct
           product.addDBRef(pref);
           // Add converse mapping reference
@@ -675,7 +725,7 @@ public class EmblEntry
             pref = new DBRefEntry(sourceDb, getVersion(), this
                     .getAccession());
             pref.setMap(pmap);
-            if (map.getTo()!=null)
+            if (map.getTo() != null)
             {
               map.getTo().addDBRef(pref);
             }
@@ -685,4 +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;
+  }
 }