X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2Fxdb%2Fembl%2FEmblEntry.java;h=0cee0b410a2bfc81cd4373ee406d05afc1085fee;hb=2253f31565d4e96edffce2fac596e2ef0578d596;hp=73ffeefecaa92eae801aff1eca7ade7888e1e997;hpb=d1f6cf53b29322601c621da9a6b3cb09dd28235e;p=jalview.git

diff --git a/src/jalview/datamodel/xdb/embl/EmblEntry.java b/src/jalview/datamodel/xdb/embl/EmblEntry.java
index 73ffeef..0cee0b4 100644
--- a/src/jalview/datamodel/xdb/embl/EmblEntry.java
+++ b/src/jalview/datamodel/xdb/embl/EmblEntry.java
@@ -67,7 +67,7 @@ public class EmblEntry
 
   /**
    * @param accession
-   *          the accession to set
+   *                the accession to set
    */
   public void setAccession(String accession)
   {
@@ -84,7 +84,7 @@ public class EmblEntry
 
   /**
    * @param dbRefs
-   *          the dbRefs to set
+   *                the dbRefs to set
    */
   public void setDbRefs(Vector dbRefs)
   {
@@ -101,7 +101,7 @@ public class EmblEntry
 
   /**
    * @param desc
-   *          the desc to set
+   *                the desc to set
    */
   public void setDesc(String desc)
   {
@@ -118,7 +118,7 @@ public class EmblEntry
 
   /**
    * @param features
-   *          the features to set
+   *                the features to set
    */
   public void setFeatures(Vector features)
   {
@@ -135,7 +135,7 @@ public class EmblEntry
 
   /**
    * @param keywords
-   *          the keywords to set
+   *                the keywords to set
    */
   public void setKeywords(Vector keywords)
   {
@@ -152,7 +152,7 @@ public class EmblEntry
 
   /**
    * @param lastUpdated
-   *          the lastUpdated to set
+   *                the lastUpdated to set
    */
   public void setLastUpdated(String lastUpdated)
   {
@@ -169,7 +169,7 @@ public class EmblEntry
 
   /**
    * @param refs
-   *          the refs to set
+   *                the refs to set
    */
   public void setRefs(Vector refs)
   {
@@ -186,7 +186,7 @@ public class EmblEntry
 
   /**
    * @param releaseCreated
-   *          the releaseCreated to set
+   *                the releaseCreated to set
    */
   public void setRcreated(String releaseCreated)
   {
@@ -203,7 +203,7 @@ public class EmblEntry
 
   /**
    * @param releaseLastUpdated
-   *          the releaseLastUpdated to set
+   *                the releaseLastUpdated to set
    */
   public void setRLastUpdated(String releaseLastUpdated)
   {
@@ -220,7 +220,7 @@ public class EmblEntry
 
   /**
    * @param sequence
-   *          the sequence to set
+   *                the sequence to set
    */
   public void setSequence(EmblSequence sequence)
   {
@@ -237,7 +237,7 @@ public class EmblEntry
 
   /**
    * @param taxDivision
-   *          the taxDivision to set
+   *                the taxDivision to set
    */
   public void setTaxDivision(String taxDivision)
   {
@@ -254,7 +254,7 @@ public class EmblEntry
 
   /**
    * @param version
-   *          the version to set
+   *                the version to set
    */
   public void setVersion(String version)
   {
@@ -396,21 +396,24 @@ public class EmblEntry
    * Recover annotated sequences from EMBL file
    * 
    * @param noNa
-   *          don't return nucleic acid sequences
+   *                don't return nucleic acid sequences
    * @param sourceDb
-   *          TODO
+   *                TODO
    * @param noProtein
-   *          don't return any translated protein sequences marked in features
+   *                don't return any translated protein sequences marked in
+   *                features
    * @return dataset sequences with DBRefs and features - DNA always comes first
    */
   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));
@@ -418,8 +421,8 @@ public class EmblEntry
       // 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
     {
@@ -453,8 +456,7 @@ public class EmblEntry
           }
         }
       }
-    } 
-    catch (Exception e)
+    } catch (Exception e)
     {
       System.err.println("EMBL Record Features parsing error!");
       System.err
@@ -477,14 +479,22 @@ 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)
@@ -552,11 +562,11 @@ 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");
@@ -570,11 +580,13 @@ public class EmblEntry
     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, prstart, prstart + prseq.length()
+              - 1);
+      product
+              .setDescription(((prname.length() == 0) ? "Protein Product from "
+                      + sourceDb
+                      : prname));
+
       if (!noPeptide)
       {
         // Protein is also added to vector of sequences returned
@@ -593,17 +605,15 @@ public class EmblEntry
           // marked.
           exon = new int[]
           { dna.getStart(), dna.getEnd() };
-          map = new jalview.datamodel.Mapping(product, exon,
-                  new int[]
-                  { prstart, prstart + prseq.length() - 1 }, 3, 1);
+          map = new jalview.datamodel.Mapping(product, exon, new int[]
+          { prstart, prstart + prseq.length() - 1 }, 3, 1);
         }
         if ((prseq.length() + 1) * 3 == 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);
+          map = new jalview.datamodel.Mapping(product, exon, new int[]
+          { prstart, prstart + prseq.length() - 1 }, 3, 1);
         }
       }
       else
@@ -612,25 +622,27 @@ public class EmblEntry
         {
           // 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);
+          map = new jalview.datamodel.Mapping(product, exon, new int[]
+          { prstart, prstart + prseq.length() - 1 }, 3, 1);
           // reconstruct the EMBLCDS entry
           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 + (prstart - 1) * 3,
+              1 + (prstart - 1) * 3 + (prseq.length() - 1) * 3 }, new int[]
+          { prstart, 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
@@ -641,8 +653,8 @@ public class EmblEntry
         sf.setEnd(exon[xint + 1]);
         sf.setType(feature.getName());
         sf.setFeatureGroup(sourceDb);
-        sf.setDescription("Exon " + (1 + (int)(xint/2)) + " 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)
@@ -667,23 +679,26 @@ 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
@@ -693,7 +708,7 @@ 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);
             }