JAL-2113 remove spaces in sequence from unmarshalling newlines

[jalview.git] / src / jalview / datamodel / xdb / embl / EmblEntry.java

diff --git a/src/jalview/datamodel/xdb/embl/EmblEntry.java b/src/jalview/datamodel/xdb/embl/EmblEntry.java
index 691a4c9..50a262f 100644 (file)
--- a/src/jalview/datamodel/xdb/embl/EmblEntry.java
+++ b/src/jalview/datamodel/xdb/embl/EmblEntry.java
@@ -29,6 +29,7 @@ import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.util.DBRefUtils;
+import jalview.util.DnaUtils;
 import jalview.util.MapList;
 import jalview.util.MappingUtils;
 import jalview.util.StringUtils;
@@ -57,7 +58,15 @@ public class EmblEntry
 
   String accession;
 
-  String version;
+  String entryVersion;
+
+  String sequenceVersion;
+
+  String moleculeType;
+
+  String topology;
+
+  String sequenceLength;
 
   String taxDivision;
 
@@ -248,20 +257,20 @@ public class EmblEntry
   }
 
   /**
-   * @return the version
+   * @return the entry version
    */
-  public String getVersion()
+  public String getEntryVersion()
   {
-    return version;
+    return entryVersion;
   }
 
   /**
    * @param version
    *          the version to set
    */
-  public void setVersion(String version)
+  public void setEntryVersion(String version)
   {
-    this.version = version;
+    this.entryVersion = version;
   }
 
   /**
@@ -277,7 +286,8 @@ public class EmblEntry
     SequenceI dna = new Sequence(sourceDb + "|" + accession,
             sequence.getSequence());
     dna.setDescription(desc);
-    DBRefEntry retrievedref = new DBRefEntry(sourceDb, version, accession);
+    DBRefEntry retrievedref = new DBRefEntry(sourceDb,
+            getSequenceVersion(), accession);
     dna.addDBRef(retrievedref);
     // add map to indicate the sequence is a valid coordinate frame for the
     // dbref
@@ -479,7 +489,8 @@ public class EmblEntry
           DBRefEntry pcdnaref = new DBRefEntry();
           pcdnaref.setAccessionId(prid);
           pcdnaref.setSource(DBRefSource.EMBLCDS);
-          pcdnaref.setVersion(getVersion()); // same as parent EMBL version.
+          pcdnaref.setVersion(getSequenceVersion()); // same as parent EMBL
+                                                     // version.
           MapList mp = new MapList(new int[] { 1, prseq.length() },
                   new int[] { 1 + (codonStart - 1),
                       (codonStart - 1) + 3 * prseq.length() }, 1, 3);
@@ -499,6 +510,7 @@ public class EmblEntry
         SequenceFeature sf = makeCdsFeature(exon, xint, prname, prid, vals,
                 codonStart);
         sf.setType(feature.getName()); // "CDS"
+        sf.setEnaLocation(feature.getLocation());
         sf.setFeatureGroup(sourceDb);
         dna.addSequenceFeature(sf);
       }
@@ -559,7 +571,7 @@ public class EmblEntry
           if (map != null)
           {
             Mapping pmap = new Mapping(dna, map.getMap().getInverse());
-            pref = new DBRefEntry(sourceDb, getVersion(),
+            pref = new DBRefEntry(sourceDb, getSequenceVersion(),
                     this.getAccession());
             pref.setMap(pmap);
             if (map.getTo() != null)
@@ -578,7 +590,7 @@ public class EmblEntry
           protEMBLCDS = new DBRefEntry();
           protEMBLCDS.setAccessionId(prid);
           protEMBLCDS.setSource(DBRefSource.EMBLCDSProduct);
-          protEMBLCDS.setVersion(getVersion());
+          protEMBLCDS.setVersion(getSequenceVersion());
           protEMBLCDS
                   .setMap(new Mapping(product, map.getMap().getInverse()));
         }
@@ -658,28 +670,31 @@ public class EmblEntry
    */
   protected int[] getCdsRanges(EmblFeature feature)
   {
-    if (feature.locations == null)
+    if (feature.location == null)
     {
       return new int[] {};
     }
-    int cdsBoundaryCount = 0; // count of all start/stop locations
-    int[][] cdsLocations = new int[feature.locations.size()][];
-    int locationNumber = 0;
-    for (EmblFeatureLocations loc : feature.locations)
-    {
-      int[] locationRanges = loc.getElementRanges(accession);
-      cdsLocations[locationNumber++] = locationRanges;
-      cdsBoundaryCount += locationRanges.length;
-    }
-    int[] cdsRanges = new int[cdsBoundaryCount];
-    int copyTo = 0;
-    for (int[] ranges : cdsLocations)
+    List<int[]> ranges = DnaUtils.parseLocation(feature.location);
+    return ranges == null ? new int[] {} : listToArray(ranges);
+  }
+
+  /**
+   * Converts a list of [start, end] ranges to a single array of [start, end,
+   * start, end ...]
+   * 
+   * @param ranges
+   * @return
+   */
+  int[] listToArray(List<int[]> ranges)
+  {
+    int[] result = new int[ranges.size() * 2];
+    int i = 0;
+    for (int[] range : ranges)
     {
-      System.arraycopy(ranges, 0, cdsRanges, copyTo, ranges.length);
-      copyTo += ranges.length;
+      result[i++] = range[0];
+      result[i++] = range[1];
     }
-    return cdsRanges;
-
+    return result;
   }
 
   /**
@@ -754,4 +769,64 @@ public class EmblEntry
     }
     return exon;
   }
+
+  public String getSequenceVersion()
+  {
+    return sequenceVersion;
+  }
+
+  public void setSequenceVersion(String sequenceVersion)
+  {
+    this.sequenceVersion = sequenceVersion;
+  }
+
+  public String getMoleculeType()
+  {
+    return moleculeType;
+  }
+
+  public void setMoleculeType(String moleculeType)
+  {
+    this.moleculeType = moleculeType;
+  }
+
+  public String getTopology()
+  {
+    return topology;
+  }
+
+  public void setTopology(String topology)
+  {
+    this.topology = topology;
+  }
+
+  public String getSequenceLength()
+  {
+    return sequenceLength;
+  }
+
+  public void setSequenceLength(String sequenceLength)
+  {
+    this.sequenceLength = sequenceLength;
+  }
+
+  public String getrCreated()
+  {
+    return rCreated;
+  }
+
+  public void setrCreated(String rCreated)
+  {
+    this.rCreated = rCreated;
+  }
+
+  public String getrLastUpdated()
+  {
+    return rLastUpdated;
+  }
+
+  public void setrLastUpdated(String rLastUpdated)
+  {
+    this.rLastUpdated = rLastUpdated;
+  }
 }