X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2Fxdb%2Fembl%2FEmblEntry.java;h=8cc81d9259b7a93b902995b9a5f96a53b8a6f1c0;hb=be762d8d9c71a7aa3121e845c45911c7192b7827;hp=fe3f6ef25c9497ae8b3e509f082de6bebc3d50fd;hpb=e327ac5df98f528afeb347ac9a79085ad0d0975b;p=jalview.git

diff --git a/src/jalview/datamodel/xdb/embl/EmblEntry.java b/src/jalview/datamodel/xdb/embl/EmblEntry.java
index fe3f6ef..8cc81d9 100644
--- a/src/jalview/datamodel/xdb/embl/EmblEntry.java
+++ b/src/jalview/datamodel/xdb/embl/EmblEntry.java
@@ -371,8 +371,8 @@ 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 (translationLength
-                * 3 == (1 - codonStart + dna.getSequence().length))
+        int dnaLength = dna.getLength();
+        if (translationLength * 3 == (1 - codonStart + dnaLength))
         {
           System.err.println(
                   "Not allowing for additional stop codon at end of cDNA fragment... !");
@@ -383,8 +383,7 @@ public class EmblEntry
                   new int[]
                   { 1, translationLength }, 3, 1);
         }
-        if ((translationLength + 1)
-                * 3 == (1 - codonStart + dna.getSequence().length))
+        if ((translationLength + 1) * 3 == (1 - codonStart + dnaLength))
         {
           System.err.println(
                   "Allowing for additional stop codon at end of cDNA fragment... will probably cause an error in VAMSAs!");
@@ -456,13 +455,27 @@ public class EmblEntry
       /*
        * add cds features to dna sequence
        */
-      for (int xint = 0; exons != null && xint < exons.length; xint += 2)
+      String cds = feature.getName(); // "CDS"
+      for (int xint = 0; exons != null && xint < exons.length - 1; xint += 2)
       {
-        SequenceFeature sf = makeCdsFeature(exons, xint, proteinName,
-                proteinId, vals, codonStart);
-        sf.setType(feature.getName()); // "CDS"
+        int exonStart = exons[xint];
+        int exonEnd = exons[xint + 1];
+        int begin = Math.min(exonStart, exonEnd);
+        int end = Math.max(exonStart, exonEnd);
+        int exonNumber = xint / 2 + 1;
+        String desc = String.format("Exon %d for protein '%s' EMBLCDS:%s",
+                exonNumber, proteinName, proteinId);
+
+        SequenceFeature sf = makeCdsFeature(cds, desc, begin, end,
+                sourceDb, vals);
+
         sf.setEnaLocation(feature.getLocation());
-        sf.setFeatureGroup(sourceDb);
+        boolean forwardStrand = exonStart <= exonEnd;
+        sf.setStrand(forwardStrand ? "+" : "-");
+        sf.setPhase(String.valueOf(codonStart - 1));
+        sf.setValue(FeatureProperties.EXONPOS, exonNumber);
+        sf.setValue(FeatureProperties.EXONPRODUCT, proteinName);
+
         dna.addSequenceFeature(sf);
       }
     }
@@ -577,33 +590,24 @@ public class EmblEntry
   /**
    * Helper method to construct a SequenceFeature for one cds range
    * 
-   * @param exons
-   *          array of cds [start, end, ...] positions
-   * @param exonStartIndex
-   *          offset into the exons array
-   * @param proteinName
-   * @param proteinAccessionId
+   * @param type
+   *          feature type ("CDS")
+   * @param desc
+   *          description
+   * @param begin
+   *          start position
+   * @param end
+   *          end position
+   * @param group
+   *          feature group
    * @param vals
    *          map of 'miscellaneous values' for feature
-   * @param codonStart
-   *          codon start position for CDS (1/2/3, normally 1)
    * @return
    */
-  protected SequenceFeature makeCdsFeature(int[] exons, int exonStartIndex,
-          String proteinName, String proteinAccessionId,
-          Map<String, String> vals, int codonStart)
-  {
-    int exonNumber = exonStartIndex / 2 + 1;
-    SequenceFeature sf = new SequenceFeature();
-    sf.setBegin(Math.min(exons[exonStartIndex], exons[exonStartIndex + 1]));
-    sf.setEnd(Math.max(exons[exonStartIndex], exons[exonStartIndex + 1]));
-    sf.setDescription(String.format("Exon %d for protein '%s' EMBLCDS:%s",
-            exonNumber, proteinName, proteinAccessionId));
-    sf.setPhase(String.valueOf(codonStart - 1));
-    sf.setStrand(
-            exons[exonStartIndex] <= exons[exonStartIndex + 1] ? "+" : "-");
-    sf.setValue(FeatureProperties.EXONPOS, exonNumber);
-    sf.setValue(FeatureProperties.EXONPRODUCT, proteinName);
+  protected SequenceFeature makeCdsFeature(String type, String desc,
+          int begin, int end, String group, Map<String, String> vals)
+  {
+    SequenceFeature sf = new SequenceFeature(type, desc, begin, end, group);
     if (!vals.isEmpty())
     {
       StringBuilder sb = new StringBuilder();