From 7ff2320a439fdf69396aff086bbfeb81411595db Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Mon, 8 May 2017 17:38:18 +0100
Subject: [PATCH] JAL-2505 refactored SequenceFeature construction so
 type,begin,end,group are set in constructor

---
 src/jalview/datamodel/xdb/embl/EmblEntry.java |   63 ++++++++++++++-----------
 1 file changed, 35 insertions(+), 28 deletions(-)

diff --git a/src/jalview/datamodel/xdb/embl/EmblEntry.java b/src/jalview/datamodel/xdb/embl/EmblEntry.java
index 4d09bdc..6f9c884 100644
--- a/src/jalview/datamodel/xdb/embl/EmblEntry.java
+++ b/src/jalview/datamodel/xdb/embl/EmblEntry.java
@@ -443,13 +443,27 @@ 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);
       }
     }
@@ -563,33 +577,26 @@ 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,
+            Float.NaN, group);
+
     if (!vals.isEmpty())
     {
       StringBuilder sb = new StringBuilder();
-- 
1.7.10.2