X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2Fgff%2FGffHelperBase.java;h=1d4d3acbe8c90e25f3003dae372a2452789873e2;hb=55eef00ac2435b5cc0ee64b92ad87a915375a709;hp=48c33e5deff795985bf817080dd4a06d80c30140;hpb=604cbee405a837565ba1a74aa9bddd62aed685ab;p=jalview.git

diff --git a/src/jalview/io/gff/GffHelperBase.java b/src/jalview/io/gff/GffHelperBase.java
index 48c33e5..1d4d3ac 100644
--- a/src/jalview/io/gff/GffHelperBase.java
+++ b/src/jalview/io/gff/GffHelperBase.java
@@ -150,8 +150,8 @@ public abstract class GffHelperBase implements GffHelperI
        * restrict from range to make them match up
        * it's kind of arbitrary which end we truncate - here it is the end
        */
-      System.err.print("Truncating mapping from " + Arrays.toString(from)
-              + " to ");
+      System.err.print(
+              "Truncating mapping from " + Arrays.toString(from) + " to ");
       if (from[1] > from[0])
       {
         from[1] -= fromOverlap / toRatio;
@@ -169,8 +169,8 @@ public abstract class GffHelperBase implements GffHelperI
       /*
        * restrict to range to make them match up
        */
-      System.err.print("Truncating mapping to " + Arrays.toString(to)
-              + " to ");
+      System.err.print(
+              "Truncating mapping to " + Arrays.toString(to) + " to ");
       if (to[1] > to[0])
       {
         to[1] -= fromOverlap / fromRatio;
@@ -261,7 +261,8 @@ public abstract class GffHelperBase implements GffHelperI
   /**
    * Parses the input line to a map of name / value(s) pairs. For example the
    * line <br>
-   * Notes=Fe-S;Method=manual curation, prediction; source = Pfam; Notes = Metal <br>
+   * Notes=Fe-S;Method=manual curation, prediction; source = Pfam; Notes = Metal
+   * <br>
    * if parsed with delimiter=";" and separators {' ', '='} <br>
    * would return a map with { Notes={Fe=S, Metal}, Method={manual curation,
    * prediction}, source={Pfam}} <br>
@@ -337,6 +338,19 @@ public abstract class GffHelperBase implements GffHelperI
   protected SequenceFeature buildSequenceFeature(String[] gff,
           Map<String, List<String>> attributes)
   {
+    return buildSequenceFeature(gff, TYPE_COL, gff[SOURCE_COL], attributes);
+  }
+
+  /**
+   * @param gff
+   * @param typeColumn
+   * @param group
+   * @param attributes
+   * @return
+   */
+  protected SequenceFeature buildSequenceFeature(String[] gff,
+          int typeColumn, String group, Map<String, List<String>> attributes)
+  {
     try
     {
       int start = Integer.parseInt(gff[START_COL]);
@@ -355,8 +369,8 @@ public abstract class GffHelperBase implements GffHelperI
         // e.g. '.' - leave as zero
       }
 
-      SequenceFeature sf = new SequenceFeature(gff[TYPE_COL],
-              gff[SOURCE_COL], start, end, score, gff[SOURCE_COL]);
+      SequenceFeature sf = new SequenceFeature(gff[typeColumn],
+              gff[SOURCE_COL], start, end, score, group);
 
       sf.setStrand(gff[STRAND_COL]);
 
@@ -375,8 +389,8 @@ public abstract class GffHelperBase implements GffHelperI
          */
         for (Entry<String, List<String>> attr : attributes.entrySet())
         {
-          String values = StringUtils.listToDelimitedString(
-                  attr.getValue(), ",");
+          String values = StringUtils.listToDelimitedString(attr.getValue(),
+                  ",");
           sf.setValue(attr.getKey(), values);
           if (NOTE.equals(attr.getKey()))
           {