From 51160e18fc93c618169ac9a4e5fda2a6a4486ec5 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Tue, 16 May 2017 11:12:04 +0100
Subject: [PATCH] JAL-2505 refactor to set type and group in SequenceFeature
 constructor

---
 src/jalview/io/gff/ExonerateHelper.java    |    8 ++++++--
 src/jalview/io/gff/Gff3Helper.java         |    4 +++-
 src/jalview/io/gff/GffHelperBase.java      |   17 +++++++++++++++--
 src/jalview/io/gff/InterProScanHelper.java |   19 +++++++++----------
 4 files changed, 33 insertions(+), 15 deletions(-)

diff --git a/src/jalview/io/gff/ExonerateHelper.java b/src/jalview/io/gff/ExonerateHelper.java
index eb74eea..873fd27 100644
--- a/src/jalview/io/gff/ExonerateHelper.java
+++ b/src/jalview/io/gff/ExonerateHelper.java
@@ -352,12 +352,16 @@ public class ExonerateHelper extends Gff2Helper
     return false;
   }
 
+  /**
+   * An override to set feature group to "exonerate" instead of the default GFF
+   * source value (column 2)
+   */
   @Override
   protected SequenceFeature buildSequenceFeature(String[] gff,
           Map<String, List<String>> set)
   {
-    SequenceFeature sf = super.buildSequenceFeature(gff, set);
-    sf.setFeatureGroup("exonerate");
+    SequenceFeature sf = super.buildSequenceFeature(gff, TYPE_COL,
+            "exonerate", set);
 
     return sf;
   }
diff --git a/src/jalview/io/gff/Gff3Helper.java b/src/jalview/io/gff/Gff3Helper.java
index 0273f9b..8af3933 100644
--- a/src/jalview/io/gff/Gff3Helper.java
+++ b/src/jalview/io/gff/Gff3Helper.java
@@ -361,9 +361,11 @@ public class Gff3Helper extends GffHelperBase
    */
   @Override
   protected SequenceFeature buildSequenceFeature(String[] gff,
+          int typeColumn, String group,
           Map<String, List<String>> attributes)
   {
-    SequenceFeature sf = super.buildSequenceFeature(gff, attributes);
+    SequenceFeature sf = super.buildSequenceFeature(gff, typeColumn, group,
+            attributes);
     String desc = getDescription(sf, attributes);
     if (desc != null)
     {
diff --git a/src/jalview/io/gff/GffHelperBase.java b/src/jalview/io/gff/GffHelperBase.java
index 48c33e5..41f141b 100644
--- a/src/jalview/io/gff/GffHelperBase.java
+++ b/src/jalview/io/gff/GffHelperBase.java
@@ -337,6 +337,19 @@ 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 +368,8 @@ 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]);
 
diff --git a/src/jalview/io/gff/InterProScanHelper.java b/src/jalview/io/gff/InterProScanHelper.java
index e1334e1..0aa3b74 100644
--- a/src/jalview/io/gff/InterProScanHelper.java
+++ b/src/jalview/io/gff/InterProScanHelper.java
@@ -73,13 +73,19 @@ public class InterProScanHelper extends Gff3Helper
   }
 
   /**
- * 
- */
+   * An override that
+   * <ul>
+   * <li>uses Source (column 2) as feature type instead of the default column 3</li>
+   * <li>sets "InterProScan" as the feature group</li>
+   * <li>extracts "signature_desc" attribute as the feature description</li>
+   * </ul>
+   */
   @Override
   protected SequenceFeature buildSequenceFeature(String[] gff,
           Map<String, List<String>> attributes)
   {
-    SequenceFeature sf = super.buildSequenceFeature(gff, attributes);
+    SequenceFeature sf = super.buildSequenceFeature(gff, SOURCE_COL,
+            INTER_PRO_SCAN, attributes);
 
     /*
      * signature_desc is a more informative source of description
@@ -91,13 +97,6 @@ public class InterProScanHelper extends Gff3Helper
       sf.setDescription(description);
     }
 
-    /*
-     * Set sequence feature group as 'InterProScan', and type as the source
-     * database for this match (e.g. 'Pfam')
-     */
-    sf.setType(gff[SOURCE_COL]);
-    sf.setFeatureGroup(INTER_PRO_SCAN);
-
     return sf;
   }
 
-- 
1.7.10.2