From 470bdf4991a8cb9d47f2bc572a2bc13b09f7565a Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Wed, 7 Oct 2015 14:54:05 +0100
Subject: [PATCH] JAL-1499 test code refactor / tidy

---
 test/jalview/io/MegaFileTest.java |   66 +++++++++++++++++--------------------
 1 file changed, 30 insertions(+), 36 deletions(-)

diff --git a/test/jalview/io/MegaFileTest.java b/test/jalview/io/MegaFileTest.java
index 1f8e4d6..881c47b 100644
--- a/test/jalview/io/MegaFileTest.java
+++ b/test/jalview/io/MegaFileTest.java
@@ -666,42 +666,36 @@ public class MegaFileTest
       // (Domain before Gene when they end together)
       assertEquals(9, sfs.length);
       // TODO settle which way round type/description go!
-      assertEquals("Exon1 (Adh Coding)", sfs[0].type);
-      assertEquals("Domain", sfs[0].description);
-      assertEquals(7, sfs[0].begin);
-      assertEquals(12, sfs[0].end);
-      assertEquals("Intron1 (Adh Noncoding)", sfs[1].type);
-      assertEquals("Domain", sfs[1].description);
-      assertEquals(13, sfs[1].begin);
-      assertEquals(18, sfs[1].end);
-      assertEquals("Exon2 (Adh Coding)", sfs[2].type);
-      assertEquals("Domain", sfs[2].description);
-      assertEquals(19, sfs[2].begin);
-      assertEquals(24, sfs[2].end);
-      assertEquals("Adh", sfs[3].type);
-      assertEquals("Gene", sfs[3].description);
-      assertEquals(7, sfs[3].begin);
-      assertEquals(24, sfs[3].end);
-      assertEquals("Intron1 (Opsin Noncoding)", sfs[4].type);
-      assertEquals("Domain", sfs[4].description);
-      assertEquals(25, sfs[4].begin);
-      assertEquals(30, sfs[4].end);
-      assertEquals("Opsin", sfs[5].type);
-      assertEquals("Gene", sfs[5].description);
-      assertEquals(25, sfs[5].begin);
-      assertEquals(30, sfs[5].end);
-      assertEquals("Exon1 (MEF2A Coding)", sfs[6].type);
-      assertEquals("Domain", sfs[6].description);
-      assertEquals(31, sfs[6].begin);
-      assertEquals(36, sfs[6].end);
-      assertEquals("MEF2A", sfs[7].type);
-      assertEquals("Gene", sfs[7].description);
-      assertEquals(31, sfs[7].begin);
-      assertEquals(36, sfs[7].end);
-      assertEquals("BindingSite", sfs[8].type);
-      assertEquals("Domain", sfs[8].description);
-      assertEquals(37, sfs[8].begin);
-      assertEquals(42, sfs[8].end);
+      verifySequenceFeature(sfs[0], "Exon1 (Adh Coding)", "Domain", 7, 12);
+      verifySequenceFeature(sfs[1], "Intron1 (Adh Noncoding)", "Domain",
+              13, 18);
+      verifySequenceFeature(sfs[2], "Exon2 (Adh Coding)", "Domain", 19, 24);
+      verifySequenceFeature(sfs[3], "Adh", "Gene", 7, 24);
+      verifySequenceFeature(sfs[4], "Intron1 (Opsin Noncoding)", "Domain",
+              25, 30);
+      verifySequenceFeature(sfs[5], "Opsin", "Gene", 25, 30);
+      verifySequenceFeature(sfs[6], "Exon1 (MEF2A Coding)", "Domain", 31,
+              36);
+      verifySequenceFeature(sfs[7], "MEF2A", "Gene", 31, 36);
+      verifySequenceFeature(sfs[8], "BindingSite", "Domain", 37, 42);
     }
   }
+
+  /**
+   * Helper method to assert properties of a SequenceFeature
+   * 
+   * @param sf
+   * @param description
+   * @param type
+   * @param begin
+   * @param end
+   */
+  protected void verifySequenceFeature(SequenceFeature sf,
+          String description, String type, int begin, int end)
+  {
+    assertEquals(description, sf.type);
+    assertEquals(type, sf.description);
+    assertEquals(begin, sf.begin);
+    assertEquals(end, sf.end);
+  }
 }
-- 
1.7.10.2