From c9439f328825bc3061835f39c81a79920f50ef32 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Mon, 30 May 2016 14:59:35 +0100
Subject: [PATCH] JAL-1670 JAL-2018 updated unit test for added example
 feature

---
 test/jalview/io/FeaturesFileTest.java |   28 +++++++++++++++++++---------
 1 file changed, 19 insertions(+), 9 deletions(-)

diff --git a/test/jalview/io/FeaturesFileTest.java b/test/jalview/io/FeaturesFileTest.java
index 73d8826..29bd567 100644
--- a/test/jalview/io/FeaturesFileTest.java
+++ b/test/jalview/io/FeaturesFileTest.java
@@ -76,53 +76,63 @@ public class FeaturesFileTest
      */
     SequenceFeature[] sfs = al.getSequenceAt(0).getDatasetSequence()
             .getSequenceFeatures(); // FER_CAPAA
-    assertEquals(7, sfs.length);
+    assertEquals(8, sfs.length);
     SequenceFeature sf = sfs[0];
+    assertEquals("Pfam family%LINK%", sf.description);
+    assertEquals(0, sf.begin);
+    assertEquals(0, sf.end);
+    assertEquals("uniprot", sf.featureGroup);
+    assertEquals("Pfam", sf.type);
+    assertEquals(1, sf.links.size());
+    assertEquals("Pfam family|http://pfam.xfam.org/family/PF00111",
+            sf.links.get(0));
+
+    sf = sfs[1];
     assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
     assertEquals(39, sf.begin);
     assertEquals(39, sf.end);
     assertEquals("uniprot", sf.featureGroup);
     assertEquals("METAL", sf.type);
-    sf = sfs[1];
+    sf = sfs[2];
     assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
     assertEquals(44, sf.begin);
     assertEquals(44, sf.end);
     assertEquals("uniprot", sf.featureGroup);
     assertEquals("METAL", sf.type);
-    sf = sfs[2];
+    sf = sfs[3];
     assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
     assertEquals(47, sf.begin);
     assertEquals(47, sf.end);
     assertEquals("uniprot", sf.featureGroup);
     assertEquals("METAL", sf.type);
-    sf = sfs[3];
+    sf = sfs[4];
     assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
     assertEquals(77, sf.begin);
     assertEquals(77, sf.end);
     assertEquals("uniprot", sf.featureGroup);
     assertEquals("METAL", sf.type);
-    sf = sfs[4];
+    sf = sfs[5];
     assertEquals("Fer2 Status: True Positive Pfam 8_8%LINK%",
             sf.description);
     assertEquals("Pfam 8_8|http://pfam.xfam.org/family/PF00111",
-            sf.links.get(0).toString());
+            sf.links.get(0));
     assertEquals(8, sf.begin);
     assertEquals(83, sf.end);
     assertEquals("uniprot", sf.featureGroup);
     assertEquals("Pfam", sf.type);
-    sf = sfs[5];
+    sf = sfs[6];
     assertEquals("Ferredoxin_fold Status: True Positive ", sf.description);
     assertEquals(3, sf.begin);
     assertEquals(93, sf.end);
     assertEquals("uniprot", sf.featureGroup);
     assertEquals("Cath", sf.type);
-    sf = sfs[6];
+    sf = sfs[7];
     assertEquals(
             "High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 89_8%LINK%",
             sf.description);
     assertEquals(
             "PHOSPHORYLATION (T) 89_8|http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P83527&amp;service=NetPhos-2.0",
-            sf.links.get(0).toString());
+            sf.links.get(0));
     assertEquals(89, sf.begin);
     assertEquals(89, sf.end);
     assertEquals("netphos", sf.featureGroup);
-- 
1.7.10.2