git://source.jalview.org / jalview.git / blobdiff
? search:
summary | shortlog | log | commit | commitdiff | tree
raw | inline | side by side
Merge branch 'features/JAL-1956_featureStyles' into merge_JAL-1956
[jalview.git] / test / jalview / io / FeaturesFileTest.java
diff --git a/test/jalview/io/FeaturesFileTest.java b/test/jalview/io/FeaturesFileTest.java
index 56305da..2f5d0c5 100644 (file)
--- a/test/jalview/io/FeaturesFileTest.java
+++ b/test/jalview/io/FeaturesFileTest.java
@@ -75,53 +75,63 @@ 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.sanger.ac.uk/family/PF00111",
-            sf.links.get(0).toString());
+    assertEquals("Pfam 8_8|http://pfam.xfam.org/family/PF00111",
+            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&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);
@@ -388,7 +398,7 @@ public class FeaturesFileTest
             + "STARTGROUP\tuniprot\n"
             + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
             + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\n"
-            + "<html>Pfam domain<a href=\"http://pfam.sanger.ac.uk/family/PF00111\">Pfam_3_4</a></html>\tFER_CAPAA\t-1\t20\t20\tPfam\n"
+            + "<html>Pfam domain<a href=\"http://pfam.xfam.org/family/PF00111\">Pfam_3_4</a></html>\tFER_CAPAA\t-1\t20\t20\tPfam\n"
             + "ENDGROUP\tuniprot\n";
     FeaturesFile featuresFile = new FeaturesFile(features,
             FormatAdapter.PASTE);
@@ -438,7 +448,7 @@ public class FeaturesFileTest
             + "\nSTARTGROUP\tuniprot\n"
             + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
             + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
-            + "<html>Pfam domain<a href=\"http://pfam.sanger.ac.uk/family/PF00111\">Pfam_3_4</a></html>\tFER_CAPAA\t-1\t20\t20\tPfam\t0.0\n"
+            + "<html>Pfam domain<a href=\"http://pfam.xfam.org/family/PF00111\">Pfam_3_4</a></html>\tFER_CAPAA\t-1\t20\t20\tPfam\t0.0\n"
             + "ENDGROUP\tuniprot\n";
     assertEquals(expected, exported);
   }