JAL-2089 patch broken merge to master for Release 2.10.0b1

[jalview.git] / test / jalview / io / FeaturesFileTest.java

diff --git a/test/jalview/io/FeaturesFileTest.java b/test/jalview/io/FeaturesFileTest.java
index 56305da..602ce9f 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);
@@ -143,7 +153,8 @@ public class FeaturesFileTest
     Map<String, FeatureColourI> colours = af.getFeatureRenderer()
             .getFeatureColours();
     // GFF2 uses space as name/value separator in column 9
-    String gffData = "METAL\tcc9900\n" + "GFF\n"
+    String gffData = "METAL\tcc9900\n"
+            + "GFF\n"
             + "FER_CAPAA\tuniprot\tMETAL\t44\t45\t4.0\t.\t.\tNote Iron-sulfur; Note 2Fe-2S\n"
             + "FER1_SOLLC\tuniprot\tPfam\t55\t130\t2.0\t.\t.";
     FeaturesFile featuresFile = new FeaturesFile(gffData,
@@ -294,7 +305,7 @@ public class FeaturesFileTest
   {
     assertEquals("no sequences extracted from GFF3 file", 2,
             dataset.getHeight());
-  
+
     SequenceI seq1 = dataset.findName("seq1");
     SequenceI seq2 = dataset.findName("seq2");
     assertNotNull(seq1);
@@ -325,7 +336,7 @@ public class FeaturesFileTest
             "Expected at least one CDNA/Protein mapping for seq1",
             dataset.getCodonFrame(seq1) != null
                     && dataset.getCodonFrame(seq1).size() > 0);
-  
+
   }
 
   @Test(groups = { "Functional" })
@@ -342,9 +353,8 @@ public class FeaturesFileTest
   public void simpleGff3FileClass() throws IOException
   {
     AlignmentI dataset = new Alignment(new SequenceI[] {});
-    FeaturesFile ffile = new FeaturesFile(simpleGffFile,
-            FormatAdapter.FILE);
-  
+    FeaturesFile ffile = new FeaturesFile(simpleGffFile, FormatAdapter.FILE);
+
     boolean parseResult = ffile.parse(dataset, null, false, false);
     assertTrue("return result should be true", parseResult);
     checkDatasetfromSimpleGff3(dataset);
@@ -365,9 +375,8 @@ public class FeaturesFileTest
   public void simpleGff3RelaxedIdMatching() throws IOException
   {
     AlignmentI dataset = new Alignment(new SequenceI[] {});
-    FeaturesFile ffile = new FeaturesFile(simpleGffFile,
-            FormatAdapter.FILE);
-  
+    FeaturesFile ffile = new FeaturesFile(simpleGffFile, FormatAdapter.FILE);
+
     boolean parseResult = ffile.parse(dataset, null, false, true);
     assertTrue("return result (relaxedID matching) should be true",
             parseResult);
@@ -388,7 +397,7 @@ 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);
@@ -398,8 +407,7 @@ public class FeaturesFileTest
      * first with no features displayed
      */
     FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
-    Map<String, FeatureColourI> visible = fr
-            .getDisplayedFeatureCols();
+    Map<String, FeatureColourI> visible = fr.getDisplayedFeatureCols();
     String exported = featuresFile.printJalviewFormat(
             al.getSequencesArray(), visible);
     String expected = "No Features Visible";
@@ -438,7 +446,7 @@ 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);
   }