file format enum wip changes

[jalview.git] / test / jalview / analysis / AlignmentUtilsTests.java

diff --git a/test/jalview/analysis/AlignmentUtilsTests.java b/test/jalview/analysis/AlignmentUtilsTests.java
index 860d979..eccfe50 100644 (file)
--- a/test/jalview/analysis/AlignmentUtilsTests.java
+++ b/test/jalview/analysis/AlignmentUtilsTests.java
@@ -40,6 +40,9 @@ import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.io.AppletFormatAdapter;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
+import jalview.io.FileFormatI;
 import jalview.io.FormatAdapter;
 import jalview.util.MapList;
 import jalview.util.MappingUtils;
@@ -69,14 +72,15 @@ public class AlignmentUtilsTests
       SequenceI s1 = ts.deriveSequence().getSubSequence(i, i + 7);
       al.addSequence(s1);
     }
-    System.out.println(new AppletFormatAdapter().formatSequences("Clustal",
+    System.out.println(new AppletFormatAdapter().formatSequences(
+            FileFormat.Clustal,
             al, true));
     for (int flnk = -1; flnk < 25; flnk++)
     {
       AlignmentI exp = AlignmentUtils.expandContext(al, flnk);
       System.out.println("\nFlank size: " + flnk);
       System.out.println(new AppletFormatAdapter().formatSequences(
-              "Clustal", exp, true));
+              FileFormat.Clustal, exp, true));
       if (flnk == -1)
       {
         /*
@@ -209,7 +213,7 @@ public class AlignmentUtilsTests
   {
     final String data = ">Seq1Name\nKQYL\n" + ">Seq2Name\nRFPW\n"
             + ">Seq1Name\nABCD\n";
-    AlignmentI al = loadAlignment(data, "FASTA");
+    AlignmentI al = loadAlignment(data, FileFormat.Fasta);
     Map<String, List<SequenceI>> map = AlignmentUtils
             .getSequencesByName(al);
     assertEquals(2, map.keySet().size());
@@ -229,11 +233,11 @@ public class AlignmentUtilsTests
    * @return
    * @throws IOException
    */
-  protected AlignmentI loadAlignment(final String data, String format)
+  protected AlignmentI loadAlignment(final String data, FileFormatI format)
           throws IOException
   {
     AlignmentI a = new FormatAdapter().readFile(data,
-            AppletFormatAdapter.PASTE, format);
+            DataSourceType.PASTE, format);
     a.setDataset(null);
     return a;
   }
@@ -1968,60 +1972,65 @@ public class AlignmentUtilsTests
     SequenceFeature sf = sfs[0];
     assertEquals(1, sf.getBegin());
     assertEquals(1, sf.getEnd());
-    assertEquals("K->E", sf.getDescription());
+    assertEquals("p.Lys1Glu", sf.getDescription());
     assertEquals("var1.125A>G", sf.getValue("ID"));
     assertNull(sf.getValue("clinical_significance"));
     assertEquals("ID=var1.125A>G", sf.getAttributes());
     assertEquals(1, sf.links.size());
     // link to variation is urlencoded
     assertEquals(
-            "K->E var1.125A>G|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var1.125A%3EG",
+            "p.Lys1Glu var1.125A>G|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var1.125A%3EG",
             sf.links.get(0));
+    assertEquals("Jalview", sf.getFeatureGroup());
     sf = sfs[1];
     assertEquals(1, sf.getBegin());
     assertEquals(1, sf.getEnd());
-    assertEquals("K->Q", sf.getDescription());
+    assertEquals("p.Lys1Gln", sf.getDescription());
     assertEquals("var2", sf.getValue("ID"));
     assertEquals("Dodgy", sf.getValue("clinical_significance"));
     assertEquals("ID=var2;clinical_significance=Dodgy", sf.getAttributes());
     assertEquals(1, sf.links.size());
     assertEquals(
-            "K->Q var2|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var2",
+            "p.Lys1Gln var2|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var2",
             sf.links.get(0));
+    assertEquals("Jalview", sf.getFeatureGroup());
     sf = sfs[2];
     assertEquals(1, sf.getBegin());
     assertEquals(1, sf.getEnd());
-    assertEquals("K->N", sf.getDescription());
+    assertEquals("p.Lys1Asn", sf.getDescription());
     assertEquals("var4", sf.getValue("ID"));
     assertEquals("Benign", sf.getValue("clinical_significance"));
     assertEquals("ID=var4;clinical_significance=Benign", sf.getAttributes());
     assertEquals(1, sf.links.size());
     assertEquals(
-            "K->N var4|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var4",
+            "p.Lys1Asn var4|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var4",
             sf.links.get(0));
+    assertEquals("Jalview", sf.getFeatureGroup());
     sf = sfs[3];
     assertEquals(3, sf.getBegin());
     assertEquals(3, sf.getEnd());
-    assertEquals("P->H", sf.getDescription());
+    assertEquals("p.Pro3His", sf.getDescription());
     assertEquals("var6", sf.getValue("ID"));
     assertEquals("Good", sf.getValue("clinical_significance"));
     assertEquals("ID=var6;clinical_significance=Good", sf.getAttributes());
     assertEquals(1, sf.links.size());
     assertEquals(
-            "P->H var6|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var6",
+            "p.Pro3His var6|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var6",
             sf.links.get(0));
     // var5 generates two distinct protein variant features
+    assertEquals("Jalview", sf.getFeatureGroup());
     sf = sfs[4];
     assertEquals(3, sf.getBegin());
     assertEquals(3, sf.getEnd());
-    assertEquals("P->R", sf.getDescription());
+    assertEquals("p.Pro3Arg", sf.getDescription());
     assertEquals("var6", sf.getValue("ID"));
     assertEquals("Good", sf.getValue("clinical_significance"));
     assertEquals("ID=var6;clinical_significance=Good", sf.getAttributes());
     assertEquals(1, sf.links.size());
     assertEquals(
-            "P->R var6|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var6",
+            "p.Pro3Arg var6|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var6",
             sf.links.get(0));
+    assertEquals("Jalview", sf.getFeatureGroup());
   }
 
   /**