X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fanalysis%2FAlignmentUtilsTests.java;h=bada3caab0b26c34685e1c37d13206e9ba2e17d8;hb=d387f0ee40a8e248ce08c97aca2e427aa75a40d8;hp=8a667b39c2842c29e29bdc8b594bc9d784fd8d16;hpb=5f4e1e4c330b045e9c8bce28ee132a0fca3834d8;p=jalview.git

diff --git a/test/jalview/analysis/AlignmentUtilsTests.java b/test/jalview/analysis/AlignmentUtilsTests.java
index 8a667b3..bada3ca 100644
--- a/test/jalview/analysis/AlignmentUtilsTests.java
+++ b/test/jalview/analysis/AlignmentUtilsTests.java
@@ -42,6 +42,9 @@ import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.gui.JvOptionPane;
 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;
@@ -79,14 +82,15 @@ 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)
       {
         /*
@@ -219,7 +223,7 @@ 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());
@@ -239,11 +243,11 @@ 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;
   }