X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FStockholmFileTest.java;h=4028913c7a30763d38a6e41adba6264e0884cb06;hb=483e7163b1fb8d4bcb9393014816c944befce328;hp=1c6a890840f6ec5bebc1b16f995a6faa94ab9c91;hpb=19424d4e1623bfcdcf30567f7a233fe81c4a9e4e;p=jalview.git

diff --git a/test/jalview/io/StockholmFileTest.java b/test/jalview/io/StockholmFileTest.java
index 1c6a890..4028913 100644
--- a/test/jalview/io/StockholmFileTest.java
+++ b/test/jalview/io/StockholmFileTest.java
@@ -56,15 +56,15 @@ public class StockholmFileTest
   @Test(groups = { "Functional" })
   public void pfamFileIO() throws Exception
   {
-    testFileIOwithFormat(new File(PfamFile), "STH", -1, 0);
+    testFileIOwithFormat(new File(PfamFile), FileFormat.Stockholm, -1, 0);
   }
 
   @Test(groups = { "Functional" })
   public void pfamFileDataExtraction() throws Exception
   {
     AppletFormatAdapter af = new AppletFormatAdapter();
-    AlignmentI al = af.readFile(PfamFile, af.FILE,
-            new IdentifyFile().identify(PfamFile, af.FILE));
+    AlignmentI al = af.readFile(PfamFile, DataSourceType.FILE,
+            new IdentifyFile().identify(PfamFile, DataSourceType.FILE));
     int numpdb = 0;
     for (SequenceI sq : al.getSequences())
     {
@@ -81,7 +81,7 @@ public class StockholmFileTest
   @Test(groups = { "Functional" })
   public void rfamFileIO() throws Exception
   {
-    testFileIOwithFormat(new File(RfamFile), "STH", 2, 1);
+    testFileIOwithFormat(new File(RfamFile), FileFormat.Stockholm, 2, 1);
   }
 
   /**
@@ -95,7 +95,7 @@ public class StockholmFileTest
    *          f
    */
 
-  public static void testFileIOwithFormat(File f, String ioformat,
+  public static void testFileIOwithFormat(File f, FileFormatI ioformat,
           int naliannot, int nminseqann)
   {
     System.out.println("Reading file: " + f);
@@ -104,8 +104,8 @@ public class StockholmFileTest
     {
       AppletFormatAdapter rf = new AppletFormatAdapter();
 
-      AlignmentI al = rf.readFile(ff, AppletFormatAdapter.FILE,
-              new IdentifyFile().identify(ff, AppletFormatAdapter.FILE));
+      AlignmentI al = rf.readFile(ff, DataSourceType.FILE,
+              new IdentifyFile().identify(ff, DataSourceType.FILE));
 
       assertNotNull("Couldn't read supplied alignment data.", al);
 
@@ -119,11 +119,11 @@ public class StockholmFileTest
               + outputfile + "\n<<EOF\n");
       // test for consistency in io
       AlignmentI al_input = new AppletFormatAdapter().readFile(outputfile,
-              AppletFormatAdapter.PASTE, ioformat);
+              DataSourceType.PASTE, ioformat);
       assertNotNull("Couldn't parse reimported alignment data.", al_input);
 
-      String identifyoutput = new IdentifyFile().identify(outputfile,
-              AppletFormatAdapter.PASTE);
+      FileFormatI identifyoutput = new IdentifyFile().identify(outputfile,
+              DataSourceType.PASTE);
       assertNotNull("Identify routine failed for outputformat " + ioformat,
               identifyoutput);
       assertTrue(