Merge branch 'develop' into trialMerge

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

diff --git a/test/jalview/io/StockholmFileTest.java b/test/jalview/io/StockholmFileTest.java
index 035f484..d0561b0 100644 (file)
--- a/test/jalview/io/StockholmFileTest.java
+++ b/test/jalview/io/StockholmFileTest.java
@@ -47,15 +47,15 @@ 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())
     {
@@ -72,7 +72,7 @@ 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);
   }
 
   /**
@@ -86,7 +86,7 @@ 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);
@@ -95,8 +95,8 @@ 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);
 
@@ -110,11 +110,11 @@ 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(