X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FStockholmFileTest.java;h=4028913c7a30763d38a6e41adba6264e0884cb06;hb=7c9fbca0e2d9be5fd05e1c89f24f81d558bf6849;hp=b034fb0e5459d0316384b694c42fc25d6f6ec974;hpb=063142d5fe1679310fd6509ad78ef94c5b345f11;p=jalview.git

diff --git a/test/jalview/io/StockholmFileTest.java b/test/jalview/io/StockholmFileTest.java
index b034fb0..4028913 100644
--- a/test/jalview/io/StockholmFileTest.java
+++ b/test/jalview/io/StockholmFileTest.java
@@ -30,32 +30,41 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
 
 import java.io.File;
 import java.util.BitSet;
 import java.util.HashMap;
 import java.util.Map;
 
+import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
 public class StockholmFileTest
 {
 
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   static String PfamFile = "examples/PF00111_seed.stk",
           RfamFile = "examples/RF00031_folded.stk";
 
   @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 +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);
   }
 
   /**
@@ -86,7 +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);
@@ -95,26 +104,26 @@ 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);
 
       // make sure dataset is initialised ? not sure about this
       for (int i = 0; i < al.getSequencesArray().length; ++i)
       {
-        al.getSequenceAt(i).setDatasetSequence(al.getSequenceAt(i));
+        al.getSequenceAt(i).createDatasetSequence();
       }
       String outputfile = rf.formatSequences(ioformat, al, true);
       System.out.println("Output file in '" + ioformat + "':\n"
               + 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(
@@ -228,7 +237,7 @@ public class StockholmFileTest
     }
     assertEquals(
             "Generated and imported alignment have different annotation sets",
-            aa_new_size, aa_original_size);
+            aa_original_size, aa_new_size);
 
     // check sequences, annotation and features
     SequenceI[] seq_original = new SequenceI[al.getSequencesArray().length];
@@ -281,8 +290,7 @@ public class StockholmFileTest
 
             assertEquals("different number of features",
                     seq_original[i].getSequenceFeatures().length,
-                    seq_new[in]
-                    .getSequenceFeatures().length);
+                    seq_new[in].getSequenceFeatures().length);
 
             for (int feat = 0; feat < seq_original[i].getSequenceFeatures().length; feat++)
             {