JAL-2344 handle null format, simplify JalviewFileChooser constructor

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

diff --git a/test/jalview/io/StockholmFileTest.java b/test/jalview/io/StockholmFileTest.java
index bdd311b..4028913 100644 (file)
--- a/test/jalview/io/StockholmFileTest.java
+++ b/test/jalview/io/StockholmFileTest.java
@@ -30,17 +30,26 @@ 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";
 
@@ -103,7 +112,7 @@ public class StockholmFileTest
       // 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"
@@ -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++)
             {