JAL-3847 Some attempts to fix a few eclipse import problems

[jalview.git] / test / jalview / io / gff / ExonerateHelperTest.java

diff --git a/test/jalview/io/gff/ExonerateHelperTest.java b/test/jalview/io/gff/ExonerateHelperTest.java
index dbacceb..49f574b 100644 (file)
--- a/test/jalview/io/gff/ExonerateHelperTest.java
+++ b/test/jalview/io/gff/ExonerateHelperTest.java
@@ -35,8 +35,9 @@ import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceDummy;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
+import jalview.gui.JvOptionPane;
+import jalview.io.DataSourceType;
 import jalview.io.FileLoader;
-import jalview.io.FormatAdapter;
 
 import java.io.IOException;
 import java.util.ArrayList;
@@ -44,17 +45,25 @@ import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 
+import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
 public class ExonerateHelperTest
 {
+
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   @Test(groups = "Functional")
   public void testGetMappingType()
   {
     // protein-to-dna:
-    assertSame(MappingType.PeptideToNucleotide,
-            ExonerateHelper
-                    .getMappingType("exonerate:protein2genome:local"));
+    assertSame(MappingType.PeptideToNucleotide, ExonerateHelper
+            .getMappingType("exonerate:protein2genome:local"));
     assertSame(MappingType.PeptideToNucleotide,
             ExonerateHelper.getMappingType("exonerate:protein2dna:local"));
 
@@ -107,11 +116,11 @@ public class ExonerateHelperTest
     assertSame(newseqs.get(0), mapping.getdnaSeqs()[0]);
     assertEquals(1, mapping.getdnaToProt().length);
     assertEquals(1, mapping.getdnaToProt()[0].getFromRanges().size());
-    assertArrayEquals(new int[] { 400, 423 }, mapping.getdnaToProt()[0]
-            .getFromRanges().get(0));
+    assertArrayEquals(new int[] { 400, 423 },
+            mapping.getdnaToProt()[0].getFromRanges().get(0));
     assertEquals(1, mapping.getdnaToProt()[0].getToRanges().size());
-    assertArrayEquals(new int[] { 3, 10 }, mapping.getdnaToProt()[0]
-            .getToRanges().get(0));
+    assertArrayEquals(new int[] { 3, 10 },
+            mapping.getdnaToProt()[0].getToRanges().get(0));
   }
 
   /**
@@ -150,11 +159,11 @@ public class ExonerateHelperTest
     assertSame(newseqs.get(0), mapping.getdnaSeqs()[0]);
     assertEquals(1, mapping.getdnaToProt().length);
     assertEquals(1, mapping.getdnaToProt()[0].getFromRanges().size());
-    assertArrayEquals(new int[] { 400, 377 }, mapping.getdnaToProt()[0]
-            .getFromRanges().get(0));
+    assertArrayEquals(new int[] { 400, 377 },
+            mapping.getdnaToProt()[0].getFromRanges().get(0));
     assertEquals(1, mapping.getdnaToProt()[0].getToRanges().size());
-    assertArrayEquals(new int[] { 3, 10 }, mapping.getdnaToProt()[0]
-            .getToRanges().get(0));
+    assertArrayEquals(new int[] { 3, 10 },
+            mapping.getdnaToProt()[0].getToRanges().get(0));
   }
 
   /**
@@ -196,11 +205,11 @@ public class ExonerateHelperTest
     assertEquals(1, mapping.getdnaSeqs().length);
     assertEquals(1, mapping.getdnaToProt().length);
     assertEquals(1, mapping.getdnaToProt()[0].getFromRanges().size());
-    assertArrayEquals(new int[] { 400, 423 }, mapping.getdnaToProt()[0]
-            .getFromRanges().get(0));
+    assertArrayEquals(new int[] { 400, 423 },
+            mapping.getdnaToProt()[0].getFromRanges().get(0));
     assertEquals(1, mapping.getdnaToProt()[0].getToRanges().size());
-    assertArrayEquals(new int[] { 3, 10 }, mapping.getdnaToProt()[0]
-            .getToRanges().get(0));
+    assertArrayEquals(new int[] { 3, 10 },
+            mapping.getdnaToProt()[0].getToRanges().get(0));
   }
 
   /**
@@ -242,11 +251,11 @@ public class ExonerateHelperTest
     assertEquals(1, mapping.getdnaSeqs().length);
     assertEquals(1, mapping.getdnaToProt().length);
     assertEquals(1, mapping.getdnaToProt()[0].getFromRanges().size());
-    assertArrayEquals(new int[] { 400, 377 }, mapping.getdnaToProt()[0]
-            .getFromRanges().get(0));
+    assertArrayEquals(new int[] { 400, 377 },
+            mapping.getdnaToProt()[0].getFromRanges().get(0));
     assertEquals(1, mapping.getdnaToProt()[0].getToRanges().size());
-    assertArrayEquals(new int[] { 3, 10 }, mapping.getdnaToProt()[0]
-            .getToRanges().get(0));
+    assertArrayEquals(new int[] { 3, 10 },
+            mapping.getdnaToProt()[0].getToRanges().get(0));
   }
 
   /**
@@ -258,10 +267,10 @@ public class ExonerateHelperTest
   {
     FileLoader loader = new FileLoader(false);
     AlignFrame af = loader.LoadFileWaitTillLoaded(
-            "examples/testdata/exonerateseqs.fa", FormatAdapter.FILE);
+            "examples/testdata/exonerateseqs.fa", DataSourceType.FILE);
 
     af.loadJalviewDataFile("examples/testdata/exonerateoutput.gff",
-            FormatAdapter.FILE, null, null);
+            DataSourceType.FILE, null, null);
 
     /*
      * verify one mapping to a dummy sequence, one to a real one