JAL-4124 comment out incomplete test bits.. for now

[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 e770a7b..49f574b 100644 (file)
--- a/test/jalview/io/gff/ExonerateHelperTest.java
+++ b/test/jalview/io/gff/ExonerateHelperTest.java
@@ -36,8 +36,8 @@ 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;
@@ -62,9 +62,8 @@ public class ExonerateHelperTest
   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"));
 
@@ -117,11 +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));
   }
 
   /**
@@ -160,11 +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));
   }
 
   /**
@@ -206,11 +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));
   }
 
   /**
@@ -252,11 +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));
   }
 
   /**
@@ -268,10 +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