Merge branch 'develop' into trialMerge

[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..825af24 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;
@@ -268,19 +268,20 @@ 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
      */
-    List<AlignedCodonFrame> mappings = af.getViewport().getAlignment()
-            .getDataset().getCodonFrames();
+    List<AlignedCodonFrame> mappings = af
+            .getViewport().getAlignment().getDataset().getCodonFrames();
     assertEquals(2, mappings.size());
     Iterator<AlignedCodonFrame> iter = mappings.iterator();
-
+  
     // first mapping is to dummy sequence
     AlignedCodonFrame mapping = iter.next();
     Mapping[] mapList = mapping.getProtMappings();
@@ -291,7 +292,7 @@ public class ExonerateHelperTest
     // 143 in protein should map to codon [11270, 11269, 11268] in dna
     int[] mappedRegion = mapList[0].getMap().locateInFrom(143, 143);
     assertArrayEquals(new int[] { 11270, 11268 }, mappedRegion);
-
+  
     // second mapping is to a sequence in the alignment
     mapping = iter.next();
     mapList = mapping.getProtMappings();
@@ -300,23 +301,23 @@ public class ExonerateHelperTest
             .findName("DDB_G0280897");
     assertSame(proteinSeq.getDatasetSequence(), mapList[0].getTo());
     assertEquals(1, mapping.getdnaToProt().length);
-
+  
     // 143 in protein should map to codon [11270, 11269, 11268] in dna
     mappedRegion = mapList[0].getMap().locateInFrom(143, 143);
     assertArrayEquals(new int[] { 11270, 11268 }, mappedRegion);
-
+  
     // 182 in protein should map to codon [11153, 11152, 11151] in dna
     mappedRegion = mapList[0].getMap().locateInFrom(182, 182);
     assertArrayEquals(new int[] { 11153, 11151 }, mappedRegion);
-
+  
     // and the reverse mapping:
     mappedRegion = mapList[0].getMap().locateInTo(11151, 11153);
     assertArrayEquals(new int[] { 182, 182 }, mappedRegion);
-
+  
     // 11150 in dna should _not_ map to protein
     mappedRegion = mapList[0].getMap().locateInTo(11150, 11150);
     assertNull(mappedRegion);
-
+  
     // similarly 183 in protein should _not_ map to dna
     mappedRegion = mapList[0].getMap().locateInFrom(183, 183);
     assertNull(mappedRegion);