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Comments added
[jalview.git]
/
test
/
jalview
/
datamodel
/
AlignedCodonFrameTest.java
diff --git
a/test/jalview/datamodel/AlignedCodonFrameTest.java
b/test/jalview/datamodel/AlignedCodonFrameTest.java
index
e782cef
..
9694a3e
100644
(file)
--- a/
test/jalview/datamodel/AlignedCodonFrameTest.java
+++ b/
test/jalview/datamodel/AlignedCodonFrameTest.java
@@
-76,10
+76,16
@@
public class AlignedCodonFrameTest
final Sequence aseq2 = new Sequence("Seq2", "-LY-");
aseq2.createDatasetSequence();
final Sequence aseq2 = new Sequence("Seq2", "-LY-");
aseq2.createDatasetSequence();
+ /*
+ * First with no mappings
+ */
AlignedCodonFrame acf = new AlignedCodonFrame();
assertNull(acf.getMappedRegion(seq1, aseq1, 1));
AlignedCodonFrame acf = new AlignedCodonFrame();
assertNull(acf.getMappedRegion(seq1, aseq1, 1));
+ /*
+ * Set up the mappings for the exons (upper-case bases)
+ */
MapList map = new MapList(new int[]
{ 2, 4, 6, 6, 8, 9 }, new int[]
{ 1, 2 }, 3, 1);
MapList map = new MapList(new int[]
{ 2, 4, 6, 6, 8, 9 }, new int[]
{ 1, 2 }, 3, 1);
@@
-98,6
+104,9
@@
public class AlignedCodonFrameTest
assertEquals("[5, 5, 7, 8]",
Arrays.toString(acf.getMappedRegion(seq2, aseq2, 2)));
assertEquals("[5, 5, 7, 8]",
Arrays.toString(acf.getMappedRegion(seq2, aseq2, 2)));
+ /*
+ * No mapping from sequence 1 to sequence 2
+ */
assertNull(acf.getMappedRegion(seq1, aseq2, 1));
}
}
assertNull(acf.getMappedRegion(seq1, aseq2, 1));
}
}