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create method to test HMM model as string
[jalview.git]
/
test
/
jalview
/
gui
/
AlignViewportTest.java
diff --git
a/test/jalview/gui/AlignViewportTest.java
b/test/jalview/gui/AlignViewportTest.java
index
e6c16b7
..
4660842
100644
(file)
--- a/
test/jalview/gui/AlignViewportTest.java
+++ b/
test/jalview/gui/AlignViewportTest.java
@@
-160,7
+160,7
@@
public class AlignViewportTest
acf2.addMap(s1, s1, new MapList(new int[] { 1, 4 }, new int[] { 4, 1 },
1, 1));
acf2.addMap(s1, s1, new MapList(new int[] { 1, 4 }, new int[] { 4, 1 },
1, 1));
- List<AlignedCodonFrame> mappings = new ArrayList<AlignedCodonFrame>();
+ List<AlignedCodonFrame> mappings = new ArrayList<>();
mappings.add(acf1);
mappings.add(acf2);
af1.getViewport().getAlignment().setCodonFrames(mappings);
mappings.add(acf1);
mappings.add(acf2);
af1.getViewport().getAlignment().setCodonFrames(mappings);
@@
-217,11
+217,11
@@
public class AlignViewportTest
acf3.addMap(cs2, cs2, new MapList(new int[] { 1, 12 }, new int[] { 1,
12 }, 1, 1));
acf3.addMap(cs2, cs2, new MapList(new int[] { 1, 12 }, new int[] { 1,
12 }, 1, 1));
- List<AlignedCodonFrame> mappings1 = new ArrayList<AlignedCodonFrame>();
+ List<AlignedCodonFrame> mappings1 = new ArrayList<>();
mappings1.add(acf1);
af1.getViewport().getAlignment().setCodonFrames(mappings1);
mappings1.add(acf1);
af1.getViewport().getAlignment().setCodonFrames(mappings1);
- List<AlignedCodonFrame> mappings2 = new ArrayList<AlignedCodonFrame>();
+ List<AlignedCodonFrame> mappings2 = new ArrayList<>();
mappings2.add(acf2);
mappings2.add(acf3);
af2.getViewport().getAlignment().setCodonFrames(mappings2);
mappings2.add(acf2);
mappings2.add(acf3);
af2.getViewport().getAlignment().setCodonFrames(mappings2);
@@
-280,12
+280,12
@@
public class AlignViewportTest
acf3.addMap(cs2, cs2, new MapList(new int[] { 1, 12 }, new int[] { 1,
12 }, 1, 1));
acf3.addMap(cs2, cs2, new MapList(new int[] { 1, 12 }, new int[] { 1,
12 }, 1, 1));
- List<AlignedCodonFrame> mappings1 = new ArrayList<AlignedCodonFrame>();
+ List<AlignedCodonFrame> mappings1 = new ArrayList<>();
mappings1.add(acf1);
mappings1.add(acf2);
af1.getViewport().getAlignment().setCodonFrames(mappings1);
mappings1.add(acf1);
mappings1.add(acf2);
af1.getViewport().getAlignment().setCodonFrames(mappings1);
- List<AlignedCodonFrame> mappings2 = new ArrayList<AlignedCodonFrame>();
+ List<AlignedCodonFrame> mappings2 = new ArrayList<>();
mappings2.add(acf2);
mappings2.add(acf3);
af2.getViewport().getAlignment().setCodonFrames(mappings2);
mappings2.add(acf2);
mappings2.add(acf3);
af2.getViewport().getAlignment().setCodonFrames(mappings2);
@@
-389,7
+389,8
@@
public class AlignViewportTest
/**
* Verify that setting the selection group has the side-effect of setting the
/**
* Verify that setting the selection group has the side-effect of setting the
- * context on the group, unless it already has one
+ * context on the group, unless it already has one, but does not change
+ * whether the group is defined or not.
*/
@Test(groups = { "Functional" })
public void testSetSelectionGroup()
*/
@Test(groups = { "Functional" })
public void testSetSelectionGroup()
@@
-399,13
+400,21
@@
public class AlignViewportTest
AlignViewport av = af.getViewport();
SequenceGroup sg1 = new SequenceGroup();
SequenceGroup sg2 = new SequenceGroup();
AlignViewport av = af.getViewport();
SequenceGroup sg1 = new SequenceGroup();
SequenceGroup sg2 = new SequenceGroup();
+ SequenceGroup sg3 = new SequenceGroup();
av.setSelectionGroup(sg1);
assertSame(sg1.getContext(), av.getAlignment()); // context set
av.setSelectionGroup(sg1);
assertSame(sg1.getContext(), av.getAlignment()); // context set
+ assertFalse(sg1.isDefined()); // group not defined
- sg2.setContext(sg1);
+ sg2.setContext(sg1, false);
av.setSelectionGroup(sg2);
av.setSelectionGroup(sg2);
+ assertFalse(sg2.isDefined()); // unchanged
assertSame(sg2.getContext(), sg1); // unchanged
assertSame(sg2.getContext(), sg1); // unchanged
+
+ // create a defined group
+ sg3.setContext(av.getAlignment(), true);
+ av.setSelectionGroup(sg3);
+ assertTrue(sg3.isDefined()); // unchanged
}
/**
* Verify that setting/clearing SHOW_OCCUPANCY preference adds or omits occupancy row from viewport
}
/**
* Verify that setting/clearing SHOW_OCCUPANCY preference adds or omits occupancy row from viewport