import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
import java.util.Arrays;
import org.testng.AssertJUnit;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class GroupingTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
Sequence s1 = new Sequence("s1", "AAAADDDDEEEE");
Sequence s2 = new Sequence("s2", "AAAADDDDEEEE");
Sequence s5 = new Sequence("s5", "AAAADDEDTTEE");
- SequenceGroup sg_12 = new SequenceGroup(Arrays.asList(new SequenceI[] {
- s1, s2 }), "Group1", null, false, false, false, 0, 5);
+ SequenceGroup sg_12 = new SequenceGroup(
+ Arrays.asList(new SequenceI[]
+ { s1, s2 }), "Group1", null, false, false, false, 0, 5);
- SequenceGroup sg_345 = new SequenceGroup(Arrays.asList(new SequenceI[] {
- s3, s4, s5 }), "Group2", null, false, false, false, 0, 5);
+ SequenceGroup sg_345 = new SequenceGroup(
+ Arrays.asList(new SequenceI[]
+ { s3, s4, s5 }), "Group2", null, false, false, false, 0, 5);
AlignmentI alignment = new Alignment(
- new SequenceI[] { s1, s2, s3, s4, s5 });
+ new SequenceI[]
+ { s1, s2, s3, s4, s5 });
/*
* test for the case where column selections are not added in
}
SequenceGroup[] seqgroupsString = Grouping.makeGroupsFrom(
alignment.getSequencesArray(), str,
- Arrays.asList(new SequenceGroup[] { sg_12, sg_345 }));
+ Arrays.asList(new SequenceGroup[]
+ { sg_12, sg_345 }));
ColumnSelection cs = new ColumnSelection();
for (int p : positions)
}
SequenceGroup[] seqgroupsColSel = Grouping.makeGroupsFromCols(
alignment.getSequencesArray(), cs,
- Arrays.asList(new SequenceGroup[] { sg_12, sg_345 }));
- AssertJUnit
- .assertEquals(seqgroupsString.length, seqgroupsColSel.length);
+ Arrays.asList(new SequenceGroup[]
+ { sg_12, sg_345 }));
+ AssertJUnit.assertEquals(seqgroupsString.length,
+ seqgroupsColSel.length);
for (int p = 0; p < seqgroupsString.length; p++)
{
AssertJUnit.assertEquals(seqgroupsString[p].getName(),