+package jalview.analysis;
+
+import static org.junit.Assert.fail;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+
+import org.junit.Assert;
+import org.junit.Test;
+
+public class GroupingTest
+{
+ Sequence s1 = new Sequence("s1", "AAAADDDDEEEE");
+
+ Sequence s2 = new Sequence("s2", "AAAADDDDEEEE");
+
+ Sequence s3 = new Sequence("s3", "ACAADDEDEEEE");
+
+ Sequence s4 = new Sequence("s4", "AAAADDEDEEEE");
+
+ Sequence s5 = new Sequence("s5", "AAAADDEDTTEE");
+
+ SequenceGroup sg1 = new SequenceGroup(Arrays.asList(new SequenceI[]
+ { s1, s2 }), "Group1", null, false, false, false, 0, 5);
+
+ SequenceGroup sg2 = 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 });
+
+ int[] positions = new int[]
+ { 1, 7, 9 };
+
+ @Test
+ public void testMakeGroupsWithBoth()
+ {
+ ArrayList<String> str = new ArrayList<String>();
+ for (SequenceI s : alignment.getSequences())
+ {
+ StringBuilder sb = new StringBuilder();
+ for (int p : positions)
+ {
+ sb.append(s.getCharAt(p));
+ }
+ str.add(sb.toString());
+ }
+ SequenceGroup[] seqgroupsString = Grouping.makeGroupsFrom(
+ alignment.getSequencesArray(),
+ str.toArray(new String[str.size()]),
+ Arrays.asList(new SequenceGroup[]
+ { sg1, sg2 }));
+ ColumnSelection cs = new ColumnSelection();
+ for (int p : positions)
+ {
+ cs.addElement(p);
+ }
+ SequenceGroup[] seqgroupsColSel = Grouping.makeGroupsFromCols(
+ alignment.getSequencesArray(), cs,
+ Arrays.asList(new SequenceGroup[]
+ { sg1, sg2 }));
+ Assert.assertEquals(seqgroupsString.length, seqgroupsColSel.length);
+ for (int p = 0; p < seqgroupsString.length; p++)
+ {
+ Assert.assertEquals(seqgroupsString[p].getName(),
+ seqgroupsColSel[p].getName());
+ Assert.assertArrayEquals(
+ seqgroupsString[p].getSequencesInOrder(alignment),
+ seqgroupsColSel[p].getSequencesInOrder(alignment));
+ if (seqgroupsString[p].getSequences().contains(s2))
+ {
+ Assert.assertTrue(seqgroupsString[p].getSize() == 2);
+ }
+ }
+ }
+
+ @Test
+ public void testMakeGroupsFromCols()
+ {
+ fail("Not yet implemented"); // TODO
+ }
+
+}