JAL-1350 cloned method and tested equivalence for using column selection to subdivide...

[jalview.git] / test / jalview / analysis / GroupingTest.java

diff --git a/test/jalview/analysis/GroupingTest.java b/test/jalview/analysis/GroupingTest.java
new file mode 100644 (file)
index 0000000..61bd480
--- /dev/null
+++ b/test/jalview/analysis/GroupingTest.java
@@ -0,0 +1,89 @@
+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
+  }
+
+}