Merge branch 'develop' into features/JAL-2094_colourInterface

[jalview.git] / test / jalview / controller / AlignViewControllerTest.java

diff --git a/test/jalview/controller/AlignViewControllerTest.java b/test/jalview/controller/AlignViewControllerTest.java
new file mode 100644 (file)
index 0000000..3eefada
--- /dev/null
+++ b/test/jalview/controller/AlignViewControllerTest.java
@@ -0,0 +1,100 @@
+package jalview.controller;
+
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertTrue;
+
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+
+import java.util.BitSet;
+
+import org.testng.annotations.Test;
+
+public class AlignViewControllerTest
+{
+  @Test(groups = "Functional")
+  public void testFindColumnsWithFeature()
+  {
+    SequenceI seq1 = new Sequence("seq1", "aMMMaaaaaaaaaaaaaaaa");
+    SequenceI seq2 = new Sequence("seq2", "aaaMMMMMMMaaaaaaaaaa");
+    SequenceI seq3 = new Sequence("seq3", "aaaaaaaaaaMMMMMaaaaa");
+    SequenceI seq4 = new Sequence("seq3", "aaaaaaaaaaaaaaaaaaaa");
+
+    /*
+     * features start/end are base 1
+     */
+    seq1.addSequenceFeature(new SequenceFeature("Metal", "desc", 2, 4, 0f,
+            null));
+    seq1.addSequenceFeature(new SequenceFeature("Helix", "desc", 1, 15, 0f,
+            null));
+    seq2.addSequenceFeature(new SequenceFeature("Metal", "desc", 4, 10, 0f,
+            null));
+    seq3.addSequenceFeature(new SequenceFeature("Metal", "desc", 11, 15,
+            0f, null));
+
+    /*
+     * select the first three columns --> Metal in seq1 2-3
+     */
+    SequenceGroup sg = new SequenceGroup();
+    sg.setStartRes(0); // base 0
+    sg.setEndRes(2);
+    sg.addSequence(seq1, false);
+    sg.addSequence(seq2, false);
+    sg.addSequence(seq3, false);
+    sg.addSequence(seq4, false);
+
+    BitSet bs = new BitSet();
+    int seqCount = AlignViewController.findColumnsWithFeature("Metal", sg,
+            bs);
+    assertEquals(1, seqCount);
+    assertEquals(2, bs.cardinality());
+    assertTrue(bs.get(1));
+    assertTrue(bs.get(2));
+    
+    /*
+     * select the first four columns: Metal in seq1 2:4, seq2 4:4
+     */
+    sg.setEndRes(3);
+    bs.clear();
+    seqCount = AlignViewController.findColumnsWithFeature("Metal", sg,
+            bs);
+    assertEquals(2, seqCount);
+    assertEquals(3, bs.cardinality());
+    assertTrue(bs.get(1));
+    assertTrue(bs.get(2));
+    assertTrue(bs.get(3));
+
+    /*
+     * select column 11: Metal in seq3 only
+     */
+    sg.setStartRes(10);
+    sg.setEndRes(10);
+    bs.clear();
+    seqCount = AlignViewController.findColumnsWithFeature("Metal", sg, bs);
+    assertEquals(1, seqCount);
+    assertEquals(1, bs.cardinality());
+    assertTrue(bs.get(10));
+
+    /*
+     * select columns 16-20: no Metal feature
+     */
+    sg.setStartRes(15);
+    sg.setEndRes(19);
+    bs.clear();
+    seqCount = AlignViewController.findColumnsWithFeature("Metal", sg, bs);
+    assertEquals(0, seqCount);
+    assertEquals(0, bs.cardinality());
+
+    /*
+     * look for a feature that isn't there
+     */
+    sg.setStartRes(0);
+    sg.setEndRes(19);
+    bs.clear();
+    seqCount = AlignViewController.findColumnsWithFeature("Pfam", sg, bs);
+    assertEquals(0, seqCount);
+    assertEquals(0, bs.cardinality());
+  }
+}