JAL-2446 FeatureStore with NCList - work in progress

[jalview.git] / test / jalview / datamodel / features / NCListTest.java

diff --git a/test/jalview/datamodel/features/NCListTest.java b/test/jalview/datamodel/features/NCListTest.java
new file mode 100644 (file)
index 0000000..38227c1
--- /dev/null
+++ b/test/jalview/datamodel/features/NCListTest.java
@@ -0,0 +1,158 @@
+package jalview.datamodel.features;
+
+import static org.testng.Assert.assertEquals;
+
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+
+import org.testng.annotations.Test;
+
+public class NCListTest
+{
+  class Range implements ContiguousI
+  {
+    int start;
+
+    int end;
+
+    @Override
+    public int getBegin()
+    {
+      return start;
+    }
+
+    @Override
+    public int getEnd()
+    {
+      return end;
+    }
+
+    Range(int i, int j)
+    {
+      start = i;
+      end = j;
+    }
+
+    @Override
+    public String toString() {
+      return String.valueOf(start) + "-" + String.valueOf(end);
+    }
+  }
+
+  /**
+   * A basic sanity test of the constructor
+   */
+  @Test(groups = "Functional")
+  public void testConstructor()
+  {
+    List<Range> ranges = new ArrayList<Range>();
+    ranges.add(new Range(20, 20));
+    ranges.add(new Range(10, 20));
+    ranges.add(new Range(15, 30));
+    ranges.add(new Range(10, 30));
+    ranges.add(new Range(11, 19));
+    ranges.add(new Range(10, 20));
+    ranges.add(new Range(1, 100));
+
+    NCList<Range> ncl = new NCList<Range>(ranges);
+    String expected = "[1-100 [10-30 [10-20 [10-20 [11-19]]]], 15-30 [20-20]]";
+    assertEquals(ncl.toString(), expected);
+
+    Collections.reverse(ranges);
+    ncl = new NCList<Range>(ranges);
+    assertEquals(ncl.toString(), expected);
+  }
+
+  @Test(groups = "Functional")
+  public void testFindOverlaps()
+  {
+    List<Range> ranges = new ArrayList<Range>();
+    ranges.add(new Range(20, 50));
+    ranges.add(new Range(30, 70));
+    ranges.add(new Range(1, 100));
+    ranges.add(new Range(70, 120));
+  
+    NCList<Range> ncl = new NCList<Range>(ranges);
+
+    List<Range> overlaps = ncl.findOverlaps(121, 122);
+    assertEquals(overlaps.size(), 0);
+
+    overlaps = ncl.findOverlaps(21, 22);
+    assertEquals(overlaps.size(), 2);
+    assertEquals(((ContiguousI) overlaps.get(0)).getBegin(), 1);
+    assertEquals(((ContiguousI) overlaps.get(0)).getEnd(), 100);
+    assertEquals(((ContiguousI) overlaps.get(1)).getBegin(), 20);
+    assertEquals(((ContiguousI) overlaps.get(1)).getEnd(), 50);
+
+    overlaps = ncl.findOverlaps(110, 110);
+    assertEquals(overlaps.size(), 1);
+    assertEquals(((ContiguousI) overlaps.get(0)).getBegin(), 70);
+    assertEquals(((ContiguousI) overlaps.get(0)).getEnd(), 120);
+  }
+
+  @Test(groups = "Functional")
+  public void testAdd_onTheEnd()
+  {
+    List<Range> ranges = new ArrayList<Range>();
+    ranges.add(new Range(20, 50));
+    NCList<Range> ncl = new NCList<Range>(ranges);
+    assertEquals(ncl.toString(), "[20-50]");
+
+    ncl.add(new Range(60, 70));
+    assertEquals(ncl.toString(), "[20-50, 60-70]");
+  }
+
+  @Test(groups = "Functional")
+  public void testAdd_inside()
+  {
+    List<Range> ranges = new ArrayList<Range>();
+    ranges.add(new Range(20, 50));
+    NCList<Range> ncl = new NCList<Range>(ranges);
+    assertEquals(ncl.toString(), "[20-50]");
+
+    ncl.add(new Range(30, 40));
+    assertEquals(ncl.toString(), "[20-50 [30-40]]");
+  }
+
+  @Test(groups = "Functional")
+  public void testAdd_onTheFront()
+  {
+    List<Range> ranges = new ArrayList<Range>();
+    ranges.add(new Range(20, 50));
+    NCList<Range> ncl = new NCList<Range>(ranges);
+    assertEquals(ncl.toString(), "[20-50]");
+
+    ncl.add(new Range(5, 15));
+    assertEquals(ncl.toString(), "[5-15, 20-50]");
+  }
+
+  @Test(groups = "Functional")
+  public void testAdd_enclosing()
+  {
+    List<Range> ranges = new ArrayList<Range>();
+    ranges.add(new Range(20, 50));
+    ranges.add(new Range(30, 60));
+    NCList<Range> ncl = new NCList<Range>(ranges);
+    assertEquals(ncl.toString(), "[20-50, 30-60]");
+
+    ncl.add(new Range(10, 70));
+    assertEquals(ncl.toString(), "[10-70 [20-50, 30-60]");
+  }
+
+  @Test(groups = "Functional")
+  public void testAdd_spanning()
+  {
+    List<Range> ranges = new ArrayList<Range>();
+    ranges.add(new Range(20, 40));
+    ranges.add(new Range(60, 70));
+    NCList<Range> ncl = new NCList<Range>(ranges);
+    assertEquals(ncl.toString(), "[20-40, 60-70]");
+
+    ncl.add(new Range(30, 50));
+    assertEquals(ncl.toString(), "[20-40, 30-50, 60-70]");
+
+    ncl.add(new Range(40, 65));
+    assertEquals(ncl.toString(), "[20-40, 30-50, 40-65, 60-70]");
+  }
+}