Merge remote-tracking branch 'origin/tasks/JAL-3070_wsinterfaces' into alpha/JAL...

[jalview.git] / test / jalview / datamodel / AlignmentAnnotationTests.java

diff --git a/test/jalview/datamodel/AlignmentAnnotationTests.java b/test/jalview/datamodel/AlignmentAnnotationTests.java
index a2c6256..ade9150 100644 (file)
--- a/test/jalview/datamodel/AlignmentAnnotationTests.java
+++ b/test/jalview/datamodel/AlignmentAnnotationTests.java
@@ -20,14 +20,15 @@
  */
 package jalview.datamodel;
 
+import static org.testng.Assert.assertNull;
 import static org.testng.AssertJUnit.assertEquals;
-import static org.testng.AssertJUnit.assertNull;
 
 import jalview.analysis.AlignSeq;
 import jalview.gui.JvOptionPane;
 import jalview.io.AppletFormatAdapter;
 import jalview.io.FileFormat;
 
+import org.testng.Assert;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
@@ -48,6 +49,11 @@ public class AlignmentAnnotationTests
     createAnnotation(sq);
     AlignmentAnnotation alc, alo = sq.getAnnotation()[0];
     alc = new AlignmentAnnotation(alo);
+
+    // TODO: this only tests string equals (which is unreliable), should use
+    // refactored tests from StockholmFileTest
+    Assert.assertEquals(alc.toString(), alo.toString());
+
     for (String key : alo.getProperties())
     {
       assertEquals("Property mismatch", alo.getProperty(key),
@@ -293,4 +299,133 @@ public class AlignmentAnnotationTests
               ann.getDefaultRnaHelixSymbol(i));
     }
   }
+
+  public static Annotation newAnnotation(String ann)
+  {
+    float val = 0f;
+    try
+    {
+      val = Float.parseFloat(ann);
+    } catch (NumberFormatException q)
+    {
+    }
+    ;
+    return new Annotation(ann, ann, '\0', val);
+  }
+
+  @Test(groups = { "Functional" })
+  public void testIsQuantitative()
+  {
+    AlignmentAnnotation ann = null;
+
+    ann = new AlignmentAnnotation("an", "some an", null);
+    Assert.assertFalse(ann.isQuantitative(),
+            "Empty annotation set should not be quantitative.");
+
+    ann = new AlignmentAnnotation("an", "some an", new Annotation[] {
+        newAnnotation("4"), newAnnotation("1"), newAnnotation("1"),
+        newAnnotation("0.1"), newAnnotation("0.3") });
+    Assert.assertTrue(ann.isQuantitative(),
+            "All numbers annotation set should be quantitative.");
+
+    ann = new AlignmentAnnotation("an", "some an", new Annotation[] {
+        newAnnotation("E"), newAnnotation("E"), newAnnotation("E"),
+        newAnnotation("E"), newAnnotation("E") });
+    Assert.assertFalse(ann.isQuantitative(),
+            "All 'E' annotation set should not be quantitative.");
+
+    ann = new AlignmentAnnotation("an", "some an", new Annotation[] {
+        newAnnotation("E"), newAnnotation("1"), newAnnotation("2"),
+        newAnnotation("3"), newAnnotation("E") });
+    Assert.assertTrue(ann.isQuantitative(),
+            "Mixed 'E' annotation set should be quantitative.");
+  }
+
+  @Test(groups = "Functional")
+  public void testMakeVisibleAnnotation()
+  {
+    HiddenColumns h = new HiddenColumns();
+    Annotation[] anns = new Annotation[] { null, null, new Annotation(1),
+        new Annotation(2), new Annotation(3), null, null, new Annotation(4),
+        new Annotation(5), new Annotation(6), new Annotation(7),
+        new Annotation(8) };
+    AlignmentAnnotation ann = new AlignmentAnnotation("an", "some an",
+            anns);
+
+    // null annotations
+    AlignmentAnnotation emptyann = new AlignmentAnnotation("an", "some ann",
+            null);
+    emptyann.makeVisibleAnnotation(h);
+    assertNull(emptyann.annotations);
+
+    emptyann.makeVisibleAnnotation(3, 4, h);
+    assertNull(emptyann.annotations);
+
+    // without bounds, does everything
+    ann.makeVisibleAnnotation(h);
+    assertEquals(12, ann.annotations.length);
+    assertNull(ann.annotations[0]);
+    assertNull(ann.annotations[1]);
+    assertEquals(1.0f, ann.annotations[2].value);
+    assertEquals(2.0f, ann.annotations[3].value);
+    assertEquals(3.0f, ann.annotations[4].value);
+    assertNull(ann.annotations[5]);
+    assertNull(ann.annotations[6]);
+    assertEquals(4.0f, ann.annotations[7].value);
+    assertEquals(5.0f, ann.annotations[8].value);
+    assertEquals(6.0f, ann.annotations[9].value);
+    assertEquals(7.0f, ann.annotations[10].value);
+    assertEquals(8.0f, ann.annotations[11].value);
+
+    // without hidden cols, just truncates
+    ann.makeVisibleAnnotation(3, 5, h);
+    assertEquals(3, ann.annotations.length);
+    assertEquals(2.0f, ann.annotations[0].value);
+    assertEquals(3.0f, ann.annotations[1].value);
+    assertNull(ann.annotations[2]);
+
+    anns = new Annotation[] { null, null, new Annotation(1),
+        new Annotation(2), new Annotation(3), null, null, new Annotation(4),
+        new Annotation(5), new Annotation(6), new Annotation(7),
+        new Annotation(8) };
+    ann = new AlignmentAnnotation("an", "some an", anns);
+    h.hideColumns(4, 7);
+    ann.makeVisibleAnnotation(1, 9, h);
+    assertEquals(5, ann.annotations.length);
+    assertNull(ann.annotations[0]);
+    assertEquals(1.0f, ann.annotations[1].value);
+    assertEquals(2.0f, ann.annotations[2].value);
+    assertEquals(5.0f, ann.annotations[3].value);
+    assertEquals(6.0f, ann.annotations[4].value);
+
+    anns = new Annotation[] { null, null, new Annotation(1),
+        new Annotation(2), new Annotation(3), null, null, new Annotation(4),
+        new Annotation(5), new Annotation(6), new Annotation(7),
+        new Annotation(8) };
+    ann = new AlignmentAnnotation("an", "some an", anns);
+    h.hideColumns(1, 2);
+    ann.makeVisibleAnnotation(1, 9, h);
+    assertEquals(3, ann.annotations.length);
+    assertEquals(2.0f, ann.annotations[0].value);
+    assertEquals(5.0f, ann.annotations[1].value);
+    assertEquals(6.0f, ann.annotations[2].value);
+
+    anns = new Annotation[] { null, null, new Annotation(1),
+        new Annotation(2), new Annotation(3), null, null, new Annotation(4),
+        new Annotation(5), new Annotation(6), new Annotation(7),
+        new Annotation(8), new Annotation(9), new Annotation(10),
+        new Annotation(11), new Annotation(12), new Annotation(13),
+        new Annotation(14), new Annotation(15) };
+    ann = new AlignmentAnnotation("an", "some an", anns);
+    h = new HiddenColumns();
+    h.hideColumns(5, 18);
+    h.hideColumns(20, 21);
+    ann.makeVisibleAnnotation(1, 21, h);
+    assertEquals(5, ann.annotations.length);
+    assertEquals(1.0f, ann.annotations[1].value);
+    assertEquals(2.0f, ann.annotations[2].value);
+    assertEquals(3.0f, ann.annotations[3].value);
+    assertNull(ann.annotations[0]);
+    assertNull(ann.annotations[4]);
+  }
 }