X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=test%2Fjalview%2Fdatamodel%2FColumnSelectionTest.java;h=5cb8cf56bb92914fb3ff3f08d3fc8e3bc0bc05d5;hb=265e81c0b3599a09c312f17188e3a892e9d96c4e;hp=8709961485e148ca9c65550086e3753a66e604c6;hpb=ad09c54f294b945fd4d037a93f5fa8eced6c1797;p=jalview.git

diff --git a/test/jalview/datamodel/ColumnSelectionTest.java b/test/jalview/datamodel/ColumnSelectionTest.java
index 8709961..5cb8cf5 100644
--- a/test/jalview/datamodel/ColumnSelectionTest.java
+++ b/test/jalview/datamodel/ColumnSelectionTest.java
@@ -25,9 +25,6 @@ import static org.testng.AssertJUnit.assertFalse;
 import static org.testng.AssertJUnit.assertTrue;
 import static org.testng.AssertJUnit.fail;
 
-import jalview.analysis.AlignmentGenerator;
-import jalview.gui.JvOptionPane;
-
 import java.util.Arrays;
 import java.util.BitSet;
 import java.util.Collections;
@@ -38,6 +35,12 @@ import java.util.List;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
+import jalview.analysis.AlignmentGenerator;
+import jalview.gui.JvOptionPane;
+import jalview.viewmodel.annotationfilter.AnnotationFilterParameter;
+import jalview.viewmodel.annotationfilter.AnnotationFilterParameter.SearchableAnnotationField;
+import jalview.viewmodel.annotationfilter.AnnotationFilterParameter.ThresholdType;
+
 public class ColumnSelectionTest
 {
 
@@ -100,8 +103,8 @@ public class ColumnSelectionTest
     cs.removeElement(1);
     List<Integer> sel = cs.getSelected();
     assertEquals(2, sel.size());
-    assertEquals(new Integer(2), sel.get(0));
-    assertEquals(new Integer(5), sel.get(1));
+    assertEquals(Integer.valueOf(2), sel.get(0));
+    assertEquals(Integer.valueOf(5), sel.get(1));
 
     // removing an element in the list removes it
     cs.removeElement(2);
@@ -109,7 +112,7 @@ public class ColumnSelectionTest
     assertEquals(1, sel.size());
     sel = cs.getSelected();
     assertEquals(1, sel.size());
-    assertEquals(new Integer(5), sel.get(0));
+    assertEquals(Integer.valueOf(5), sel.get(0));
   }
 
   /**
@@ -408,7 +411,8 @@ public class ColumnSelectionTest
    */
   @Test(
     groups = "Functional",
-    expectedExceptions = { ConcurrentModificationException.class })
+    expectedExceptions =
+    { ConcurrentModificationException.class })
   public void testGetSelected_concurrentModification()
   {
     ColumnSelection cs = new ColumnSelection();
@@ -535,7 +539,6 @@ public class ColumnSelectionTest
     assertEquals("[3, 1]", cs2.getSelected().toString());
   }
 
-
   @Test(groups = { "Functional" })
   public void testStretchGroup_expand()
   {
@@ -598,4 +601,124 @@ public class ColumnSelectionTest
     assertEquals(sg.getStartRes(), 10);
     assertEquals(sg.getEndRes(), 19);
   }
+
+  @Test(groups = { "Functional" })
+  public void testFilterAnnotations()
+  {
+    ColumnSelection cs = new ColumnSelection();
+    AlignmentAnnotation alann = new AlignmentAnnotation("dummy",
+            "dummyDesc", null);
+
+    /*
+     * filter with no conditions clears the selection
+     */
+    Annotation[] anns = new Annotation[] { null };
+    AnnotationFilterParameter filter = new AnnotationFilterParameter();
+    cs.addElement(3);
+    alann.annotations = anns;
+    int added = cs.filterAnnotations(alann, filter);
+    assertEquals(0, added);
+    assertTrue(cs.isEmpty());
+
+    /*
+     * select on description (regex)
+     */
+    filter.setRegexString("w.rld");
+    filter.addRegexSearchField(SearchableAnnotationField.DESCRIPTION);
+    Annotation helix = new Annotation("(", "hello", '<', 2f);
+    Annotation sheet = new Annotation("(", "world", '<', 2f);
+    alann.annotations = new Annotation[] { null, helix, sheet };
+    added = cs.filterAnnotations(alann, filter);
+    assertEquals(1, added);
+    assertTrue(cs.contains(2));
+
+    /*
+     * select on label (invalid regex, exact match)
+     */
+    filter = new AnnotationFilterParameter();
+    filter.setRegexString("(");
+    filter.addRegexSearchField(SearchableAnnotationField.DISPLAY_STRING);
+    alann.annotations = new Annotation[] { null, helix, sheet };
+    added = cs.filterAnnotations(alann, filter);
+    assertEquals(2, added);
+    assertTrue(cs.contains(1));
+    assertTrue(cs.contains(2));
+
+    /*
+     * select Helix (secondary structure symbol H)
+     */
+    filter = new AnnotationFilterParameter();
+    filter.setFilterAlphaHelix(true);
+    helix = new Annotation("x", "desc", 'H', 0f);
+    sheet = new Annotation("x", "desc", 'E', 1f);
+    Annotation turn = new Annotation("x", "desc", 'S', 2f);
+    Annotation ann4 = new Annotation("x", "desc", 'Y', 3f);
+    alann.annotations = new Annotation[] { null, helix, sheet, turn, ann4 };
+    added = cs.filterAnnotations(alann, filter);
+    assertEquals(1, added);
+    assertTrue(cs.contains(1));
+
+    /*
+     * select Helix and Sheet (E)
+     */
+    filter.setFilterBetaSheet(true);
+    alann.annotations = new Annotation[] { null, helix, sheet, turn, ann4 };
+    added = cs.filterAnnotations(alann, filter);
+    assertEquals(2, added);
+    assertTrue(cs.contains(1));
+    assertTrue(cs.contains(2));
+
+    /*
+     * select Sheet and Turn (S)
+     */
+    filter.setFilterAlphaHelix(false);
+    filter.setFilterTurn(true);
+    alann.annotations = new Annotation[] { null, helix, sheet, turn, ann4 };
+    added = cs.filterAnnotations(alann, filter);
+    assertEquals(2, added);
+    assertTrue(cs.contains(2));
+    assertTrue(cs.contains(3));
+
+    /*
+     * select value < 2f (ann1, ann2)
+     */
+    filter = new AnnotationFilterParameter();
+    filter.setThresholdType(ThresholdType.BELOW_THRESHOLD);
+    filter.setThresholdValue(2f);
+    alann.annotations = new Annotation[] { null, helix, sheet, turn, ann4 };
+    added = cs.filterAnnotations(alann, filter);
+    assertEquals(2, added);
+    assertTrue(cs.contains(1));
+    assertTrue(cs.contains(2));
+
+    /*
+     * select value > 2f (ann4 only)
+     */
+    filter.setThresholdType(ThresholdType.ABOVE_THRESHOLD);
+    alann.annotations = new Annotation[] { null, helix, sheet, turn, ann4 };
+    added = cs.filterAnnotations(alann, filter);
+    assertEquals(1, added);
+    assertTrue(cs.contains(4));
+
+    /*
+     * select >2f or Helix
+     */
+    filter.setFilterAlphaHelix(true);
+    alann.annotations = new Annotation[] { null, helix, sheet, turn, ann4 };
+    added = cs.filterAnnotations(alann, filter);
+    assertEquals(2, added);
+    assertTrue(cs.contains(1));
+    assertTrue(cs.contains(4));
+
+    /*
+     * select < 1f or Helix; one annotation matches both
+     * return value should only count it once
+     */
+    filter.setThresholdType(ThresholdType.BELOW_THRESHOLD);
+    filter.setThresholdValue(1f);
+    alann.annotations = new Annotation[] { null, helix, sheet, turn, ann4 };
+    added = cs.filterAnnotations(alann, filter);
+    assertEquals(1, added);
+    assertTrue(cs.contains(1));
+  }
 }