Merge branch 'Jalview-JS/jim/JAL-3253-JAL-3418' into Jalview-JS/JAL-3253-applet

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

diff --git a/test/jalview/datamodel/ColumnSelectionTest.java b/test/jalview/datamodel/ColumnSelectionTest.java
index ce2949f..2dda4d3 100644 (file)
--- a/test/jalview/datamodel/ColumnSelectionTest.java
+++ b/test/jalview/datamodel/ColumnSelectionTest.java
@@ -27,11 +27,15 @@ import static org.testng.AssertJUnit.fail;
 
 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;
 
 import java.util.Arrays;
 import java.util.BitSet;
 import java.util.Collections;
 import java.util.ConcurrentModificationException;
+import java.util.Iterator;
 import java.util.List;
 
 import org.testng.annotations.BeforeClass;
@@ -132,9 +136,9 @@ public class ColumnSelectionTest
     // hide column 5 (and adjacent):
     cs.hideSelectedColumns(5, al.getHiddenColumns());
     // 4,5,6 now hidden:
-    List<int[]> hidden = al.getHiddenColumns().getListOfCols();
-    assertEquals(1, hidden.size());
-    assertEquals("[4, 6]", Arrays.toString(hidden.get(0)));
+    Iterator<int[]> regions = al.getHiddenColumns().iterator();
+    assertEquals(1, al.getHiddenColumns().getNumberOfRegions());
+    assertEquals("[4, 6]", Arrays.toString(regions.next()));
     // none now selected:
     assertTrue(cs.getSelected().isEmpty());
 
@@ -145,9 +149,9 @@ public class ColumnSelectionTest
     cs.addElement(5);
     cs.addElement(6);
     cs.hideSelectedColumns(4, al.getHiddenColumns());
-    hidden = al.getHiddenColumns().getListOfCols();
-    assertEquals(1, hidden.size());
-    assertEquals("[4, 6]", Arrays.toString(hidden.get(0)));
+    regions = al.getHiddenColumns().iterator();
+    assertEquals(1, al.getHiddenColumns().getNumberOfRegions());
+    assertEquals("[4, 6]", Arrays.toString(regions.next()));
     assertTrue(cs.getSelected().isEmpty());
 
     // repeat, hiding column (4, 5 and) 6
@@ -157,9 +161,9 @@ public class ColumnSelectionTest
     cs.addElement(5);
     cs.addElement(6);
     cs.hideSelectedColumns(6, al.getHiddenColumns());
-    hidden = al.getHiddenColumns().getListOfCols();
-    assertEquals(1, hidden.size());
-    assertEquals("[4, 6]", Arrays.toString(hidden.get(0)));
+    regions = al.getHiddenColumns().iterator();
+    assertEquals(1, al.getHiddenColumns().getNumberOfRegions());
+    assertEquals("[4, 6]", Arrays.toString(regions.next()));
     assertTrue(cs.getSelected().isEmpty());
 
     // repeat, with _only_ adjacent columns selected
@@ -168,9 +172,9 @@ public class ColumnSelectionTest
     cs.addElement(4);
     cs.addElement(6);
     cs.hideSelectedColumns(5, al.getHiddenColumns());
-    hidden = al.getHiddenColumns().getListOfCols();
-    assertEquals(1, hidden.size());
-    assertEquals("[4, 6]", Arrays.toString(hidden.get(0)));
+    regions = al.getHiddenColumns().iterator();
+    assertEquals(1, al.getHiddenColumns().getNumberOfRegions());
+    assertEquals("[4, 6]", Arrays.toString(regions.next()));
     assertTrue(cs.getSelected().isEmpty());
   }
 
@@ -196,12 +200,12 @@ public class ColumnSelectionTest
 
     cs.hideSelectedColumns(al);
     assertTrue(cs.getSelected().isEmpty());
-    List<int[]> hidden = cols.getListOfCols();
-    assertEquals(4, hidden.size());
-    assertEquals("[2, 4]", Arrays.toString(hidden.get(0)));
-    assertEquals("[7, 9]", Arrays.toString(hidden.get(1)));
-    assertEquals("[15, 18]", Arrays.toString(hidden.get(2)));
-    assertEquals("[20, 22]", Arrays.toString(hidden.get(3)));
+    Iterator<int[]> regions = cols.iterator();
+    assertEquals(4, cols.getNumberOfRegions());
+    assertEquals("[2, 4]", Arrays.toString(regions.next()));
+    assertEquals("[7, 9]", Arrays.toString(regions.next()));
+    assertEquals("[15, 18]", Arrays.toString(regions.next()));
+    assertEquals("[20, 22]", Arrays.toString(regions.next()));
   }
 
   /**
@@ -597,4 +601,129 @@ public class ColumnSelectionTest
     assertEquals(sg.getStartRes(), 10);
     assertEquals(sg.getEndRes(), 19);
   }
+
+  @Test(groups = { "Functional" })
+  public void testFilterAnnotations()
+  {
+    ColumnSelection cs = new ColumnSelection();
+
+    /*
+     * filter with no conditions clears the selection
+     */
+    Annotation[] anns = new Annotation[] { null };
+    AnnotationFilterParameter filter = new AnnotationFilterParameter();
+    cs.addElement(3);
+    int added = cs.filterAnnotations(anns, 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);
+    added = cs.filterAnnotations(new Annotation[] { null, helix, sheet },
+            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);
+    added = cs.filterAnnotations(new Annotation[] { null, helix, sheet },
+            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);
+    added = cs
+            .filterAnnotations(new Annotation[]
+            { null, helix, sheet, turn, ann4 },
+            filter);
+    assertEquals(1, added);
+    assertTrue(cs.contains(1));
+
+    /*
+     * select Helix and Sheet (E)
+     */
+    filter.setFilterBetaSheet(true);
+    added = cs
+            .filterAnnotations(new Annotation[]
+            { null, helix, sheet, turn, ann4 }, filter);
+    assertEquals(2, added);
+    assertTrue(cs.contains(1));
+    assertTrue(cs.contains(2));
+
+    /*
+     * select Sheet and Turn (S)
+     */
+    filter.setFilterAlphaHelix(false);
+    filter.setFilterTurn(true);
+    added = cs
+            .filterAnnotations(new Annotation[]
+            { null, helix, sheet, turn, ann4 }, 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);
+    added = cs
+            .filterAnnotations(new Annotation[]
+            { null, helix, sheet, turn, ann4 }, filter);
+    assertEquals(2, added);
+    assertTrue(cs.contains(1));
+    assertTrue(cs.contains(2));
+
+    /*
+     * select value > 2f (ann4 only)
+     */
+    filter.setThresholdType(ThresholdType.ABOVE_THRESHOLD);
+    added = cs
+            .filterAnnotations(new Annotation[]
+            { null, helix, sheet, turn, ann4 }, filter);
+    assertEquals(1, added);
+    assertTrue(cs.contains(4));
+
+    /*
+     * select >2f or Helix
+     */
+    filter.setFilterAlphaHelix(true);
+    added = cs
+            .filterAnnotations(new Annotation[]
+            { null, helix, sheet, turn, ann4 }, 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);
+    added = cs
+            .filterAnnotations(new Annotation[]
+            { null, helix, sheet, turn, ann4 }, filter);
+    assertEquals(1, added);
+    assertTrue(cs.contains(1));
+  }
 }