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;
import java.util.ConcurrentModificationException;
+import java.util.Iterator;
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
{
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);
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));
}
/**
// hide column 5 (and adjacent):
cs.hideSelectedColumns(5, al.getHiddenColumns());
// 4,5,6 now hidden:
- List<int[]> hidden = al.getHiddenColumns().getHiddenRegions();
- 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());
cs.addElement(5);
cs.addElement(6);
cs.hideSelectedColumns(4, al.getHiddenColumns());
- hidden = al.getHiddenColumns().getHiddenRegions();
- 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
cs.addElement(5);
cs.addElement(6);
cs.hideSelectedColumns(6, al.getHiddenColumns());
- hidden = al.getHiddenColumns().getHiddenRegions();
- 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
cs.addElement(4);
cs.addElement(6);
cs.hideSelectedColumns(5, al.getHiddenColumns());
- hidden = al.getHiddenColumns().getHiddenRegions();
- 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());
}
cs.hideSelectedColumns(al);
assertTrue(cs.getSelected().isEmpty());
- List<int[]> hidden = cols.getHiddenRegions();
- 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()));
}
/**
*/
@Test(
groups = "Functional",
- expectedExceptions = { ConcurrentModificationException.class })
+ expectedExceptions =
+ { ConcurrentModificationException.class })
public void testGetSelected_concurrentModification()
{
ColumnSelection cs = new ColumnSelection();
assertEquals("[3, 1]", cs2.getSelected().toString());
}
-
@Test(groups = { "Functional" })
public void testStretchGroup_expand()
{
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));
+ }
}
git://source.jalview.org / jalview.git / blobdiff