X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2FColumnSelectionTest.java;h=5cb8cf56bb92914fb3ff3f08d3fc8e3bc0bc05d5;hb=refs%2Fheads%2Ffeatures%2Fr2_11_2_alphafold%2FJAL-2349_JAL-3855;hp=ce2949fa361ac2eac31e5d8c07e1a100f3a38b74;hpb=b70c7ff4b002103401ccceb917114b954e18d50c;p=jalview.git diff --git a/test/jalview/datamodel/ColumnSelectionTest.java b/test/jalview/datamodel/ColumnSelectionTest.java index ce2949f..5cb8cf5 100644 --- a/test/jalview/datamodel/ColumnSelectionTest.java +++ b/test/jalview/datamodel/ColumnSelectionTest.java @@ -25,18 +25,22 @@ 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; 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 { @@ -99,8 +103,8 @@ public class ColumnSelectionTest cs.removeElement(1); List 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); @@ -108,7 +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)); } /** @@ -132,9 +136,9 @@ public class ColumnSelectionTest // hide column 5 (and adjacent): cs.hideSelectedColumns(5, al.getHiddenColumns()); // 4,5,6 now hidden: - List hidden = al.getHiddenColumns().getListOfCols(); - assertEquals(1, hidden.size()); - assertEquals("[4, 6]", Arrays.toString(hidden.get(0))); + Iterator 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 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 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())); } /** @@ -407,7 +411,8 @@ public class ColumnSelectionTest */ @Test( groups = "Functional", - expectedExceptions = { ConcurrentModificationException.class }) + expectedExceptions = + { ConcurrentModificationException.class }) public void testGetSelected_concurrentModification() { ColumnSelection cs = new ColumnSelection(); @@ -534,7 +539,6 @@ public class ColumnSelectionTest assertEquals("[3, 1]", cs2.getSelected().toString()); } - @Test(groups = { "Functional" }) public void testStretchGroup_expand() { @@ -597,4 +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)); + } }