+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.datamodel;
import static org.testng.AssertJUnit.assertEquals;
+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 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;
import org.testng.annotations.Test;
public class ColumnSelectionTest
{
- @Test(groups ={ "Functional" })
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
+ @Test(groups = { "Functional" })
public void testAddElement()
{
ColumnSelection cs = new ColumnSelection();
cs.addElement(2);
cs.addElement(5);
+ cs.addElement(3);
+ cs.addElement(5); // ignored
List<Integer> sel = cs.getSelected();
- assertEquals(2, sel.size());
- assertEquals(new Integer(2), sel.get(0));
- assertEquals(new Integer(5), sel.get(1));
+ assertEquals("[2, 5, 3]", sel.toString());
+ }
+
+ @Test(groups = { "Functional" })
+ public void testSetElementsFrom()
+ {
+ ColumnSelection fromcs = new ColumnSelection();
+ ColumnSelection tocs = new ColumnSelection();
+ HiddenColumns hidden = new HiddenColumns();
+
+ fromcs.addElement(2);
+ fromcs.addElement(3);
+ fromcs.addElement(5);
+
+ tocs.setElementsFrom(fromcs, hidden);
+ assertTrue(tocs.equals(fromcs));
+
+ hidden.hideColumns(4, 6);
+ tocs.setElementsFrom(fromcs, hidden);
+
+ // expect cols 2 and 3 to be selected but not 5
+ ColumnSelection expectcs = new ColumnSelection();
+ expectcs.addElement(2);
+ expectcs.addElement(3);
+ assertTrue(tocs.equals(expectcs));
}
/**
* Test the remove method - in particular to verify that remove(int i) removes
* the element whose value is i, _NOT_ the i'th element.
*/
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testRemoveElement()
{
ColumnSelection cs = new ColumnSelection();
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);
+ // ...and also from the read-only view
+ 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));
+ }
+
+ /**
+ * Test the method that hides a specified column including any adjacent
+ * selected columns. This is a convenience method for the case where multiple
+ * column regions are selected and then hidden using menu option View | Hide |
+ * Selected Columns.
+ */
+ @Test(groups = { "Functional" })
+ public void testHideColumns_withSelection()
+ {
+ // create random alignment
+ AlignmentGenerator gen = new AlignmentGenerator(false);
+ AlignmentI al = gen.generate(50, 20, 123, 5, 5);
+
+ ColumnSelection cs = new ColumnSelection();
+ // select columns 4-6
+ cs.addElement(4);
+ cs.addElement(5);
+ cs.addElement(6);
+ // hide column 5 (and adjacent):
+ cs.hideSelectedColumns(5, al.getHiddenColumns());
+ // 4,5,6 now hidden:
+ 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());
+
+ // repeat, hiding column 4 (5 and 6)
+ al = gen.generate(50, 20, 123, 5, 5);
+ cs = new ColumnSelection();
+ cs.addElement(4);
+ cs.addElement(5);
+ cs.addElement(6);
+ cs.hideSelectedColumns(4, al.getHiddenColumns());
+ 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
+ al = gen.generate(50, 20, 123, 5, 5);
+ cs = new ColumnSelection();
+ cs.addElement(4);
+ cs.addElement(5);
+ cs.addElement(6);
+ cs.hideSelectedColumns(6, al.getHiddenColumns());
+ 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
+ al = gen.generate(50, 20, 123, 5, 5);
+ cs = new ColumnSelection();
+ cs.addElement(4);
+ cs.addElement(6);
+ cs.hideSelectedColumns(5, al.getHiddenColumns());
+ regions = al.getHiddenColumns().iterator();
+ assertEquals(1, al.getHiddenColumns().getNumberOfRegions());
+ assertEquals("[4, 6]", Arrays.toString(regions.next()));
+ assertTrue(cs.getSelected().isEmpty());
+ }
+
+ /**
+ * Test the method that hides all (possibly disjoint) selected column ranges
+ */
+ @Test(groups = { "Functional" })
+ public void testHideSelectedColumns()
+ {
+ // create random alignment
+ AlignmentGenerator gen = new AlignmentGenerator(false);
+ AlignmentI al = gen.generate(50, 20, 123, 5, 5);
+
+ ColumnSelection cs = new ColumnSelection();
+ int[] sel = { 2, 3, 4, 7, 8, 9, 20, 21, 22 };
+ for (int col : sel)
+ {
+ cs.addElement(col);
+ }
+
+ HiddenColumns cols = al.getHiddenColumns();
+ cols.hideColumns(15, 18);
+
+ cs.hideSelectedColumns(al);
+ assertTrue(cs.getSelected().isEmpty());
+ 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 the method that gets runs of selected columns ordered by column. If
+ * this fails, HideSelectedColumns may also fail
+ */
+ @Test(groups = { "Functional" })
+ public void testGetSelectedRanges()
+ {
+ /*
+ * getSelectedRanges returns ordered columns regardless
+ * of the order in which they are added
+ */
+ ColumnSelection cs = new ColumnSelection();
+ int[] sel = { 4, 3, 7, 21, 9, 20, 8, 22, 2 };
+ for (int col : sel)
+ {
+ cs.addElement(col);
+ }
+ List<int[]> range;
+ range = cs.getSelectedRanges();
+ assertEquals(3, range.size());
+ assertEquals("[2, 4]", Arrays.toString(range.get(0)));
+ assertEquals("[7, 9]", Arrays.toString(range.get(1)));
+ assertEquals("[20, 22]", Arrays.toString(range.get(2)));
+ cs.addElement(0);
+ cs.addElement(1);
+ range = cs.getSelectedRanges();
+ assertEquals(3, range.size());
+ assertEquals("[0, 4]", Arrays.toString(range.get(0)));
+ }
+
+ @Test(groups = { "Functional" })
+ public void testInvertColumnSelection()
+ {
+ // create random alignment
+ AlignmentGenerator gen = new AlignmentGenerator(false);
+ AlignmentI al = gen.generate(50, 20, 123, 5, 5);
+
+ ColumnSelection cs = new ColumnSelection();
+ cs.addElement(4);
+ cs.addElement(6);
+ cs.addElement(8);
+
+ HiddenColumns cols = al.getHiddenColumns();
+ cols.hideColumns(3, 3);
+ cols.hideColumns(6, 6);
+
+ // invert selection from start (inclusive) to end (exclusive)
+ cs.invertColumnSelection(2, 9, al);
+ assertEquals("[2, 5, 7]", cs.getSelected().toString());
+
+ cs.invertColumnSelection(1, 9, al);
+ assertEquals("[1, 4, 8]", cs.getSelected().toString());
+ }
+
+ @Test(groups = { "Functional" })
+ public void testMaxColumnSelection()
+ {
+ ColumnSelection cs = new ColumnSelection();
+ cs.addElement(0);
+ cs.addElement(513);
+ cs.addElement(1);
+ assertEquals(513, cs.getMax());
+ cs.removeElement(513);
+ assertEquals(1, cs.getMax());
+ cs.removeElement(1);
+ assertEquals(0, cs.getMax());
+ cs.addElement(512);
+ cs.addElement(513);
+ assertEquals(513, cs.getMax());
+
+ }
+
+ @Test(groups = { "Functional" })
+ public void testMinColumnSelection()
+ {
+ ColumnSelection cs = new ColumnSelection();
+ cs.addElement(0);
+ cs.addElement(513);
+ cs.addElement(1);
+ assertEquals(0, cs.getMin());
+ cs.removeElement(0);
+ assertEquals(1, cs.getMin());
+ cs.addElement(0);
+ assertEquals(0, cs.getMin());
+ }
+
+ @Test(groups = { "Functional" })
+ public void testEquals()
+ {
+ ColumnSelection cs = new ColumnSelection();
+ cs.addElement(0);
+ cs.addElement(513);
+ cs.addElement(1);
+
+ // same selections added in a different order
+ ColumnSelection cs2 = new ColumnSelection();
+ cs2.addElement(1);
+ cs2.addElement(513);
+ cs2.addElement(0);
+
+ assertTrue(cs.equals(cs2));
+ assertTrue(cs.equals(cs));
+ assertTrue(cs2.equals(cs));
+ assertTrue(cs2.equals(cs2));
+
+ cs2.addElement(12);
+ assertFalse(cs.equals(cs2));
+ assertFalse(cs2.equals(cs));
+
+ cs2.removeElement(12);
+ assertTrue(cs.equals(cs2));
}
+ /*
+ cs2.hideSelectedColumns(88);
+ assertFalse(cs.equals(cs2));
+ /*
+ * unhiding a column adds it to selection!
+ */
+ /* cs2.revealHiddenColumns(88);
+ assertFalse(cs.equals(cs2));
+ cs.addElement(88);
+ assertTrue(cs.equals(cs2));
+ */
+
/**
- * Test the method that finds the visible column position of an alignment
- * column, allowing for hidden columns.
+ * Test the method that returns selected columns, in the order in which they
+ * were added
*/
- @Test(groups ={ "Functional" })
- public void testFindColumnPosition()
+ @Test(groups = { "Functional" })
+ public void testGetSelected()
+ {
+ ColumnSelection cs = new ColumnSelection();
+ int[] sel = { 4, 3, 7, 21 };
+ for (int col : sel)
+ {
+ cs.addElement(col);
+ }
+
+ List<Integer> selected = cs.getSelected();
+ assertEquals(4, selected.size());
+ assertEquals("[4, 3, 7, 21]", selected.toString());
+
+ /*
+ * getSelected returns a read-only view of the list
+ * verify the view follows any changes in it
+ */
+ cs.removeElement(7);
+ cs.addElement(1);
+ cs.removeElement(4);
+ assertEquals("[3, 21, 1]", selected.toString());
+ }
+
+ /**
+ * Test to verify that the list returned by getSelection cannot be modified
+ */
+ @Test(groups = { "Functional" })
+ public void testGetSelected_isReadOnly()
+ {
+ ColumnSelection cs = new ColumnSelection();
+ cs.addElement(3);
+
+ List<Integer> selected = cs.getSelected();
+ try
+ {
+ selected.clear();
+ fail("expected exception");
+ } catch (UnsupportedOperationException e)
+ {
+ // expected
+ }
+ try
+ {
+ selected.add(1);
+ fail("expected exception");
+ } catch (UnsupportedOperationException e)
+ {
+ // expected
+ }
+ try
+ {
+ selected.remove(3);
+ fail("expected exception");
+ } catch (UnsupportedOperationException e)
+ {
+ // expected
+ }
+ try
+ {
+ Collections.sort(selected);
+ fail("expected exception");
+ } catch (UnsupportedOperationException e)
+ {
+ // expected
+ }
+ }
+
+ /**
+ * Test that demonstrates a ConcurrentModificationException is thrown if you
+ * change the selection while iterating over it
+ */
+ @Test(
+ groups = "Functional",
+ expectedExceptions =
+ { ConcurrentModificationException.class })
+ public void testGetSelected_concurrentModification()
+ {
+ ColumnSelection cs = new ColumnSelection();
+ cs.addElement(0);
+ cs.addElement(1);
+ cs.addElement(2);
+
+ /*
+ * simulate changing the list under us (e.g. in a separate
+ * thread) while iterating over it -> ConcurrentModificationException
+ */
+ List<Integer> selected = cs.getSelected();
+ for (Integer col : selected)
+ {
+ if (col.intValue() == 0)
+ {
+ cs.removeElement(1);
+ }
+ }
+ }
+
+ @Test(groups = "Functional")
+ public void testMarkColumns()
+ {
+ ColumnSelection cs = new ColumnSelection();
+ cs.addElement(5); // this will be cleared
+ BitSet toMark = new BitSet();
+ toMark.set(1);
+ toMark.set(3);
+ toMark.set(6);
+ toMark.set(9);
+
+ assertTrue(cs.markColumns(toMark, 3, 8, false, false, false));
+ List<Integer> selected = cs.getSelected();
+ assertEquals(2, selected.size());
+ assertTrue(selected.contains(3));
+ assertTrue(selected.contains(6));
+ }
+
+ @Test(groups = "Functional")
+ public void testMarkColumns_extend()
+ {
+ ColumnSelection cs = new ColumnSelection();
+ cs.addElement(1);
+ cs.addElement(5);
+ BitSet toMark = new BitSet();
+ toMark.set(1);
+ toMark.set(3);
+ toMark.set(6);
+ toMark.set(9);
+
+ /*
+ * extending selection of {3, 6} should leave {1, 3, 5, 6} selected
+ */
+ assertTrue(cs.markColumns(toMark, 3, 8, false, true, false));
+ List<Integer> selected = cs.getSelected();
+ assertEquals(4, selected.size());
+ assertTrue(selected.contains(1));
+ assertTrue(selected.contains(3));
+ assertTrue(selected.contains(5));
+ assertTrue(selected.contains(6));
+ }
+
+ @Test(groups = "Functional")
+ public void testMarkColumns_invert()
{
ColumnSelection cs = new ColumnSelection();
- assertEquals(5, cs.findColumnPosition(5));
+ cs.addElement(5); // this will be cleared
+ BitSet toMark = new BitSet();
+ toMark.set(1);
+ toMark.set(3);
+ toMark.set(6);
+ toMark.set(9);
+
+ /*
+ * inverted selection of {3, 6} should select {4, 5, 7, 8}
+ */
+ assertTrue(cs.markColumns(toMark, 3, 8, true, false, false));
+ List<Integer> selected = cs.getSelected();
+ assertEquals(4, selected.size());
+ assertTrue(selected.contains(4));
+ assertTrue(selected.contains(5));
+ assertTrue(selected.contains(7));
+ assertTrue(selected.contains(8));
+ }
+
+ @Test(groups = "Functional")
+ public void testMarkColumns_toggle()
+ {
+ ColumnSelection cs = new ColumnSelection();
+ cs.addElement(1); // outside change range
+ cs.addElement(3);
+ cs.addElement(4);
+ cs.addElement(10); // outside change range
+ BitSet toMark = new BitSet();
+ toMark.set(1);
+ toMark.set(3);
+ toMark.set(6);
+ toMark.set(9);
+
+ /*
+ * toggling state of {3, 6} should leave {1, 4, 6, 10} selected
+ */
+ assertTrue(cs.markColumns(toMark, 3, 8, false, false, true));
+ List<Integer> selected = cs.getSelected();
+ assertEquals(4, selected.size());
+ assertTrue(selected.contains(1));
+ assertTrue(selected.contains(4));
+ assertTrue(selected.contains(6));
+ assertTrue(selected.contains(10));
+ }
+
+ @Test(groups = "Functional")
+ public void testCopyConstructor()
+ {
+ ColumnSelection cs = new ColumnSelection();
+ cs.addElement(3);
+ cs.addElement(1);
+
+ ColumnSelection cs2 = new ColumnSelection(cs);
+ assertTrue(cs2.hasSelectedColumns());
+
+ // order of column selection is preserved
+ assertEquals("[3, 1]", cs2.getSelected().toString());
+ }
+
+ @Test(groups = { "Functional" })
+ public void testStretchGroup_expand()
+ {
+ /*
+ * test that emulates clicking column 4 (selected)
+ * and dragging right to column 5 (all base 0)
+ */
+ ColumnSelection cs = new ColumnSelection();
+ cs.addElement(4);
+ SequenceGroup sg = new SequenceGroup();
+ sg.setStartRes(4);
+ sg.setEndRes(4);
+ cs.stretchGroup(5, sg, 4, 4);
+ assertEquals(cs.getSelected().size(), 2);
+ assertTrue(cs.contains(4));
+ assertTrue(cs.contains(5));
+ assertEquals(sg.getStartRes(), 4);
+ assertEquals(sg.getEndRes(), 5);
+
+ /*
+ * emulate drag right with columns 10-20 already selected
+ */
+ cs.clear();
+ for (int i = 10; i <= 20; i++)
+ {
+ cs.addElement(i);
+ }
+ assertEquals(cs.getSelected().size(), 11);
+ sg = new SequenceGroup();
+ sg.setStartRes(10);
+ sg.setEndRes(20);
+ cs.stretchGroup(21, sg, 10, 20);
+ assertEquals(cs.getSelected().size(), 12);
+ assertTrue(cs.contains(10));
+ assertTrue(cs.contains(21));
+ assertEquals(sg.getStartRes(), 10);
+ assertEquals(sg.getEndRes(), 21);
+ }
+
+ @Test(groups = { "Functional" })
+ public void testStretchGroup_shrink()
+ {
+ /*
+ * emulate drag left to 19 with columns 10-20 already selected
+ */
+ ColumnSelection cs = new ColumnSelection();
+ for (int i = 10; i <= 20; i++)
+ {
+ cs.addElement(i);
+ }
+ assertEquals(cs.getSelected().size(), 11);
+ SequenceGroup sg = new SequenceGroup();
+ sg.setStartRes(10);
+ sg.setEndRes(20);
+ cs.stretchGroup(19, sg, 10, 20);
+ assertEquals(cs.getSelected().size(), 10);
+ assertTrue(cs.contains(10));
+ assertTrue(cs.contains(19));
+ assertFalse(cs.contains(20));
+ 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));
- // hiding column 6 makes no difference
- cs.hideColumns(6, 6);
- assertEquals(5, cs.findColumnPosition(5));
+ /*
+ * 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));
- // hiding column 5 makes no difference
- cs.hideColumns(5, 5);
- assertEquals(5, cs.findColumnPosition(5));
+ /*
+ * 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));
- // hiding column 4 moves column 5 to column 4
- cs.hideColumns(4, 4);
- assertEquals(4, cs.findColumnPosition(5));
+ /*
+ * 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));
- // hiding columns 1 and 2 moves column 5 to column 2
- cs.hideColumns(1, 2);
- assertEquals(2, cs.findColumnPosition(5));
+ /*
+ * 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));
}
}
git://source.jalview.org / jalview.git / blobdiff