import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;
-import static org.testng.AssertJUnit.assertSame;
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;
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.
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));
- }
-
- /**
- * Test the method that finds the visible column position of an alignment
- * column, allowing for hidden columns.
- */
- @Test(groups = { "Functional" })
- public void testFindColumnPosition()
- {
- ColumnSelection cs = new ColumnSelection();
- assertEquals(5, cs.findColumnPosition(5));
-
- // hiding column 6 makes no difference
- cs.hideColumns(6, 6);
- assertEquals(5, cs.findColumnPosition(5));
-
- // hiding column 4 moves column 5 to column 4
- cs.hideColumns(4, 4);
- assertEquals(4, cs.findColumnPosition(5));
-
- // hiding column 4 moves column 4 to position 3
- assertEquals(3, cs.findColumnPosition(4));
-
- // hiding columns 1 and 2 moves column 5 to column 2
- cs.hideColumns(1, 2);
- assertEquals(2, cs.findColumnPosition(5));
-
- // check with > 1 hidden column regions
- // where some columns are in the hidden regions
- ColumnSelection cs2 = new ColumnSelection();
- cs2.hideColumns(5, 10);
- cs2.hideColumns(20, 27);
- cs2.hideColumns(40, 44);
-
- // hiding columns 5-10 and 20-27 moves column 8 to column 4
- assertEquals(4, cs2.findColumnPosition(8));
-
- // and moves column 24 to 13
- assertEquals(13, cs2.findColumnPosition(24));
-
- // and moves column 28 to 14
- assertEquals(14, cs2.findColumnPosition(28));
-
- // and moves column 40 to 25
- assertEquals(25, cs2.findColumnPosition(40));
-
- // check when hidden columns start at 0 that the visible column
- // is returned as 0
- ColumnSelection cs3 = new ColumnSelection();
- cs3.hideColumns(0, 4);
- assertEquals(0, cs3.findColumnPosition(2));
-
- }
-
- /**
- * Test the code used to locate the reference sequence ruler origin
- */
- @Test(groups = { "Functional" })
- public void testLocateVisibleBoundsofSequence()
- {
- ColumnSelection cs = new ColumnSelection();
- SequenceI seq = new Sequence("RefSeq", "-A-SD-ASD--E---");
- assertEquals(2, seq.findIndex(seq.getStart()));
-
- // no hidden columns
- assertEquals(
- Arrays.toString(new int[] { seq.findIndex(seq.getStart()) - 1,
- seq.findIndex(seq.getEnd()) - 1, seq.getStart(),
- seq.getEnd(), seq.findIndex(seq.getStart()) - 1,
- seq.findIndex(seq.getEnd()) - 1 }),
- Arrays.toString(cs.locateVisibleBoundsOfSequence(seq)));
-
- // hidden column on gap after end of sequence - should not affect bounds
- cs.hideColumns(13);
- assertEquals(
- Arrays.toString(new int[] { seq.findIndex(seq.getStart()) - 1,
- seq.findIndex(seq.getEnd()) - 1, seq.getStart(),
- seq.getEnd(), seq.findIndex(seq.getStart()) - 1,
- seq.findIndex(seq.getEnd()) - 1 }),
- Arrays.toString(cs.locateVisibleBoundsOfSequence(seq)));
-
- cs.revealAllHiddenColumns();
- // hidden column on gap before beginning of sequence - should vis bounds by
- // one
- cs.hideColumns(0);
- assertEquals(
- Arrays.toString(new int[] { seq.findIndex(seq.getStart()) - 2,
- seq.findIndex(seq.getEnd()) - 2, seq.getStart(),
- seq.getEnd(), seq.findIndex(seq.getStart()) - 1,
- seq.findIndex(seq.getEnd()) - 1 }),
- Arrays.toString(cs.locateVisibleBoundsOfSequence(seq)));
-
- cs.revealAllHiddenColumns();
- // hide columns around most of sequence - leave one residue remaining
- cs.hideColumns(1, 3);
- cs.hideColumns(6, 11);
- assertEquals("-D",
- cs.getVisibleSequenceStrings(0, 5, new SequenceI[] { seq })[0]);
- assertEquals(
- Arrays.toString(new int[] { 1, 1, 3, 3,
- seq.findIndex(seq.getStart()) - 1,
- seq.findIndex(seq.getEnd()) - 1 }),
- Arrays.toString(cs.locateVisibleBoundsOfSequence(seq)));
- cs.revealAllHiddenColumns();
-
- // hide whole sequence - should just get location of hidden region
- // containing sequence
- cs.hideColumns(1, 11);
- assertEquals(
- Arrays.toString(new int[] { 0, 1, 0, 0,
- seq.findIndex(seq.getStart()) - 1,
- seq.findIndex(seq.getEnd()) - 1 }),
- Arrays.toString(cs.locateVisibleBoundsOfSequence(seq)));
-
- }
-
- @Test(groups = { "Functional" })
- public void testLocateVisibleBoundsPathologicals()
- {
- // test some pathological cases we missed
- AlignmentI al = new Alignment(new SequenceI[] { new Sequence(
- "refseqGaptest", "KTDVTI----------NFI-----G----L") });
- ColumnSelection cs = new ColumnSelection();
- cs.hideInsertionsFor(al.getSequenceAt(0));
- assertEquals(
- "G",
- ""
- + al.getSequenceAt(0).getCharAt(
- cs.adjustForHiddenColumns(9)));
-
- }
-
- @Test(groups = { "Functional" })
- public void testHideColumns()
- {
- ColumnSelection cs = new ColumnSelection();
- cs.hideColumns(5);
- List<int[]> hidden = cs.getHiddenColumns();
- assertEquals(1, hidden.size());
- assertEquals("[5, 5]", Arrays.toString(hidden.get(0)));
-
- cs.hideColumns(3);
- assertEquals(2, hidden.size());
- // two hidden ranges, in order:
- assertSame(hidden, cs.getHiddenColumns());
- assertEquals("[3, 3]", Arrays.toString(hidden.get(0)));
- assertEquals("[5, 5]", Arrays.toString(hidden.get(1)));
-
- // hiding column 4 expands [3, 3] to [3, 4]
- // and merges to [5, 5] to make [3, 5]
- cs.hideColumns(4);
- hidden = cs.getHiddenColumns();
- assertEquals(1, hidden.size());
- assertEquals("[3, 5]", Arrays.toString(hidden.get(0)));
-
- // clear hidden columns (note they are added to selected)
- cs.revealAllHiddenColumns();
- // it is now actually null but getter returns an empty list
- assertTrue(cs.getHiddenColumns().isEmpty());
-
- cs.hideColumns(3, 6);
- hidden = cs.getHiddenColumns();
- int[] firstHiddenRange = hidden.get(0);
- assertEquals("[3, 6]", Arrays.toString(firstHiddenRange));
-
- // adding a subrange of already hidden should do nothing
- cs.hideColumns(4, 5);
- assertEquals(1, hidden.size());
- assertSame(firstHiddenRange, cs.getHiddenColumns().get(0));
- cs.hideColumns(3, 5);
- assertEquals(1, hidden.size());
- assertSame(firstHiddenRange, cs.getHiddenColumns().get(0));
- cs.hideColumns(4, 6);
- assertEquals(1, hidden.size());
- assertSame(firstHiddenRange, cs.getHiddenColumns().get(0));
- cs.hideColumns(3, 6);
- assertEquals(1, hidden.size());
- assertSame(firstHiddenRange, cs.getHiddenColumns().get(0));
-
- cs.revealAllHiddenColumns();
- cs.hideColumns(2, 4);
- hidden = cs.getHiddenColumns();
- assertEquals(1, hidden.size());
- assertEquals("[2, 4]", Arrays.toString(hidden.get(0)));
-
- // extend contiguous with 2 positions overlap
- cs.hideColumns(3, 5);
- assertEquals(1, hidden.size());
- assertEquals("[2, 5]", Arrays.toString(hidden.get(0)));
-
- // extend contiguous with 1 position overlap
- cs.hideColumns(5, 6);
- assertEquals(1, hidden.size());
- assertEquals("[2, 6]", Arrays.toString(hidden.get(0)));
-
- // extend contiguous with overlap both ends:
- cs.hideColumns(1, 7);
- assertEquals(1, hidden.size());
- assertEquals("[1, 7]", Arrays.toString(hidden.get(0)));
+ assertEquals(Integer.valueOf(5), sel.get(0));
}
/**
@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.hideColumns(5);
+ cs.hideSelectedColumns(5, al.getHiddenColumns());
// 4,5,6 now hidden:
- List<int[]> hidden = cs.getHiddenColumns();
- 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());
// 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.hideColumns(4);
- hidden = cs.getHiddenColumns();
- assertEquals(1, hidden.size());
- assertEquals("[4, 6]", Arrays.toString(hidden.get(0)));
+ 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.hideColumns(6);
- hidden = cs.getHiddenColumns();
- assertEquals(1, hidden.size());
- assertEquals("[4, 6]", Arrays.toString(hidden.get(0)));
+ 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.hideColumns(5);
- hidden = cs.getHiddenColumns();
- assertEquals(1, hidden.size());
- assertEquals("[4, 6]", Arrays.toString(hidden.get(0)));
+ 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(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);
}
- cs.hideColumns(15, 18);
- cs.hideSelectedColumns();
+ HiddenColumns cols = al.getHiddenColumns();
+ cols.hideColumns(15, 18);
+
+ cs.hideSelectedColumns(al);
assertTrue(cs.getSelected().isEmpty());
- List<int[]> hidden = cs.getHiddenColumns();
- 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()));
}
/**
assertEquals("[0, 4]", Arrays.toString(range.get(0)));
}
- /**
- * Test the method that reveals a range of hidden columns given the start
- * column of the range
- */
- @Test(groups = { "Functional" })
- public void testRevealHiddenColumns()
- {
- ColumnSelection cs = new ColumnSelection();
- cs.hideColumns(5, 8);
- cs.addElement(10);
- cs.revealHiddenColumns(5);
- // hidden columns list now null but getter returns empty list:
- assertTrue(cs.getHiddenColumns().isEmpty());
- // revealed columns are marked as selected (added to selection):
- assertEquals("[10, 5, 6, 7, 8]", cs.getSelected().toString());
-
- // calling with a column other than the range start does nothing:
- cs = new ColumnSelection();
- cs.hideColumns(5, 8);
- List<int[]> hidden = cs.getHiddenColumns();
- cs.revealHiddenColumns(6);
- assertSame(hidden, cs.getHiddenColumns());
- assertTrue(cs.getSelected().isEmpty());
- }
-
- @Test(groups = { "Functional" })
- public void testRevealAllHiddenColumns()
- {
- ColumnSelection cs = new ColumnSelection();
- cs.hideColumns(5, 8);
- cs.hideColumns(2, 3);
- cs.addElement(11);
- cs.addElement(1);
- cs.revealAllHiddenColumns();
-
- /*
- * revealing hidden columns adds them (in order) to the (unordered)
- * selection list
- */
- assertTrue(cs.getHiddenColumns().isEmpty());
- assertEquals("[11, 1, 2, 3, 5, 6, 7, 8]", cs.getSelected().toString());
- }
-
- @Test(groups = { "Functional" })
- public void testIsVisible()
- {
- ColumnSelection cs = new ColumnSelection();
- cs.hideColumns(2, 4);
- cs.hideColumns(6, 7);
- assertTrue(cs.isVisible(0));
- assertTrue(cs.isVisible(-99));
- assertTrue(cs.isVisible(1));
- assertFalse(cs.isVisible(2));
- assertFalse(cs.isVisible(3));
- assertFalse(cs.isVisible(4));
- assertTrue(cs.isVisible(5));
- assertFalse(cs.isVisible(6));
- assertFalse(cs.isVisible(7));
- }
-
- @Test(groups = { "Functional" })
- public void testGetVisibleContigs()
- {
- ColumnSelection cs = new ColumnSelection();
- cs.hideColumns(3, 6);
- cs.hideColumns(8, 9);
- cs.hideColumns(12, 12);
-
- // start position is inclusive, end position exclusive:
- int[] visible = cs.getVisibleContigs(1, 13);
- assertEquals("[1, 2, 7, 7, 10, 11]", Arrays.toString(visible));
-
- visible = cs.getVisibleContigs(4, 14);
- assertEquals("[7, 7, 10, 11, 13, 13]", Arrays.toString(visible));
-
- visible = cs.getVisibleContigs(3, 10);
- assertEquals("[7, 7]", Arrays.toString(visible));
-
- visible = cs.getVisibleContigs(4, 6);
- assertEquals("[]", Arrays.toString(visible));
- }
-
@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);
- cs.hideColumns(3, 3);
- cs.hideColumns(6, 6);
+
+ HiddenColumns cols = al.getHiddenColumns();
+ cols.hideColumns(3, 3);
+ cols.hideColumns(6, 6);
// invert selection from start (inclusive) to end (exclusive)
- // hidden columns are _not_ changed
- cs.invertColumnSelection(2, 9);
+ cs.invertColumnSelection(2, 9, al);
assertEquals("[2, 5, 7]", cs.getSelected().toString());
- cs.invertColumnSelection(1, 9);
+ cs.invertColumnSelection(1, 9, al);
assertEquals("[1, 4, 8]", cs.getSelected().toString());
}
cs.addElement(0);
cs.addElement(513);
cs.addElement(1);
- cs.hideColumns(3);
- cs.hideColumns(7);
- cs.hideColumns(5, 9);
// same selections added in a different order
ColumnSelection cs2 = new ColumnSelection();
cs2.addElement(513);
cs2.addElement(0);
- // with no hidden columns
- assertFalse(cs.equals(cs2));
- assertFalse(cs2.equals(cs));
-
- // with hidden columns added in a different order
- cs2.hideColumns(6, 9);
- cs2.hideColumns(5, 8);
- cs2.hideColumns(3);
-
assertTrue(cs.equals(cs2));
assertTrue(cs.equals(cs));
assertTrue(cs2.equals(cs));
cs2.removeElement(12);
assertTrue(cs.equals(cs2));
-
- cs2.hideColumns(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));
}
+ /*
+ 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 returns selected columns, in the order in which they
* were added
*/
@Test(
groups = "Functional",
- expectedExceptions = { ConcurrentModificationException.class })
+ expectedExceptions =
+ { ConcurrentModificationException.class })
public void testGetSelected_concurrentModification()
{
ColumnSelection cs = new ColumnSelection();
ColumnSelection cs = new ColumnSelection();
cs.addElement(3);
cs.addElement(1);
- cs.hideColumns(10, 11);
- cs.hideColumns(5, 7);
- assertEquals("[5, 7]", Arrays.toString(cs.getHiddenColumns().get(0)));
ColumnSelection cs2 = new ColumnSelection(cs);
assertTrue(cs2.hasSelectedColumns());
- assertTrue(cs2.hasHiddenColumns());
+
// order of column selection is preserved
assertEquals("[3, 1]", cs2.getSelected().toString());
- assertEquals(2, cs2.getHiddenColumns().size());
- // hidden columns are held in column order
- assertEquals("[5, 7]", Arrays.toString(cs2.getHiddenColumns().get(0)));
- assertEquals("[10, 11]", Arrays.toString(cs2.getHiddenColumns().get(1)));
- }
-
- /**
- * Test for the case when a hidden range encloses more one already hidden
- * range
- */
- @Test(groups = { "Functional" })
- public void testHideColumns_subsumingHidden()
- {
- /*
- * JAL-2370 bug scenario:
- * two hidden ranges subsumed by a third
- */
- ColumnSelection cs = new ColumnSelection();
- cs.hideColumns(49, 59);
- cs.hideColumns(69, 79);
- List<int[]> hidden = cs.getHiddenColumns();
- assertEquals(2, hidden.size());
- assertEquals("[49, 59]", Arrays.toString(hidden.get(0)));
- assertEquals("[69, 79]", Arrays.toString(hidden.get(1)));
-
- cs.hideColumns(48, 80);
- hidden = cs.getHiddenColumns();
- assertEquals(1, hidden.size());
- assertEquals("[48, 80]", Arrays.toString(hidden.get(0)));
-
- /*
- * another...joining hidden ranges
- */
- cs = new ColumnSelection();
- cs.hideColumns(10, 20);
- cs.hideColumns(30, 40);
- cs.hideColumns(50, 60);
- // hiding 21-49 should merge to one range
- cs.hideColumns(21, 49);
- hidden = cs.getHiddenColumns();
- assertEquals(1, hidden.size());
- assertEquals("[10, 60]", Arrays.toString(hidden.get(0)));
-
- /*
- * another...lef overlap, subsumption, right overlap,
- * no overlap of existing hidden ranges
- */
- cs = new ColumnSelection();
- cs.hideColumns(10, 20);
- cs.hideColumns(10, 20);
- cs.hideColumns(30, 35);
- cs.hideColumns(40, 50);
- cs.hideColumns(60, 70);
-
- cs.hideColumns(15, 45);
- hidden = cs.getHiddenColumns();
- assertEquals(2, hidden.size());
- assertEquals("[10, 50]", Arrays.toString(hidden.get(0)));
- assertEquals("[60, 70]", Arrays.toString(hidden.get(1)));
}
@Test(groups = { "Functional" })
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));
+ }
}
git://source.jalview.org / jalview.git / blobdiff