import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.SearchResults;
-import jalview.datamodel.SearchResults.Match;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.SearchResultMatchI;
+import jalview.datamodel.SearchResultsI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignViewport;
+import jalview.gui.JvOptionPane;
import jalview.io.DataSourceType;
import jalview.io.FileFormat;
import jalview.io.FileFormatI;
import java.util.Arrays;
import java.util.List;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class MappingUtilsTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
private AlignViewportI dnaView;
private AlignViewportI proteinView;
/*
* Check protein residue 12 maps to codon 5-7, 13 to codon 8-10
*/
- SearchResults sr = MappingUtils.buildSearchResults(aseq1, 12, acfList);
+ SearchResultsI sr = MappingUtils.buildSearchResults(aseq1, 12, acfList);
assertEquals(1, sr.getResults().size());
- Match m = sr.getResults().get(0);
+ SearchResultMatchI m = sr.getResults().get(0);
assertEquals(seq1.getDatasetSequence(), m.getSequence());
assertEquals(5, m.getStart());
assertEquals(7, m.getEnd());
/*
* Check protein residue 8 maps to [6, 8, 9]
*/
- SearchResults sr = MappingUtils.buildSearchResults(aseq1, 8, acfList);
+ SearchResultsI sr = MappingUtils.buildSearchResults(aseq1, 8, acfList);
assertEquals(2, sr.getResults().size());
- Match m = sr.getResults().get(0);
+ SearchResultMatchI m = sr.getResults().get(0);
assertEquals(seq1.getDatasetSequence(), m.getSequence());
assertEquals(6, m.getStart());
assertEquals(6, m.getEnd());
setupMappedAlignments();
ColumnSelection colsel = new ColumnSelection();
+ HiddenColumns hidden = new HiddenColumns();
/*
* Column 0 in protein picks up Seq2/L, Seq3/G which map to cols 0-4 and 0-3
* in dna respectively, overall 0-4
*/
colsel.addElement(0);
- ColumnSelection cs = MappingUtils.mapColumnSelection(colsel,
- proteinView, dnaView);
+ ColumnSelection cs = new ColumnSelection();
+ HiddenColumns hs = new HiddenColumns();
+ MappingUtils.mapColumnSelection(colsel, hidden, proteinView, dnaView,
+ cs, hs);
assertEquals("[0, 1, 2, 3, 4]", cs.getSelected().toString());
/*
* Column 1 in protein picks up Seq1/K which maps to cols 0-3 in dna
*/
+ cs.clear();
colsel.clear();
colsel.addElement(1);
- cs = MappingUtils.mapColumnSelection(colsel, proteinView, dnaView);
+ MappingUtils.mapColumnSelection(colsel, hidden, proteinView, dnaView,
+ cs, hs);
assertEquals("[0, 1, 2, 3]", cs.getSelected().toString());
/*
* Column 2 in protein picks up gaps only - no mapping
*/
+ cs.clear();
colsel.clear();
colsel.addElement(2);
- cs = MappingUtils.mapColumnSelection(colsel, proteinView, dnaView);
+ MappingUtils.mapColumnSelection(colsel, hidden, proteinView,
+ dnaView, cs, hs);
assertEquals("[]", cs.getSelected().toString());
/*
* Column 3 in protein picks up Seq1/P, Seq2/Q, Seq3/S which map to columns
* 6-9, 6-10, 5-8 respectively, overall to 5-10
*/
+ cs.clear();
colsel.clear();
colsel.addElement(3);
- cs = MappingUtils.mapColumnSelection(colsel, proteinView, dnaView);
+ MappingUtils.mapColumnSelection(colsel, hidden, proteinView,
+ dnaView, cs, hs);
assertEquals("[5, 6, 7, 8, 9, 10]", cs.getSelected().toString());
/*
* Combine selection of columns 1 and 3 to get a discontiguous mapped
* selection
*/
+ cs.clear();
colsel.clear();
colsel.addElement(1);
colsel.addElement(3);
- cs = MappingUtils.mapColumnSelection(colsel, proteinView, dnaView);
+ MappingUtils.mapColumnSelection(colsel, hidden, proteinView,
+ dnaView, cs, hs);
assertEquals("[0, 1, 2, 3, 5, 6, 7, 8, 9, 10]", cs.getSelected()
.toString());
}
setupMappedAlignments();
ColumnSelection colsel = new ColumnSelection();
+ HiddenColumns hidden = new HiddenColumns();
/*
* Column 0 in dna picks up first bases which map to residue 1, columns 0-1
* in protein.
*/
+ ColumnSelection cs = new ColumnSelection();
+ HiddenColumns hs = new HiddenColumns();
colsel.addElement(0);
- ColumnSelection cs = MappingUtils.mapColumnSelection(colsel, dnaView,
- proteinView);
+ MappingUtils.mapColumnSelection(colsel, hidden, dnaView, proteinView,
+ cs, hs);
assertEquals("[0, 1]", cs.getSelected().toString());
/*
colsel.addElement(3);
colsel.addElement(4);
colsel.addElement(5);
- cs = MappingUtils.mapColumnSelection(colsel, dnaView, proteinView);
+ cs.clear();
+ MappingUtils.mapColumnSelection(colsel, hidden, dnaView, proteinView,
+ cs, hs);
assertEquals("[0, 1, 3]", cs.getSelected().toString());
}
public void testMapColumnSelection_null() throws IOException
{
setupMappedAlignments();
- ColumnSelection cs = MappingUtils.mapColumnSelection(null, dnaView,
- proteinView);
+ ColumnSelection cs = new ColumnSelection();
+ HiddenColumns hs = new HiddenColumns();
+ MappingUtils.mapColumnSelection(null, null, dnaView, proteinView, cs,
+ hs);
assertTrue("mapped selection not empty", cs.getSelected().isEmpty());
}
AlignedCodonFrame acf3 = new AlignedCodonFrame();
acf3.addMap(seq3.getDatasetSequence(), seq1.getDatasetSequence(), map);
- List<AlignedCodonFrame> mappings = new ArrayList<AlignedCodonFrame>();
+ List<AlignedCodonFrame> mappings = new ArrayList<>();
mappings.add(acf1);
mappings.add(acf2);
mappings.add(acf3);
assertEquals(0, result.size());
}
+ /**
+ * just like the one above, but this time, we provide a set of sequences to
+ * subselect the mapping search
+ */
+ @Test(groups = { "Functional" })
+ public void testFindMappingsForSequenceAndOthers()
+ {
+ SequenceI seq1 = new Sequence("Seq1", "ABC");
+ SequenceI seq2 = new Sequence("Seq2", "ABC");
+ SequenceI seq3 = new Sequence("Seq3", "ABC");
+ SequenceI seq4 = new Sequence("Seq4", "ABC");
+ seq1.createDatasetSequence();
+ seq2.createDatasetSequence();
+ seq3.createDatasetSequence();
+ seq4.createDatasetSequence();
+
+ /*
+ * Create mappings from seq1 to seq2, seq2 to seq1, seq3 to seq1, seq3 to seq4
+ */
+ AlignedCodonFrame acf1 = new AlignedCodonFrame();
+ MapList map = new MapList(new int[] { 1, 3 }, new int[] { 1, 3 }, 1, 1);
+ acf1.addMap(seq1.getDatasetSequence(), seq2.getDatasetSequence(), map);
+ AlignedCodonFrame acf2 = new AlignedCodonFrame();
+ acf2.addMap(seq2.getDatasetSequence(), seq1.getDatasetSequence(), map);
+ AlignedCodonFrame acf3 = new AlignedCodonFrame();
+ acf3.addMap(seq3.getDatasetSequence(), seq1.getDatasetSequence(), map);
+ AlignedCodonFrame acf4 = new AlignedCodonFrame();
+ acf4.addMap(seq3.getDatasetSequence(), seq4.getDatasetSequence(), map);
+
+ List<AlignedCodonFrame> mappings = new ArrayList<>();
+ mappings.add(acf1);
+ mappings.add(acf2);
+ mappings.add(acf3);
+ mappings.add(acf4);
+
+ /*
+ * test for null args
+ */
+ List<AlignedCodonFrame> result = MappingUtils
+ .findMappingsForSequenceAndOthers(null, mappings,
+ Arrays.asList(new SequenceI[] { seq1, seq2 }));
+ assertTrue(result.isEmpty());
+
+ result = MappingUtils.findMappingsForSequenceAndOthers(seq1, null,
+ Arrays.asList(new SequenceI[] { seq1, seq2 }));
+ assertTrue(result.isEmpty());
+
+ /*
+ * Seq1 has three mappings, but filter argument will only accept
+ * those to seq2
+ */
+ result = MappingUtils.findMappingsForSequenceAndOthers(
+ seq1,
+ mappings,
+ Arrays.asList(new SequenceI[] { seq1, seq2,
+ seq1.getDatasetSequence() }));
+ assertEquals(2, result.size());
+ assertTrue(result.contains(acf1));
+ assertTrue(result.contains(acf2));
+ assertFalse("Did not expect to find mapping acf3 - subselect failed",
+ result.contains(acf3));
+ assertFalse(
+ "Did not expect to find mapping acf4 - doesn't involve sequence",
+ result.contains(acf4));
+
+ /*
+ * and verify the no filter case
+ */
+ result = MappingUtils.findMappingsForSequenceAndOthers(seq1, mappings,
+ null);
+ assertEquals(3, result.size());
+ assertTrue(result.contains(acf1));
+ assertTrue(result.contains(acf2));
+ assertTrue(result.contains(acf3));
+ }
+
@Test(groups = { "Functional" })
public void testMapEditCommand()
{
AlignedCodonFrame acf = new AlignedCodonFrame();
MapList map = new MapList(new int[] { 8, 16 }, new int[] { 5, 7 }, 3, 1);
acf.addMap(dna.getDatasetSequence(), protein.getDatasetSequence(), map);
- List<AlignedCodonFrame> mappings = new ArrayList<AlignedCodonFrame>();
+ List<AlignedCodonFrame> mappings = new ArrayList<>();
mappings.add(acf);
AlignmentI prot = new Alignment(new SequenceI[] { protein });
public void testMapColumnSelection_hiddenColumns() throws IOException
{
setupMappedAlignments();
-
+
ColumnSelection proteinSelection = new ColumnSelection();
+ HiddenColumns hiddenCols = new HiddenColumns();
/*
* Column 0 in protein picks up Seq2/L, Seq3/G which map to cols 0-4 and 0-3
* in dna respectively, overall 0-4
*/
- proteinSelection.hideColumns(0);
- ColumnSelection dnaSelection = MappingUtils.mapColumnSelection(proteinSelection,
- proteinView, dnaView);
+ proteinSelection.hideSelectedColumns(0, hiddenCols);
+ ColumnSelection dnaSelection = new ColumnSelection();
+ HiddenColumns dnaHidden = new HiddenColumns();
+ MappingUtils.mapColumnSelection(proteinSelection, hiddenCols,
+ proteinView, dnaView, dnaSelection, dnaHidden);
assertEquals("[]", dnaSelection.getSelected().toString());
- List<int[]> hidden = dnaSelection.getHiddenColumns();
+ List<int[]> hidden = dnaHidden.getHiddenColumnsCopy();
assertEquals(1, hidden.size());
assertEquals("[0, 4]", Arrays.toString(hidden.get(0)));
/*
* Column 1 in protein picks up Seq1/K which maps to cols 0-3 in dna
*/
- proteinSelection.revealAllHiddenColumns();
+ dnaSelection = new ColumnSelection();
+ dnaHidden = new HiddenColumns();
+ hiddenCols.revealAllHiddenColumns(proteinSelection);
// the unhidden columns are now marked selected!
assertEquals("[0]", proteinSelection.getSelected().toString());
// deselect these or hideColumns will be expanded to include 0
proteinSelection.clear();
- proteinSelection.hideColumns(1);
- dnaSelection = MappingUtils.mapColumnSelection(proteinSelection, proteinView, dnaView);
- hidden = dnaSelection.getHiddenColumns();
+ proteinSelection.hideSelectedColumns(1, hiddenCols);
+ MappingUtils.mapColumnSelection(proteinSelection, hiddenCols,
+ proteinView, dnaView, dnaSelection, dnaHidden);
+ hidden = dnaHidden.getHiddenColumnsCopy();
assertEquals(1, hidden.size());
assertEquals("[0, 3]", Arrays.toString(hidden.get(0)));
/*
* Column 2 in protein picks up gaps only - no mapping
*/
- proteinSelection.revealAllHiddenColumns();
+ dnaSelection = new ColumnSelection();
+ dnaHidden = new HiddenColumns();
+ hiddenCols.revealAllHiddenColumns(proteinSelection);
proteinSelection.clear();
- proteinSelection.hideColumns(2);
- dnaSelection = MappingUtils.mapColumnSelection(proteinSelection, proteinView, dnaView);
- assertTrue(dnaSelection.getHiddenColumns().isEmpty());
+ proteinSelection.hideSelectedColumns(2, hiddenCols);
+ MappingUtils.mapColumnSelection(proteinSelection, hiddenCols,
+ proteinView, dnaView, dnaSelection, dnaHidden);
+ assertTrue(dnaHidden.getHiddenColumnsCopy().isEmpty());
/*
* Column 3 in protein picks up Seq1/P, Seq2/Q, Seq3/S which map to columns
* 6-9, 6-10, 5-8 respectively, overall to 5-10
*/
- proteinSelection.revealAllHiddenColumns();
+ dnaSelection = new ColumnSelection();
+ dnaHidden = new HiddenColumns();
+ hiddenCols.revealAllHiddenColumns(proteinSelection);
proteinSelection.clear();
- proteinSelection.hideColumns(3); // 5-10 hidden in dna
+ proteinSelection.hideSelectedColumns(3, hiddenCols); // 5-10 hidden in dna
proteinSelection.addElement(1); // 0-3 selected in dna
- dnaSelection = MappingUtils.mapColumnSelection(proteinSelection, proteinView, dnaView);
+ MappingUtils.mapColumnSelection(proteinSelection, hiddenCols,
+ proteinView, dnaView, dnaSelection, dnaHidden);
assertEquals("[0, 1, 2, 3]", dnaSelection.getSelected().toString());
- hidden = dnaSelection.getHiddenColumns();
+ hidden = dnaHidden.getHiddenColumnsCopy();
assertEquals(1, hidden.size());
assertEquals("[5, 10]", Arrays.toString(hidden.get(0)));
/*
* Combine hiding columns 1 and 3 to get discontiguous hidden columns
*/
- proteinSelection.revealAllHiddenColumns();
+ dnaSelection = new ColumnSelection();
+ dnaHidden = new HiddenColumns();
+ hiddenCols.revealAllHiddenColumns(proteinSelection);
proteinSelection.clear();
- proteinSelection.hideColumns(1);
- proteinSelection.hideColumns(3);
- dnaSelection = MappingUtils.mapColumnSelection(proteinSelection, proteinView, dnaView);
- hidden = dnaSelection.getHiddenColumns();
+ proteinSelection.hideSelectedColumns(1, hiddenCols);
+ proteinSelection.hideSelectedColumns(3, hiddenCols);
+ MappingUtils.mapColumnSelection(proteinSelection, hiddenCols,
+ proteinView, dnaView, dnaSelection, dnaHidden);
+ hidden = dnaHidden.getHiddenColumnsCopy();
assertEquals(2, hidden.size());
assertEquals("[0, 3]", Arrays.toString(hidden.get(0)));
assertEquals("[5, 10]", Arrays.toString(hidden.get(1)));
/*
* [start, end] ranges
*/
- List<int[]> ranges = new ArrayList<int[]>();
+ List<int[]> ranges = new ArrayList<>();
assertEquals(0, MappingUtils.getLength(ranges));
ranges.add(new int[] { 1, 1 });
assertEquals(1, MappingUtils.getLength(ranges));
public void testContains()
{
assertFalse(MappingUtils.contains(null, 1));
- List<int[]> ranges = new ArrayList<int[]>();
+ List<int[]> ranges = new ArrayList<>();
assertFalse(MappingUtils.contains(ranges, 1));
ranges.add(new int[] { 1, 4 });
int[] adjusted = MappingUtils.removeStartPositions(0, ranges);
assertEquals("[10, 1]", Arrays.toString(adjusted));
assertEquals("[10, 1]", Arrays.toString(ranges));
-
+
ranges = adjusted;
adjusted = MappingUtils.removeStartPositions(1, ranges);
assertEquals("[9, 1]", Arrays.toString(adjusted));
assertEquals("[10, 1]", Arrays.toString(ranges));
-
+
ranges = adjusted;
adjusted = MappingUtils.removeStartPositions(1, ranges);
assertEquals("[8, 1]", Arrays.toString(adjusted));
assertEquals("[9, 1]", Arrays.toString(ranges));
-
+
ranges = new int[] { 12, 11, 9, 6 };
adjusted = MappingUtils.removeStartPositions(1, ranges);
assertEquals("[11, 11, 9, 6]", Arrays.toString(adjusted));
assertEquals("[12, 11, 9, 6]", Arrays.toString(ranges));
-
+
ranges = new int[] { 12, 12, 8, 4 };
adjusted = MappingUtils.removeStartPositions(1, ranges);
assertEquals("[8, 4]", Arrays.toString(adjusted));
assertEquals("[12, 12, 8, 4]", Arrays.toString(ranges));
-
+
ranges = new int[] { 12, 12, 8, 4 };
adjusted = MappingUtils.removeStartPositions(2, ranges);
assertEquals("[7, 4]", Arrays.toString(adjusted));
assertEquals("[12, 12, 8, 4]", Arrays.toString(ranges));
-
+
ranges = new int[] { 12, 12, 10, 10, 8, 4 };
adjusted = MappingUtils.removeStartPositions(1, ranges);
assertEquals("[10, 10, 8, 4]", Arrays.toString(adjusted));
assertEquals("[12, 12, 10, 10, 8, 4]", Arrays.toString(ranges));
-
+
ranges = new int[] { 12, 12, 10, 10, 8, 4 };
adjusted = MappingUtils.removeStartPositions(2, ranges);
assertEquals("[8, 4]", Arrays.toString(adjusted));
assertEquals("[12, 12, 10, 10, 8, 4]", Arrays.toString(ranges));
-
+
ranges = new int[] { 12, 11, 8, 4 };
adjusted = MappingUtils.removeStartPositions(3, ranges);
assertEquals("[7, 4]", Arrays.toString(adjusted));
assertEquals("[12, 11, 8, 4]", Arrays.toString(ranges));
}
+ @Test(groups = { "Functional" })
+ public void testRangeContains()
+ {
+ /*
+ * both forward ranges
+ */
+ assertTrue(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+ 1, 10 }));
+ assertTrue(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+ 2, 10 }));
+ assertTrue(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+ 1, 9 }));
+ assertTrue(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+ 4, 5 }));
+ assertFalse(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+ 0, 9 }));
+ assertFalse(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+ -10, -9 }));
+ assertFalse(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+ 1, 11 }));
+ assertFalse(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+ 11, 12 }));
+
+ /*
+ * forward range, reverse query
+ */
+ assertTrue(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+ 10, 1 }));
+ assertTrue(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+ 9, 1 }));
+ assertTrue(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+ 10, 2 }));
+ assertTrue(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+ 5, 5 }));
+ assertFalse(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+ 11, 1 }));
+ assertFalse(MappingUtils.rangeContains(new int[] { 1, 10 }, new int[] {
+ 10, 0 }));
+
+ /*
+ * reverse range, forward query
+ */
+ assertTrue(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+ 1, 10 }));
+ assertTrue(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+ 1, 9 }));
+ assertTrue(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+ 2, 10 }));
+ assertTrue(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+ 6, 6 }));
+ assertFalse(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+ 6, 11 }));
+ assertFalse(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+ 11, 20 }));
+ assertFalse(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+ -3, -2 }));
+
+ /*
+ * both reverse
+ */
+ assertTrue(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+ 10, 1 }));
+ assertTrue(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+ 9, 1 }));
+ assertTrue(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+ 10, 2 }));
+ assertTrue(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+ 3, 3 }));
+ assertFalse(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+ 11, 1 }));
+ assertFalse(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+ 10, 0 }));
+ assertFalse(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+ 12, 11 }));
+ assertFalse(MappingUtils.rangeContains(new int[] { 10, 1 }, new int[] {
+ -5, -8 }));
+
+ /*
+ * bad arguments
+ */
+ assertFalse(MappingUtils.rangeContains(new int[] { 1, 10, 12 },
+ new int[] {
+ 1, 10 }));
+ assertFalse(MappingUtils.rangeContains(new int[] { 1, 10 },
+ new int[] { 1 }));
+ assertFalse(MappingUtils.rangeContains(new int[] { 1, 10 }, null));
+ assertFalse(MappingUtils.rangeContains(null, new int[] { 1, 10 }));
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff