package jalview.util;
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 java.awt.Color;
import java.io.IOException;
+import java.util.ArrayList;
import java.util.Arrays;
-import java.util.Collections;
-import java.util.HashSet;
-import java.util.LinkedHashSet;
import java.util.List;
-import java.util.Set;
import org.testng.annotations.Test;
MapList map = new MapList(new int[] { 5, 10 }, new int[] { 12, 13 }, 3,
1);
acf.addMap(seq1.getDatasetSequence(), aseq1.getDatasetSequence(), map);
- Set<AlignedCodonFrame> acfList = Collections.singleton(acf);
+ List<AlignedCodonFrame> acfList = Arrays.asList(new AlignedCodonFrame[]
+ { acf });
/*
* Check protein residue 12 maps to codon 5-7, 13 to codon 8-10
MapList map = new MapList(new int[] { 6, 6, 8, 9, 11, 11, 13, 13, 15,
15 }, new int[] { 8, 9 }, 3, 1);
acf.addMap(seq1.getDatasetSequence(), aseq1.getDatasetSequence(), map);
- Set<AlignedCodonFrame> acfList = Collections.singleton(acf);
+ List<AlignedCodonFrame> acfList = Arrays.asList(new AlignedCodonFrame[]
+ { acf });
/*
* Check protein residue 8 maps to [6, 8, 9]
acf.addMap(cdna.getSequenceAt(seq).getDatasetSequence(), protein
.getSequenceAt(seq).getDatasetSequence(), map);
}
- Set<AlignedCodonFrame> acfList = Collections.singleton(acf);
+ List<AlignedCodonFrame> acfList = Arrays.asList(new AlignedCodonFrame[]
+ { acf });
AlignViewportI dnaView = new AlignViewport(cdna);
AlignViewportI proteinView = new AlignViewport(protein);
protected void setupMappedAlignments() throws IOException
{
/*
- * Set up dna and protein Seq1/2/3 with mappings (held on the protein
- * viewport). Lower case for introns.
+ * Map (upper-case = coding):
+ * Seq1/10-18 AC-GctGtC-T to Seq1/40 -K-P
+ * Seq2/20-27 Tc-GA-G-T-T to Seq2/20-27 L--Q
+ * Seq3/30-38 TtTT-AaCGg- to Seq3/60-61\nG--S
*/
AlignmentI cdna = loadAlignment(">Seq1/10-18\nAC-GctGtC-T\n"
+ ">Seq2/20-27\nTc-GA-G-T-Tc\n" + ">Seq3/30-38\nTtTT-AaCGg-\n",
61 }, 3, 1);
acf.addMap(cdna.getSequenceAt(2).getDatasetSequence(), protein
.getSequenceAt(2).getDatasetSequence(), map);
- Set<AlignedCodonFrame> acfList = Collections.singleton(acf);
+ List<AlignedCodonFrame> acfList = Arrays.asList(new AlignedCodonFrame[]
+ { acf });
dnaView = new AlignViewport(cdna);
proteinView = new AlignViewport(protein);
acf.addMap(cdna.getSequenceAt(seq).getDatasetSequence(), protein
.getSequenceAt(seq).getDatasetSequence(), map);
}
- Set<AlignedCodonFrame> acfList = Collections.singleton(acf);
+ List<AlignedCodonFrame> acfList = Arrays.asList(new AlignedCodonFrame[]
+ { acf });
AlignViewportI dnaView = new AlignViewport(cdna);
AlignViewportI proteinView = new AlignViewport(protein);
acf.addMap(cdna.getSequenceAt(seq).getDatasetSequence(), protein
.getSequenceAt(seq).getDatasetSequence(), map);
}
- Set<AlignedCodonFrame> acfList = Collections.singleton(acf);
+ List<AlignedCodonFrame> acfList = Arrays.asList(new AlignedCodonFrame[]
+ { acf });
AlignViewportI dnaView = new AlignViewport(cdna);
AlignViewportI proteinView = new AlignViewport(protein);
AlignedCodonFrame acf3 = new AlignedCodonFrame();
acf3.addMap(seq3.getDatasetSequence(), seq1.getDatasetSequence(), map);
- Set<AlignedCodonFrame> mappings = new HashSet<AlignedCodonFrame>();
+ List<AlignedCodonFrame> mappings = new ArrayList<AlignedCodonFrame>();
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<AlignedCodonFrame>();
+ 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);
- Set<AlignedCodonFrame> mappings = new LinkedHashSet<AlignedCodonFrame>();
+ List<AlignedCodonFrame> mappings = new ArrayList<AlignedCodonFrame>();
mappings.add(acf);
AlignmentI prot = new Alignment(new SequenceI[] { protein });
Arrays.toString(MappingUtils.flattenRanges(new int[] { 12, 12,
9, 7, 4, 2, 1 })));
}
+
+ /**
+ * Test mapping a column selection including hidden columns
+ *
+ * @throws IOException
+ */
+ @Test(groups = { "Functional" })
+ public void testMapColumnSelection_hiddenColumns() throws IOException
+ {
+ setupMappedAlignments();
+
+ ColumnSelection proteinSelection = new ColumnSelection();
+
+ /*
+ * 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);
+ assertEquals("[]", dnaSelection.getSelected().toString());
+ List<int[]> hidden = dnaSelection.getHiddenColumns();
+ 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();
+ // 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();
+ assertEquals(1, hidden.size());
+ assertEquals("[0, 3]", Arrays.toString(hidden.get(0)));
+
+ /*
+ * Column 2 in protein picks up gaps only - no mapping
+ */
+ proteinSelection.revealAllHiddenColumns();
+ proteinSelection.clear();
+ proteinSelection.hideColumns(2);
+ dnaSelection = MappingUtils.mapColumnSelection(proteinSelection,
+ proteinView, dnaView);
+ assertTrue(dnaSelection.getHiddenColumns().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();
+ proteinSelection.clear();
+ proteinSelection.hideColumns(3); // 5-10 hidden in dna
+ proteinSelection.addElement(1); // 0-3 selected in dna
+ dnaSelection = MappingUtils.mapColumnSelection(proteinSelection,
+ proteinView, dnaView);
+ assertEquals("[0, 1, 2, 3]", dnaSelection.getSelected().toString());
+ hidden = dnaSelection.getHiddenColumns();
+ 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();
+ proteinSelection.clear();
+ proteinSelection.hideColumns(1);
+ proteinSelection.hideColumns(3);
+ dnaSelection = MappingUtils.mapColumnSelection(proteinSelection,
+ proteinView, dnaView);
+ hidden = dnaSelection.getHiddenColumns();
+ assertEquals(2, hidden.size());
+ assertEquals("[0, 3]", Arrays.toString(hidden.get(0)));
+ assertEquals("[5, 10]", Arrays.toString(hidden.get(1)));
+ }
+
+ @Test(groups = { "Functional" })
+ public void testGetLength()
+ {
+ assertEquals(0, MappingUtils.getLength(null));
+
+ /*
+ * [start, end] ranges
+ */
+ List<int[]> ranges = new ArrayList<int[]>();
+ assertEquals(0, MappingUtils.getLength(ranges));
+ ranges.add(new int[] { 1, 1 });
+ assertEquals(1, MappingUtils.getLength(ranges));
+ ranges.add(new int[] { 2, 10 });
+ assertEquals(10, MappingUtils.getLength(ranges));
+ ranges.add(new int[] { 20, 10 });
+ assertEquals(21, MappingUtils.getLength(ranges));
+
+ /*
+ * [start, end, start, end...] ranges
+ */
+ ranges.clear();
+ ranges.add(new int[] { 1, 5, 8, 4 });
+ ranges.add(new int[] { 8, 2 });
+ ranges.add(new int[] { 12, 12 });
+ assertEquals(18, MappingUtils.getLength(ranges));
+ }
+
+ @Test(groups = { "Functional" })
+ public void testContains()
+ {
+ assertFalse(MappingUtils.contains(null, 1));
+ List<int[]> ranges = new ArrayList<int[]>();
+ assertFalse(MappingUtils.contains(ranges, 1));
+
+ ranges.add(new int[] { 1, 4 });
+ ranges.add(new int[] { 6, 6 });
+ ranges.add(new int[] { 8, 10 });
+ ranges.add(new int[] { 30, 20 });
+ ranges.add(new int[] { -16, -44 });
+
+ assertFalse(MappingUtils.contains(ranges, 0));
+ assertTrue(MappingUtils.contains(ranges, 1));
+ assertTrue(MappingUtils.contains(ranges, 2));
+ assertTrue(MappingUtils.contains(ranges, 3));
+ assertTrue(MappingUtils.contains(ranges, 4));
+ assertFalse(MappingUtils.contains(ranges, 5));
+
+ assertTrue(MappingUtils.contains(ranges, 6));
+ assertFalse(MappingUtils.contains(ranges, 7));
+
+ assertTrue(MappingUtils.contains(ranges, 8));
+ assertTrue(MappingUtils.contains(ranges, 9));
+ assertTrue(MappingUtils.contains(ranges, 10));
+
+ assertFalse(MappingUtils.contains(ranges, 31));
+ assertTrue(MappingUtils.contains(ranges, 30));
+ assertTrue(MappingUtils.contains(ranges, 29));
+ assertTrue(MappingUtils.contains(ranges, 20));
+ assertFalse(MappingUtils.contains(ranges, 19));
+
+ assertFalse(MappingUtils.contains(ranges, -15));
+ assertTrue(MappingUtils.contains(ranges, -16));
+ assertTrue(MappingUtils.contains(ranges, -44));
+ assertFalse(MappingUtils.contains(ranges, -45));
+ }
+
+ /**
+ * Test the method that drops positions from the start of a mapped range
+ */
+ @Test(groups = "Functional")
+ public void testRemoveStartPositions()
+ {
+ int[] ranges = new int[] { 1, 10 };
+ int[] adjusted = MappingUtils.removeStartPositions(0, ranges);
+ assertEquals("[1, 10]", Arrays.toString(adjusted));
+
+ adjusted = MappingUtils.removeStartPositions(1, ranges);
+ assertEquals("[2, 10]", Arrays.toString(adjusted));
+ assertEquals("[1, 10]", Arrays.toString(ranges));
+
+ ranges = adjusted;
+ adjusted = MappingUtils.removeStartPositions(1, ranges);
+ assertEquals("[3, 10]", Arrays.toString(adjusted));
+ assertEquals("[2, 10]", Arrays.toString(ranges));
+
+ ranges = new int[] { 2, 3, 10, 12 };
+ adjusted = MappingUtils.removeStartPositions(1, ranges);
+ assertEquals("[3, 3, 10, 12]", Arrays.toString(adjusted));
+ assertEquals("[2, 3, 10, 12]", Arrays.toString(ranges));
+
+ ranges = new int[] { 2, 2, 8, 12 };
+ adjusted = MappingUtils.removeStartPositions(1, ranges);
+ assertEquals("[8, 12]", Arrays.toString(adjusted));
+ assertEquals("[2, 2, 8, 12]", Arrays.toString(ranges));
+
+ ranges = new int[] { 2, 2, 8, 12 };
+ adjusted = MappingUtils.removeStartPositions(2, ranges);
+ assertEquals("[9, 12]", Arrays.toString(adjusted));
+ assertEquals("[2, 2, 8, 12]", Arrays.toString(ranges));
+
+ ranges = new int[] { 2, 2, 4, 4, 9, 12 };
+ adjusted = MappingUtils.removeStartPositions(1, ranges);
+ assertEquals("[4, 4, 9, 12]", Arrays.toString(adjusted));
+ assertEquals("[2, 2, 4, 4, 9, 12]", Arrays.toString(ranges));
+
+ ranges = new int[] { 2, 2, 4, 4, 9, 12 };
+ adjusted = MappingUtils.removeStartPositions(2, ranges);
+ assertEquals("[9, 12]", Arrays.toString(adjusted));
+ assertEquals("[2, 2, 4, 4, 9, 12]", Arrays.toString(ranges));
+
+ ranges = new int[] { 2, 3, 9, 12 };
+ adjusted = MappingUtils.removeStartPositions(3, ranges);
+ assertEquals("[10, 12]", Arrays.toString(adjusted));
+ assertEquals("[2, 3, 9, 12]", Arrays.toString(ranges));
+ }
+
+ /**
+ * Test the method that drops positions from the start of a mapped range, on
+ * the reverse strand
+ */
+ @Test(groups = "Functional")
+ public void testRemoveStartPositions_reverseStrand()
+ {
+ int[] ranges = new int[] { 10, 1 };
+ 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));
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff