--- /dev/null
+package jalview.util;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertSame;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+import jalview.api.AlignViewportI;
+import jalview.datamodel.AlignedCodonFrame;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SearchResults.Match;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.gui.AlignViewport;
+import jalview.io.AppletFormatAdapter;
+import jalview.io.FormatAdapter;
+
+import java.awt.Color;
+import java.io.IOException;
+import java.util.Collections;
+import java.util.Set;
+
+import org.junit.Test;
+
+public class MappingUtilsTest
+{
+ private AlignViewportI dnaView;
+ private AlignViewportI proteinView;
+
+ /**
+ * Simple test of mapping with no intron involved.
+ */
+ @Test
+ public void testBuildSearchResults()
+ {
+ final Sequence seq1 = new Sequence("Seq1", "C-G-TA-GC");
+ seq1.createDatasetSequence();
+
+ final Sequence aseq1 = new Sequence("Seq1", "-P-R");
+ aseq1.createDatasetSequence();
+
+ /*
+ * Map dna bases 1-6 to protein residues 1-2
+ */
+ AlignedCodonFrame acf = new AlignedCodonFrame();
+ MapList map = new MapList(new int[]
+ { 1, 6 }, new int[]
+ { 1, 2 }, 3, 1);
+ acf.addMap(seq1.getDatasetSequence(), aseq1.getDatasetSequence(), map);
+ Set<AlignedCodonFrame> acfList = Collections.singleton(acf);
+
+ /*
+ * Check protein residue 1 maps to codon 1-3, 2 to codon 4-6
+ */
+ SearchResults sr = MappingUtils.buildSearchResults(aseq1, 1, acfList);
+ assertEquals(1, sr.getResults().size());
+ Match m = sr.getResults().get(0);
+ assertEquals(seq1.getDatasetSequence(), m.getSequence());
+ assertEquals(1, m.getStart());
+ assertEquals(3, m.getEnd());
+ sr = MappingUtils.buildSearchResults(aseq1, 2, acfList);
+ assertEquals(1, sr.getResults().size());
+ m = sr.getResults().get(0);
+ assertEquals(seq1.getDatasetSequence(), m.getSequence());
+ assertEquals(4, m.getStart());
+ assertEquals(6, m.getEnd());
+
+ /*
+ * Check inverse mappings, from codons 1-3, 4-6 to protein 1, 2
+ */
+ for (int i = 1; i < 7; i++)
+ {
+ sr = MappingUtils.buildSearchResults(seq1, i, acfList);
+ assertEquals(1, sr.getResults().size());
+ m = sr.getResults().get(0);
+ assertEquals(aseq1.getDatasetSequence(), m.getSequence());
+ int residue = i > 3 ? 2 : 1;
+ assertEquals(residue, m.getStart());
+ assertEquals(residue, m.getEnd());
+ }
+ }
+
+ /**
+ * Simple test of mapping with introns involved.
+ */
+ @Test
+ public void testBuildSearchResults_withIntro()
+ {
+ final Sequence seq1 = new Sequence("Seq1", "C-G-TAGA-GCAGCTT");
+ seq1.createDatasetSequence();
+
+ final Sequence aseq1 = new Sequence("Seq1", "-P-R");
+ aseq1.createDatasetSequence();
+
+ /*
+ * Map dna bases [2, 4, 5], [7, 9, 11] to protein residues 1 and 2
+ */
+ AlignedCodonFrame acf = new AlignedCodonFrame();
+ MapList map = new MapList(new int[]
+ { 2, 2, 4, 5, 7, 7, 9, 9, 11, 11 }, new int[]
+ { 1, 2 }, 3, 1);
+ acf.addMap(seq1.getDatasetSequence(), aseq1.getDatasetSequence(), map);
+ Set<AlignedCodonFrame> acfList = Collections.singleton(acf);
+
+ /*
+ * Check protein residue 1 maps to [2, 4, 5]
+ */
+ SearchResults sr = MappingUtils.buildSearchResults(aseq1, 1, acfList);
+ assertEquals(2, sr.getResults().size());
+ Match m = sr.getResults().get(0);
+ assertEquals(seq1.getDatasetSequence(), m.getSequence());
+ assertEquals(2, m.getStart());
+ assertEquals(2, m.getEnd());
+ m = sr.getResults().get(1);
+ assertEquals(seq1.getDatasetSequence(), m.getSequence());
+ assertEquals(4, m.getStart());
+ assertEquals(5, m.getEnd());
+
+ /*
+ * Check protein residue 2 maps to [7, 9, 11]
+ */
+ sr = MappingUtils.buildSearchResults(aseq1, 2, acfList);
+ assertEquals(3, sr.getResults().size());
+ m = sr.getResults().get(0);
+ assertEquals(seq1.getDatasetSequence(), m.getSequence());
+ assertEquals(7, m.getStart());
+ assertEquals(7, m.getEnd());
+ m = sr.getResults().get(1);
+ assertEquals(seq1.getDatasetSequence(), m.getSequence());
+ assertEquals(9, m.getStart());
+ assertEquals(9, m.getEnd());
+ m = sr.getResults().get(2);
+ assertEquals(seq1.getDatasetSequence(), m.getSequence());
+ assertEquals(11, m.getStart());
+ assertEquals(11, m.getEnd());
+
+ /*
+ * Check inverse mappings, from codons to protein
+ */
+ for (int i = 1; i < 14; i++)
+ {
+ sr = MappingUtils.buildSearchResults(seq1, i, acfList);
+ int residue = (i == 2 || i == 4 || i == 5) ? 1 : (i == 7 || i == 9
+ || i == 11 ? 2 : 0);
+ if (residue == 0)
+ {
+ assertEquals(0, sr.getResults().size());
+ continue;
+ }
+ assertEquals(1, sr.getResults().size());
+ m = sr.getResults().get(0);
+ assertEquals(aseq1.getDatasetSequence(), m.getSequence());
+ assertEquals(residue, m.getStart());
+ assertEquals(residue, m.getEnd());
+ }
+ }
+
+ /**
+ * Test mapping a sequence group.
+ *
+ * @throws IOException
+ */
+ @Test
+ public void testMapSequenceGroup() throws IOException
+ {
+ /*
+ * Set up dna and protein Seq1/2/3 with mappings (held on the protein
+ * viewport).
+ */
+ AlignmentI cdna = loadAlignment(">Seq1\nACG\n>Seq2\nTGA\n>Seq3\nTAC\n",
+ "FASTA");
+ cdna.setDataset(null);
+ AlignmentI protein = loadAlignment(">Seq1\nK\n>Seq2\nL\n>Seq3\nQ\n",
+ "FASTA");
+ protein.setDataset(null);
+ AlignedCodonFrame acf = new AlignedCodonFrame();
+ MapList map = new MapList(new int[]
+ { 1, 3 }, new int[]
+ { 1, 1 }, 3, 1);
+ for (int seq = 0; seq < 3; seq++)
+ {
+ acf.addMap(cdna.getSequenceAt(seq).getDatasetSequence(), protein
+ .getSequenceAt(seq).getDatasetSequence(), map);
+ }
+ Set<AlignedCodonFrame> acfList = Collections.singleton(acf);
+
+ AlignViewportI dnaView = new AlignViewport(cdna);
+ AlignViewportI proteinView = new AlignViewport(protein);
+ protein.setCodonFrames(acfList);
+
+ /*
+ * Select Seq1 and Seq3 in the protein
+ */
+ SequenceGroup sg = new SequenceGroup();
+ sg.setColourText(true);
+ sg.setIdColour(Color.GREEN);
+ sg.setOutlineColour(Color.LIGHT_GRAY);
+ sg.addSequence(protein.getSequenceAt(0), false);
+ sg.addSequence(protein.getSequenceAt(2), false);
+
+ /*
+ * Verify the mapped sequence group in dna
+ */
+ SequenceGroup mappedGroup = MappingUtils.mapSequenceGroup(sg, proteinView, dnaView);
+ assertTrue(mappedGroup.getColourText());
+ assertSame(sg.getIdColour(), mappedGroup.getIdColour());
+ assertSame(sg.getOutlineColour(), mappedGroup.getOutlineColour());
+ assertEquals(2, mappedGroup.getSequences().size());
+ assertSame(cdna.getSequenceAt(0), mappedGroup.getSequences().get(0));
+ assertSame(cdna.getSequenceAt(2), mappedGroup.getSequences().get(1));
+
+ /*
+ * Verify mapping sequence group from dna to protein
+ */
+ sg.clear();
+ sg.addSequence(cdna.getSequenceAt(1), false);
+ sg.addSequence(cdna.getSequenceAt(0), false);
+ mappedGroup = MappingUtils.mapSequenceGroup(sg, dnaView, proteinView);
+ assertTrue(mappedGroup.getColourText());
+ assertSame(sg.getIdColour(), mappedGroup.getIdColour());
+ assertSame(sg.getOutlineColour(), mappedGroup.getOutlineColour());
+ assertEquals(2, mappedGroup.getSequences().size());
+ assertSame(protein.getSequenceAt(1), mappedGroup.getSequences().get(0));
+ assertSame(protein.getSequenceAt(0), mappedGroup.getSequences().get(1));
+ }
+
+ /**
+ * Helper method to load an alignment and ensure dataset sequences are set up.
+ *
+ * @param data
+ * @param format
+ * TODO
+ * @return
+ * @throws IOException
+ */
+ protected AlignmentI loadAlignment(final String data, String format)
+ throws IOException
+ {
+ Alignment a = new FormatAdapter().readFile(data,
+ AppletFormatAdapter.PASTE, format);
+ a.setDataset(null);
+ return a;
+ }
+
+ /**
+ * Test mapping a column selection in protein to its dna equivalent
+ *
+ * @throws IOException
+ */
+ @Test
+ public void testMapColumnSelection_proteinToDna() throws IOException
+ {
+ setupMappedAlignments();
+
+ ColumnSelection colsel = 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
+ */
+ colsel.addElement(0);
+ ColumnSelection cs = MappingUtils.mapColumnSelection(colsel,
+ proteinView, dnaView);
+ 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
+ */
+ colsel.clear();
+ colsel.addElement(1);
+ cs = MappingUtils.mapColumnSelection(colsel, proteinView, dnaView);
+ assertEquals("[0, 1, 2, 3]", cs.getSelected().toString());
+
+ /*
+ * Column 2 in protein picks up gaps only - no mapping
+ */
+ colsel.clear();
+ colsel.addElement(2);
+ cs = MappingUtils.mapColumnSelection(colsel, proteinView, dnaView);
+ 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
+ */
+ colsel.clear();
+ colsel.addElement(3);
+ cs = MappingUtils.mapColumnSelection(colsel, proteinView, dnaView);
+ assertEquals("[5, 6, 7, 8, 9, 10]", cs.getSelected().toString());
+
+ /*
+ * Combine selection of columns 1 and 3 to get a discontiguous mapped
+ * selection
+ */
+ colsel.clear();
+ colsel.addElement(1);
+ colsel.addElement(3);
+ cs = MappingUtils.mapColumnSelection(colsel, proteinView, dnaView);
+ assertEquals("[0, 1, 2, 3, 5, 6, 7, 8, 9, 10]", cs.getSelected()
+ .toString());
+ }
+
+ /**
+ * @throws IOException
+ */
+ protected void setupMappedAlignments() throws IOException
+ {
+ /*
+ * Set up dna and protein Seq1/2/3 with mappings (held on the protein
+ * viewport). Lower case for introns.
+ */
+ AlignmentI cdna = loadAlignment(">Seq1\nAC-GctGtC-T\n"
+ + ">Seq2\nTc-GA-G-T-Tc\n" + ">Seq3\nTtTT-AaCGg-\n",
+ "FASTA");
+ cdna.setDataset(null);
+ AlignmentI protein = loadAlignment(
+ ">Seq1\n-K-P\n>Seq2\nL--Q\n>Seq3\nG--S\n",
+ "FASTA");
+ protein.setDataset(null);
+ AlignedCodonFrame acf = new AlignedCodonFrame();
+ MapList map = new MapList(new int[]
+ { 1, 3, 6, 6, 8, 9 }, new int[]
+ { 1, 2 }, 3, 1);
+ acf.addMap(cdna.getSequenceAt(0).getDatasetSequence(), protein
+ .getSequenceAt(0).getDatasetSequence(), map);
+ map = new MapList(new int[]
+ { 1, 1, 3, 4, 5, 7 }, new int[]
+ { 1, 2 }, 3, 1);
+ acf.addMap(cdna.getSequenceAt(1).getDatasetSequence(), protein
+ .getSequenceAt(1).getDatasetSequence(), map);
+ map = new MapList(new int[]
+ { 1, 1, 3, 4, 5, 5, 7, 8 }, new int[]
+ { 1, 2 }, 3, 1);
+ acf.addMap(cdna.getSequenceAt(2).getDatasetSequence(), protein
+ .getSequenceAt(2).getDatasetSequence(), map);
+ Set<AlignedCodonFrame> acfList = Collections.singleton(acf);
+
+ dnaView = new AlignViewport(cdna);
+ proteinView = new AlignViewport(protein);
+ protein.setCodonFrames(acfList);
+ }
+
+ /**
+ * Test mapping a column selection including hidden columns
+ *
+ * @throws IOException
+ */
+ @Test
+ public void testMapColumnSelection_hiddenColumns() throws IOException
+ {
+ setupMappedAlignments();
+
+ ColumnSelection colsel = 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
+ */
+ colsel.addElement(0);
+ ColumnSelection cs = MappingUtils.mapColumnSelection(colsel,
+ proteinView, dnaView);
+ assertEquals("[0, 1, 2, 3, 4]", cs.getSelected().toString());
+
+ fail("write me");
+ }
+
+ /**
+ * Test mapping a column selection in dna to its protein equivalent
+ *
+ * @throws IOException
+ */
+ @Test
+ public void testMapColumnSelection_dnaToProtein() throws IOException
+ {
+ setupMappedAlignments();
+
+ ColumnSelection colsel = new ColumnSelection();
+
+ /*
+ * Column 0 in dna picks up first bases which map to residue 1, columns 0-1
+ * in protein.
+ */
+ colsel.addElement(0);
+ ColumnSelection cs = MappingUtils.mapColumnSelection(colsel, dnaView,
+ proteinView);
+ assertEquals("[0, 1]", cs.getSelected().toString());
+
+ /*
+ * Columns 3-5 in dna map to the first residues in protein Seq1, Seq2, and
+ * the first two in Seq3. Overall to columns 0, 1, 3 (col2 is all gaps).
+ */
+ colsel.addElement(3);
+ colsel.addElement(4);
+ colsel.addElement(5);
+ cs = MappingUtils.mapColumnSelection(colsel, dnaView, proteinView);
+ assertEquals("[0, 1, 3]", cs.getSelected().toString());
+ }
+}
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