//--------------------------------------
package org.xerial.lens;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.*;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
-import java.util.Map;
import org.junit.After;
import org.junit.Before;
+import org.junit.Ignore;
import org.junit.Test;
import org.xerial.core.XerialException;
+import org.xerial.lens.relation.NodeBase;
+import org.xerial.lens.relation.Tuple;
+import org.xerial.silk.SilkParser;
import org.xerial.silk.SilkUtilTest;
import org.xerial.util.FileResource;
-import org.xerial.util.Pair;
+import org.xerial.util.HashedArrayList;
+import org.xerial.util.StringUtil;
import org.xerial.util.log.Logger;
-public class LensTest
-{
+public class LensTest {
private static Logger _logger = Logger.getLogger(LensTest.class);
@Before
- public void setUp() throws Exception
- {}
+ public void setUp() throws Exception {}
@After
- public void tearDown() throws Exception
- {}
+ public void tearDown() throws Exception {}
- static class GeneTableOneToMany
- {
- public String trackName;
- public Map<Coordinate, List<Gene>> sequenceTable;
- }
+ public static class GeneTable {
+ private HashedArrayList<Coordinate, Gene> sequenceTable = new HashedArrayList<Coordinate, Gene>();
- /**
- * Example of showing that adder with two arguments corresponds to a
- * Map<Key, Collection<Value>> parameter.
- *
- * @author leo
- *
- */
- static class GeneTableWithMapAdder
- {
- private Map<Coordinate, List<Gene>> sequenceTable;
-
- @OneToMany(key = "coordinate", value = "gene")
- public void add(Coordinate coordinate, Gene gene)
- {
- List<Gene> geneList = sequenceTable.get(coordinate);
- if (geneList == null)
- {
- geneList = new ArrayList<Gene>();
- sequenceTable.put(coordinate, geneList);
- }
- geneList.add(gene);
+ public void add(Coordinate coordinate, Gene gene) {
+ sequenceTable.put(coordinate, gene);
}
}
- static class GeneTableOneToOne
- {
- public List<Pair<Coordinate, Gene>> geneList;
- }
-
- static class GeneTableOneToOneWithAdder
- {
- public List<Pair<Coordinate, Gene>> geneList;
-
- @OneToMany(key = "coordinate", value = "gene")
- public void add(Coordinate coordinate, Gene gene)
- {
- geneList.add(Pair.newPair(coordinate, gene));
- }
- }
-
- static class Gene
- {
+ static class Gene {
private String name;
private long start;
private String strand;
- private String sequence;
+ private StringBuilder sequence = new StringBuilder();
+
+ public void appendSequence(String sequence) {}
}
@Test
- public void testTranslateSilk() throws IOException, XerialException
- {
- GeneTableOneToMany g = Lens.translateSilk(FileResource.find(LensTest.class, "../silk/sequence.silk"),
- GeneTableOneToMany.class);
+ public void testTranslateSilk() throws IOException, XerialException {
+ GeneTable g = Lens.loadSilk(GeneTable.class, FileResource.find(LensTest.class,
+ "sequence.silk"));
assertNotNull(g);
assertEquals(2, g.sequenceTable.size());
+ for (Coordinate each : g.sequenceTable.keySet()) {
+ List<Gene> gl = g.sequenceTable.get(each);
+ assertEquals(2, gl.size());
+ }
}
+ @Ignore
@Test
- public void testMapping() throws Exception
- {
- Coordinate c = Lens.translateSilk(FileResource.find(SilkUtilTest.class, "../silk/sequence.silk"),
- Coordinate.class);
+ public void testMapping() throws Exception {
+ // TODO: How to resolve nested scope when the information of gene class is not available
+ // -coordinate(name:chr1)
+ // -gene(name:gene1)
+
+ Coordinate c = Lens.loadSilk(Coordinate.class, FileResource.find(SilkUtilTest.class,
+ "sequence.silk"));
+
_logger.info(c);
assertNotNull(c);
assertEquals("utgb", c.group);
assertEquals("chr1", c.name);
}
+
+ @Test
+ public void testBED() throws Exception {
+ BEDQuery result = new BEDQuery("chr7", 1L, 1000000000L);
+ Lens.loadSilk(result, FileResource.find(LensTest.class, "sample.bed.silk"));
+
+ _logger.debug(StringUtil.join(result.geneList, "\n"));
+
+ assertEquals("Item,RGB,Demo2", result.track.name);
+ assertEquals("Item RGBdemonstration2", result.track.description);
+ assertEquals(2, result.track.visibility);
+ assertEquals("On", result.track.itemRgb);
+ assertEquals(1, result.track.useScore);
+ assertEquals("0,128,0", result.track.color);
+ assertEquals("http://genome.ucsc.edu/goldenPath/help/clones.html#$$", result.track.url);
+ }
+
+ public static class Locus {
+ public long start;
+ public long end;
+
+ public Locus() {}
+
+ public Locus(long start, long end) {
+ this.start = start;
+ this.end = end;
+ }
+
+ public boolean hasOverlap(Locus other) {
+ return (this.start <= other.end) && (this.end >= other.start);
+ }
+
+ @Override
+ public String toString() {
+ return String.format("(%s, %s)", start, end);
+ }
+ }
+
+ public static class CDS extends Locus {
+
+ }
+
+ public static class Exon extends Locus {
+
+ }
+
+ public static class BEDGene extends Locus {
+ public String coordinate;
+ public String name;
+ public String color;
+ public String strand;
+ public List<CDS> cds;
+ public List<Exon> exon;
+
+ @Override
+ public String toString() {
+ return ObjectLens.toJSON(this);
+ }
+ }
+
+ public static class BEDTrack {
+ public String name;
+ public String description;
+ public String itemRgb;
+ public int visibility;
+ public String color;
+ public int useScore;
+ public String url;
+ }
+
+ public static class BEDQuery {
+ private String coordinate;
+ private Locus queryRange;
+ private List<BEDGene> geneList = new ArrayList<BEDGene>();
+
+ public BEDTrack track;
+
+ public BEDQuery(String coordinate, long startOnGenome, long endOnGenome) {
+ this.coordinate = coordinate;
+ this.queryRange = new Locus(startOnGenome, endOnGenome);
+ }
+
+ public void addGene(BEDGene gene) {
+ // where conditions
+ if (coordinate.equals(gene.coordinate) && queryRange.hasOverlap(gene)) {
+ // draw the gene on the canvas
+ geneList.add(gene);
+ }
+ }
+ }
+
+ public static class DASFeature {
+ public DASGFF gff;
+ public Segment segment;
+
+ @Override
+ public String toString() {
+ return ObjectLens.toJSON(this);
+ }
+
+ }
+
+ public static class DASGFF {
+ public String version;
+ public String href;
+
+ }
+
+ public static class Segment {
+ public String id;
+ public long start;
+ public long stop;
+ public List<Feature> feature;
+ }
+
+ public static class Feature {
+ public String id;
+ public long start;
+ public long end;
+
+ public String score;
+ public String orientation;
+
+ public Method method;
+ public FeatureType type;
+ public Group group;
+ public Target target;
+
+ }
+
+ public static class Target {
+ public String id;
+ public long start;
+ public long stop;
+ }
+
+ public static class FeatureType {
+ public String id;
+ public String category;
+ public String value;
+
+ }
+
+ public static class Group {
+ public String id;
+ public String type;
+ public String label;
+ public Link link;
+
+ }
+
+ public static class Link {
+ public String href;
+ public String value;
+ }
+
+ public static class Method {
+ public String id;
+ public String value;
+ }
+
+ /*
+ * <pre>
+ <SEGMENT id="13" start="1800000" stop="18100000">
+ <FEATURE id="ENSE00001471274">
+ <START>17957458</START>
+ <END>17957578</END>
+ <TYPE id="exon:coding:ensembl" category="transcription">exon:coding:ensembl</TYPE>
+ <METHOD id="ensembl">ensembl</METHOD>
+ <SCORE>-</SCORE>
+ <ORIENTATION>-</ORIENTATION>
+ <GROUP id="ENST00000342944" type="transcript:ensembl" label="ENST00000342944 (AL138715.11-201)">
+ <LINK href="http://www.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000342944;db=core">TransView ENST00000342944</LINK>
+ </GROUP>
+ <TARGET id="ENST00000342944" start="1" stop="121" />
+ </FEATURE>
+ </SEGMENT>
+ </pre>
+ */
+ @Test
+ public void dasTest() throws Exception {
+ DASFeature das = Lens.loadXML(DASFeature.class, FileResource
+ .find(LensTest.class, "das.xml"));
+ assertEquals(1, das.segment.feature.size());
+ Feature f = das.segment.feature.get(0);
+ _logger.debug(das);
+ assertEquals("ENSE00001471274", f.id);
+ assertEquals(17957458L, f.start);
+ assertEquals(17957578L, f.end);
+ assertEquals("-", f.score);
+ assertEquals("-", f.orientation);
+ Target t = f.target;
+ assertEquals("ENST00000342944", t.id);
+ assertEquals(1L, t.start);
+ assertEquals(121L, t.stop);
+
+ }
+
+ public static class Text {
+ public String value;
+ }
+
+ public static class TextQuery {
+ public Text text;
+ }
+
+ @Test
+ public void textData() throws Exception {
+ TextQuery q = Lens
+ .loadSilk(TextQuery.class, FileResource.find(LensTest.class, "text.silk"));
+ assertNotNull(q.text);
+ assertEquals("hello world", q.text.value);
+ }
+
+ public static class ArrayData {
+ public List<String> list = new ArrayList<String>();
+ }
+
+ @Test
+ public void toJSONTest() throws Exception {
+ ArrayData d = new ArrayData();
+ assertEquals("{\"list\":[]}", Lens.toJSON(d));
+ }
+
+ public static class MyGene {
+ public String name;
+ public long start;
+ public String link;
+ }
+
+ public static class MyGeneQuery {
+ private List<MyGene> geneList = new ArrayList<MyGene>();
+
+ public void addGene_Coordinate(MyGene gene, Chr c) {
+ if (c.name.equals("chr1"))
+ geneList.add(gene);
+ }
+
+ public List<MyGene> getGeneList() {
+ return geneList;
+ }
+ }
+
+ public static class Chr {
+ public String name;
+ }
+
+ @Test
+ public void testLens() throws Exception {
+
+ MyGeneQuery result = Lens.loadSilk(MyGeneQuery.class, FileResource.open(LensTest.class,
+ "sequence.silk"));
+
+ _logger.debug(Lens.toJSON(result));
+ }
+
+ @Ignore
+ @Test
+ public void testFind() throws Exception {
+ Lens.find(MyGene.class, "gene", new SilkParser(FileResource.find(LensTest.class,
+ "sequence.silk")), new ObjectHandler<MyGene>() {
+
+ public void handle(MyGene input) throws Exception {
+ _logger.info(Lens.toJSON(input));
+ }
+ });
+ }
+
+ public static class TupleNode extends NodeBase<TupleNode> {
+ public final int id;
+ public final String name;
+
+ public TupleNode(int id, String name) {
+ this.id = id;
+ this.name = name;
+ }
+ }
+
+ @Test
+ public void testToSilkTuple() throws Exception {
+ Tuple<TupleNode> t = new Tuple<TupleNode>();
+ t.add(new TupleNode(1, "A"));
+ t.add(new TupleNode(2, "B"));
+
+ String s = Lens.toSilk(t);
+ _logger.debug(s);
+ }
+
}
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