return load(result, new SilkWalker(silkResource));
}
+ public static <Result> Result loadSilk(Result result, Reader silkReader) throws XerialException, IOException
+ {
+ return load(result, new SilkWalker(silkReader));
+ }
+
+ public static <Result> Result loadSilk(Class<Result> resultType, Reader silkReader) throws XerialException,
+ IOException
+ {
+ return loadSilk(TypeInfo.createInstance(resultType), silkReader);
+ }
+
public static <Result> Result loadXML(Result result, URL xmlResource) throws IOException, XerialException
{
if (xmlResource == null)
\r
import org.xerial.util.Pair;\r
import org.xerial.util.bean.TypeInfo;\r
+import org.xerial.util.reflect.ReflectionUtil;\r
\r
/**\r
* Tree to Object lens\r
{\r
Class< ? > fieldType = eachField.getType();\r
String paramName = getCanonicalParameterName(eachField.getName());\r
- SetterType setterType = SetterType.SETTER;\r
\r
if (TypeInfo.isArray(fieldType))\r
{\r
}\r
else if (TypeInfo.isMap(fieldType))\r
{\r
- setterType = SetterType.PUTTER;\r
+\r
+ // TODO map putter\r
+\r
}\r
if (TypeInfo.isCollection(fieldType))\r
{\r
- setterType = SetterType.ADDER;\r
+ Class< ? > elementType = ReflectionUtil.getGenericCollectionElementType(eachField);\r
+ setterContainer.add(ParameterSetter.newSetter(elementType, paramName, eachField));\r
}\r
-\r
- setterContainer.add(ParameterSetter.newSetter(fieldType, paramName, eachField));\r
+ else\r
+ setterContainer.add(ParameterSetter.newSetter(fieldType, paramName, eachField));\r
\r
}\r
\r
if (relName == null)\r
{\r
// infer relation node names\r
- relName = new Pair<String, String>(argTypes[0].getSimpleName(), argTypes[1].getSimpleName());\r
+ relName = new Pair<String, String>(getCanonicalParameterName(argTypes[0].getSimpleName()),\r
+ getCanonicalParameterName(argTypes[1].getSimpleName()));\r
}\r
\r
relationSetterContainer.add(RelationSetter.newRelationSetter(relName.getFirst(), relName\r
return paramName.toLowerCase();\r
}\r
\r
- private enum SetterType {\r
- ADDER, SETTER, PUTTER, APPENDER\r
- };\r
-\r
}\r
import org.xerial.core.XerialErrorCode;
import org.xerial.core.XerialException;
import org.xerial.relation.Node;
-import org.xerial.relation.query.AmoebaJoinHandler;
+import org.xerial.relation.query.AmoebaJoinHandlerBase;
import org.xerial.relation.query.QuerySet;
import org.xerial.relation.query.StreamAmoebaJoin;
import org.xerial.relation.query.QuerySet.QuerySetBuilder;
public void build(Class< ? > targetType, String alias)
{
- if (TypeInfo.isBasicType(targetType))
+ if (TypeInfo.isBasicType(targetType) || TypeInfo.isCollection(targetType))
return;
if (processedClasses.contains(targetType))
processedClasses.add(targetType);
ObjectLens lens = ObjectLens.getObjectLens(targetType);
- if (_logger.isDebugEnabled())
- _logger.debug(String.format("class %s: %s\n", targetType.getSimpleName(), lens));
+ if (_logger.isTraceEnabled())
+ _logger.trace(String.format("class %s: %s\n", targetType.getSimpleName(), lens));
for (ParameterSetter each : lens.getSetterList())
{
}
- private class RelationExtracter implements AmoebaJoinHandler
+ private class RelationExtracter extends AmoebaJoinHandlerBase
{
public void leaveNode(Schema schema, Node node) throws Exception
public void newAmoeba(Schema schema, Node coreNode, Node attributeNode) throws Exception
{
- if (_logger.isTraceEnabled())
- _logger.trace(String.format("amoeba: (%s, %s) in %s", coreNode, attributeNode, schema));
+ if (_logger.isDebugEnabled())
+ _logger.debug(String.format("amoeba: (%s, %s) in %s", coreNode, attributeNode, schema));
Binder binder = schema2binder.get(schema);
if (binder == null)
public interface AmoebaJoinHandler
{
+ public void init();
+
public void newAmoeba(Schema schema, Node coreNode, Node attributeNode) throws Exception;
public void leaveNode(Schema schema, Node node) throws Exception;
public void text(Schema schema, Node coreNode, String nodeName, String text) throws Exception;
+
+ public void finish();
}
\r
}\r
\r
+ public void finish()\r
+ {\r
+\r
+ }\r
+\r
+ public void init()\r
+ {\r
+\r
+ }\r
+\r
}\r
{
leaveNode("root", walker);
_logger.debug("sweep finished");
+ handler.finish();
}
public void init(TreeWalker walker) throws XerialException
latticeCursor = nodeNameLattice.cursor();
stateStack.addLast(latticeCursor.getNode());
+ handler.init();
+
visitNode("root", null, walker);
}
}
catch (Exception e)
{
- throw new XerialError(XerialErrorCode.INHERITED, e);
+ if (e instanceof XerialException)
+ throw (XerialException) e;
+ else
+ throw new XerialException(XerialErrorCode.INHERITED, e);
}
}
Deque<Node> nodeStack = getNodeStack(nodeName);
Node currentNode = nodeStack.getLast();
- currentPath.removeLast();
-
try
{
back(currentNode);
}
catch (Exception e)
{
- throw new XerialException(XerialErrorCode.INHERITED, e);
+ if (e instanceof XerialException)
+ throw (XerialException) e;
+ else if (e instanceof XerialError)
+ throw (XerialError) e;
+ else
+ throw new XerialException(XerialErrorCode.INHERITED, e);
}
+ currentPath.removeLast();
+
nodeStack.removeLast();
}
* @param input
* @throws IOException
*/
- protected SilkWalker(Reader input) throws IOException
+ public SilkWalker(Reader input) throws IOException
{
super(new SilkStreamReader(input));
}
if (constractableClass != null)
{
cons = getPublicDefaultConstructor(constractableClass);
+ assert cons != null;
constructorTable.put(c, cons);
return constractableClass.newInstance();
}
}
}
+ // search hidden constructors
+ for (Constructor< ? > constructor : c.getDeclaredConstructors())
+ {
+ try
+ {
+ constructor.setAccessible(true);
+ Object instance = createInstance(constructor);
+ constructorTable.put(c, constructor);
+ return (T) instance;
+ }
+ catch (Exception e)
+ {
+
+ }
+ }
+
throw new BeanException(BeanErrorCode.NoPublicConstructor, "No public constructor for the class: "
+ c.getName() + " is available");
import static org.junit.Assert.*;
import java.io.IOException;
+import java.util.List;
import org.junit.After;
import org.junit.Before;
-import org.junit.Ignore;
import org.junit.Test;
import org.xerial.core.XerialException;
import org.xerial.silk.SilkUtilTest;
static class GeneTable
{
- private HashedArrayList<Coordinate, Gene> sequenceTable;
+ private HashedArrayList<Coordinate, Gene> sequenceTable = new HashedArrayList<Coordinate, Gene>();
public void add(Coordinate coordinate, Gene gene)
{
{}
}
- @Ignore
@Test
public void testTranslateSilk() throws IOException, XerialException
{
assertNotNull(g);
assertEquals(2, g.sequenceTable.size());
- assertEquals(4, g.sequenceTable.values().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
{
assertEquals("chr1", c.name);
}
+
+ @Test
+ public void testBED() throws Exception
+ {
+ BEDGene g = Lens.loadSilk(BEDGene.class, FileResource.find(LensTest.class, "sample.bed.silk"));
+ }
+
+ public static class CDS
+ {
+ public long start;
+ public long end;
+ }
+
+ public static class Exon extends CDS
+ {
+
+ }
+
+ public static class BEDGene
+ {
+
+ public List<CDS> cds;
+ public List<Exon> exon;
+
+ }
+
}
--- /dev/null
+%silk(version:1.0)\r
+\r
+-track(name:"Item,RGB,Demo2", description:"Item RGBdemonstration2", visibility:2, itemRgb:"On", useScore:1, color:"0,128,0", url:"http://genome.ucsc.edu/goldenPath/help/clones.html#$$")\r
+ -gene(coordinate, start, end, name, strand, cds(start, end), exon(start, end)*, color, _[json])|\r
+chr7 127471197 127472364 Pos1 + [127471197, 127472364] #ff0000 {"score":300}\r
+chr7 127472364 127473531 Pos2 + [127472364, 127473531] #ff0000 {"score":200}\r
+chr7 127473531 127474698 Pos3 + [127473531, 127474698] #ff0000 {"score":900}\r
+chr7 127474698 127475865 Pos4 + [127474698, 127475865] #ff0000 {"score":400}\r
+chr7 127475865 127477032 Neg1 - [127475865, 127477032] #0000ff {"score":100}\r
+chr7 127477032 127478199 Neg2 - [127477032, 127478199] #0000ff {"score":500}\r
+chr7 127478199 127479366 Neg3 - [127478199, 127479366] #0000ff {"score":200}\r
+chr7 127479366 127480533 Pos5 + [127479366, 127480533] #ff0000 {"score":200}\r
+chr7 127480533 127481700 Neg4 - [127480533, 127481700] #0000ff {"score":600}\r
+chr22 2001 7001 itemB - [2201, 6951] [[1, 433], [501, 600], [2001, 2550], [3501, 5000]] {"score":200}\r
+chr22 2001 6001 cloneB - [2001, 6001] [[1, 433], [3602, 4000]] {"score":900}\r
+chr22 1001 5001 itemA + [1101, 4701] [[1, 1567], [2513, 4000]] {"score":960}\r
+chr22 1001 5001 itemA + [1101, 4701] [[1, 1567], [2513, 4000]] {"score":960}\r
+chr22 2001 7001 itemB - [2201, 6951] [[1, 433], [501, 600], [2001, 2550], [3501, 5000]] {"score":200}\r
+chr22 20100001 20100002 \r
+chr22 20110001 20110002 \r
+chr22 20100001 20100101 first \r
+chr22 20100201 20100301 second \r
+chr22 20100401 20100501 thirds \r
+chr7 127472364 127473531 Pos2 {"score":200}\r
+chr7 127472364 127473531 Pos2 + {"score":200}\r
+chr7 127472364 127473531 Pos2 + [127472364, 127473531] {"score":200}\r
+chr7 127472364 127473531 Pos2 + [127472364, 127473531] #ff0000 {"score":200}
\ No newline at end of file
//--------------------------------------\r
package org.xerial.relation.query;\r
\r
+import static org.junit.Assert.*;\r
+\r
import org.junit.After;\r
import org.junit.Before;\r
import org.junit.Test;\r
qs.addQueryTarget(new SchemaBuilder().add("gene").add("id").add("name").add("start").add("end").add("sequence")\r
.build());\r
\r
- StreamAmoebaJoin aj = new StreamAmoebaJoin(qs.build(), new AmoebaJoinHandler() {\r
+ StreamAmoebaJoin aj = new StreamAmoebaJoin(qs.build(), new AmoebaJoinHandlerBase() {\r
\r
public void newAmoeba(Schema schema, Node n1, Node n2)\r
{\r
\r
aj.sweep(new SilkWalker(FileResource.find(StreamAmoebaJoinTest.class, "sample.silk")));\r
}\r
+\r
+ @Test\r
+ public void amoebaTest() throws Exception\r
+ {\r
+ QuerySetBuilder qs = new QuerySetBuilder();\r
+ qs.addQueryTarget(new SchemaBuilder().add("coordinate").add("revision").build());\r
+\r
+ StreamAmoebaJoin aj = new StreamAmoebaJoin(qs.build(), new AmoebaJoinHandlerBase() {\r
+\r
+ int count = 0;\r
+\r
+ public void newAmoeba(Schema schema, Node n1, Node n2)\r
+ {\r
+ _logger.debug(String.format("relation (%s, %s)", n1, n2));\r
+ count++;\r
+ }\r
+\r
+ public void finish()\r
+ {\r
+ assertEquals(2, count);\r
+ }\r
+\r
+ });\r
+\r
+ aj.sweep(new SilkWalker(FileResource.find(StreamAmoebaJoinTest.class, "gene.silk")));\r
+\r
+ }\r
+\r
}\r
--- /dev/null
+-coordinate(revision:hg18)\r
+ \r
+-(revision:hg17)\r
+ -coordinate\r
+
\ No newline at end of file
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