1 /*--------------------------------------------------------------------------
2 * Copyright 2008 utgenome.org
3 *
4 * Licensed under the Apache License, Version 2.0 (the "License");
5 * you may not use this file except in compliance with the License.
6 * You may obtain a copy of the License at
7 *
8 * http://www.apache.org/licenses/LICENSE-2.0
9 *
10 * Unless required by applicable law or agreed to in writing, software
11 * distributed under the License is distributed on an "AS IS" BASIS,
12 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
13 * See the License for the specific language governing permissions and
14 * limitations under the License.
15 *--------------------------------------------------------------------------*/
16 //--------------------------------------
17 // utgb-shell Project
18 //
19 // BED2SilkReader.java
20 // Since: May 26, 2009
21 //
22 // $URL: http://svn.utgenome.org/utgb/trunk/utgb/utgb-shell/src/main/java/org/utgenome/shell/db/bed/BED2SilkReader.java $
23 // $Author: leo $
24 //--------------------------------------
25 package org.utgenome.format.bed;
26
27 import java.io.IOException;
28 import java.io.PrintWriter;
29 import java.io.Reader;
30 import java.io.Writer;
31
32 import org.utgenome.UTGBException;
33 import org.utgenome.format.FormatConversionReader;
34 import org.xerial.lens.SilkLens;
35
36 /**
37 * BED2SilkReader read the input BED data, and the user can read it as if it were a Silk format.
38 *
39 * @author leo
40 *
41 */
42 public class BED2SilkReader extends FormatConversionReader {
43
44 public BED2SilkReader(Reader bedReader) throws IOException {
45 super(bedReader, new PipeConsumer() {
46 @Override
47 public void consume(Reader in, Writer out) throws Exception {
48 BED2Silk converter = new BED2Silk(in);
49 PrintWriter pout = new PrintWriter(out);
50 converter.toSilk(pout);
51 }
52 });
53
54 }
55
56 /**
57 * Read an input BED data, and retrieves {@link BEDTrack} and {@link BEDEntry} information through the
58 * {@link BEDQuery} interface.
59 *
60 * @param input
61 * @param query
62 * @return
63 * @throws UTGBException
64 */
65 public static BEDQuery scan(Reader input, BEDQuery query) throws UTGBException {
66
67 try {
68 BED2SilkReader in = new BED2SilkReader(input);
69 SilkLens.loadSilk(query, in);
70 return query;
71 }
72 catch (Exception e) {
73 throw UTGBException.convert(e);
74 }
75 }
76
77 }