1 /*--------------------------------------------------------------------------
2 * Copyright 2009 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
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15 *--------------------------------------------------------------------------*/
16 //--------------------------------------
17 // utgb-core Project
18 //
19 // BEDQuery.java
20 // Since: May 20, 2010
21 //
22 // $URL$
23 // $Author$
24 //--------------------------------------
25 package org.utgenome.format.bed;
26
27 /**
28 * An interface for extracting BED entries using {@link BED2SilkReader}.
29 *
30 * <h3>usage:</h3>
31 *
32 * <pre>
33 * BEDQuery q = new BEDQuery() {
34 * public void addTrack(BEDTrack track) {
35 * // called when a track entry is found
36 * }
37 * public void addGene(BEDGene gene) {
38 * // called when a gene entry is found
39 * }
40 * };
41 * Lens.loadSilk(q, new BufferedReader(new FileReader(...)));
42 * </pre>
43 *
44 * @author leo
45 *
46 */
47 public interface BEDQuery {
48
49 public void addTrack(BEDTrack track);
50
51 public void addGene(BEDEntry gene);
52
53 public void reportError(Exception e);
54 }