1 /*--------------------------------------------------------------------------
2 * Copyright 2011 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 // RegionQueryExpr.java
20 // Since: 2011/01/06
21 //
22 // $URL$
23 // $Author$
24 //--------------------------------------
25 package org.utgenome.shell;
26
27 import java.util.regex.Matcher;
28 import java.util.regex.Pattern;
29
30 import org.utgenome.gwt.utgb.client.bio.ChrLoc;
31
32 public class RegionQueryExpr {
33
34 private static Pattern p = Pattern.compile("([^:]+)(:([0-9]+)-([0-9]+))?");
35
36 public static ChrLoc parse(String expr) throws UTGBShellException {
37 Matcher m = p.matcher(expr.replaceAll(",", "")); // remove comma
38 if (!m.matches())
39 throw new UTGBShellException("invalid query format:" + expr);
40 String chr = m.group(1);
41 String sStart = m.group(3);
42 String sEnd = m.group(4);
43
44 int start = 0;
45 if (sStart != null)
46 start = Integer.parseInt(sStart);
47 int end = Integer.MAX_VALUE;
48 if (sEnd != null)
49 end = Integer.parseInt(sEnd);
50
51 return new ChrLoc(chr, start, end);
52 }
53 }