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1   /*--------------------------------------------------------------------------
2    *  Copyright 2007 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 Common Project
18  //
19  // FASTASequence.java
20  // Since: Jun 4, 2007
21  //
22  // $URL$ 
23  // $Author$
24  //--------------------------------------
25  package org.utgenome.format.fasta;
26  
27  /**
28   * A FASTASequence represents an entry in FASTA files
29   * 
30   * @author leo
31   * 
32   */
33  public class FASTASequence {
34  	private String sequence = "";
35  	private String descriptionLine;
36  
37  	/**
38  	 * @param _sequence
39  	 * @param _description
40  	 */
41  	public FASTASequence(String rawDescription, String sequence) {
42  		this.descriptionLine = rawDescription;
43  		this.sequence = sequence;
44  	}
45  
46  	public FASTASequence() {
47  	}
48  
49  	/**
50  	 * Extract a sequence name from the description line
51  	 * 
52  	 * @return
53  	 */
54  	public String getSequenceName() {
55  		return CompactFASTA.pickSequenceName(descriptionLine);
56  	}
57  
58  	public String getDescriptionLine() {
59  		return descriptionLine;
60  	}
61  
62  	public String getSequence() {
63  		return sequence;
64  	}
65  
66  	public void setSequence(String sequence) {
67  		this.sequence = sequence;
68  	}
69  
70  	@Override
71  	public String toString() {
72  		return descriptionLine + ":" + sequence;
73  	}
74  }