Change the way to deal with Limits to simplify wrapper writing and enable couping...
[jabaws.git] / runner / compbio / runner / msa / Probcons.java
1 /* Copyright (c) 2009 Peter Troshin\r
2  *  \r
3  *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0\r
4  * \r
5  *  This library is free software; you can redistribute it and/or modify it under the terms of the\r
6  *  Apache License version 2 as published by the Apache Software Foundation\r
7  * \r
8  *  This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without\r
9  *  even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache \r
10  *  License for more details.\r
11  * \r
12  *  A copy of the license is in apache_license.txt. It is also available here:\r
13  * @see: http://www.apache.org/licenses/LICENSE-2.0.txt\r
14  * \r
15  * Any republication or derived work distributed in source code form\r
16  * must include this copyright and license notice.\r
17  */\r
18 \r
19 package compbio.runner.msa;\r
20 \r
21 import java.io.FileNotFoundException;\r
22 import java.io.IOException;\r
23 import java.util.Arrays;\r
24 import java.util.List;\r
25 \r
26 import org.apache.log4j.Logger;\r
27 \r
28 import compbio.data.sequence.Alignment;\r
29 import compbio.data.sequence.UnknownFileFormatException;\r
30 import compbio.engine.client.Executable;\r
31 import compbio.engine.client.PipedExecutable;\r
32 import compbio.engine.client.SkeletalExecutable;\r
33 import compbio.metadata.ResultNotAvailableException;\r
34 import compbio.runner.Util;\r
35 \r
36 public class Probcons extends SkeletalExecutable<Probcons>\r
37                 implements\r
38                         PipedExecutable<Probcons> {\r
39 \r
40         private static Logger log = Logger.getLogger(Probcons.class);\r
41 \r
42         private final static String ANNOTATION = "annotation.txt";\r
43 \r
44         public static final String KEY_VALUE_SEPARATOR = Util.SPACE;\r
45 \r
46         /**\r
47          * \r
48          * @param workDirectory\r
49          */\r
50         public Probcons() {\r
51                 addParameters(Arrays.asList("-v", "-clustalw", "-annot", ANNOTATION));\r
52                 /*\r
53                  * Could either have probabilities or the alignment, but not both "-t",\r
54                  * "probabilities"\r
55                  */\r
56         }\r
57 \r
58         @SuppressWarnings("unchecked")\r
59         @Override\r
60         public Alignment getResults(String workDirectory)\r
61                         throws ResultNotAvailableException {\r
62                 try {\r
63                         return Util.readClustalFile(workDirectory, getOutput());\r
64                 } catch (FileNotFoundException e) {\r
65                         log.error(e.getMessage(), e.getCause());\r
66                         throw new ResultNotAvailableException(e);\r
67                 } catch (IOException e) {\r
68                         log.error(e.getMessage(), e.getCause());\r
69                         throw new ResultNotAvailableException(e);\r
70                 } catch (UnknownFileFormatException e) {\r
71                         log.error(e.getMessage(), e.getCause());\r
72                         throw new ResultNotAvailableException(e);\r
73                 } catch (NullPointerException e) {\r
74                         log.error(e.getMessage(), e.getCause());\r
75                         throw new ResultNotAvailableException(e);\r
76                 }\r
77         }\r
78 \r
79         @Override\r
80         public List<String> getCreatedFiles() {\r
81                 return Arrays.asList(getOutput(), ANNOTATION, getError());\r
82         }\r
83 \r
84         @Override\r
85         public Probcons setInput(String inFile) {\r
86                 String input = getInput();\r
87                 super.setInput(inFile);\r
88                 // TODO replace with setLast\r
89                 cbuilder.setParam(inFile);\r
90                 return this;\r
91         }\r
92 \r
93         @SuppressWarnings("unchecked")\r
94         @Override\r
95         public Class<Executable<Probcons>> getType() {\r
96                 return (Class<Executable<Probcons>>) this.getClass();\r
97         }\r
98 }\r