Add JRonn runner, tester, methods to parse jronn output files.

[jabaws.git] / runner / compbio / runner / disorder / Jronn.java

diff --git a/runner/compbio/runner/disorder/Jronn.java b/runner/compbio/runner/disorder/Jronn.java
new file mode 100644 (file)
index 0000000..0c4245a
--- /dev/null
+++ b/runner/compbio/runner/disorder/Jronn.java
@@ -0,0 +1,164 @@
+/* Copyright (c) 2009 Peter Troshin\r
+ *  \r
+ *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0     \r
+ * \r
+ *  This library is free software; you can redistribute it and/or modify it under the terms of the\r
+ *  Apache License version 2 as published by the Apache Software Foundation\r
+ * \r
+ *  This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without\r
+ *  even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache \r
+ *  License for more details.\r
+ * \r
+ *  A copy of the license is in apache_license.txt. It is also available here:\r
+ * @see: http://www.apache.org/licenses/LICENSE-2.0.txt\r
+ * \r
+ * Any republication or derived work distributed in source code form\r
+ * must include this copyright and license notice.\r
+ */\r
+\r
+package compbio.runner.disorder;\r
+\r
+import java.io.File;\r
+import java.io.FileInputStream;\r
+import java.io.FileNotFoundException;\r
+import java.io.IOException;\r
+import java.io.InputStream;\r
+import java.util.Arrays;\r
+import java.util.List;\r
+\r
+import org.apache.log4j.Logger;\r
+\r
+import compbio.data.sequence.AnnotatedSequence;\r
+import compbio.data.sequence.SequenceUtil;\r
+import compbio.data.sequence.UnknownFileFormatException;\r
+import compbio.engine.client.Executable;\r
+import compbio.engine.client.SkeletalExecutable;\r
+import compbio.metadata.Limit;\r
+import compbio.metadata.LimitsManager;\r
+import compbio.metadata.ResultNotAvailableException;\r
+import compbio.runner.Util;\r
+\r
+/**\r
+ * Command line\r
+ * \r
+ * java -Xmx512 -jar jronn_v3.jar -i=test_seq.txt -n=1 -o=out.txt -s=stat.out\r
+ * \r
+ * @author pvtroshin\r
+ * \r
+ */\r
+public class Jronn extends SkeletalExecutable<Jronn> {\r
+\r
+    private static Logger log = Logger.getLogger(Jronn.class);\r
+\r
+    // Cache for Limits information\r
+    private static LimitsManager<Jronn> limits;\r
+\r
+    public static final String KEY_VALUE_SEPARATOR = Util.SPACE;\r
+    public static final String STAT_FILE = "stat.txt";\r
+\r
+    public Jronn() {\r
+       addParameters(Arrays.asList("-jar", getLibPath(), "-n=1", "-s="\r
+               + STAT_FILE, "-f=H"));\r
+    }\r
+\r
+    @SuppressWarnings("unchecked")\r
+    @Override\r
+    public List<AnnotatedSequence> getResults(String workDirectory)\r
+           throws ResultNotAvailableException {\r
+       List<AnnotatedSequence> sequences = null;\r
+       try {\r
+           InputStream inStream = new FileInputStream(new File(workDirectory,\r
+                   getOutput()));\r
+           sequences = SequenceUtil.readJRonn(inStream);\r
+           inStream.close();\r
+       } catch (FileNotFoundException e) {\r
+           log.error(e.getMessage(), e.getCause());\r
+           throw new ResultNotAvailableException(e);\r
+       } catch (IOException e) {\r
+           log.error(e.getMessage(), e.getCause());\r
+           throw new ResultNotAvailableException(e);\r
+       } catch (UnknownFileFormatException e) {\r
+           log.error(e.getMessage(), e.getCause());\r
+           throw new ResultNotAvailableException(e);\r
+       } catch (NullPointerException e) {\r
+           log.error(e.getMessage(), e.getCause());\r
+           throw new ResultNotAvailableException(e);\r
+       }\r
+       return sequences;\r
+    }\r
+\r
+    private static String getLibPath() {\r
+\r
+       String settings = ph.getProperty("jronn.jar.file");\r
+       if (compbio.util.Util.isEmpty(settings)) {\r
+           throw new NullPointerException(\r
+                   "Please define jronn.jar.file property in Executable.properties file"\r
+                           + "and initialize it with the location of jronn jar file");\r
+       }\r
+       if (new File(settings).isAbsolute()) {\r
+           // Jronn jar can be found so no actions necessary\r
+           // no further actions is necessary\r
+           return settings;\r
+       }\r
+       return compbio.engine.client.Util.convertToAbsolute(settings);\r
+    }\r
+\r
+    @Override\r
+    public List<String> getCreatedFiles() {\r
+       return Arrays.asList(getOutput(), getError());\r
+    }\r
+\r
+    @Override\r
+    public Jronn setInput(String inFile) {\r
+       super.setInput(inFile);\r
+       cbuilder.setParam("-i=" + inFile);\r
+       return this;\r
+    }\r
+\r
+    @Override\r
+    public Jronn setOutput(String outFile) {\r
+       super.setOutput(outFile);\r
+       cbuilder.setParam("-o=" + outFile);\r
+       return this;\r
+    }\r
+\r
+    @Override\r
+    public Limit<Jronn> getLimit(String presetName) {\r
+       if (limits == null) {\r
+           limits = getLimits();\r
+       }\r
+       Limit<Jronn> limit = null;\r
+       if (limits != null) {\r
+           // this returns default limit if preset is undefined!\r
+           limit = limits.getLimitByName(presetName);\r
+       }\r
+       // If limit is not defined for a particular preset, then return default\r
+       // limit\r
+       if (limit == null) {\r
+           log.debug("Limit for the preset " + presetName\r
+                   + " is not found. Using default");\r
+           limit = limits.getDefaultLimit();\r
+       }\r
+       return limit;\r
+    }\r
+\r
+    @Override\r
+    public LimitsManager<Jronn> getLimits() {\r
+       // synchronise on static field\r
+       synchronized (log) {\r
+           if (limits == null) {\r
+               limits = Util.getLimits(this.getClass());\r
+           }\r
+       }\r
+       return limits;\r
+    }\r
+\r
+    @Override\r
+    public Class<? extends Executable<?>> getType() {\r
+       return this.getClass();\r
+    }\r
+\r
+    public static String getStatFile() {\r
+       return STAT_FILE;\r
+    }\r
+}\r