Add Java wrapper class for Jpred

diff --git a/runner/compbio/runner/predictors/Jpred.java b/runner/compbio/runner/predictors/Jpred.java
new file mode 100644 (file)
index 0000000..017dcfc
--- /dev/null
+++ b/runner/compbio/runner/predictors/Jpred.java
@@ -0,0 +1,143 @@
+/* Copyright (c) 2013 Alexander Sherstnev\r
+ *  \r
+ *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 3.0     \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.predictors;\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.ScoreManager;\r
+import compbio.data.sequence.SequenceUtil;\r
+import compbio.engine.client.CommandBuilder;\r
+import compbio.engine.client.Executable;\r
+import compbio.engine.client.SkeletalExecutable;\r
+import compbio.metadata.ResultNotAvailableException;\r
+\r
+/**\r
+ * Command line\r
+ * \r
+ * jpred.pl -in d16vpa_.fas -out res_d16vpa_ -dbname ported_db -dbpath /data/UNIREFdb -ncpu 4\r
+ * \r
+ * @author asherstnev\r
+ * \r
+ */\r
+public class Jpred extends SkeletalExecutable<Jpred> {\r
+\r
+       private static Logger log = Logger.getLogger(Jpred.class);\r
+\r
+       /**\r
+        * Number of cores to use, defaults to 1 for local execution or the value of\r
+        * "jpred.cluster.cpunum" property for cluster execution\r
+        */\r
+       private int ncoreNumber = 0;\r
+\r
+       public static final String KEY_VALUE_SEPARATOR = " ";\r
+       public static final String STAT_FILE = "stat.txt";\r
+\r
+       public Jpred() {\r
+//             addParameters(Arrays.asList());\r
+       }\r
+       // HashMap<Method, float[]>\r
+       @Override\r
+       public ScoreManager getResults(String workDirectory)\r
+                       throws ResultNotAvailableException {\r
+               ScoreManager annotations = null;\r
+               try {\r
+                       InputStream inStream = new FileInputStream(new File(workDirectory, getOutput()));\r
+                       annotations = ScoreManager.newInstanceSingleSequence(SequenceUtil.readAAConResults(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 (NullPointerException e) {\r
+                       log.error(e.getMessage(), e.getCause());\r
+                       throw new ResultNotAvailableException(e);\r
+               }\r
+               return annotations;\r
+       }\r
+\r
+       @Override\r
+       public List<String> getCreatedFiles() {\r
+               return Arrays.asList(getOutput(), getError());\r
+       }\r
+\r
+       @Override\r
+       public Jpred setInput(String inFile) {\r
+               super.setInput(inFile);\r
+               cbuilder.setParam("-in " + inFile);\r
+               return this;\r
+       }\r
+\r
+       @Override\r
+       public Jpred setOutput(String outFile) {\r
+               super.setOutput(outFile);\r
+               cbuilder.setParam("-out " + outFile);\r
+               return this;\r
+       }\r
+\r
+       @SuppressWarnings("unchecked")\r
+       @Override\r
+       public Class<Jpred> getType() {\r
+               return (Class<Jpred>) this.getClass();\r
+       }\r
+\r
+       public static String getStatFile() {\r
+               return STAT_FILE;\r
+       }\r
+\r
+       public void setNCore(int ncoreNumber) {\r
+               if (0 < ncoreNumber && ncoreNumber < 9) {\r
+                       this.ncoreNumber = ncoreNumber;\r
+                       cbuilder.setParam("-ncpu " + Integer.toString(getNCore()));\r
+               } else {\r
+                       throw new IndexOutOfBoundsException("Number of cores must be between 1 and 8 ");\r
+               }\r
+       }\r
+\r
+       int getNCore() {\r
+               return ncoreNumber;\r
+       }\r
+\r
+       @Override\r
+       public CommandBuilder<Jpred> getParameters(ExecProvider provider) {\r
+               // If number of cores is provided, set it for the cluster execution only!\r
+               if (provider == Executable.ExecProvider.Cluster) {\r
+                       int cpunum = SkeletalExecutable.getClusterCpuNum(getType());\r
+                       cpunum = (cpunum == 0) ? 1 : cpunum;\r
+                       setNCore(cpunum);\r
+               } else {\r
+                       // Limit number of cores to 1 for ANY execution which does not set\r
+                       // Ncores explicitly using setNCore method or is run on local VM\r
+                       if (ncoreNumber == 0) {\r
+                               setNCore(1);\r
+                       }\r
+               }\r
+               return super.getParameters(provider);\r
+       }\r
+\r
+}\r