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/RonnWrapper.java b/runner/compbio/runner/disorder/Jronn.java
similarity index 58%
rename from runner/compbio/runner/disorder/RonnWrapper.java
rename to runner/compbio/runner/disorder/Jronn.java
index 0bd621e..0c4245a 100644 (file)
--- a/runner/compbio/runner/disorder/RonnWrapper.java
+++ b/runner/compbio/runner/disorder/Jronn.java
@@ -18,52 +18,59 @@
 \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.Alignment;\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.PipedExecutable;\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
-public class RonnWrapper extends SkeletalExecutable<RonnWrapper> implements\r
-       PipedExecutable<RonnWrapper> {\r
-    /*\r
-     * RONN does not accept stdin the file name must be defined as parameter It\r
-     * can only analyse ONE sequence per run! (or may be not, but the results\r
-     * gets overriden!) FASTA format is accepted.\r
-     * \r
-     * To run it do the following:\r
-     * \r
-     * 1) copy ronn executables and task file to work directory\r
-     * \r
-     * 2) execute run processes one by one for each sequence\r
-     */\r
-\r
-    private static final String command = "/homes/pvtroshin/soft/RONNv3_fasta/Ronn_runner.sh";\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(RonnWrapper.class);\r
+    private static Logger log = Logger.getLogger(Jronn.class);\r
 \r
     // Cache for Limits information\r
-    private static LimitsManager<RonnWrapper> limits;\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 Alignment getResults(String workDirectory)\r
+    public List<AnnotatedSequence> getResults(String workDirectory)\r
            throws ResultNotAvailableException {\r
+       List<AnnotatedSequence> sequences = null;\r
        try {\r
-           return Util.readClustalFile(workDirectory, getOutput());\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
@@ -77,6 +84,23 @@ public class RonnWrapper extends SkeletalExecutable<RonnWrapper> implements
            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
@@ -85,18 +109,25 @@ public class RonnWrapper extends SkeletalExecutable<RonnWrapper> implements
     }\r
 \r
     @Override\r
-    public RonnWrapper setInput(String inFile) {\r
-       String input = getInput();\r
+    public Jronn setInput(String inFile) {\r
        super.setInput(inFile);\r
+       cbuilder.setParam("-i=" + inFile);\r
        return this;\r
     }\r
 \r
     @Override\r
-    public Limit<RonnWrapper> getLimit(String presetName) {\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<RonnWrapper> limit = null;\r
+       Limit<Jronn> limit = null;\r
        if (limits != null) {\r
            // this returns default limit if preset is undefined!\r
            limit = limits.getLimitByName(presetName);\r
@@ -112,7 +143,7 @@ public class RonnWrapper extends SkeletalExecutable<RonnWrapper> implements
     }\r
 \r
     @Override\r
-    public LimitsManager<RonnWrapper> getLimits() {\r
+    public LimitsManager<Jronn> getLimits() {\r
        // synchronise on static field\r
        synchronized (log) {\r
            if (limits == null) {\r
@@ -126,4 +157,8 @@ public class RonnWrapper extends SkeletalExecutable<RonnWrapper> implements
     public Class<? extends Executable<?>> getType() {\r
        return this.getClass();\r
     }\r
+\r
+    public static String getStatFile() {\r
+       return STAT_FILE;\r
+    }\r
 }\r