Adding disembl wrapper

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

diff --git a/runner/compbio/runner/disorder/Disembl.java b/runner/compbio/runner/disorder/Disembl.java
new file mode 100644 (file)
index 0000000..4c76854
--- /dev/null
+++ b/runner/compbio/runner/disorder/Disembl.java
@@ -0,0 +1,133 @@
+/* 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.FileNotFoundException;\r
+import java.io.IOException;\r
+import java.util.Arrays;\r
+\r
+import org.apache.log4j.Logger;\r
+\r
+import com.sun.xml.internal.bind.api.impl.NameConverter.Standard;\r
+import compbio.data.sequence.Alignment;\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
+/**\r
+ * @see Standard DisEMBL DisEMBL.py smooth_frame peak_frame join_frame\r
+ *      fold_coils fold_hotloops fold_rem465 sequence_file print 'A default run\r
+ *      would be: ./DisEMBL.py 8 8 4 1.2 1.4 1.2 fasta_file > out'\r
+ * \r
+ *      new DisEMBL is at /homes/pvtroshin/soft/DisEMBL-1.4raw This is not a\r
+ *      standard DisEMBL! The script has been modified! DisEMBL.py smooth_frame\r
+ *      peak_frame join_frame fold_coils fold_hotloops fold_rem465 [mode] <\r
+ *      fasta_file > out print 'A default run would be: ./DisEMBL.py 8 8 4 1.2\r
+ *      1.4 1.2 < fasta_file' print 'Mode: "default"(nothing) or "scores" which\r
+ *      will give scores per residue in TAB separated format'\r
+ * \r
+ */\r
+public class Disembl extends SkeletalExecutable<Disembl> implements\r
+       PipedExecutable<Disembl> {\r
+\r
+    private static Logger log = Logger.getLogger(Disembl.class);\r
+\r
+    // Cache for Limits information\r
+    private static LimitsManager<Disembl> limits;\r
+\r
+    public static final String KEY_VALUE_SEPARATOR = Util.SPACE;\r
+\r
+    public Disembl() {\r
+       // remove default input to prevent it to appear in the parameters list\r
+       // that could happen if the parameters are set first\r
+       // super.setInput("");\r
+       addParameters(Arrays.asList("8", "8", "4", "1.2", "1.4", "1.2",\r
+               "scores"));\r
+    }\r
+\r
+    @SuppressWarnings("unchecked")\r
+    public Alignment getResults(String workDirectory)\r
+           throws ResultNotAvailableException {\r
+       try {\r
+           return Util.readClustalFile(workDirectory, getOutput());\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
+    }\r
+\r
+    @Override\r
+    public Disembl setInput(String inFile) {\r
+       super.setInput(inFile);\r
+       cbuilder.setLast(inFile);\r
+       return this;\r
+    }\r
+\r
+    @Override\r
+    public Limit<Disembl> getLimit(String presetName) {\r
+       if (limits == null) {\r
+           limits = getLimits();\r
+       }\r
+\r
+       Limit<Disembl> 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<Disembl> 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
+}\r