runner/compbio/runner/structure/RNAalifold.java

   1 package compbio.runner.structure;\r
   2 \r
   3 import java.io.FileNotFoundException;\r
   4 import java.io.IOException;\r
   5 \r
   6 import org.apache.log4j.Logger;\r
   7 \r
   8 import compbio.data.sequence.RNAStructScoreManager;\r
   9 import compbio.engine.client.PipedExecutable;\r
  10 import compbio.engine.client.SkeletalExecutable;\r
  11 import compbio.metadata.ResultNotAvailableException;\r
  12 import compbio.runner.Util;\r
  13 \r
  14 public class RNAalifold extends SkeletalExecutable<RNAalifold> \r
  15                 implements PipedExecutable<RNAalifold> {\r
  16 \r
  17         private static Logger log = Logger.getLogger(RNAalifold.class);\r
  18 \r
  19         // May not be necessary as defult is "<space>" but still dont know\r
  20         // How to deal with different key value separators for different params\r
  21         public static final String KEY_VALUE_SEPARATOR = " ";\r
  22         \r
  23         public RNAalifold() {\r
  24                 super(KEY_VALUE_SEPARATOR);\r
  25         }\r
  26         \r
  27         @Override\r
  28         public RNAalifold setOutput(String outFile) {\r
  29                 super.setOutput(outFile);\r
  30                 return this;\r
  31         }\r
  32         \r
  33         @Override\r
  34         public RNAalifold setInput(String inFile) {\r
  35                 cbuilder.setLast(inFile);\r
  36                 super.setInput(inFile);\r
  37                 return this;\r
  38         }\r
  39         \r
  40         @SuppressWarnings("unchecked")\r
  41         @Override\r
  42         public Class<RNAalifold> getType() {\r
  43                 return (Class<RNAalifold>) this.getClass();\r
  44         }\r
  45         \r
  46         @SuppressWarnings("unchecked")\r
  47         @Override\r
  48         public RNAStructScoreManager getResults(String workDirectory)\r
  49                         throws ResultNotAvailableException {\r
  50                 try {\r
  51                         return Util.readRNAStruct(workDirectory, getOutput());\r
  52                 } catch (FileNotFoundException e) {\r
  53                         log.error(e.getMessage(), e.getCause());\r
  54                         throw new ResultNotAvailableException(e);\r
  55                 } catch (IOException e) {\r
  56                         log.error(e.getMessage(), e.getCause());\r
  57                         throw new ResultNotAvailableException(e);\r
  58                 }\r
  59         }\r
  60 \r
  61 }\r