runner/compbio/runner/structure/RNAalifold.java

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