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