runner/compbio/runner/structure/RNAalifold.java

   1 package compbio.runner.structure;
   2
   3
   4 import java.io.FileNotFoundException;
   5 import java.io.IOException;
   6 import java.util.Arrays;
   7 import java.util.List;
   8
   9 import org.apache.log4j.Logger;
  10
  11 import compbio.data.sequence.Alignment;
  12 import compbio.data.sequence.UnknownFileFormatException;
  13 import compbio.engine.client.PipedExecutable;
  14 import compbio.engine.client.SkeletalExecutable;
  15 import compbio.metadata.ResultNotAvailableException;
  16 import compbio.runner.Util;
  17
  18 public class RNAalifold extends SkeletalExecutable<RNAalifold>
  19                 implements PipedExecutable<RNAalifold> {
  20
  21
  22
  23         private static Logger log = Logger.getLogger(RNAalifold.class);
  24
  25
  26         @SuppressWarnings("unchecked")
  27         @Override
  28         // PlaceHolder method
  29         public String getResults(String resultFile)
  30                         throws ResultNotAvailableException {
  31                 return "null";
  32         }
  33
  34
  35         @Override
  36         public RNAalifold setOutput(String outFile) {
  37                 log.info("Set ouput file: " + outFile.toString());
  38                 super.setOutput(outFile);
  39                 return this;
  40         }
  41
  42         @Override
  43         public RNAalifold setInput(String inFile) {
  44                 log.info("Set input file: " + inFile.toString());
  45                 cbuilder.setLast(inFile);
  46                 super.setInput(inFile);
  47                 return this;
  48         }
  49
  50         @SuppressWarnings("unchecked")
  51         @Override
  52         public Class<RNAalifold> getType() {
  53                 return (Class<RNAalifold>) this.getClass();
  54         }
  55
  56
  57 }