runner/compbio/runner/structure/RNAalifold.java

   1 package compbio.runner.structure;
   2
   3 import java.util.Scanner; //temp
   4 import java.io.File; //temp
   5
   6 import java.io.FileNotFoundException;
   7 import java.io.IOException;
   8 import java.util.Arrays;
   9 import java.util.List;
  10
  11 import org.apache.log4j.Logger;
  12
  13 import compbio.data.sequence.Alignment;
  14 import compbio.data.sequence.UnknownFileFormatException;
  15 import compbio.engine.client.SkeletalExecutable;
  16 import compbio.metadata.ResultNotAvailableException;
  17 import compbio.runner.Util;
  18
  19 public class RNAalifold extends SkeletalExecutable<RNAalifold> {
  20
  21         @SuppressWarnings("unchecked")
  22         @Override
  23         //temp
  24         public String getResults(String resultFile)
  25                         throws ResultNotAvailableException {
  26                 Scanner s;
  27                 try {
  28                         System.out.println("testfrom RNAalifold.getResults");
  29                         s = new Scanner(new File(resultFile));
  30                         System.out.println(s.nextLine());
  31                         return "null";
  32                 } catch (FileNotFoundException e) {
  33                         System.out.println("file not found");
  34                         throw new ResultNotAvailableException(e);
  35                 }
  36         }
  37
  38
  39         @Override
  40         public RNAalifold setOutput(String outFile) {
  41                 System.out.println("Set ouput file: " + outFile.toString());
  42                 super.setOutput(outFile);
  43                 return this;
  44         }
  45
  46         @Override
  47         public RNAalifold setInput(String inFile) {
  48                 System.out.println("Set input file: " + inFile.toString());
  49                 super.setInput(inFile);
  50                 return this;
  51         }
  52
  53         @SuppressWarnings("unchecked")
  54         @Override
  55         public Class<RNAalifold> getType() {
  56                 return (Class<RNAalifold>) this.getClass();
  57         }
  58
  59
  60 }