1 package compbio.runner.structure;
3 import java.util.Scanner; //temp
4 import java.io.File; //temp
6 import java.io.FileNotFoundException;
7 import java.io.IOException;
8 import java.util.Arrays;
11 import org.apache.log4j.Logger;
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;
19 public class RNAalifold extends SkeletalExecutable<RNAalifold> {
21 @SuppressWarnings("unchecked")
24 public String getResults(String resultFile)
25 throws ResultNotAvailableException {
28 System.out.println("testfrom RNAalifold.getResults");
29 s = new Scanner(new File(resultFile));
30 System.out.println(s.nextLine());
32 } catch (FileNotFoundException e) {
33 System.out.println("file not found");
34 throw new ResultNotAvailableException(e);
40 public RNAalifold setOutput(String outFile) {
41 System.out.println("Set ouput file: " + outFile.toString());
42 super.setOutput(outFile);
47 public RNAalifold setInput(String inFile) {
48 System.out.println("Set input file: " + inFile.toString());
49 super.setInput(inFile);
53 @SuppressWarnings("unchecked")
55 public Class<RNAalifold> getType() {
56 return (Class<RNAalifold>) this.getClass();