1 package compbio.runner.structure;
4 import java.io.FileNotFoundException;
5 import java.io.IOException;
6 import java.util.Arrays;
9 import org.apache.log4j.Logger;
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;
18 public class RNAalifold extends SkeletalExecutable<RNAalifold>
19 implements PipedExecutable<RNAalifold> {
23 private static Logger log = Logger.getLogger(RNAalifold.class);
26 @SuppressWarnings("unchecked")
29 public String getResults(String resultFile)
30 throws ResultNotAvailableException {
36 public RNAalifold setOutput(String outFile) {
37 log.info("Set ouput file: " + outFile.toString());
38 super.setOutput(outFile);
43 public RNAalifold setInput(String inFile) {
44 log.info("Set input file: " + inFile.toString());
45 cbuilder.setLast(inFile);
46 super.setInput(inFile);
50 @SuppressWarnings("unchecked")
52 public Class<RNAalifold> getType() {
53 return (Class<RNAalifold>) this.getClass();