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 //imports for filereader method
  10 import java.io.FileReader;
  11 import java.io.BufferedReader;
  12 import java.io.File;
  13
  14 import org.apache.log4j.Logger;
  15
  16 import compbio.data.sequence.Alignment;
  17 import compbio.data.sequence.UnknownFileFormatException;
  18 import compbio.engine.client.PipedExecutable;
  19 import compbio.engine.client.SkeletalExecutable;
  20 import compbio.metadata.ResultNotAvailableException;
  21 import compbio.runner.Util;
  22
  23
  24 import compbio.engine.client.CommandBuilder;
  25
  26 public class RNAalifold extends SkeletalExecutable<RNAalifold>
  27                 implements PipedExecutable<RNAalifold> {
  28
  29
  30         private static Logger log = Logger.getLogger(RNAalifold.class);
  31
  32
  33         @Override
  34         public RNAalifold setOutput(String outFile) {
  35                 log.info("Set ouput file: " + outFile.toString());
  36                 super.setOutput(outFile);
  37                 return this;
  38         }
  39
  40         @Override
  41         public RNAalifold setInput(String inFile) {
  42                 log.info("Set input file: " + inFile.toString());
  43                 cbuilder.setLast(inFile);
  44                 super.setInput(inFile);
  45                 return this;
  46         }
  47
  48         @SuppressWarnings("unchecked")
  49         @Override
  50         public Class<RNAalifold> getType() {
  51                 return (Class<RNAalifold>) this.getClass();
  52         }
  53
  54         @SuppressWarnings("unchecked")
  55         @Override
  56         // PlaceHolder method
  57         public String getResults(String workDirectory)
  58                         throws ResultNotAvailableException {
  59                 try {
  60                         // System.out.print(readRNAStruct(workDirectory, getOutput()));
  61                         return readRNAStruct(workDirectory, getOutput());
  62                 } catch (FileNotFoundException e) {
  63                         log.error(e.getMessage(), e.getCause());
  64                         throw new ResultNotAvailableException(e);
  65                 } catch (IOException e) {
  66                         log.error(e.getMessage(), e.getCause());
  67                         throw new ResultNotAvailableException(e);
  68                 }
  69         }
  70
  71
  72         // Simple and generic methods for reading a whole file
  73         // Should surfice until a more detailed datamodel and parser are developed
  74         private static String readRNAStruct(String workDirectory,
  75                         String structFile) throws IOException, FileNotFoundException {
  76                 assert !compbio.util.Util.isEmpty(workDirectory);
  77                 assert !compbio.util.Util.isEmpty(structFile);
  78                 File sfile = new File(compbio.engine.client.Util.getFullPath(
  79                                 workDirectory, structFile));
  80                 log.trace("RNAALIFOLD OUTPUT FILE PATH: " + sfile.getAbsolutePath());
  81                 if(!(sfile.exists() && sfile.length() > 0)) {
  82                         throw new FileNotFoundException("Result for the jobId "
  83                                         + workDirectory + "with file name " + structFile
  84                                         + " is not found!");
  85                 }
  86                 return readFile(sfile);
  87         }
  88
  89         private static BufferedReader input;
  90         public static String readFile(File inputFile) throws
  91                         FileNotFoundException, IOException {
  92
  93                 input   = new BufferedReader(new FileReader(inputFile));
  94
  95                 String file = new String();
  96                 String line = new String();
  97
  98                 while (true) {
  99                         line = input.readLine();
 100
 101                         if (line != null) {
 102                                 file = file + line + "\r\n";
 103                         } else break;
 104                 }
 105                 // Close file
 106                 input.close();
 107                 return file;
 108         }
 109
 110 }