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
  15
  16 import org.apache.log4j.Logger;
  17
  18 import compbio.data.sequence.RNAstruct;
  19 import compbio.data.sequence.UnknownFileFormatException;
  20 import compbio.engine.client.PipedExecutable;
  21 import compbio.engine.client.SkeletalExecutable;
  22 import compbio.metadata.ResultNotAvailableException;
  23 import compbio.runner.Util;
  24
  25
  26 import compbio.engine.client.CommandBuilder;
  27
  28 public class RNAalifold extends SkeletalExecutable<RNAalifold>
  29                 implements PipedExecutable<RNAalifold> {
  30
  31
  32         private static Logger log = Logger.getLogger(RNAalifold.class);
  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         @SuppressWarnings("unchecked")
  57         @Override
  58         // PlaceHolder method
  59         public RNAstruct getResults(String workDirectory)
  60                         throws ResultNotAvailableException {
  61                 try {
  62                         // System.out.println("Specialread " + Util.readRNAStructFile(workDirectory, getOutput()).toString());
  63                         return Util.readRNAStructFile(workDirectory, getOutput());
  64
  65                 } catch (FileNotFoundException e) {
  66                         log.error(e.getMessage(), e.getCause());
  67                         throw new ResultNotAvailableException(e);
  68                 } catch (IOException e) {
  69                         log.error(e.getMessage(), e.getCause());
  70                         throw new ResultNotAvailableException(e);
  71                 }
  72         }
  73
  74
  75         // OLD :- the new methods for reading are found in
  76         // - compbio.data.sequence.SequenceUtil and
  77         // - compbio.runner.Util
  78
  79         // Simple and generic methods for reading a whole file
  80         // Should surfice until a more detailed datamodel and parser are developed
  81 //      private static String readRNAStruct(String workDirectory,
  82 //                      String structFile) throws IOException, FileNotFoundException {
  83 //              assert !compbio.util.Util.isEmpty(workDirectory);
  84 //              assert !compbio.util.Util.isEmpty(structFile);
  85 //              File sfile = new File(compbio.engine.client.Util.getFullPath(
  86 //                              workDirectory, structFile));
  87 //              log.trace("RNAALIFOLD OUTPUT FILE PATH: " + sfile.getAbsolutePath());
  88 //              if(!(sfile.exists() && sfile.length() > 0)) {
  89 //                      throw new FileNotFoundException("Result for the jobId "
  90 //                                      + workDirectory + "with file name " + structFile
  91 //                                      + " is not found!");
  92 //              }
  93 //              return readFile(sfile);
  94 //      }
  95 //
  96 //      private static BufferedReader input;
  97 //      public static String readFile(File inputFile) throws
  98 //                      FileNotFoundException, IOException {
  99 //
 100 //              input   = new BufferedReader(new FileReader(inputFile));
 101 //
 102 //              String file = new String();
 103 //              String line = new String();
 104 //
 105 //              while (true) {
 106 //                      line = input.readLine();
 107 //
 108 //                      if (line != null) {
 109 //                              file = file + line + "\r\n";
 110 //                      } else break;
 111 //              }
 112 //              // Close file
 113 //              input.close();
 114 //              return file;
 115 //      }
 116
 117 }