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         // May not be necessary as defult is "<space>" but still dont know
  35         // How to deal with different key value separators for different params
  36         public static final String KEY_VALUE_SEPARATOR = " ";
  37
  38         public RNAalifold() {
  39                 super(KEY_VALUE_SEPARATOR);
  40         }
  41
  42         @Override
  43         public RNAalifold setOutput(String outFile) {
  44                 super.setOutput(outFile);
  45                 return this;
  46         }
  47
  48         @Override
  49         public RNAalifold setInput(String inFile) {
  50                 cbuilder.setLast(inFile);
  51                 super.setInput(inFile);
  52                 return this;
  53         }
  54
  55         @SuppressWarnings("unchecked")
  56         @Override
  57         public Class<RNAalifold> getType() {
  58                 return (Class<RNAalifold>) this.getClass();
  59         }
  60
  61         @SuppressWarnings("unchecked")
  62         @Override
  63         // PlaceHolder method
  64         public RNAstruct getResults(String workDirectory)
  65                         throws ResultNotAvailableException {
  66                 try {
  67                         // System.out.println("Specialread " + Util.readRNAStructFile(workDirectory, getOutput()).toString());
  68                         return Util.readRNAStructFile(workDirectory, getOutput());
  69
  70                 } catch (FileNotFoundException e) {
  71                         log.error(e.getMessage(), e.getCause());
  72                         throw new ResultNotAvailableException(e);
  73                 } catch (IOException e) {
  74                         log.error(e.getMessage(), e.getCause());
  75                         throw new ResultNotAvailableException(e);
  76                 }
  77         }
  78
  79
  80         // the new currently used methods for reading are found in
  81         // - compbio.data.sequence.SequenceUtil and
  82         // - compbio.runner.Util
  83
  84         // Simple and generic methods for reading a whole file
  85 //      private static String readRNAStruct(String workDirectory,
  86 //                      String structFile) throws IOException, FileNotFoundException {
  87 //              assert !compbio.util.Util.isEmpty(workDirectory);
  88 //              assert !compbio.util.Util.isEmpty(structFile);
  89 //              File sfile = new File(compbio.engine.client.Util.getFullPath(
  90 //                              workDirectory, structFile));
  91 //              log.trace("RNAALIFOLD OUTPUT FILE PATH: " + sfile.getAbsolutePath());
  92 //              if(!(sfile.exists() && sfile.length() > 0)) {
  93 //                      throw new FileNotFoundException("Result for the jobId "
  94 //                                      + workDirectory + "with file name " + structFile
  95 //                                      + " is not found!");
  96 //              }
  97 //              return readFile(sfile);
  98 //      }
  99 //
 100 //      private static BufferedReader input;
 101 //      public static String readFile(File inputFile) throws
 102 //                      FileNotFoundException, IOException {
 103 //
 104 //              input   = new BufferedReader(new FileReader(inputFile));
 105 //
 106 //              String file = new String();
 107 //              String line = new String();
 108 //
 109 //              while (true) {
 110 //                      line = input.readLine();
 111 //
 112 //                      if (line != null) {
 113 //                              file = file + line + "\r\n";
 114 //                      } else break;
 115 //              }
 116 //              // Close file
 117 //              input.close();
 118 //              return file;
 119 //      }
 120
 121 }