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
  10
  11
  12
  13 import org.apache.log4j.Logger;
  14
  15 import compbio.data.sequence.ScoreManager;
  16 import compbio.data.sequence.RNAStruct;
  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         // May not be necessary as defult is "<space>" but still dont know
  33         // How to deal with different key value separators for different params
  34         public static final String KEY_VALUE_SEPARATOR = " ";
  35
  36         public RNAalifold() {
  37                 super(KEY_VALUE_SEPARATOR);
  38         }
  39
  40         @Override
  41         public RNAalifold setOutput(String outFile) {
  42                 super.setOutput(outFile);
  43                 return this;
  44         }
  45
  46         @Override
  47         public RNAalifold setInput(String inFile) {
  48                 cbuilder.setLast(inFile);
  49                 super.setInput(inFile);
  50                 return this;
  51         }
  52
  53         @SuppressWarnings("unchecked")
  54         @Override
  55         public Class<RNAalifold> getType() {
  56                 return (Class<RNAalifold>) this.getClass();
  57         }
  58
  59         @SuppressWarnings("unchecked")
  60         @Override
  61         // PlaceHolder method
  62         public ScoreManager getResults(String workDirectory)
  63                         throws ResultNotAvailableException {
  64                 try {
  65                         return Util.readRNAStruct(workDirectory, getOutput());
  66
  67                 } catch (FileNotFoundException e) {
  68                         log.error(e.getMessage(), e.getCause());
  69                         throw new ResultNotAvailableException(e);
  70                 } catch (IOException e) {
  71                         log.error(e.getMessage(), e.getCause());
  72                         throw new ResultNotAvailableException(e);
  73                 }
  74         }
  75
  76
  77         // the new currently used methods for reading are found in
  78         // - compbio.data.sequence.SequenceUtil and
  79         // - compbio.runner.Util
  80
  81         // Simple and generic methods for reading a whole file
  82 //      private static String readRNAStruct(String workDirectory,
  83 //                      String structFile) throws IOException, FileNotFoundException {
  84 //              assert !compbio.util.Util.isEmpty(workDirectory);
  85 //              assert !compbio.util.Util.isEmpty(structFile);
  86 //              File sfile = new File(compbio.engine.client.Util.getFullPath(
  87 //                              workDirectory, structFile));
  88 //              log.trace("RNAALIFOLD OUTPUT FILE PATH: " + sfile.getAbsolutePath());
  89 //              if(!(sfile.exists() && sfile.length() > 0)) {
  90 //                      throw new FileNotFoundException("Result for the jobId "
  91 //                                      + workDirectory + "with file name " + structFile
  92 //                                      + " is not found!");
  93 //              }
  94 //              return readFile(sfile);
  95 //      }
  96 //
  97 //      private static BufferedReader input;
  98 //      public static String readFile(File inputFile) throws
  99 //                      FileNotFoundException, IOException {
 100 //
 101 //              input   = new BufferedReader(new FileReader(inputFile));
 102 //
 103 //              String file = new String();
 104 //              String line = new String();
 105 //
 106 //              while (true) {
 107 //                      line = input.readLine();
 108 //
 109 //                      if (line != null) {
 110 //                              file = file + line + "\r\n";
 111 //                      } else break;
 112 //              }
 113 //              // Close file
 114 //              input.close();
 115 //              return file;
 116 //      }
 117
 118 }