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.RNAstruct;
  16 import compbio.data.sequence.UnknownFileFormatException;
  17 import compbio.engine.client.PipedExecutable;
  18 import compbio.engine.client.SkeletalExecutable;
  19 import compbio.metadata.ResultNotAvailableException;
  20 import compbio.runner.Util;
  21
  22
  23 import compbio.engine.client.CommandBuilder;
  24
  25 public class RNAalifold extends SkeletalExecutable<RNAalifold>
  26                 implements PipedExecutable<RNAalifold> {
  27
  28
  29         private static Logger log = Logger.getLogger(RNAalifold.class);
  30
  31         // May not be necessary as defult is "<space>" but still dont know
  32         // How to deal with different key value separators for different params
  33         public static final String KEY_VALUE_SEPARATOR = " ";
  34
  35         public RNAalifold() {
  36                 super(KEY_VALUE_SEPARATOR);
  37         }
  38
  39         @Override
  40         public RNAalifold setOutput(String outFile) {
  41                 super.setOutput(outFile);
  42                 return this;
  43         }
  44
  45         @Override
  46         public RNAalifold setInput(String inFile) {
  47                 cbuilder.setLast(inFile);
  48                 super.setInput(inFile);
  49                 return this;
  50         }
  51
  52         @SuppressWarnings("unchecked")
  53         @Override
  54         public Class<RNAalifold> getType() {
  55                 return (Class<RNAalifold>) this.getClass();
  56         }
  57
  58         @SuppressWarnings("unchecked")
  59         @Override
  60         // PlaceHolder method
  61         public String getResults(String workDirectory)
  62                         throws ResultNotAvailableException {
  63                 try {
  64                         return Util.readRNAStruct(workDirectory, getOutput());
  65
  66                 } catch (FileNotFoundException e) {
  67                         log.error(e.getMessage(), e.getCause());
  68                         throw new ResultNotAvailableException(e);
  69                 } catch (IOException e) {
  70                         log.error(e.getMessage(), e.getCause());
  71                         throw new ResultNotAvailableException(e);
  72                 }
  73         }
  74
  75
  76         // the new currently used methods for reading are found in
  77         // - compbio.data.sequence.SequenceUtil and
  78         // - compbio.runner.Util
  79
  80         // Simple and generic methods for reading a whole file
  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 }