Package versusSNP.blast

Examples of versusSNP.blast.BlastParser

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        JOptionPane.showMessageDialog(null, UICaption.dialog_error_path_empty, UICaption.dialog_caption_error, JOptionPane.ERROR_MESSAGE);
        loopAlignmentLoader(dialog);
      }
      document.setQueryGenome(dialog.getId1());
      document.setSubjectGenome(dialog.getId2());
      new Thread(new BlastParser(dialog.getPath(), document)).start();
    }
  }
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      new ORFFile().readFile(args[1] + ".txt", genome2);
      genome2.sortOrfList();
      FastaFile fastaFile2 = new FastaFile();
      fastaFile2.readFile(args[1] + ".fasta", genome2);
      genome2.attachSequences(fastaFile2.getSequences());
      BlastParser parser = new BlastParser();
      parser.parse(args[0] + "-" + args[1]);
      genome1.attachBlastSets(parser.getBlastList(), genome2, true);
      genome1.printSNPSummary(genome2);
    } else {
      new VersusSNP().setVisible(true);
    }
  }
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Related Classes of versusSNP.blast.BlastParser

  • versusSNP.blast.util.SNPFinder
  • versusSNP.gui.widgets.ProgressBar
  • versusSNP.Main
  • versusSNP.VersusSNP
  • java.io.File
  • java.io.InputStreamReader
  • java.io.FileInputStream
  • java.io.BufferedReader
  • java.util.regex.Matcher
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