/// <summary> /// Validation method for input box for sequence data /// </summary> /// <param name="sender"></param> /// <param name="e"></param> private void inputBox_SequenceValidating(object sender, InputBoxValidatingArgs e) { if (e.Text.Trim().Length == 0) { e.Cancel = true; e.Message = "Required"; } else if (Nucleotide.isDNA(e.Text.Trim()) == false) { e.Cancel = true; e.Message = "Required"; } }
/// <summary> /// Creates an array of nucleotides from the whole sequence /// </summary> /// <returns>An array of Nucleotide objects</returns> public override Nucleotide createNucleotideArray() { Nucleotide nucleotide = new Nucleotide(header); for (int i = 0; i < index; i++) { for (int j = 0; i < fastqSeq[i].getFastqSeqSize(); j++) { nucleotide.addCharNucleotideArray(Fq_FILE_MAP[fastqSeq[i].getFastqSeqAtPosition(j)].getNucleotide()); } } Console.Write("An array of nucleotides has been created"); return(nucleotide); }
public Boolean CheckStandardFormat() { header = new String[FQ_BLOCKS_TO_CHECK]; seq = new String[FQ_BLOCKS_TO_CHECK]; info = new String[FQ_BLOCKS_TO_CHECK]; qscore = new String[FQ_BLOCKS_TO_CHECK]; BufferedStream bs = new BufferedStream(fileReader); StreamReader reader = new StreamReader(bs); // Build sets of fastq blocks to check for (int i = 0; i < FQ_BLOCKS_TO_CHECK; i++) { header[i] = reader.ReadLine(); seq[i] = reader.ReadLine(); info[i] = reader.ReadLine(); qscore[i] = reader.ReadLine(); } // Check sets for (int i = 0; i < FQ_BLOCKS_TO_CHECK; i++) { if ((char)header[i][0] != IFqFile.INITIAL_HEADER_CHARACTER) { return(false); } if ((char)info[i][0] != IFqFile.INITIAL_INFO_LINE_CHARACTER) { return(false); } if (Nucleotide.isDNA(seq[i]) != true) { return(false); } if (seq[i].Length != qscore[i].Length) { return(false); } } fileReader.Seek(0, SeekOrigin.Begin); Console.WriteLine("FileReader Position: {0}", fileReader.Position); Console.WriteLine("File is found to be a fastqFile"); return(true); }
/// <summary> /// Creates an array of nucleotides from the whole sequence /// </summary> /// <returns>An array of Nucleotide objects</returns> public override Nucleotide createNucleotideArray() { Nucleotide nucleotide = new Nucleotide(header); for (int i = 0; i < index; i++) { for (int j = 0; i < fastqSeq[i].getFastqSeqSize(); j++) { nucleotide.addCharNucleotideArray(Fq_FILE_MAP[fastqSeq[i].getFastqSeqAtPosition(j)].getNucleotide()); } } Console.Write("An array of nucleotides has been created"); return nucleotide; }