/// <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;
}