internal info_blast_pssm_entry(info_blast_pssm_entry pssm_entry)
{
const string module_name = nameof(pssm_entry);
const string method_name = nameof(pssm_entry);
if (pssm_entry == null)
{
throw new ArgumentNullException(nameof(pssm_entry));
}
this.matrix_column_index = pssm_entry.matrix_column_index;
this.matrix_row_index = pssm_entry.matrix_row_index;
this.position_aa = pssm_entry.position_aa;
this.score = pssm_entry.score;
this.query_sequence_aa = pssm_entry.query_sequence_aa;
this.query_sequence_aa_pos = pssm_entry.query_sequence_aa_pos;
}
internal static List <info_blast_pssm_entry> load_psi_blast_pssm(string pssm_filename, bool normalise_pssm = false)
{
const string module_name = nameof(info_blast_pssm);
const string method_name = nameof(load_psi_blast_pssm);
var pssm = new List <info_blast_pssm_entry>();
if (!File.Exists(pssm_filename) || new FileInfo(pssm_filename).Length == 0)
{
return(new List <info_blast_pssm_entry>());
}
var line_list = io_proxy.ReadAllLines(pssm_filename, module_name, method_name).Skip(2).ToList();
var pssm_end_index = line_list.IndexOf(/*program.string_debug*/ ($@""));
if (pssm_end_index > -1)
{
line_list = line_list.GetRange(0, pssm_end_index);
}
line_list[0] = /*program.string_debug*/ ($@"ID AA {line_list[0]} W1 W2");
//lineList = lineList.Skip(1).ToList();
var line_list_split = line_list.Select(a => a.Split(new char[] { ' ' }, StringSplitOptions.RemoveEmptyEntries).ToList()).ToList();
line_list_split = line_list_split.Select(a => a.Take(22).ToList()).ToList();
for (var row = 1; row < line_list_split.Count; row++)
{
for (var col = 2; col < line_list_split[row].Count; col++)
{
if (!double.TryParse(line_list_split[row][col], out var score))
{
score = 0;
}
var col_aa_provided = line_list_split[0][col][0];
var row_aa_provided = line_list_split[row][1][0];
var row_index_provided = int.Parse(line_list_split[row][0], NumberStyles.Integer, NumberFormatInfo.InvariantInfo);
var e = new info_blast_pssm_entry()
{
query_sequence_aa_pos = row_index_provided,
query_sequence_aa = row_aa_provided,
matrix_row_index = row - 1,
matrix_column_index = col - 2,
position_aa = col_aa_provided,
score = score
};
pssm.Add(e);
}
}
if (normalise_pssm)
{
pssm = dimorphics_dataset.info_blast_pssm.normalise_pssm(pssm);
}
return(pssm);
}
