public Colchar_column_line_class Deep_copy()
{
Colchar_column_line_class copy = (Colchar_column_line_class)this.MemberwiseClone();
copy.SampleName = (string)this.SampleName.Clone();
return(copy);
}
private Colchar_column_line_class[] Deep_copy_columns()
{
int columns_length = Columns.Length;
Colchar_column_line_class[] copy_columns = new Colchar_column_line_class[columns_length];
for (int indexC = 0; indexC < columns_length; indexC++)
{
copy_columns[indexC] = this.Columns[indexC].Deep_copy();
}
return(copy_columns);
}
public void Keep_only_input_columns(params int[] inputColumns)
{
Correctness_check();
int inputColumns_length = inputColumns.Length;
Colchar_column_line_class[] new_columns = new Colchar_column_line_class[inputColumns_length];
for (int indexInput = 0; indexInput < inputColumns_length; indexInput++)
{
new_columns[indexInput] = this.Columns[inputColumns[indexInput]].Deep_copy();
}
Columns = new_columns;
Column_rearrangements_adopted = false;
}
public void Correctness_check()
{
int col_length = Columns_length;
Colchar_column_line_class[] columns_copy = Deep_copy_columns();
columns_copy = Colchar_column_line_class.Order_in_standard_way(columns_copy);
for (int indexC = 1; indexC < col_length; indexC++)
{
if (columns_copy[indexC].Equal_in_standard_way(columns_copy[indexC - 1]))
{
throw new Exception("duplicated column charactarization");
}
}
if (!Column_rearrangements_adopted)
{
throw new Exception("column rearrangements are not adopted");
}
}
public int[] Order_columns_in_standard_way_and_get_old_new_index_array()
{
Correctness_check();
Column_rearrangements_adopted = false;
Colchar_column_line_class[] old_columns = Deep_copy_columns();
Columns = Colchar_column_line_class.Order_in_standard_way(Columns);
int columns_length = Columns.Length;
#region Initialize index old new (and fill with -1 entries)
int[] old_new_index_array = new int[columns_length];
for (int indexOld = 0; indexOld < columns_length; indexOld++)
{
old_new_index_array[indexOld] = -1;
}
#endregion
#region Fill index old new
Colchar_column_line_class old_column;
Colchar_column_line_class new_column;
for (int indexOld = 0; indexOld < columns_length; indexOld++)
{
old_column = old_columns[indexOld];
for (int indexNew = 0; indexNew < columns_length; indexNew++)
{
new_column = Columns[indexNew];
if (old_column.Equal_in_standard_way(new_column))
{
old_new_index_array[indexOld] = indexNew;
break;
}
}
}
#endregion
return(old_new_index_array);
}
public void Merge_all_columns()
{
int columns_count = this.Columns_length;
Colchar_column_line_class column_line;
StringBuilder sb_new_name = new StringBuilder();
sb_new_name.AppendFormat("Merged");
Entry_type_enum entryType = this.Columns[0].EntryType;
for (int indexC = 0; indexC < columns_count; indexC++)
{
column_line = this.Columns[indexC];
if (!column_line.EntryType.Equals(entryType))
{
throw new Exception();
}
sb_new_name.AppendFormat("-");
sb_new_name.AppendFormat("{0}", column_line.Timepoint);
}
Colchar_column_line_class new_column_line = new Colchar_column_line_class(entryType, 0, sb_new_name.ToString());
this.Columns = new Colchar_column_line_class[] { new_column_line };
}
public void Add_to_data_instance(IAdd_to_data[] add_data)
{
int old_columns_length = ColChar.Columns_length;
int add_data_length = add_data.Length;
IAdd_to_data add_data_interface_line;
#region Analyze, if new columns needed and add to colChar
add_data = add_data.OrderBy(l => l.EntryType_for_data).ThenBy(l => l.Timepoint_for_data).ThenBy(l => l.SampleName_for_data).ToArray();
List <Colchar_column_line_class> colChar_column_list = new List <Colchar_column_line_class>();
Colchar_column_line_class colChar_column_line;
for (int indexAdd = 0; indexAdd < add_data_length; indexAdd++)
{
add_data_interface_line = add_data[indexAdd];
if ((indexAdd == 0) ||
(!add_data_interface_line.EntryType_for_data.Equals(add_data[indexAdd - 1].EntryType_for_data)) ||
(!add_data_interface_line.Timepoint_for_data.Equals(add_data[indexAdd - 1].Timepoint_for_data)) ||
(!add_data_interface_line.SampleName_for_data.Equals(add_data[indexAdd - 1].SampleName_for_data)))
{
colChar_column_line = new Colchar_column_line_class();
colChar_column_line.EntryType = add_data_interface_line.EntryType_for_data;
colChar_column_line.Timepoint = add_data_interface_line.Timepoint_for_data;
colChar_column_line.SampleName = (string)add_data_interface_line.SampleName_for_data.Clone();
colChar_column_list.Add(colChar_column_line);
}
}
ColChar.Identify_new_columns_and_add_at_right_site(colChar_column_list.ToArray());
int new_columns_length = ColChar.Columns.Length;
#endregion
int data_length = this.Data_length;
Data_line_class data_line;
#region Extend data lines by adding zero values at right site
float[] new_columns;
for (int indexD = 0; indexD < data_length; indexD++)
{
data_line = this.Data[indexD];
new_columns = new float[new_columns_length];
for (int indexOld = 0; indexOld < old_columns_length; indexOld++)
{
new_columns[indexOld] = data_line.Columns[indexOld];
}
data_line.Columns = new_columns.ToArray();
}
#endregion
#region Add to data and generate ordered data add lines to data
add_data = add_data.OrderBy(l => l.NCBI_official_symbol_for_data).ThenBy(l => l.EntryType_for_data).ThenBy(l => l.SampleName_for_data).ToArray();
int indexColumn;
int indexData = 0;
int stringCompare;
Data_line_class new_data_line;
List <Data_line_class> add_lines_to_data_list = new List <Data_line_class>();
int indexCol = -1;
for (int indexAdd = 0; indexAdd < add_data_length; indexAdd++)
{
add_data_interface_line = add_data[indexAdd];
indexColumn = ColChar.Get_columnIndex(add_data_interface_line);
stringCompare = -2;
while ((indexData < data_length) && (stringCompare < 0))
{
data_line = Data[indexData];
stringCompare = data_line.NCBI_official_symbol.CompareTo(add_data_interface_line.NCBI_official_symbol_for_data);
if (stringCompare < 0)
{
indexData++;
}
else if (stringCompare == 0)
{
indexCol = ColChar.Get_columnIndex(add_data_interface_line);
data_line.Add_to_this_line_after_checking_if_this_line_has_empty_entry(add_data_interface_line, indexCol);
}
}
if (stringCompare != 0)
{
new_data_line = new Data_line_class(add_data_interface_line.NCBI_official_symbol_for_data, new_columns_length);
new_data_line.Columns[indexColumn] = add_data_interface_line.Value_for_data;
add_lines_to_data_list.Add(new_data_line);
}
}
Data_line_class[] add_lines_to_data = add_lines_to_data_list.OrderBy(l => l.NCBI_official_symbol).ToArray();
#endregion
#region Combine add_lines_to_data to generate final add_data_lines
int add_lines_length = add_lines_to_data.Length;
int firstIndex_same_rowName = -1;
Data_line_class add_data_line;
Data_line_class inner_add_data_line;
List <Data_line_class> final_add_data_list = new List <Data_line_class>();
for (int indexAL = 0; indexAL < add_lines_length; indexAL++)
{
add_data_line = add_lines_to_data[indexAL];
if ((indexAL == 0) || (!add_data_line.NCBI_official_symbol.Equals(add_lines_to_data[indexAL - 1].NCBI_official_symbol)))
{
firstIndex_same_rowName = indexAL;
}
if ((indexAL == add_lines_length - 1) || (!add_data_line.NCBI_official_symbol.Equals(add_lines_to_data[indexAL + 1].NCBI_official_symbol)))
{
for (int indexInner = firstIndex_same_rowName; indexInner < indexAL; indexInner++)
{
inner_add_data_line = add_lines_to_data[indexInner];
add_data_line.Sum_values_to_this_in_consideration_of_empty_entry(inner_add_data_line);
}
final_add_data_list.Add(add_data_line);
}
}
#endregion
#region Add final data line to data
int final_data_length = final_add_data_list.Count;
int new_data_length = final_data_length + data_length;
Data_line_class[] new_data = new Data_line_class[new_data_length];
int indexNew = -1;
for (int indexOld = 0; indexOld < data_length; indexOld++)
{
indexNew++;
new_data[indexNew] = Data[indexOld];
}
for (int indexFinal = 0; indexFinal < final_data_length; indexFinal++)
{
indexNew++;
new_data[indexNew] = final_add_data_list[indexFinal];
}
Data = new_data;
#endregion
Keep_only_lines_that_contain_at_least_one_non_zero_value();
}
public void Identify_new_columns_and_add_at_right_site(Colchar_column_line_class[] add_data)
{
Correctness_check();
int old_columns_length = Columns_length;
Colchar_column_line_class[] add_columns;
#region Identify add columns
List <Colchar_column_line_class> add_columns_list = new List <Colchar_column_line_class>();
add_data = Colchar_column_line_class.Order_in_standard_way(add_data);
int add_data_length = add_data.Length;
Colchar_column_line_class add_line;
bool old_columns_contain_new_combination = false;
Colchar_column_line_class old_column_line;
Colchar_column_line_class add_column_line;
for (int indexAdd = 0; indexAdd < add_data_length; indexAdd++)
{
add_line = add_data[indexAdd];
if ((indexAdd == 0) || (!Colchar_column_line_class.Equal_in_standard_way(add_line, add_data[indexAdd - 1])))
{
old_columns_contain_new_combination = false;
for (int indexOld = 0; indexOld < old_columns_length; indexOld++)
{
old_column_line = Columns[indexOld];
if (old_column_line.Equal_in_standard_way(add_line))
{
old_columns_contain_new_combination = true;
break;
}
}
if (!old_columns_contain_new_combination)
{
add_column_line = new Colchar_column_line_class(add_line.EntryType, add_line.Timepoint, add_line.SampleName);
add_columns_list.Add(add_column_line);
}
}
}
add_columns = add_columns_list.ToArray();
#endregion
#region Add add columns at right site
int add_columns_length = add_columns.Length;
int new_columns_length = add_columns_length + old_columns_length;
Colchar_column_line_class[] new_columns = new Colchar_column_line_class[new_columns_length];
int indexNew = -1;
for (int indexOld = 0; indexOld < old_columns_length; indexOld++)
{
indexNew++;
new_columns[indexNew] = this.Columns[indexOld].Deep_copy();
}
for (int indexAdd = 0; indexAdd < add_columns_length; indexAdd++)
{
indexNew++;
new_columns[indexNew] = add_columns[indexAdd].Deep_copy();
}
Columns = new_columns;
#endregion
Correctness_check();
}
public Colchar_class()
{
Column_rearrangements_adopted = true;
Columns = new Colchar_column_line_class[0];
}
public static bool Equal_in_standard_way(Colchar_column_line_class line1, Colchar_column_line_class line2)
{
return((line1.EntryType.Equals(line2.EntryType)) &&
(line1.Timepoint.Equals(line2.Timepoint)) &&
(line1.SampleName.Equals(line2.SampleName)));
}
public bool Equal_in_standard_way(Colchar_column_line_class other)
{
return((this.EntryType.Equals(other.EntryType)) &&
(this.Timepoint.Equals(other.Timepoint)) &&
(this.SampleName.Equals(other.SampleName)));
}