public PeptideExtractionManager(int sizeOfOneSide, DataTable dtSource, string nameOfPIDFieldName, string nameOfSequenceFeild, bool isExtendedSequenceField, string nameOfPositionFeild, bool markClassificationLabel, string classificationLabel)
{
_SizeOfOneSide = sizeOfOneSide;
_SourceDataTable = dtSource;
_IsExtendedSequence = isExtendedSequenceField;
_NameOfPositionFeildName = nameOfPositionFeild;
_NamePIDFeildName = nameOfPIDFieldName;
_NameOfSequenceFeildName = nameOfSequenceFeild;
_ClassificationLabel = classificationLabel;
_MarkClassificationLabel = markClassificationLabel;
_PeptideDataTable = new DataTable("Peptides");
_PeptideDataTable.Columns.Add("PeptideID");
_PeptideDataTable.Columns.Add("ExtendedSequence");
if (_MarkClassificationLabel == true)
{
_PeptideDataTable.Columns.Add("Class");
}
PeptideExtractionCompletedEventArg = new WorkerCompletedEventArg();
PeptideExtractionProgressEventArg = new WorkerProgressEventArg();
for (index = (-1 * _SizeOfOneSide); index <= _SizeOfOneSide; index++)
{
_PeptideDataTable.Columns.Add("P" + index.ToString());
}
}
public void Run()
{
int rowIndex;
DataRow row;
int totalRows;
float progress;
int tableIndex = 0;
foreach (DataTable dt in _ListOfDataTables)
{
tableIndex++;
totalRows = dt.Rows.Count;
for (rowIndex = 0; rowIndex < totalRows; rowIndex++)
{
row = dt.Rows[rowIndex];
_MegeredDataTable.ImportRow(row);
progress = (((float)(rowIndex + 1)) / ((float)(totalRows)) * 100);
if (ProgressUpdate != null)
{
ProgressArg.ProgressPercentage = progress;
ProgressArg.UserState = "Merging table no. " + tableIndex.ToString();
ProgressUpdate(this, ProgressArg);
}
}
}
if (ProgressCompleted != null)
{
WorkerCompletedEventArg e = new WorkerCompletedEventArg();
e.Result = _MegeredDataTable;
e.UserStateMessage = "Finished";
ProgressCompleted(this, e);
}
}
public NeuralNetwork(int id)
{
ID = id;
NeuralNetworkTaskCompletedArgs = new WorkerCompletedEventArg();
NeuralNetworkTaskProgressArgs = new WorkerProgressEventArg();
NeuralNetworkTaskStartedArgs = new WorkerStartedEventArg();
}
void dtmanager_ProgressCompleted(object sender, WorkerCompletedEventArg e)
{
_MergedDataTable = (DataTable)e.Result;
dataGridView2.DataSource = _MergedDataTable;
lblStatus.Text = "Total Merged Records: " + _MergedDataTable.Rows.Count.ToString();
progressBar1.Value = 0;
Application.DoEvents();
}
void _BootStrapAgent_SamplingCompleted(object sender, WorkerCompletedEventArg e)
{
lblStatus.Text = "Bootstrapping Done...";
_TrainingDataTable = _BootStrapAgent.TrainingDataTable;
_ValidationDataTable = _BootStrapAgent.ValidateDataTable;
gridTraining.DataSource = _TrainingDataTable;
gridValidaton.DataSource = _ValidationDataTable;
lblTrainingRecordCount.Text = _BootStrapAgent.TrainingDataTable.Rows.Count.ToString();
lblValidationRecordCount.Text = _BootStrapAgent.ValidateDataTable.Rows.Count.ToString();
}
void encodingManager_EncodingCompleted(object sender, WorkerCompletedEventArg e)
{
_EncodedTable = (DataTable)e.Result;
dataGridView3.DataSource = _EncodedTable;
lblEncodedTableRecordCount.Text = _EncodedTable.Rows.Count.ToString();
}
void _ProteinDataSeperator_SeperationCompleted(object sender, WorkerCompletedEventArg e)
{
lblStatus.Text = "Done";
Application.DoEvents();
}
public void Run()
{
if (SeperationStarted != null)
{
SeperationStarted(this);
}
SeperationEventArgs = new WorkerCompletedEventArg();
SeperationProgressEventArgs = new WorkerProgressEventArg();
int total = _SiteDataTable.Rows.Count;
string positionString;
string pid;
string sequence;
int position;
_ProteinDataTable = new DataTable("ProteinDataTable");
_ProteinDataTable.Columns.Add("PID");
_ProteinDataTable.Columns.Add("Sequence");
_ProteinDataTable.Columns.Add("SequenceLength");
_ProteinDataTable.Columns.Add("Position");
DataRow row;
Dictionary <string, string> proteinSequenceDictionary;
Dictionary <string, List <int> > proteinPositionDictionary;
proteinPositionDictionary = new Dictionary <string, List <int> >();
proteinSequenceDictionary = new Dictionary <string, string>();
int index;
if (SeperationProgressUpdate != null)
{
SeperationProgressEventArgs.ProgressPercentage = 0;
SeperationProgressEventArgs.UserState = "Extracting and Grouping Protein's Sequence and Position Related Data";
SeperationProgressUpdate(this, SeperationProgressEventArgs);
}
for (index = 0; index < total; index++)
{
row = _SiteDataTable.Rows[index];
pid = row[_PIDFieldName].ToString();
if (proteinSequenceDictionary.ContainsKey(pid) == false)
{
sequence = row[_SequenceFieldName].ToString();
proteinSequenceDictionary.Add(pid, sequence);
proteinPositionDictionary.Add(pid, new List <int>());
}
position = int.Parse(row[_PositionFieldName].ToString());
//if (proteinPositionDictionary[pid] == null)
// proteinPositionDictionary[pid] = new List<int>();
if (proteinPositionDictionary[pid].Contains(position) == false)
{
proteinPositionDictionary[pid].Add(position);
}
if (SeperationProgressUpdate != null)
{
SeperationProgressEventArgs.ProgressPercentage = (float)(((float)index / (float)total) * 100.00f);
SeperationProgressEventArgs.UserState = "Extracting and Grouping Protein's Sequence and Position Related Data";
SeperationProgressUpdate(this, SeperationProgressEventArgs);
}
}
total = proteinPositionDictionary.Keys.Count;
index = 1;
int ctr;
List <int> positionList;
if (SeperationProgressUpdate != null)
{
SeperationProgressEventArgs.ProgressPercentage = 0.00f;
SeperationProgressEventArgs.UserState = "Preparing Protein Profiles and Importing Them to DataTable";
SeperationProgressUpdate(this, SeperationProgressEventArgs);
}
foreach (string id in proteinSequenceDictionary.Keys)
{
positionString = "";
positionList = proteinPositionDictionary[id];
positionList.Sort();
for (ctr = 0; ctr < positionList.Count; ctr++)
{
position = positionList[ctr];
positionString = positionString + position.ToString();
if (ctr != (positionList.Count - 1))
{
positionString = positionString + ",";
}
}
row = _ProteinDataTable.NewRow();
row["PID"] = id;
row["Sequence"] = proteinSequenceDictionary[id];
row["SequenceLength"] = proteinSequenceDictionary[id].Length;
row["Position"] = positionString;
_ProteinDataTable.Rows.Add(row);
if (SeperationProgressUpdate != null)
{
SeperationProgressEventArgs.ProgressPercentage = (float)(((float)index / (float)total) * 100.00f);
SeperationProgressEventArgs.UserState = "Preparing Protein Profiles and Importing Them to DataTable";
SeperationProgressUpdate(this, SeperationProgressEventArgs);
}
index++;
}
if (SeperationCompleted != null)
{
SeperationCompleted(this, null);
}
}
void _PeptideExtractionManager_PeptideExtractionCompleted(object sender, WorkerCompletedEventArg e)
{
lblStatus.Text = "Peptde Extraction Done...";
gridPeptides.DataSource = _PeptideExtractionManager.PeptideDataTable;
}
public void Run()
{
ProgressArgs = new WorkerProgressEventArg();
int ctr;
if (_UseBinarySplitMode == true)
{
sizeOfCodeString = 0;
foreach (string key in _EncodingDictionary.Keys)
{
if (sizeOfCodeString <= _EncodingDictionary[key].Length)
{
sizeOfCodeString = _EncodingDictionary[key].Length;
}
}
_EncodedDataTable = new DataTable("Encoded");
string columnName;
foreach (DataColumn col in _DataTableToEncode.Columns)
{
columnName = col.ColumnName;
if (_ListOfAttributes.Contains(columnName) == false)
{
_EncodedDataTable.Columns.Add(columnName);
}
else
{
for (ctr = 1; ctr <= sizeOfCodeString; ctr++)
{
_EncodedDataTable.Columns.Add(columnName + "_" + ctr.ToString());
}
}
}
}
else
{
_EncodedDataTable = _DataTableToEncode.Clone();
}
if (_AddBinaryStringAttribute == true)
{
_EncodedDataTable.Columns.Add("EncodedString");
_EncodedDataTable.Columns.Add("EncodedStringLength");
}
int attributeIndex;
string attribute;
int rowIndex;
int totalRows = _DataTableToEncode.Rows.Count;
int totalAttributes = _DataTableToEncode.Columns.Count;
float progress;
DataRow row;
DataRow encodedRow;
string item;
string encodeditem;
string encodedString = "";
char [] encodingStringArray;
//int ctr;
for (rowIndex = 0; rowIndex < totalRows; rowIndex++)
{
row = _DataTableToEncode.Rows[rowIndex];
encodedRow = _EncodedDataTable.NewRow();
for (attributeIndex = 0; attributeIndex < totalAttributes; attributeIndex++)
{
attribute = _DataTableToEncode.Columns[attributeIndex].ColumnName;
item = row[attribute].ToString();
if (_ListOfAttributes.Contains(attribute) == true)
{
encodeditem = _EncodingDictionary[item];
if (_UseBinarySplitMode == true)
{
encodingStringArray = encodeditem.ToCharArray();
for (ctr = 1; ctr <= sizeOfCodeString; ctr++)
{
encodedRow[attribute + "_" + ctr.ToString()] = encodingStringArray[ctr - 1].ToString();
}
}
else
{
encodedRow[attribute] = encodeditem;
}
if (_AddBinaryStringAttribute == true)
{
encodedString = encodedString + encodeditem;
}
}
else
{
encodedRow[attribute] = item;
}
}
if (_AddBinaryStringAttribute == true)
{
encodedRow["EncodedString"] = encodedString;
encodedRow["EncodedStringLength"] = encodedString.Length;
encodedString = "";
}
_EncodedDataTable.Rows.Add(encodedRow);
progress = (((float)(rowIndex + 1)) / ((float)(totalRows)) * 100);
if (EncodingProgress != null)
{
ProgressArgs.ProgressPercentage = progress;
ProgressArgs.UserState = "";
EncodingProgress(this, ProgressArgs);
}
}
if (EncodingCompleted != null)
{
CompletedArgs = new WorkerCompletedEventArg();
CompletedArgs.Result = _EncodedDataTable;
CompletedArgs.UserStateMessage = "Finished";
EncodingCompleted(this, CompletedArgs);
}
}
