private void button2_Click(object sender, EventArgs e)
{
string[] filePath = null;
filePath = this.textBox1.Text.Split(',');
for (int i = 0; i < filePath.Length - 1; i++)
{
FileStream fs = new FileStream(filePath[i], System.IO.FileMode.Open, System.IO.FileAccess.Read);
StreamReader sr = new StreamReader(fs, Encoding.UTF8);
string strLine = "";
string[] aryLine = null;
ArrayList HMMinfo = new ArrayList();
bool accession = false;
while ((strLine = sr.ReadLine()) != null)
{
aryLine = strLine.Split(' ');
if (string.Equals(aryLine[0], "Query:"))
{
aryLine = aryLine.Where(s => !string.IsNullOrEmpty(s)).ToArray();
HMMinfo.Add(aryLine[1].ToString());
}
else if (string.Equals(aryLine[0], "Accession:"))
{
accession = true;
aryLine = aryLine.Where(s => !string.IsNullOrEmpty(s)).ToArray();
HMMinfo.Add(aryLine[1].ToString());
}
else if (aryLine.Length > 5)
{
if (string.Equals(aryLine[4], "(domZ):"))
{
aryLine = aryLine.Where(s => !string.IsNullOrEmpty(s)).ToArray();
HMMinfo.Add(int.Parse(aryLine[4]).ToString());
}
}
}
sr.Close();
fs.Close();
int QueryNum;
DataTable dt = new DataTable();
if (accession)
{
dt.Columns.Add("Accession", typeof(string));
QueryNum = HMMinfo.Count / 3;
}
else
{
dt.Columns.Add("Query", typeof(string));
QueryNum = HMMinfo.Count / 2;
}
dt.Columns.Add("Number", typeof(Int32));
for (int j = 0; j < QueryNum; j++)
{
DataRow dr = dt.NewRow();
if (accession)
{
dr[0] = HMMinfo[3 * j + 1].ToString();
dr[1] = int.Parse(HMMinfo[3 * j + 2].ToString());
}
else
{
dr[0] = HMMinfo[2 * j].ToString();
dr[1] = int.Parse(HMMinfo[2 * j + 1].ToString());
}
dt.Rows.Add(dr);
}
if (app.Profile == null)
{
app.Profile = new DataTable();
app.Profile.Columns.Add("Feature", typeof(string));
app.Profile.Columns.Add("File1", typeof(int));
for (int m = 0; m < dt.Rows.Count; m++)
{
app.Profile.Rows.Add(dt.Rows[m][0], dt.Rows[m][1]);
}
}
else
{
int FileNum = app.Profile.Columns.Count;
string newfilename = "File" + FileNum.ToString();
DataColumn newfile = new DataColumn(newfilename, typeof(int));
newfile.DefaultValue = 0;
app.Profile.Columns.Add(newfile);
for (int m = 0; m < dt.Rows.Count; m++)
{
bool k = true;;
for (int j = 0; j < app.Profile.Rows.Count; j++)
{
if (string.Equals(dt.Rows[m][0].ToString(), app.Profile.Rows[j][0].ToString()))
{
app.Profile.Rows[j][FileNum] = int.Parse(dt.Rows[m][1].ToString());
k = false;
break;
}
}
if (k)
{
DataRow drtemp;
drtemp = app.Profile.NewRow();
drtemp[0] = dt.Rows[m][0].ToString();
for (int n = 1; n < FileNum; n++)
{
drtemp[n] = 0;
}
drtemp[FileNum] = int.Parse(dt.Rows[m][1].ToString());
app.Profile.Rows.Add(drtemp);
}
}
}
}
app.FeaName = new string[app.Profile.Rows.Count];
for (int i = 0; i < app.Profile.Rows.Count; i++)
{
app.FeaName[i] = app.Profile.Rows[i][0].ToString();
}
app.SamName = new string[app.Profile.Columns.Count - 1];
for (int i = 0; i < app.Profile.Columns.Count - 1; i++)
{
app.SamName[i] = app.Profile.Columns[i + 1].ColumnName;
}
int FeatureNum = app.FeaName.GetLength(0);
int SampleNum = app.SamName.GetLength(0);
app.CountMatrix = new double[FeatureNum, SampleNum];
for (int i = 0; i < FeatureNum; i++)
{
for (int j = 0; j < SampleNum; j++)
{
app.CountMatrix[i, j] = Convert.ToDouble(app.Profile.Rows[i][j + 1]);
}
}
app.SampleTotal = new double[SampleNum];
for (int i = 0; i < SampleNum; i++)
{
for (int j = 0; j < FeatureNum; j++)
{
app.SampleTotal[i] = app.SampleTotal[i] + Convert.ToDouble(app.Profile.Rows[j][i + 1]);
}
}
app.FreqMatrix = new double[FeatureNum, SampleNum];
for (int i = 0; i < FeatureNum; i++)
{
for (int j = 0; j < SampleNum; j++)
{
app.FreqMatrix[i, j] = app.CountMatrix[i, j] / app.SampleTotal[j];
}
}
Data_Output loaddata = new Data_Output();
loaddata.MdiParent = this.MdiParent;
loaddata.Show();
this.Close();
}
private void button2_Click_1(object sender, EventArgs e)
{
string filePath = this.textBox1.Text;
DataTable dt = new DataTable();
FileStream fs = new FileStream(filePath, System.IO.FileMode.Open, System.IO.FileAccess.Read);
StreamReader sr = new StreamReader(fs, Encoding.UTF8);
string strLine = "";
string[] aryLine = null;
string[] tableHead = null;
int columnCount = 0;
bool IsFirst = true;
while ((strLine = sr.ReadLine()) != null)
{
if (IsFirst == true)
{
tableHead = strLine.Split('\t');
IsFirst = false;
columnCount = tableHead.Length;
for (int i = 0; i < columnCount; i++)
{
tableHead[i] = tableHead[i].Replace("\"", "");
DataColumn dc = new DataColumn(tableHead[i]);
dt.Columns.Add(dc);
}
}
else
{
aryLine = strLine.Split('\t');
DataRow dr = dt.NewRow();
for (int j = 0; j < columnCount; j++)
{
dr[j] = aryLine[j].Replace("\"", "");
}
dt.Rows.Add(dr);
}
}
sr.Close();
fs.Close();
app.Profile = dt;
app.FeaName = new string[app.Profile.Rows.Count];
for (int i = 0; i < app.Profile.Rows.Count; i++)
{
app.FeaName[i] = app.Profile.Rows[i][0].ToString();
}
app.SamName = new string[app.Profile.Columns.Count - 1];
for (int i = 0; i < app.Profile.Columns.Count - 1; i++)
{
app.SamName[i] = app.Profile.Columns[i + 1].ColumnName;
}
int FeatureNum = app.FeaName.GetLength(0);
int SampleNum = app.SamName.GetLength(0);
app.CountMatrix = new double[FeatureNum, SampleNum];
for (int i = 0; i < FeatureNum; i++)
{
for (int j = 0; j < SampleNum; j++)
{
app.CountMatrix[i, j] = Convert.ToDouble(app.Profile.Rows[i][j + 1]);
}
}
app.SampleTotal = new double[SampleNum];
for (int i = 0; i < SampleNum; i++)
{
for (int j = 0; j < FeatureNum; j++)
{
app.SampleTotal[i] = app.SampleTotal[i] + Convert.ToDouble(app.Profile.Rows[j][i + 1]);
}
}
app.FreqMatrix = new double[FeatureNum, SampleNum];
for (int i = 0; i < FeatureNum; i++)
{
for (int j = 0; j < SampleNum; j++)
{
app.FreqMatrix[i, j] = app.CountMatrix[i, j] / app.SampleTotal[j];
}
}
Data_Output loaddata = new Data_Output();
loaddata.MdiParent = this.MdiParent;
loaddata.Show();
this.Close();
}
private void button3_Click(object sender, EventArgs e)
{
string[] filePath = null;
filePath = this.textBox1.Text.Split(',');
for (int i = 0; i < filePath.Length - 1; i++)
{
FileStream fs = new FileStream(filePath[i], System.IO.FileMode.Open, System.IO.FileAccess.Read);
StreamReader sr = new StreamReader(fs, Encoding.UTF8);
string strLine = "";
string[] aryLine = null;
DataTable dt = new DataTable();
dt.Columns.Add("Subject ID", typeof(string));
dt.Columns.Add("Hit Num", typeof(int));
if (this.radioButton1.Checked)
{
for (int j = 0; j < 5665; j++)
{
DataRow dr = dt.NewRow();
dr["Subject ID"] = "COG" + j.ToString("0000");
dr["Hit Num"] = 0;
dt.Rows.Add(dr);
}
}
else if (this.radioButton2.Checked)
{
for (int j = 0; j < 20519; j++)
{
DataRow dr = dt.NewRow();
dr["Subject ID"] = "KO" + j.ToString("00000");
dr["Hit Num"] = 0;
dt.Rows.Add(dr);
}
}
bool Newquery = true;
while ((strLine = sr.ReadLine()) != null)
{
aryLine = strLine.Split('\t');
if (aryLine.Length > 1)
{
if (Newquery)
{
if (this.radioButton1.Checked)
{
string COGpath = System.IO.Path.Combine(System.Windows.Forms.Application.StartupPath + @"./database/COG.csv");
FileStream COGfs = new FileStream(COGpath, System.IO.FileMode.Open, System.IO.FileAccess.Read);
StreamReader COGsr = new StreamReader(COGfs, Encoding.UTF8);
string COGstrLine = "";
string[] COGaryLine = null;
app.COGdatabase = new DataTable();
app.COGdatabase.Columns.Add("ID", typeof(string));
app.COGdatabase.Columns.Add("COG", typeof(string));
while ((COGstrLine = COGsr.ReadLine()) != null)
{
COGaryLine = COGstrLine.Split(',');
DataRow dr = app.COGdatabase.NewRow();
dr[0] = COGaryLine[0].Replace("\"", "");
dr[1] = COGaryLine[6].Replace("\"", "");
app.COGdatabase.Rows.Add(dr);
}
int cogNum = app.COGdatabase.Rows.Count;
int subject_ID = Convert.ToInt32(aryLine[1].Split('|')[1].Replace("\"", ""));
for (int j = 0; j < cogNum; j++)
{
if (subject_ID == Convert.ToInt32(app.COGdatabase.Rows[j][0].ToString()))
{
for (int k = 0; k < 5665; k++)
{
if (string.Equals(dt.Rows[k][0], app.COGdatabase.Rows[j][1]))
{
dt.Rows[k][1] = Convert.ToInt32(dt.Rows[k][1]) + 1;
break;
}
}
break;
}
}
}
else if (this.radioButton2.Checked)
{
string KEGGpath = System.IO.Path.Combine(System.Windows.Forms.Application.StartupPath + @"./database/ko_genes.list");
FileStream KEGGfs = new FileStream(KEGGpath, System.IO.FileMode.Open, System.IO.FileAccess.Read);
StreamReader KEGGsr = new StreamReader(KEGGfs, Encoding.UTF8);
string KEGGstrLine = "";
string[] KEGGaryLine = null;
app.KEGGdatabase = new DataTable();
app.KEGGdatabase.Columns.Add("ID", typeof(string));
app.KEGGdatabase.Columns.Add("KEGG", typeof(string));
while ((KEGGstrLine = KEGGsr.ReadLine()) != null)
{
KEGGaryLine = KEGGstrLine.Split('\t');
DataRow dr = app.KEGGdatabase.NewRow();
dr[0] = KEGGaryLine[1].Replace("\"", "");
dr[1] = KEGGaryLine[0].Replace("\"", "");
app.KEGGdatabase.Rows.Add(dr);
}
int keggNum = app.KEGGdatabase.Rows.Count;
string subject_ID = aryLine[1].Replace("\"", "");
for (int j = 0; j < keggNum; j++)
{
if (string.Equals(subject_ID, app.KEGGdatabase.Rows[j][0].ToString()))
{
for (int k = 0; k < 20519; k++)
{
if (string.Equals(dt.Rows[k][0], app.KEGGdatabase.Rows[j][0]))
{
dt.Rows[k][1] = Convert.ToInt32(dt.Rows[k][1]) + 1;
break;
}
}
break;
}
}
}
else
{
string subject_ID = aryLine[1];
if (dt.Rows.Count == 0)
{
DataRow dr = dt.NewRow();
dr["Subject ID"] = subject_ID;
dr["Hit Num"] = 1;
dt.Rows.Add(dr);
}
else
{
bool newFea = true;
for (int j = 0; j < dt.Rows.Count; j++)
{
if (string.Equals(subject_ID, dt.Rows[j][0]))
{
dt.Rows[j][1] = Convert.ToInt32(dt.Rows[j][1]) + 1;
newFea = false;
break;
}
}
if (newFea)
{
DataRow dr = dt.NewRow();
dr["Subject ID"] = subject_ID;
dr["Hit Num"] = 1;
dt.Rows.Add(dr);
}
}
}
Newquery = false;
}
}
else
{
Newquery = true;
}
}
sr.Close();
fs.Close();
if (app.Profile == null)
{
app.Profile = new DataTable();
app.Profile.Columns.Add("Feature", typeof(string));
app.Profile.Columns.Add("File1", typeof(int));
for (int m = 0; m < dt.Rows.Count; m++)
{
app.Profile.Rows.Add(dt.Rows[m][0].ToString(), Convert.ToInt32(dt.Rows[m][1]));
}
}
else
{
int FileNum = app.Profile.Columns.Count;
string newfilename = "File" + FileNum.ToString();
DataColumn newfile = new DataColumn(newfilename, typeof(int));
newfile.DefaultValue = 0;
app.Profile.Columns.Add(newfile);
for (int m = 0; m < dt.Rows.Count; m++)
{
bool k = true;;
for (int j = 0; j < app.Profile.Rows.Count; j++)
{
if (string.Equals(dt.Rows[m][0].ToString(), app.Profile.Rows[j][0].ToString()))
{
app.Profile.Rows[j][FileNum] = int.Parse(dt.Rows[m][1].ToString());
k = false;
break;
}
}
if (k)
{
DataRow drtemp;
drtemp = app.Profile.NewRow();
drtemp[0] = dt.Rows[m][0].ToString();
for (int n = 1; n < FileNum; n++)
{
drtemp[n] = 0;
}
drtemp[FileNum] = int.Parse(dt.Rows[m][1].ToString());
app.Profile.Rows.Add(drtemp);
}
}
}
}
app.FeaName = new string[app.Profile.Rows.Count];
for (int i = 0; i < app.Profile.Rows.Count; i++)
{
app.FeaName[i] = app.Profile.Rows[i][0].ToString();
}
app.SamName = new string[app.Profile.Columns.Count - 1];
for (int i = 0; i < app.Profile.Columns.Count - 1; i++)
{
app.SamName[i] = app.Profile.Columns[i + 1].ColumnName;
}
int FeatureNum = app.FeaName.GetLength(0);
int SampleNum = app.SamName.GetLength(0);
app.CountMatrix = new double[FeatureNum, SampleNum];
for (int i = 0; i < FeatureNum; i++)
{
for (int j = 0; j < SampleNum; j++)
{
app.CountMatrix[i, j] = Convert.ToDouble(app.Profile.Rows[i][j + 1]);
}
}
app.SampleTotal = new double[SampleNum];
for (int i = 0; i < SampleNum; i++)
{
for (int j = 0; j < FeatureNum; j++)
{
app.SampleTotal[i] = app.SampleTotal[i] + Convert.ToDouble(app.Profile.Rows[j][i + 1]);
}
}
app.FreqMatrix = new double[FeatureNum, SampleNum];
for (int i = 0; i < FeatureNum; i++)
{
for (int j = 0; j < SampleNum; j++)
{
app.FreqMatrix[i, j] = app.CountMatrix[i, j] / app.SampleTotal[j];
}
}
Data_Output loaddata = new Data_Output();
loaddata.MdiParent = this.MdiParent;
loaddata.Show();
this.Close();
}
private void button2_Click(object sender, EventArgs e)
{
string[] filePath = null;
filePath = this.textBox1.Text.Split(',');
for (int i = 0; i < filePath.Length - 1; i++)
{
FileStream fs = new FileStream(filePath[i], System.IO.FileMode.Open, System.IO.FileAccess.Read);
StreamReader sr = new StreamReader(fs, Encoding.UTF8);
string strLine = "";
string[] aryLine = null;
bool IsFirst = true;
DataTable dt = new DataTable();
dt.Columns.Add("Subject ID", typeof(string));
dt.Columns.Add("Hit Num", typeof(int));
while ((strLine = sr.ReadLine()) != null)
{
if (IsFirst == true)
{
IsFirst = false;
}
else
{
aryLine = strLine.Split('\t');
if (dt.Rows.Count == 0)
{
DataRow dr = dt.NewRow();
dr[0] = aryLine[1].ToString();
dr[1] = 1;
dt.Rows.Add(dr);
}
else
{
bool newFea = true;
for (int j = 0; j < dt.Rows.Count; j++)
{
if (string.Equals(aryLine[1].ToString(), dt.Rows[j][0]))
{
dt.Rows[j][1] = Convert.ToInt32(dt.Rows[j][1]) + 1;
newFea = false;
break;
}
}
if (newFea)
{
DataRow dr = dt.NewRow();
dr[0] = aryLine[1].ToString();
dr[1] = 1;
dt.Rows.Add(dr);
}
}
}
}
sr.Close();
fs.Close();
if (app.Profile == null)
{
app.Profile = new DataTable();
app.Profile.Columns.Add("Feature", typeof(string));
app.Profile.Columns.Add("File1", typeof(int));
for (int m = 0; m < dt.Rows.Count; m++)
{
app.Profile.Rows.Add(dt.Rows[m][0].ToString(), dt.Rows[m][1]);
}
}
else
{
int FileNum = app.Profile.Columns.Count;
string newfilename = "File" + FileNum.ToString();
DataColumn newfile = new DataColumn(newfilename, typeof(int));
newfile.DefaultValue = 0;
app.Profile.Columns.Add(newfile);
for (int m = 0; m < dt.Rows.Count; m++)
{
bool k = true;;
for (int j = 0; j < app.Profile.Rows.Count; j++)
{
if (string.Equals(dt.Rows[m][0].ToString(), app.Profile.Rows[j][0].ToString()))
{
app.Profile.Rows[j][FileNum] = int.Parse(dt.Rows[m][1].ToString());
k = false;
break;
}
}
if (k)
{
DataRow drtemp;
drtemp = app.Profile.NewRow();
drtemp[0] = dt.Rows[m][0].ToString();
for (int n = 1; n < FileNum; n++)
{
drtemp[n] = 0;
}
drtemp[FileNum] = int.Parse(dt.Rows[m][1].ToString());
app.Profile.Rows.Add(drtemp);
}
}
}
}
app.FeaName = new string[app.Profile.Rows.Count];
for (int i = 0; i < app.Profile.Rows.Count; i++)
{
app.FeaName[i] = app.Profile.Rows[i][0].ToString();
}
app.SamName = new string[app.Profile.Columns.Count - 1];
for (int i = 0; i < app.Profile.Columns.Count - 1; i++)
{
app.SamName[i] = app.Profile.Columns[i + 1].ColumnName;
}
int FeatureNum = app.FeaName.GetLength(0);
int SampleNum = app.SamName.GetLength(0);
app.CountMatrix = new double[FeatureNum, SampleNum];
for (int i = 0; i < FeatureNum; i++)
{
for (int j = 0; j < SampleNum; j++)
{
app.CountMatrix[i, j] = Convert.ToDouble(app.Profile.Rows[i][j + 1]);
}
}
app.SampleTotal = new double[SampleNum];
for (int i = 0; i < SampleNum; i++)
{
for (int j = 0; j < FeatureNum; j++)
{
app.SampleTotal[i] = app.SampleTotal[i] + Convert.ToDouble(app.Profile.Rows[j][i + 1]);
}
}
app.FreqMatrix = new double[FeatureNum, SampleNum];
for (int i = 0; i < FeatureNum; i++)
{
for (int j = 0; j < SampleNum; j++)
{
app.FreqMatrix[i, j] = app.CountMatrix[i, j] / app.SampleTotal[j];
}
}
Data_Output loaddata = new Data_Output();
loaddata.MdiParent = this.MdiParent;
loaddata.Show();
this.Close();
}
private void button1_Click(object sender, EventArgs e)
{
string[] filePath = null;
filePath = this.textBox1.Text.Split(',');
for (int i = 0; i < filePath.Length - 1; i++)
{
FileStream fs = new FileStream(filePath[i], System.IO.FileMode.Open, System.IO.FileAccess.Read);
DataTable dt = new DataTable();
dt.Columns.Add("Query", typeof(string));
dt.Columns.Add("Result", typeof(string));
StreamReader sr = new StreamReader(fs, Encoding.UTF8);
string strLine = "";
string[] aryLine = null;
while ((strLine = sr.ReadLine()) != null)
{
aryLine = strLine.Split('\t');
DataRow dr = dt.NewRow();
for (int j = 0; j < aryLine.Length; j++)
{
dr[j] = aryLine[j].Replace("\"", "");
}
dt.Rows.Add(dr);
}
sr.Close();
fs.Close();
if (app.Profile == null)
{
app.Profile = new DataTable();
app.Profile.Columns.Add("Feature", typeof(string));
app.Profile.Columns.Add("File1", typeof(int));
DataRow drfirst;
drfirst = app.Profile.NewRow();
app.Profile.Rows.Add(dt.Rows[0][1].ToString(), 1);
for (int m = 1; m < dt.Rows.Count; m++)
{
int k = 0;
for (int j = 0; j < app.Profile.Rows.Count; j++)
{
if (string.Equals(dt.Rows[m][1].ToString(), app.Profile.Rows[j][0].ToString()))
{
app.Profile.Rows[j][1] = (int)app.Profile.Rows[j][1] + 1;
k = 1;
break;
}
}
if (k == 0)
{
app.Profile.Rows.Add(dt.Rows[m][1].ToString(), 1);
}
}
}
else
{
int FileNum = app.Profile.Columns.Count;
string newfilename = "File" + FileNum.ToString();
DataColumn newfile = new DataColumn(newfilename, typeof(int));
newfile.DefaultValue = 0;
app.Profile.Columns.Add(newfile);
for (int m = 0; m < dt.Rows.Count; m++)
{
int k = 0;
for (int j = 0; j < app.Profile.Rows.Count; j++)
{
if (string.Equals(dt.Rows[m][1].ToString(), app.Profile.Rows[j][0].ToString()))
{
app.Profile.Rows[j][FileNum] = (int)app.Profile.Rows[j][FileNum] + 1;
k = 1;
break;
}
}
if (k == 0)
{
DataRow dr;
dr = app.Profile.NewRow();
dr[0] = dt.Rows[m][1].ToString();
for (int n = 1; n < FileNum; n++)
{
dr[n] = 0;
}
dr[FileNum] = 1;
app.Profile.Rows.Add(dr);
}
}
}
}
app.FeaName = new string[app.Profile.Rows.Count];
for (int i = 0; i < app.Profile.Rows.Count; i++)
{
app.FeaName[i] = app.Profile.Rows[i][0].ToString();
}
app.SamName = new string[app.Profile.Columns.Count - 1];
for (int i = 0; i < app.Profile.Columns.Count - 1; i++)
{
app.SamName[i] = app.Profile.Columns[i + 1].ColumnName;
}
int FeatureNum = app.FeaName.GetLength(0);
int SampleNum = app.SamName.GetLength(0);
app.CountMatrix = new double[FeatureNum, SampleNum];
for (int i = 0; i < FeatureNum; i++)
{
for (int j = 0; j < SampleNum; j++)
{
app.CountMatrix[i, j] = Convert.ToDouble(app.Profile.Rows[i][j + 1]);
}
}
app.SampleTotal = new double[SampleNum];
for (int i = 0; i < SampleNum; i++)
{
for (int j = 0; j < FeatureNum; j++)
{
app.SampleTotal[i] = app.SampleTotal[i] + Convert.ToDouble(app.Profile.Rows[j][i + 1]);
}
}
app.FreqMatrix = new double[FeatureNum, SampleNum];
for (int i = 0; i < FeatureNum; i++)
{
for (int j = 0; j < SampleNum; j++)
{
app.FreqMatrix[i, j] = app.CountMatrix[i, j] / app.SampleTotal[j];
}
}
Data_Output loaddata = new Data_Output();
loaddata.MdiParent = this.MdiParent;
loaddata.Show();
this.Close();
}