private List <string> GenerateGlycoPeptide()
{
List <ProteinInfo> PInfos = FastaReader.ReadFasta(_fastaFile);
List <string> GlycoPeptide = new List <string>();
foreach (ProteinInfo Prot in PInfos)
{
GlycoPeptide.AddRange(Prot.NGlycopeptide(_MissCLeavage, _ProteaseType, _peptideMutation));
}
return(GlycoPeptide);
}
public Prot Clone()
{
Prot P = new Prot();
P.ID = ID;
P.Desc = Desc;
P.RefAbunds = RefAbunds;
P.Peptides = Peptides;
P.IPIS = new List <string>();
P.IPIS.AddRange(IPIS);
P.Abunds = new List <double>();
P.Abunds.AddRange(Abunds);
return(P);
}
public static extern int mprotect(IntPtr addr, UIntPtr len, Prot prot);
private void GoButton_Click(object sender, EventArgs e)
{
//merge by IPIs
ProtMatrix Merged = new ProtMatrix();
//samples
for (int i = 0; i < FileList.Items.Count; i++)
{
Merged.Samples.AddRange(PM[i].Samples);
}
//make a proterin list
List <List <string> > ProteinsIPIs = new List <List <string> >();
if (radioButton1.Checked)
{
//skip proteins
for (int i = 0; i < PM[0].Proteins.Count; i++)
{
List <string> PIPIs = PM[0].Proteins[i].IPIS;
bool GlobalFlag = true;
for (int j = 1; j < PM.GetLength(0); j++)
{
bool flag = false;
foreach (Prot PS in PM[j].Proteins)
{
if (Cross(PIPIs, PS.IPIS))
{
flag = true;
break;
}
}
GlobalFlag &= flag;
}
if (GlobalFlag)
{
ProteinsIPIs.Add(PIPIs);
}
}
}
else
{
//keep proteins
for (int k = 0; k < PM.GetLength(0); k++)
{
for (int i = 0; i < PM[k].Proteins.Count; i++)
{
bool flag = false;
foreach (List <string> PS in ProteinsIPIs)
{
if (Cross(PM[k].Proteins[i].IPIS, PS))
{
flag = true;
break;
}
}
if (!flag)
{
ProteinsIPIs.Add(PM[k].Proteins[i].IPIS);
}
}
}
}
//proteins
for (int i = 0; i < ProteinsIPIs.Count; i++)
{
List <string> PL = ProteinsIPIs[i];
Prot P = null;
for (int j = 0; j < PM.GetLength(0); j++)
{
bool flag = false;
foreach (Prot PS in PM[j].Proteins)
{
if (Cross(PL, PS.IPIS))
{
flag = true;
if (P == null)
{
P = PS.Clone();
//leading zeroes
for (int k = 0; k < j; k++)
{
foreach (string S in PM[k].Samples)
{
P.Abunds.Insert(0, 0.0);
}
}
}
else
{
P.Abunds.AddRange(PS.Abunds);
}
break;
}
}
if (P != null && !flag)
{
foreach (string S in PM[j].Samples)
{
P.Abunds.Add(0.0);
}
}
}
if (P.Abunds.Count == Merged.Samples.Count)
{
//maximum zero filtering
int ZeroCount = 0;
for (int j = 0; j < P.Abunds.Count; j++)
{
ZeroCount += P.Abunds[j] == 0.0 ? 1 : 0;
}
if (ZeroCount < Convert.ToInt32(textBox2.Text))
{
Merged.Proteins.Add(P);
}
}
}
//writing
StreamWriter sw = new StreamWriter(OutFileBox.Text);
//Caption
sw.WriteLine(Text);
sw.WriteLine("Original Fies:");
for (int i = 0; i < FileList.Items.Count; i++)
{
sw.WriteLine(FileList.Items[i].ToString());
}
sw.WriteLine("Unique proteins has {0}; Maximum zeroes {1}.", radioButton1.Checked ? "skipped" : "kept", textBox2.Text);
//Matrix
Merged.Save(sw);
sw.Close();
}
public void Load(string ProtMatrFile)
{
//отбрасываем заголовки
StreamReader sr = new StreamReader(ProtMatrFile);
List <string> tokens = new List <string>();
while (!sr.EndOfStream)
{
string Caption = sr.ReadLine();
tokens = Caption.Split(new char[] { '\t' }).ToList();
if (tokens.Count > 2)
{
break;
}
}
int[] Delims = new int[5];
Delims[0] = tokens.IndexOf("PROTEIN ID");
Delims[1] = tokens.IndexOf("DESCRIPTION");
Delims[2] = tokens.IndexOf("PEPTIDES");
Delims[3] = tokens.IndexOf("PROTEIN IDs");
Delims[4] = tokens.IndexOf("REF ABUNDANCE");
int Shift = 5;
for (int i = 0; i < 5; i++)
{
if (Delims[i] == -1)
{
Shift--;
}
}
int Count = tokens.Count - Shift;
for (int i = 0; i < Count; i++)
{
if (tokens[i + Shift] == "")
{
Count = i;
break;
}
Samples.Add(tokens[i + Shift]);
}
while (!sr.EndOfStream)
{
string str = sr.ReadLine();
tokens = str.Split(new char[] { '\t' }).ToList();
Prot P = new Prot();
if (Delims[0] != -1)
{
P.ID = tokens[Delims[0]];
}
if (Delims[1] != -1)
{
P.Desc = tokens[Delims[1]];
}
if (Delims[2] != -1)
{
P.Peptides = Convert.ToInt32(tokens[Delims[2]]);
}
if (Delims[3] != -1)
{
P.IPIS = (tokens[Delims[3]].Split(new char[] { ';' })).ToList();
}
if (Delims[4] != -1)
{
P.RefAbunds = Convert.ToDouble(tokens[Delims[4]]);
}
P.Abunds = new List <double>();
for (int i = 0; i < Count; i++)
{
//if empty
if (tokens[i + Shift] == "")
{
P.Abunds.Add(0.0);
continue;
}
//if 1
if (Convert.ToDouble(tokens[i + Shift]) == 1.0)
{
//if all alternativbe are 0.0 - then 1.0 otherwise 0.0
bool flag = true;
for (int j = 0; j < Count; j++)
{
if (i != j)
{
flag &= Convert.ToDouble(tokens[i + Shift]) == 0.0;
}
}
P.Abunds.Add(flag?1.0:0.0);
}
else
{
//if normal value
P.Abunds.Add(Convert.ToDouble(tokens[i + Shift]));
}
}
Proteins.Add(P);
}
}
public void Load(string ProtMatrFile)
{
//отбрасываем заголовки
StreamReader sr = new StreamReader(ProtMatrFile);
List<string> tokens = new List<string>();
while (!sr.EndOfStream){
string Caption = sr.ReadLine();
tokens = Caption.Split(new char[] {'\t'}).ToList();
if (tokens.Count > 2) break;
}
int[] Delims = new int[5];
Delims[0] = tokens.IndexOf("PROTEIN ID");
Delims[1] = tokens.IndexOf("DESCRIPTION");
Delims[2] = tokens.IndexOf("PEPTIDES");
Delims[3] = tokens.IndexOf("PROTEIN IDs");
Delims[4] = tokens.IndexOf("REF ABUNDANCE");
int Shift = 5;
for (int i = 0 ; i < 5 ; i++){
if (Delims[i] == -1){
Shift--;
}
}
int Count = tokens.Count - Shift;
for ( int i = 0 ; i < Count ; i++ ){
if (tokens[i+Shift] == ""){
Count = i;
break;
}
Samples.Add(tokens[i+Shift]);
}
while (!sr.EndOfStream){
string str = sr.ReadLine();
tokens = str.Split(new char[] {'\t'}).ToList();
Prot P = new Prot();
if (Delims[0]!=-1){
P.ID = tokens[Delims[0]];
}
if (Delims[1]!=-1){
P.Desc = tokens[Delims[1]];
}
if (Delims[2]!=-1){
P.Peptides = Convert.ToInt32(tokens[Delims[2]]);
}
if (Delims[3]!=-1){
P.IPIS = (tokens[Delims[3]].Split(new char[] {';'})).ToList();
}
if (Delims[4]!=-1){
P.RefAbunds = Convert.ToDouble(tokens[Delims[4]]);
}
P.Abunds = new List<double>();
for ( int i = 0 ; i < Count ; i++){
//if empty
if (tokens[i+Shift] == ""){
P.Abunds.Add(0.0);
continue;
}
//if 1
if (Convert.ToDouble(tokens[i+Shift]) == 1.0){
//if all alternativbe are 0.0 - then 1.0 otherwise 0.0
bool flag = true;
for ( int j = 0 ; j < Count ; j++){
if (i!=j){
flag &= Convert.ToDouble(tokens[i + Shift]) == 0.0;
}
}
P.Abunds.Add(flag?1.0:0.0);
}else{
//if normal value
P.Abunds.Add(Convert.ToDouble(tokens[i+Shift]));
}
}
Proteins.Add(P);
}
}
public Prot Clone()
{
Prot P = new Prot();
P.ID = ID;
P.Desc = Desc;
P.RefAbunds = RefAbunds;
P.Peptides = Peptides;
P.IPIS = new List<string>();
P.IPIS.AddRange(IPIS);
P.Abunds = new List<double>();
P.Abunds.AddRange(Abunds);
return P;
}
