private void AddButtonClick(object sender, EventArgs e)
{
if (openFileDialog1.ShowDialog() != DialogResult.OK)
{
return;
}
for (int i = 0; i < openFileDialog1.FileNames.Length; i++)
{
if (FileList.Items.IndexOf(openFileDialog1.FileNames[i]) == -1)
{
FileList.Items.Add(openFileDialog1.FileNames[i]);
}
}
MakeOutName();
//loading
PM = new ProtMatrix[FileList.Items.Count];
for (int i = 0; i < FileList.Items.Count; i++)
{
PM[i] = new ProtMatrix(FileList.Items[i].ToString());
}
//count samples
int CountSamples = 0;
for (int i = 0; i < FileList.Items.Count; i++)
{
CountSamples += PM[i].Samples.Count;
}
textBox2.Text = (CountSamples - 1).ToString();
}
private void AddButtonClick(object sender, EventArgs e)
{
if(openFileDialog1.ShowDialog() != DialogResult.OK) {
return;
}
for (int i = 0 ; i < openFileDialog1.FileNames.Length ; i++){
if (FileList.Items.IndexOf(openFileDialog1.FileNames[i]) == -1){
FileList.Items.Add(openFileDialog1.FileNames[i]);
}
}
MakeOutName();
//loading
PM = new ProtMatrix[FileList.Items.Count];
for (int i = 0 ; i < FileList.Items.Count ; i++ ){
PM[i] = new ProtMatrix(FileList.Items[i].ToString());
}
//count samples
int CountSamples = 0;
for (int i = 0 ; i < FileList.Items.Count ; i++ ){
CountSamples += PM[i].Samples.Count;
}
textBox2.Text = (CountSamples - 1).ToString();
}
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();
}
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();
}
