private void button4_Click(object sender, EventArgs e)
{
if (combometabolites.Text.Length > 0)
{
if (Sbml.There(combometabolites, combometabolites.Text))
{
sbml.AgregaraMetabolitosExternos(combometabolites.Text);
if (!Principal.txt)
{
Read read = new Read();
read.ActualizarBoundaryCondition(Principal.doc, combometabolites.Text.ToLower());
}
// Principal.doc.PreserveWhitespace = true;
combometabolites.Items.Remove(combometabolites.Text);
Principal.mysbml = sbml;
MessageBox.Show("Correctly Converted!!!", "Ok", MessageBoxButtons.OK, MessageBoxIcon.Information);
}
else
{
MessageBox.Show("not exist a metabolite with this name", "Error", MessageBoxButtons.OK, MessageBoxIcon.Error);
}
}
else
{
MessageBox.Show("Select the metabolite to be removed of the internal metabolites", "Error", MessageBoxButtons.OK, MessageBoxIcon.Error);
}
}
private void sbmlToolStripMenuItem_Click(object sender, EventArgs e)
{
if (this.openfile.ShowDialog() == DialogResult.OK)
{
string aux = openfile.FileName.Split('.')[1];
if (aux == "xml")
{
fileaddres = openfile.FileName;
Read read = new Read();
mysbml = read.ReadXml(fileaddres);
if (mysbml.ListReaction.Length == 0 || mysbml.ListSpecie.Length == 0)
{
MessageBox.Show("Unreadable file,\n verify complies with the standard", "Error", MessageBoxButtons.OK, MessageBoxIcon.Error);
}
else
{
doc.Load(fileaddres);
optimize.Enabled = true;
optimizer2.Enabled = true;
toolStripButton2.Enabled = true;
toolStripMenuItem1.Enabled = true;
save2toolStrip.Enabled = true;
save1toolStrip.Enabled = true;
txt = false;
if (yaabri)
{
mod.Close();
mod = new Model();
mod.MdiParent = this;
mod.Show();
}
else
{
mod = new Model();
mod.MdiParent = this;
mod.Show();
yaabri = true;
}
fba2 = false;
}
//MessageBox.Show("Successfully Loaded", "Information", MessageBoxButtons.OK, MessageBoxIcon.Information);
}
else
{
MessageBox.Show("Incorrect Extension", "Error", MessageBoxButtons.OK, MessageBoxIcon.Error);
}
}
}
private void Model_Load(object sender, EventArgs e)
{
mysbml = Principal.mysbml;
Principal.abierto = true;
foreach (Reaction aux in mysbml.ListReaction)
{
string[] row = new string[4] {
aux.Name, aux.LowerBound.ToString(), aux.UpperBound.ToString(), aux.IsExchange().ToString()
};
ListViewItem list = new ListViewItem(row);
listView2.Items.Add(list);
}
}
private void Setup_Constraints_Load(object sender, EventArgs e)
{
valuee = "";
objetive = FVA.objetive;
sbml = Principal.mysbml;
dataGridView1.Rows.Clear();
for (int i = 0; i < sbml.ListReaction.Length; i++)
{
dataGridView1.Rows.Add();
dataGridView1.Rows[i].Cells[0].Value = sbml.ListReaction[i].Id;
dataGridView1.Rows[i].Cells[1].Value = sbml.ListReaction[i].Reversible;
dataGridView1.Rows[i].Cells[2].Value = sbml.ListReaction[i].LowerBound;
dataGridView1.Rows[i].Cells[3].Value = sbml.ListReaction[i].UpperBound;
}
}
private void Rna_Load(object sender, EventArgs e)
{
fileTextBox.Text = Principal.FileAddres;
reactionObjetiveComboBox.Text = Principal.objetivefuntion;
readsbml = new Read();
results = false;
sbml = Principal.mysbml;
foreach (Reaction item in sbml.ListReaction)
{
reactionObjetiveComboBox.Items.Add(item.Id);
comboconstrain.Items.Add(item.Id);
comboreactionexchange.Items.Add(item.Id);
}
foreach (Specie item in sbml.ListSpecie)
{
combometabolites.Items.Add(item.Id);
}
}
private void button6_Click(object sender, EventArgs e)
{
if (reactionObjetiveComboBox.Text.Length == 0)
{
MessageBox.Show("Select the function to optimize", "Error", MessageBoxButtons.OK, MessageBoxIcon.Error);
}
else
{
if (Sbml.There(reactionObjetiveComboBox, reactionObjetiveComboBox.Text))
{
Principal.objetivefuntion = reactionObjetiveComboBox.Text;
Principal.yaabriconstraint = true;
sc = new Setup_Constraints();
sc.MdiParent = Principal.ActiveForm;
objetive = reactionObjetiveComboBox.Text;
this.Close();
sc.Show();
}
else
{
MessageBox.Show("This reaction not exist in the model", "Error", MessageBoxButtons.OK, MessageBoxIcon.Error);
}
}
}
private void button1_Click(object sender, EventArgs e)
{
if (reactionObjetiveComboBox.Text.Length > 0 && comboreactionexchange.Text.Length > 0)
{
if (Sbml.There(reactionObjetiveComboBox, reactionObjetiveComboBox.Text) && Sbml.There(comboreactionexchange, comboreactionexchange.Text))
{
if ((aNumericUpDown.Value != bNumericUpDown.Value) && (aNumericUpDown.Value < bNumericUpDown.Value))
{
makefba = new MakeFba();
int i = 0;
bool find = false;
foreach (Reaction item in sbml.ListReaction)
{
if (item.Id == reactionObjetiveComboBox.Text)
{
reactionoptimize = reactionObjetiveComboBox.Text;
find = true;
break;
}
i++;
}
if (find)
{
if (radiomax.Checked)
{
pd = OptimisationDirection.MAXIMISE;
}
else
{
pd = OptimisationDirection.MINIMISE;
}
pointresult = makefba.Rna(sbml, i, pd, (int)aNumericUpDown.Value, (int)bNumericUpDown.Value, comboreactionexchange.Text);
resultlist.Items.Clear();
string[] str;
ListViewItem list;
for (int k = 0; k < pointresult.Length; k++)
{
int kaux = k + 1;
str = new string[3] {
kaux.ToString(), pointresult[k].X.ToString(), pointresult[k].Y.ToString()
};
list = new ListViewItem(str);
resultlist.Items.Add(list);
}
results = true;
button3.Enabled = true;
}
else
{
results = false;
button3.Enabled = false;
MessageBox.Show("This reaction not exist in the model", "Error", MessageBoxButtons.OK, MessageBoxIcon.Error);
}
}
else
{
MessageBox.Show("The values of A and B must be different, and A less than B", "Error", MessageBoxButtons.OK, MessageBoxIcon.Error);
}
}
else
{
MessageBox.Show("Select the objective functions to optimize and to be varied", "Error", MessageBoxButtons.OK, MessageBoxIcon.Error);
}
}
else
{
MessageBox.Show("Select the objective functions to optimize and to be varied", "Error", MessageBoxButtons.OK, MessageBoxIcon.Error);
}
}
private void updateButton_Click(object sender, EventArgs e)
{
if (comboconstrain.Text.Length > 0)
{
if (Sbml.There(comboconstrain, comboconstrain.Text))
{
if (isReversibleTextBox.Text == "False")
{
if (double.Parse(lowertextBox1.Text, CultureInfo.InvariantCulture.NumberFormat) < 0)
{
MessageBox.Show("This reaction is irreversible, the Lower Bound must be less than zero", "Error", MessageBoxButtons.OK, MessageBoxIcon.Error);
}
else
{
foreach (Reaction item in sbml.ListReaction)
{
if (item.Id == comboconstrain.Text)
{
item.LowerBound = double.Parse(lowertextBox1.Text, CultureInfo.InvariantCulture.NumberFormat);
item.UpperBound = double.Parse(uppertextBox2.Text, CultureInfo.InvariantCulture.NumberFormat);
Principal.mysbml = sbml;
if (!Principal.txt)
{
Read red = new Read();
red.ActualizarRestricciones(Principal.doc, comboconstrain.Text.ToLower(), lowertextBox1.Text, uppertextBox2.Text);
}
MessageBox.Show("Update!!!!!!", "Ok", MessageBoxButtons.OK, MessageBoxIcon.Information);
break;
}
}
}
}
else
{
foreach (Reaction item in sbml.ListReaction)
{
if (item.Id == comboconstrain.Text)
{
item.LowerBound = double.Parse(lowertextBox1.Text, CultureInfo.InvariantCulture.NumberFormat);
item.UpperBound = double.Parse(uppertextBox2.Text, CultureInfo.InvariantCulture.NumberFormat);
Principal.mysbml = sbml;
if (!Principal.txt)
{
Read red = new Read();
red.ActualizarRestricciones(Principal.doc, comboconstrain.Text.ToLower(), lowertextBox1.Text, uppertextBox2.Text);
}
MessageBox.Show("Update!!!!!!", "Ok", MessageBoxButtons.OK, MessageBoxIcon.Information);
break;
}
}
}
}
else
{
MessageBox.Show("Not exist a reaction with this name", "Error", MessageBoxButtons.OK, MessageBoxIcon.Error);
}
}
else
{
MessageBox.Show("Select the reaction to be configured", "Error", MessageBoxButtons.OK, MessageBoxIcon.Error);
}
}
private void button1_Click(object sender, EventArgs e)
{
if (reactionObjetiveComboBox.Text.Length > 0 && reactionObjetiveComboBox2.Text.Length > 0)
{
if (Sbml.There(reactionObjetiveComboBox, reactionObjetiveComboBox.Text) && Sbml.There(reactionObjetiveComboBox2, reactionObjetiveComboBox2.Text))
{
makefba = new MakeFba();
int i = 0;
int j = 0;
int ii = 0;
int jj = 0;
int find = 0;
foreach (Reaction item in sbml.ListReaction)
{
if (item.Id == reactionObjetiveComboBox.Text)
{
reactionoptimize1 = reactionObjetiveComboBox.Text;
find++;
ii = i;
}
if (item.Id == reactionObjetiveComboBox2.Text)
{
reactionoptimize2 = reactionObjetiveComboBox2.Text;
find++;
jj = j;
}
if (find == 2)
{
break;
}
j++;
i++;
}
if (find == 2)
{
if (radiomax.Checked)
{
pd = OptimisationDirection.MAXIMISE;
}
else
{
pd = OptimisationDirection.MINIMISE;
}
fva = makefba.Fva(sbml, ii, jj, pd);
double z1 = fva.Lp1.GetObjectiveValue();
double z2 = fva.Lp2.GetObjectiveValue();
resultlist.Items.Clear();
string[] str = new string[3] {
"Z1,Z2", "Z1 = " + z1.ToString(), "Z2 = " + z2.ToString()
};
ListViewItem list = new ListViewItem(str, 0, Color.Black, Color.YellowGreen, new Font("Arial", 12));
resultlist.Items.Add(list);
for (int k = 0; k < sbml.ListReaction.Length; k++)
{
str = new string[3] {
sbml.ListReaction[k].Id, fva.Lp1.GetColPrimal(k + 1).ToString(), fva.Lp2.GetColPrimal(k + 1).ToString()
};
if (fva.Lp1.GetColPrimal(k + 1) == fva.Lp2.GetColPrimal(k + 1))
{
list = new ListViewItem(str);
resultlist.Items.Add(list);
}
else
{
list = new ListViewItem(str, 0, Color.Black, Color.YellowGreen, new Font("Arial", 12));
resultlist.Items.Add(list);
}
}
results = true;
button3.Enabled = true;
}
else
{
results = false;
button3.Enabled = false;
MessageBox.Show("This reaction not exist in the model", "Error", MessageBoxButtons.OK, MessageBoxIcon.Error);
}
}
else
{
MessageBox.Show("One of the functions not exist in the model", "Error", MessageBoxButtons.OK, MessageBoxIcon.Error);
}
}
else
{
MessageBox.Show("Select the functions to optimize", "Error", MessageBoxButtons.OK, MessageBoxIcon.Error);
}
}
