//This function is used by generateHypo to get the mass of a composition in the composition table.
public Double getcompMass(GlycanCompositionTable CT, List<string> elementIDs)
{
Double Mass = 0;
PeriodicTable PT = new PeriodicTable();
for (int i = 0; i < CT.elementAmount.Count(); i++)
{
Mass = Mass + CT.elementAmount[i] * PT.getMass(elementIDs[i]);
}
return Mass;
}
//This function reads the generate composition page and save it to a variable of class "generator".
public GlycanHypothesisCombinatorialGenerator getGenerator()
{
//compotable is used to store the data from the composition table before they are used.
List<GlycanCompositionTable> compotable = new List<GlycanCompositionTable>();
//arTable is used to store the data from additional rules table before they're used.
List<Boundary> arTable = new List<Boundary>();
//GD is used to store all the data that will be returned.
GlycanHypothesisCombinatorialGenerator GD = new GlycanHypothesisCombinatorialGenerator();
String currentpath = Application.StartupPath + "\\compositionsCurrent.cpos";
try
{
FileStream reading = new FileStream(currentpath, FileMode.Open, FileAccess.Read);
StreamReader readcompo = new StreamReader(reading);
//Read the first line to skip the column names:
String Line1 = readcompo.ReadLine();
String[] headers = Line1.Split(',');
List<string> elementIDs = new List<string>();
bool moreElements = true;
int sh= 2;
while (moreElements)
{
if (headers[sh] != "Lower Bound")
{
elementIDs.Add(headers[sh]);
sh++;
}
else
moreElements = false;
}
bool firstrow = true;
//Read the other lines for compTable data.
while (readcompo.Peek() >= 0)
{
GlycanCompositionTable compTable = new GlycanCompositionTable();
if (firstrow)
{
compTable.elementIDs = elementIDs;
firstrow = false;
}
String Line = readcompo.ReadLine();
String[] eachentry = Line.Split(',');
//When next line is the Modification line, it breaks.
if (eachentry[0] == "Modification%^&!@#*()iop")
break;
compTable.Letter = eachentry[0];
compTable.Molecule = eachentry[1];
for (int i = 2; i < elementIDs.Count + 2; i++)
{
compTable.elementAmount.Add(Convert.ToInt32(eachentry[i]));
}
List<String> bounds = new List<String>();
bounds.Add(eachentry[elementIDs.Count + 2]);
bounds.Add(eachentry[elementIDs.Count + 3]);
compTable.Bound = bounds;
compotable.Add(compTable);
}
//Send compotable data to GD
GD.comTable = compotable;
//Populate the Modification Table
String modiLine = readcompo.ReadLine();
//Send Modification data to GD
GD.Modification = modiLine.Split(',');
//Populate the additional rules table
while (readcompo.Peek() >= 0)
{
String Line = readcompo.ReadLine();
String[] eachentry = Line.Split(',');
if (eachentry[0] != "" && eachentry[2] != "")
{
Boundary areTable = new Boundary();
areTable.Formula = eachentry[0];
areTable.Relationship = eachentry[1];
areTable.Constraint = Convert.ToString(eachentry[2]);
arTable.Add(areTable);
}
}
//Send arTable data to GD.
GD.aTable = arTable;
readcompo.Close();
reading.Close();
}
catch (Exception compoex)
{
MessageBox.Show("Error in loading GlycanCompositions Table. Error:" + compoex);
}
return GD;
}
//This function is used to read the cpos file and translate it to generatorData format.
private GlycanHypothesisCombinatorialGenerator extractFile(String path)
{
//table is used to store the data before the calculation
GlycanHypothesisCombinatorialGenerator DATA = new GlycanHypothesisCombinatorialGenerator();
List<GlycanCompositionTable> GD = new List<GlycanCompositionTable>();
try
{
FileStream reading = new FileStream(path, FileMode.Open, FileAccess.Read);
StreamReader readcompo = new StreamReader(reading);
//Read the first line to throw the column names:
String Line1 = readcompo.ReadLine();
String[] headers = Line1.Split(',');
int sh = 2;
bool moreElements = true;
List<string> elementIDs = new List<string>();
while (moreElements)
{
if (headers[sh] != "Lower Bound")
{
elementIDs.Add(headers[sh]);
sh++;
}
else
{
moreElements = false;
}
}
bool firstRow = true;
while (readcompo.Peek() >= 0)
{
String Line = readcompo.ReadLine();
String[] eachentry = Line.Split(',');
if (eachentry[0] == "Modification%^&!@#*()iop")
break;
GlycanCompositionTable CT = new GlycanCompositionTable();
CT.Letter = eachentry[0];
CT.Molecule = eachentry[1];
if (firstRow)
{
CT.elementIDs = elementIDs;
firstRow = false;
}
for (int i = 0; i < elementIDs.Count(); i++)
{
CT.elementAmount.Add(Convert.ToInt32(eachentry[2 + i]));
}
//Random the lower bound and upper bound to get random composition hypothesis
CT.Bound = new List<String>();
CT.Bound.Add(eachentry[2 + elementIDs.Count()]);
CT.Bound.Add(eachentry[2 + elementIDs.Count() + 1]);
GD.Add(CT);
}
String Line2 = readcompo.ReadLine();
String[] eachentry2 = Line2.Split(',');
DATA.comTable = GD;
DATA.Modification = eachentry2;
readcompo.Close();
reading.Close();
}
catch (Exception compoex)
{
MessageBox.Show("Error in loading GlycanCompositions Table (cpos). Error:" + compoex);
}
DATA.aTable = new List<Boundary>();
DATA.comTable = GD;
return DATA;
}
