public Parameters GetParameters(IMatrixData mdata, ref string errorString)
{
List <string> colChoice = mdata.StringColumnNames;
int colInd = 0;
for (int i = 0; i < colChoice.Count; i++)
{
if (colChoice[i].ToUpper().Equals("UNIPROT"))
{
colInd = i;
break;
}
}
string[] choice = PhosphoSitePlusParser.GetAllMods();
return
(new Parameters(
new MultiChoiceParam("Modifications")
{
Value = ArrayUtils.ConsecutiveInts(choice.Length), Values = choice
},
new SingleChoiceParam("Uniprot column")
{
Value = colInd,
Help = "Specify here the column that contains Uniprot identifiers.",
Values = colChoice
}));
}
public Parameters GetParameters(IMatrixData mdata, ref string errorString)
{
List <string> colChoice = mdata.StringColumnNames;
int colInd = 0;
for (int i = 0; i < colChoice.Count; i++)
{
if (colChoice[i].ToUpper().Equals("UNIPROT"))
{
colInd = i;
break;
}
}
int colSeqInd = 0;
for (int i = 0; i < colChoice.Count; i++)
{
if (colChoice[i].ToUpper().Equals("SEQUENCE WINDOW"))
{
colSeqInd = i;
break;
}
}
string[] choice = PhosphoSitePlusParser.GetAllMods();
int ind = ArrayUtils.IndexOf(choice, "Phosphorylation");
return
(new Parameters(
new SingleChoiceParam("Modification")
{
Value = ind,
Values = choice,
Help = "Select here the kind of modification for which information should be added."
},
new SingleChoiceParam("Uniprot column")
{
Value = colInd,
Help = "Specify here the column that contains Uniprot identifiers.",
Values = colChoice
},
new SingleChoiceParam("Sequence window")
{
Value = colSeqInd,
Help = "Specify here the column that contains the sequence windows around the site.",
Values = colChoice
}));
}
