public static void enterTextMutPred(UVSearch main, ref WebBrowser webBrowserProvean)
{
HtmlElementCollection collection;
collection = webBrowserProvean.Document.GetElementsByTagName("textarea");
//change fasta header to put gene name first
string fasta = ">" + main._Gene + "_" + main._RefSeq + "_" + main._protRefSeq + "\n" + main._FastaNH;
foreach (HtmlElement element in collection)
{
string name = element.GetAttribute("name");
if (name == "pseq")
{
element.SetAttribute("Value", fasta);
}
}
collection = webBrowserProvean.Document.GetElementsByTagName("input");
foreach (HtmlElement element in collection)
{
string name = element.GetAttribute("name");
if (name == "mut")
{
element.SetAttribute("Value", main._Variant);
}
if (name == "email")
{
element.SetAttribute("Value", main._Email);
}
}
}
public static void enterTextPMut(UVSearch main, ref WebBrowser webBrowserPMut)
{
//Comma or blank separated mutations
HtmlElement inputFasta = webBrowserPMut.Document.GetElementById("sequence-input");
HtmlElementCollection collection = inputFasta.GetElementsByTagName("textarea");
HtmlElement textbox = collection[0];
textbox.SetAttribute("Value", main._Fasta);
HtmlElement searchButton = webBrowserPMut.Document.GetElementById("search-sequences");
searchButton.InvokeMember("click");
HtmlElement chooseButton = webBrowserPMut.Document.GetElementById("choose-sequence");
chooseButton.InvokeMember("click");
HtmlElement mutationList = webBrowserPMut.Document.GetElementById("mutations-list");
string mutation = main._VarArray[0] + main._VarArray[1] + main._VarArray[2];
mutationList.SetAttribute("Value", mutation);
webBrowserPMut.Document.InvokeScript("update_variants");
HtmlElement analysisButton = webBrowserPMut.Document.GetElementById("start-analysis");
analysisButton.InvokeMember("click");
}
public static void saveTextFile(UVSearch main, string filename, string URL)
{
string fpath = main._Path + "\\" + main._Gene + "_" + main._Variant + "_" + filename;
TextWriter tw = new StreamWriter(fpath, false);
tw.Write(URL);
tw.Close();
}
public static void enterTextSNAP(UVSearch main, ref WebBrowser webBrowserMain)
{
HtmlElement element;
element = webBrowserMain.Document.GetElementById("sequence");
element.SetAttribute("Value", main._Fasta);
element = webBrowserMain.Document.GetElementById("email");
element.SetAttribute("Value", main._Email);
submitSNAP(ref webBrowserMain);
}
public static void enterTextPROVEAN(UVSearch main, ref WebBrowser webBrowserProvean)
{
// Format <uniprot code> <position> <wild type AA> <variant AA>
string variantEntry = main._protRefSeq + " " + main._VarArray[1] + " " + main._VarArray[0] + " " + main._VarArray[2];
HtmlElement element;
element = webBrowserProvean.Document.GetElementById("variants");
element.SetAttribute("Value", variantEntry);
submitProvean(ref webBrowserProvean);
}
public static void savePage(UVSearch main, string fileName, string documentText, Encoding wbrowserEncoding)
{
string fpath = "";
if (main._Gene != null)
{
fpath = main._Path + "\\" + main._Gene + "_" + main._Variant + "_" + fileName;
}
File.WriteAllText(fpath,
documentText,
wbrowserEncoding);
}
public static bool enterTextSNPsandGO(UVSearch main, WebBrowser webBrowserSandGo)
{
//Find GO Terms
string terms = GoTerms.GetGOs(main._RefSeq);
if (!Regex.IsMatch(terms, @"^GO:\d+(?:\sGO:\d+){0,}") && terms != "")
{
Go_Manual frm = new Go_Manual();
DialogResult dlg = frm.ShowDialog();
if (dlg == System.Windows.Forms.DialogResult.OK)
{
terms = GoTerms.GetGOs(frm.Terms);
}
}
if (terms == "")
{
terms = GOTerms();
if (terms == "" || terms == null)
{
return(false);
}
}
//save GO terms
Utilities.saveTextFile(main, "GOTerms.txt", terms);
//Comma or blank separated mutations
HtmlElementCollection collection;
collection = webBrowserSandGo.Document.GetElementsByTagName("textarea");
foreach (HtmlElement element in collection)
{
string name = element.GetAttribute("name");
if (name == "proteina")
{
element.SetAttribute("Value", main._Fasta);
}
else if (name == "posizione")
{
element.SetAttribute("Value", main._Variant);
}
else if (name == "gos")
{
element.SetAttribute("Value", terms);
}
}
return(true);
}
public static void enterTextPanther(UVSearch main, WebBrowser webBrowserMain)
{
//Comma or blank separated mutations
HtmlElementCollection collection;
collection = webBrowserMain.Document.GetElementsByTagName("textarea");
foreach (HtmlElement element in collection)
{
string name = element.GetAttribute("name");
if (name == "sequence")
{
element.SetAttribute("Value", main._FastaNH);
}
if (name == "substitutions")
{
element.SetAttribute("Value", main._Variant);
}
}
}
public static void enterTextMutAssess(UVSearch main, WebBrowser webBrowserMain)
{
//Needs the shorter version of the refseq code (!?)
string[] splitStr = main._protRefSeq.Split('.');
string shortPRefSeq = splitStr[0];
string varMA = shortPRefSeq + " " + main._Variant;
HtmlElementCollection collection;
collection = webBrowserMain.Document.GetElementsByTagName("textarea");
foreach (HtmlElement element in collection)
{
string name = element.GetAttribute("name");
if (name == "vars")
{
element.SetAttribute("Value", varMA);
}
}
}
public static void enterTextHANSA(UVSearch main, ref WebBrowser webBrowserHansa)
{
string variantEntry = main._VarArray[0] + " " + main._VarArray[1] + " " + main._VarArray[2];
HtmlElementCollection collection;
collection = webBrowserHansa.Document.GetElementsByTagName("textarea");
foreach (HtmlElement element in collection)
{
string name = element.GetAttribute("name");
if (name == "fsequence")
{
element.SetAttribute("Value", main._Fasta);
}
if (name == "mutlist")
{
element.SetAttribute("Value", variantEntry);
}
}
Utilities.submit(ref webBrowserHansa);
}
public static void enterTextPolyPhen2(UVSearch main, ref WebBrowser webBrowserPP2)
{
HtmlElementCollection collection;
collection = webBrowserPP2.Document.GetElementsByTagName("textarea");
foreach (HtmlElement element in collection)
{
string name = element.GetAttribute("name");
if (name == "seqres")
{
element.SetAttribute("Value", main._Fasta);
}
}
collection = webBrowserPP2.Document.GetElementsByTagName("input");
foreach (HtmlElement element in collection)
{
string name = element.GetAttribute("name");
if (name == "seqpos")
{
element.SetAttribute("Value", main._VarArray[1]);
}
if (name == "description")
{
element.SetAttribute("Value", main._Gene + ' ' + main._Variant);
}
}
HtmlElement AAelement;
AAelement = webBrowserPP2.Document.GetElementById("v1" + main._VarArray[0]);
AAelement.InvokeMember("click");
AAelement = webBrowserPP2.Document.GetElementById("v2" + main._VarArray[2]);
AAelement.InvokeMember("click");
PP2.submitPP2(ref webBrowserPP2);
}
public SelectTranscript(UVSearch main)
{
InitializeComponent();
_main = main;
}