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; }