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AdvancedSetting.xaml.cs
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using BUDDY.FormulaData;
using BUDDY.MS2LibrarySearch;
using System;
using System.Collections.Generic;
using System.Collections.ObjectModel;
using System.ComponentModel;
using System.Diagnostics;
using System.IO;
using System.Linq;
using System.Runtime.InteropServices.WindowsRuntime;
using System.Text.RegularExpressions;
using Windows.Foundation.Collections;
using Windows.Graphics.Display;
using Windows.Storage;
using Windows.UI.ViewManagement;
using Windows.UI.Xaml;
using Windows.UI.Xaml.Controls;
using Windows.UI.Xaml.Controls.Primitives;
using Windows.UI.Xaml.Data;
using Windows.UI.Xaml.Input;
using Windows.UI.Xaml.Media;
using Windows.UI.Xaml.Navigation;
// The Blank Page item template is documented at https://go.microsoft.com/fwlink/?LinkId=234238
namespace BUDDY
{
/// <summary>
/// An empty page that can be used on its own or navigated to within a Frame.
/// </summary>
public sealed partial class AdvancedSetting : Page
{
ApplicationDataContainer localSettings = ApplicationData.Current.LocalSettings;
StorageFolder storageFolder = ApplicationData.Current.LocalFolder;
string currTab = "general";
ObservableCollection<Adduct> adductList_Pos;
ObservableCollection<Adduct> adductList_Neg;
bool throwInvalidInputError = false;
StorageFile customMS2DB = null;
List<MS2DBEntry> newDB = new List<MS2DBEntry>();
public AdvancedSetting()
{
//adduct list
using (Stream stream = File.Open(storageFolder.Path + @"\adductList_Pos.bin", FileMode.Open))
{
var bformatter = new System.Runtime.Serialization.Formatters.Binary.BinaryFormatter();
adductList_Pos = new ObservableCollection<Adduct>((IEnumerable<Adduct>)bformatter.Deserialize(stream));
}
using (Stream stream = File.Open(storageFolder.Path + @"\adductList_Neg.bin", FileMode.Open))
{
var bformatter = new System.Runtime.Serialization.Formatters.Binary.BinaryFormatter();
adductList_Neg = new ObservableCollection<Adduct>((IEnumerable<Adduct>)bformatter.Deserialize(stream));
}
this.InitializeComponent();
this.Loaded += AdvancedSetting_Page_Loaded;
#region
general_panel.Visibility = Visibility.Visible;
//general
MS2LibrarySearch_checkbox.IsChecked = (bool)localSettings.Values["MS2LibrarySearch_include"];
BUDDY_checkbox.IsChecked = (bool)localSettings.Values["BUDDY_include"];
ExpSpecificGlobalAnnotation_checkbox.IsChecked = (bool)localSettings.Values["ExpSpecificGlobalAnnotation_include"];
ms_instrument_selection.SelectedIndex = (int)localSettings.Values["selectedMSinstrument"];
ms1tol_box.Text = localSettings.Values["ms1tol"].ToString();
ms2tol_box.Text = localSettings.Values["ms2tol"].ToString();
ms1tol_switch.IsOn = (bool)localSettings.Values["ms1tol_ppmON"];
ms2tol_switch.IsOn = (bool)localSettings.Values["ms2tol_ppmON"];
topFrag_box.Text = localSettings.Values["topFrag"].ToString();
use_topFrag_checkbox.IsChecked = (bool)localSettings.Values["use_topFrag"];
use_allFrag_checkbox.IsChecked = (bool)localSettings.Values["use_allFrag"];
ms2Deisotope_checkbox.IsChecked = (bool)localSettings.Values["ms2Deisotope"];
ms2Denoise_checkbox.IsChecked = (bool)localSettings.Values["ms2Denoise"];
maxNoiseInt_box.Text = localSettings.Values["maxNoiseInt"].ToString();
maxNoiseFragRatio_box.Text = localSettings.Values["maxNoiseFragRatio"].ToString();
maxNoiseRSD_box.Text = localSettings.Values["maxNoiseRSD"].ToString();
MetaScore_checkbox.IsChecked = (bool)localSettings.Values["MetaScore_include"];
//ms2_library_search
useCustomMS2DB_checkbox.IsChecked = (bool)localSettings.Values["useCustomMS2DB_include"];
if ((bool)localSettings.Values["useCustomMS2DB_include"])
{
string fullPath = (string)localSettings.Values["customMS2DBName"];
loadedMS2DB_text.Text = fullPath.Substring(fullPath.LastIndexOf("\\") + 1);
}
else
{
loadedMS2DB_text.Text = "";
}
ms2MatchingAlgorithm_selection.SelectedIndex = (int)localSettings.Values["ms2MatchingAlgorithm"];
metaboliteIdentificationMS2SimilarityScoreThreshold_box.Text = localSettings.Values["metaboliteIdentificationMS2SimilarityScoreThreshold"].ToString();
string recommendedMetaIdenMS2ScoreStr = "0.7";
string recommendedMetaIdenMS2MinMatchedFragNoStr = "";
switch (ms2MatchingAlgorithm_selection.SelectedIndex)
{
case 0:
recommendedMetaIdenMS2ScoreStr = "0.7";
recommendedMetaIdenMS2MinMatchedFragNoStr = "6";
break;
case 1:
recommendedMetaIdenMS2ScoreStr = "0.7";
recommendedMetaIdenMS2MinMatchedFragNoStr = "6";
break;
case 2:
recommendedMetaIdenMS2ScoreStr = "0.75";
recommendedMetaIdenMS2MinMatchedFragNoStr = "0";
break;
default:
break;
}
recommendedMetaIdenMS2Score_text.Text = recommendedMetaIdenMS2ScoreStr;
recommendedMetaIdenMS2MinMatchedFragNo_text.Text = recommendedMetaIdenMS2MinMatchedFragNoStr;
metaboliteIdentificationMS2MinMatchedFrag_checkbox.IsChecked = (bool)localSettings.Values["metaboliteIdentificationMS2MinMatchedFrag_include"];
metaboliteIdentificationMS2MinMatchedFragNo_box.Text = localSettings.Values["metaboliteIdentificationMS2MinMatchedFragNo"].ToString();
metaboliteIdentificationRT_checkbox.IsChecked = (bool)localSettings.Values["metaboliteIdentificationRT_include"];
metaboliteIdentificationRTtol_box.Text = localSettings.Values["metaboliteIdentificationRTtol"].ToString();
//elements
C_RangeSelector.RangeStart = (int)localSettings.Values["c_min"];
C_RangeSelector.RangeEnd = (int)localSettings.Values["c_max"];
ele_C_checkbox.IsChecked = (bool)localSettings.Values["c_include"];
H_RangeSelector.RangeStart = (int)localSettings.Values["h_min"];
H_RangeSelector.RangeEnd = (int)localSettings.Values["h_max"];
ele_H_checkbox.IsChecked = (bool)localSettings.Values["h_include"];
N_RangeSelector.RangeStart = (int)localSettings.Values["n_min"];
N_RangeSelector.RangeEnd = (int)localSettings.Values["n_max"];
ele_N_checkbox.IsChecked = (bool)localSettings.Values["n_include"];
O_RangeSelector.RangeStart = (int)localSettings.Values["o_min"];
O_RangeSelector.RangeEnd = (int)localSettings.Values["o_max"];
ele_O_checkbox.IsChecked = (bool)localSettings.Values["o_include"];
P_RangeSelector.RangeStart = (int)localSettings.Values["p_min"];
P_RangeSelector.RangeEnd = (int)localSettings.Values["p_max"];
ele_P_checkbox.IsChecked = (bool)localSettings.Values["p_include"];
S_RangeSelector.RangeStart = (int)localSettings.Values["s_min"];
S_RangeSelector.RangeEnd = (int)localSettings.Values["s_max"];
ele_S_checkbox.IsChecked = (bool)localSettings.Values["s_include"];
F_RangeSelector.RangeStart = (int)localSettings.Values["f_min"];
F_RangeSelector.RangeEnd = (int)localSettings.Values["f_max"];
ele_F_checkbox.IsChecked = (bool)localSettings.Values["f_include"];
Cl_RangeSelector.RangeStart = (int)localSettings.Values["cl_min"];
Cl_RangeSelector.RangeEnd = (int)localSettings.Values["cl_max"];
ele_Cl_checkbox.IsChecked = (bool)localSettings.Values["cl_include"];
Br_RangeSelector.RangeStart = (int)localSettings.Values["br_min"];
Br_RangeSelector.RangeEnd = (int)localSettings.Values["br_max"];
ele_Br_checkbox.IsChecked = (bool)localSettings.Values["br_include"];
I_RangeSelector.RangeStart = (int)localSettings.Values["i_min"];
I_RangeSelector.RangeEnd = (int)localSettings.Values["i_max"];
ele_I_checkbox.IsChecked = (bool)localSettings.Values["i_include"];
Si_RangeSelector.RangeStart = (int)localSettings.Values["si_min"];
Si_RangeSelector.RangeEnd = (int)localSettings.Values["si_max"];
ele_Si_checkbox.IsChecked = (bool)localSettings.Values["si_include"];
B_RangeSelector.RangeStart = (int)localSettings.Values["b_min"];
B_RangeSelector.RangeEnd = (int)localSettings.Values["b_max"];
ele_B_checkbox.IsChecked = (bool)localSettings.Values["b_include"];
Se_RangeSelector.RangeStart = (int)localSettings.Values["se_min"];
Se_RangeSelector.RangeEnd = (int)localSettings.Values["se_max"];
ele_Se_checkbox.IsChecked = (bool)localSettings.Values["se_include"];
//formula database
noResDB_checkbox.IsChecked = (bool)localSettings.Values["NoResDB_include"];
pubchem_checkbox.IsChecked = (bool)localSettings.Values["PubChem_include"];
mtb_lpd_checkbox.IsChecked = (bool)localSettings.Values["mtb_lpd_include"];
BMDB_checkbox.IsChecked = (bool)localSettings.Values["BMDB_include"];
ChEBI_checkbox.IsChecked = (bool)localSettings.Values["ChEBI_include"];
ECMDB_checkbox.IsChecked = (bool)localSettings.Values["ECMDB_include"];
FooDB_checkbox.IsChecked = (bool)localSettings.Values["FooDB_include"];
HMDB_checkbox.IsChecked = (bool)localSettings.Values["HMDB_include"];
KEGG_checkbox.IsChecked = (bool)localSettings.Values["KEGG_include"];
LMSD_checkbox.IsChecked = (bool)localSettings.Values["LMSD_include"];
MarkerDB_checkbox.IsChecked = (bool)localSettings.Values["MarkerDB_include"];
MCDB_checkbox.IsChecked = (bool)localSettings.Values["MCDB_include"];
PlantCyc_checkbox.IsChecked = (bool)localSettings.Values["PlantCyc_include"];
SMPDB_checkbox.IsChecked = (bool)localSettings.Values["SMPDB_include"];
YMDB_checkbox.IsChecked = (bool)localSettings.Values["YMDB_include"];
drug_txn_checkbox.IsChecked = (bool)localSettings.Values["drug_txn_include"];
DrugBank_checkbox.IsChecked = (bool)localSettings.Values["DrugBank_include"];
DSSTOX_checkbox.IsChecked = (bool)localSettings.Values["DSSTOX_include"];
HSDB_checkbox.IsChecked = (bool)localSettings.Values["HSDB_include"];
T3DB_checkbox.IsChecked = (bool)localSettings.Values["T3DB_include"];
TTD_checkbox.IsChecked = (bool)localSettings.Values["TTD_include"];
natProducts_checkbox.IsChecked = (bool)localSettings.Values["natProducts_include"];
ANPDB_checkbox.IsChecked = (bool)localSettings.Values["ANPDB_include"];
COCONUT_checkbox.IsChecked = (bool)localSettings.Values["COCONUT_include"];
NPASS_checkbox.IsChecked = (bool)localSettings.Values["NPASS_include"];
UNPD_checkbox.IsChecked = (bool)localSettings.Values["UNPD_include"];
xbiotics_checkbox.IsChecked = (bool)localSettings.Values["xbiotics_include"];
BLEXP_checkbox.IsChecked = (bool)localSettings.Values["BLEXP_include"];
NORMAN_checkbox.IsChecked = (bool)localSettings.Values["NORMAN_include"];
STF_IDENT_checkbox.IsChecked = (bool)localSettings.Values["STF_IDENT_include"];
contaminants_checkbox.IsChecked = (bool)localSettings.Values["contaminants_include"];
MaConDa_checkbox.IsChecked = (bool)localSettings.Values["MaConDa_include"];
//raw data processing
//isotopicPT_checkbox.IsChecked = (bool)localSettings.Values["isotopic_pattern_imp"];
featureClusterMsdial_checkbox.IsChecked = (bool)localSettings.Values["featureClusterMsdial_include"];
max_ispPeaks_box.Text = localSettings.Values["max_isotopic_peaks"].ToString();
ispAbundance_cut_box.Text = localSettings.Values["isotopic_abundance_cutoff"].ToString();
isp_group_masstol_box.Text = localSettings.Values["isotopologue_grp_masstol"].ToString();
ms2Group_checkbox.IsChecked = (bool)localSettings.Values["ms2_group_imp"];
cosSim_cut_box.Text = localSettings.Values["cos_similarity_cutoff"].ToString();
max_peakWidth_box.Text = localSettings.Values["max_peak_width"].ToString();
ms2Merge_checkbox.IsChecked = (bool)localSettings.Values["ms2_merging"];
//candidate refinement
topCandidates_box.Text = localSettings.Values["topCandidates"].ToString();
use_topCandidates_checkbox.IsChecked = (bool)localSettings.Values["use_topCandidates"];
use_allCandidates_checkbox.IsChecked = (bool)localSettings.Values["use_allCandidates"];
//expMS2fragNum_checkbox.IsChecked = (bool)localSettings.Values["expMS2fragNum_include"];
//expMS2fragNum_box.Text = localSettings.Values["expMS2fragNum"].ToString();
//expMS2fragInt_checkbox.IsChecked = (bool)localSettings.Values["expMS2fragInt_include"];
//expMS2fragInt_box.Text = localSettings.Values["expMS2fragInt"].ToString();
isp_sim_checkbox.IsChecked = (bool)localSettings.Values["ispPatternSim_include"];
isp_sim_box.Text = localSettings.Values["ispPatternSim"].ToString();
h_c_ratio_checkbox.IsChecked = (bool)localSettings.Values["h_c_ratio_include"];
h_c_ratio_box1.Text = localSettings.Values["h_c_ratio_box1"].ToString();
h_c_ratio_box2.Text = localSettings.Values["h_c_ratio_box2"].ToString();
o_c_ratio_checkbox.IsChecked = (bool)localSettings.Values["o_c_ratio_include"];
o_c_ratio_box1.Text = localSettings.Values["o_c_ratio_box1"].ToString();
o_c_ratio_box2.Text = localSettings.Values["o_c_ratio_box2"].ToString();
n_c_ratio_checkbox.IsChecked = (bool)localSettings.Values["n_c_ratio_include"];
n_c_ratio_box1.Text = localSettings.Values["n_c_ratio_box1"].ToString();
n_c_ratio_box2.Text = localSettings.Values["n_c_ratio_box2"].ToString();
p_c_ratio_checkbox.IsChecked = (bool)localSettings.Values["p_c_ratio_include"];
p_c_ratio_box1.Text = localSettings.Values["p_c_ratio_box1"].ToString();
p_c_ratio_box2.Text = localSettings.Values["p_c_ratio_box2"].ToString();
s_c_ratio_checkbox.IsChecked = (bool)localSettings.Values["s_c_ratio_include"];
s_c_ratio_box1.Text = localSettings.Values["s_c_ratio_box1"].ToString();
s_c_ratio_box2.Text = localSettings.Values["s_c_ratio_box2"].ToString();
f_c_ratio_checkbox.IsChecked = (bool)localSettings.Values["f_c_ratio_include"];
f_c_ratio_box1.Text = localSettings.Values["f_c_ratio_box1"].ToString();
f_c_ratio_box2.Text = localSettings.Values["f_c_ratio_box2"].ToString();
cl_c_ratio_checkbox.IsChecked = (bool)localSettings.Values["cl_c_ratio_include"];
cl_c_ratio_box1.Text = localSettings.Values["cl_c_ratio_box1"].ToString();
cl_c_ratio_box2.Text = localSettings.Values["cl_c_ratio_box2"].ToString();
br_c_ratio_checkbox.IsChecked = (bool)localSettings.Values["br_c_ratio_include"];
br_c_ratio_box1.Text = localSettings.Values["br_c_ratio_box1"].ToString();
br_c_ratio_box2.Text = localSettings.Values["br_c_ratio_box2"].ToString();
si_c_ratio_checkbox.IsChecked = (bool)localSettings.Values["si_c_ratio_include"];
si_c_ratio_box1.Text = localSettings.Values["si_c_ratio_box1"].ToString();
si_c_ratio_box2.Text = localSettings.Values["si_c_ratio_box2"].ToString();
o_p_ratio_checkbox.IsChecked = (bool)localSettings.Values["o_p_ratio_include"];
//timeout
timeout_single_checkbox.IsChecked = (bool)localSettings.Values["timeout_single_include"];
timeout_single_box.Text = localSettings.Values["timeout_single"].ToString();
//timeout_batch_checkbox.IsChecked = (bool)localSettings.Values["timeout_batch_include"];
//timeout_batch_box.Text = localSettings.Values["timeout_batch"].ToString();
MS2FragReannotate_checkbox.IsChecked = (bool)localSettings.Values["MS2FragReannotate_include"];
#endregion
}
private void AdvancedSetting_Page_Loaded(object sender, RoutedEventArgs e)
{
var s = ApplicationView.GetForCurrentView();
s.TryResizeView(new Windows.Foundation.Size { Width = 800.0, Height = 800.0 });
}
private void general_button_Click(object sender, RoutedEventArgs e)
{
general_button.IsChecked = true;
ms2_library_search_button.IsChecked = false;
element_button.IsChecked = false;
formulaDB_button.IsChecked = false;
adduct_button.IsChecked = false;
raw_data_button.IsChecked = false;
candidate_refinement_button.IsChecked = false;
others_button.IsChecked = false;
//general_button.Background = (SolidColorBrush)Resources["MenuLightGrey"];
//general_button.Foreground = (SolidColorBrush)Resources["MenuDarkGrey"];
//element_button.Background = (SolidColorBrush)Resources["MenuDarkGrey"];
//element_button.Foreground = (SolidColorBrush)Resources["MenuLightGrey"];
//formulaDB_button.Background = (SolidColorBrush)Resources["MenuDarkGrey"];
//formulaDB_button.Foreground = (SolidColorBrush)Resources["MenuLightGrey"];
//adduct_button.Background = (SolidColorBrush)Resources["MenuDarkGrey"];
//adduct_button.Foreground = (SolidColorBrush)Resources["MenuLightGrey"];
//raw_data_button.Background = (SolidColorBrush)Resources["MenuDarkGrey"];
//raw_data_button.Foreground = (SolidColorBrush)Resources["MenuLightGrey"];
//candidate_refinement_button.Background = (SolidColorBrush)Resources["MenuDarkGrey"];
//candidate_refinement_button.Foreground = (SolidColorBrush)Resources["MenuLightGrey"];
//others_button.Background = (SolidColorBrush)Resources["MenuDarkGrey"];
//others_button.Foreground = (SolidColorBrush)Resources["MenuLightGrey"];
currTab = "general";
general_panel.Visibility = Visibility.Visible;
ms2_library_search_panel.Visibility = Visibility.Collapsed;
element_panel.Visibility = Visibility.Collapsed;
fdb_res_panel.Visibility = Visibility.Collapsed;
adduct_panel.Visibility = Visibility.Collapsed;
raw_data_panel.Visibility = Visibility.Collapsed;
candidate_refinement_panel.Visibility = Visibility.Collapsed;
others_panel.Visibility = Visibility.Collapsed;
}
private void ms2_library_search_button_Click(object sender, RoutedEventArgs e)
{
general_button.IsChecked = false;
ms2_library_search_button.IsChecked = true;
element_button.IsChecked = false;
formulaDB_button.IsChecked = false;
adduct_button.IsChecked = false;
raw_data_button.IsChecked = false;
candidate_refinement_button.IsChecked = false;
others_button.IsChecked = false;
currTab = "ms2_library_search";
general_panel.Visibility = Visibility.Collapsed;
ms2_library_search_panel.Visibility = Visibility.Visible;
element_panel.Visibility = Visibility.Collapsed;
fdb_res_panel.Visibility = Visibility.Collapsed;
adduct_panel.Visibility = Visibility.Collapsed;
raw_data_panel.Visibility = Visibility.Collapsed;
candidate_refinement_panel.Visibility = Visibility.Collapsed;
others_panel.Visibility = Visibility.Collapsed;
}
private void element_button_Click(object sender, RoutedEventArgs e)
{
general_button.IsChecked = false;
ms2_library_search_button.IsChecked = false;
element_button.IsChecked = true;
formulaDB_button.IsChecked = false;
adduct_button.IsChecked = false;
raw_data_button.IsChecked = false;
candidate_refinement_button.IsChecked = false;
others_button.IsChecked = false;
//general_button.Background = (SolidColorBrush)Resources["MenuDarkGrey"];
//general_button.Foreground = (SolidColorBrush)Resources["MenuLightGrey"];
//element_button.Background = (SolidColorBrush)Resources["MenuLightGrey"];
//element_button.Foreground = (SolidColorBrush)Resources["MenuDarkGrey"];
//formulaDB_button.Background = (SolidColorBrush)Resources["MenuDarkGrey"];
//formulaDB_button.Foreground = (SolidColorBrush)Resources["MenuLightGrey"];
//adduct_button.Background = (SolidColorBrush)Resources["MenuDarkGrey"];
//adduct_button.Foreground = (SolidColorBrush)Resources["MenuLightGrey"];
//raw_data_button.Background = (SolidColorBrush)Resources["MenuDarkGrey"];
//raw_data_button.Foreground = (SolidColorBrush)Resources["MenuLightGrey"];
//candidate_refinement_button.Background = (SolidColorBrush)Resources["MenuDarkGrey"];
//candidate_refinement_button.Foreground = (SolidColorBrush)Resources["MenuLightGrey"];
//others_button.Background = (SolidColorBrush)Resources["MenuDarkGrey"];
//others_button.Foreground = (SolidColorBrush)Resources["MenuLightGrey"];
currTab = "element";
general_panel.Visibility = Visibility.Collapsed;
ms2_library_search_panel.Visibility = Visibility.Collapsed;
element_panel.Visibility = Visibility.Visible;
fdb_res_panel.Visibility = Visibility.Collapsed;
adduct_panel.Visibility = Visibility.Collapsed;
raw_data_panel.Visibility = Visibility.Collapsed;
candidate_refinement_panel.Visibility = Visibility.Collapsed;
others_panel.Visibility = Visibility.Collapsed;
}
private void formulaDB_button_Click(object sender, RoutedEventArgs e)
{
general_button.IsChecked = false;
ms2_library_search_button.IsChecked = false;
element_button.IsChecked = false;
formulaDB_button.IsChecked = true;
adduct_button.IsChecked = false;
raw_data_button.IsChecked = false;
candidate_refinement_button.IsChecked = false;
others_button.IsChecked = false;
//general_button.Background = (SolidColorBrush)Resources["MenuDarkGrey"];
//general_button.Foreground = (SolidColorBrush)Resources["MenuLightGrey"];
//element_button.Background = (SolidColorBrush)Resources["MenuDarkGrey"];
//element_button.Foreground = (SolidColorBrush)Resources["MenuLightGrey"];
//formulaDB_button.Background = (SolidColorBrush)Resources["MenuLightGrey"];
//formulaDB_button.Foreground = (SolidColorBrush)Resources["MenuDarkGrey"];
//adduct_button.Background = (SolidColorBrush)Resources["MenuDarkGrey"];
//adduct_button.Foreground = (SolidColorBrush)Resources["MenuLightGrey"];
//raw_data_button.Background = (SolidColorBrush)Resources["MenuDarkGrey"];
//raw_data_button.Foreground = (SolidColorBrush)Resources["MenuLightGrey"];
//candidate_refinement_button.Background = (SolidColorBrush)Resources["MenuDarkGrey"];
//candidate_refinement_button.Foreground = (SolidColorBrush)Resources["MenuLightGrey"];
//others_button.Background = (SolidColorBrush)Resources["MenuDarkGrey"];
//others_button.Foreground = (SolidColorBrush)Resources["MenuLightGrey"];
currTab = "formulaDB";
general_panel.Visibility = Visibility.Collapsed;
ms2_library_search_panel.Visibility = Visibility.Collapsed;
element_panel.Visibility = Visibility.Collapsed;
fdb_res_panel.Visibility = Visibility.Visible;
adduct_panel.Visibility = Visibility.Collapsed;
raw_data_panel.Visibility = Visibility.Collapsed;
candidate_refinement_panel.Visibility = Visibility.Collapsed;
others_panel.Visibility = Visibility.Collapsed;
}
private void adduct_button_Click(object sender, RoutedEventArgs e)
{
general_button.IsChecked = false;
ms2_library_search_button.IsChecked = false;
element_button.IsChecked = false;
formulaDB_button.IsChecked = false;
adduct_button.IsChecked = true;
raw_data_button.IsChecked = false;
candidate_refinement_button.IsChecked = false;
others_button.IsChecked = false;
currTab = "adduct";
general_panel.Visibility = Visibility.Collapsed;
ms2_library_search_panel.Visibility = Visibility.Collapsed;
element_panel.Visibility = Visibility.Collapsed;
fdb_res_panel.Visibility = Visibility.Collapsed;
adduct_panel.Visibility = Visibility.Visible;
raw_data_panel.Visibility = Visibility.Collapsed;
candidate_refinement_panel.Visibility = Visibility.Collapsed;
others_panel.Visibility = Visibility.Collapsed;
}
private void raw_data_button_Click(object sender, RoutedEventArgs e)
{
general_button.IsChecked = false;
ms2_library_search_button.IsChecked = false;
element_button.IsChecked = false;
formulaDB_button.IsChecked = false;
adduct_button.IsChecked = false;
raw_data_button.IsChecked = true;
candidate_refinement_button.IsChecked = false;
others_button.IsChecked = false;
currTab = "raw_data";
general_panel.Visibility = Visibility.Collapsed;
ms2_library_search_panel.Visibility = Visibility.Collapsed;
element_panel.Visibility = Visibility.Collapsed;
fdb_res_panel.Visibility = Visibility.Collapsed;
adduct_panel.Visibility = Visibility.Collapsed;
raw_data_panel.Visibility = Visibility.Visible;
candidate_refinement_panel.Visibility = Visibility.Collapsed;
others_panel.Visibility = Visibility.Collapsed;
}
private void candidate_refinement_button_Click(object sender, RoutedEventArgs e)
{
general_button.IsChecked = false;
ms2_library_search_button.IsChecked = false;
element_button.IsChecked = false;
formulaDB_button.IsChecked = false;
adduct_button.IsChecked = false;
raw_data_button.IsChecked = false;
candidate_refinement_button.IsChecked = true;
others_button.IsChecked = false;
currTab = "candidate_refinement";
general_panel.Visibility = Visibility.Collapsed;
ms2_library_search_panel.Visibility = Visibility.Collapsed;
element_panel.Visibility = Visibility.Collapsed;
fdb_res_panel.Visibility = Visibility.Collapsed;
adduct_panel.Visibility = Visibility.Collapsed;
raw_data_panel.Visibility = Visibility.Collapsed;
candidate_refinement_panel.Visibility = Visibility.Visible;
others_panel.Visibility = Visibility.Collapsed;
}
private void others_button_Click(object sender, RoutedEventArgs e)
{
general_button.IsChecked = false;
ms2_library_search_button.IsChecked = false;
element_button.IsChecked = false;
formulaDB_button.IsChecked = false;
adduct_button.IsChecked = false;
raw_data_button.IsChecked = false;
candidate_refinement_button.IsChecked = false;
others_button.IsChecked = true;
currTab = "others";
general_panel.Visibility = Visibility.Collapsed;
ms2_library_search_panel.Visibility = Visibility.Collapsed;
element_panel.Visibility = Visibility.Collapsed;
fdb_res_panel.Visibility = Visibility.Collapsed;
adduct_panel.Visibility = Visibility.Collapsed;
raw_data_panel.Visibility = Visibility.Collapsed;
candidate_refinement_panel.Visibility = Visibility.Collapsed;
others_panel.Visibility = Visibility.Visible;
}
private void ADV_Restore(object sender, RoutedEventArgs e)
{
switch (currTab)
{
case "general":
ms_instrument_selection.SelectedIndex = (int)localSettings.Values["selectedMSinstrument_default"];
ms1tol_box.Text = localSettings.Values["ms1tol_default"].ToString();
ms2tol_box.Text = localSettings.Values["ms2tol_default"].ToString();
ms1tol_switch.IsOn = (bool)localSettings.Values["ms1tol_ppmON_default"];
ms2tol_switch.IsOn = (bool)localSettings.Values["ms2tol_ppmON_default"];
topFrag_box.Text = localSettings.Values["topFrag_default"].ToString();
use_topFrag_checkbox.IsChecked = (bool)localSettings.Values["use_topFrag_default"];
use_allFrag_checkbox.IsChecked = (bool)localSettings.Values["use_allFrag_default"];
ms2Deisotope_checkbox.IsChecked = (bool)localSettings.Values["ms2Deisotope_default"];
ms2Denoise_checkbox.IsChecked = (bool)localSettings.Values["ms2Denoise_default"];
maxNoiseInt_box.Text = localSettings.Values["maxNoiseInt_default"].ToString();
maxNoiseFragRatio_box.Text = localSettings.Values["maxNoiseFragRatio_default"].ToString();
maxNoiseRSD_box.Text = localSettings.Values["maxNoiseRSD_default"].ToString();
ExpSpecificGlobalAnnotation_checkbox.IsChecked = (bool)localSettings.Values["ExpSpecificGlobalAnnotation_include_default"];
MS2LibrarySearch_checkbox.IsChecked = (bool)localSettings.Values["MS2LibrarySearch_include_default"];
BUDDY_checkbox.IsChecked = (bool)localSettings.Values["BUDDY_include_default"];
MetaScore_checkbox.IsChecked = (bool)localSettings.Values["MetaScore_include_default"];
break;
case "ms2_library_search":
useCustomMS2DB_checkbox.IsChecked = (bool)localSettings.Values["useCustomMS2DB_include_default"];
ms2MatchingAlgorithm_selection.SelectedIndex = (int)localSettings.Values["ms2MatchingAlgorithm_default"];
metaboliteIdentificationMS2SimilarityScoreThreshold_box.Text = localSettings.Values["metaboliteIdentificationMS2SimilarityScoreThreshold_default"].ToString();
metaboliteIdentificationMS2MinMatchedFrag_checkbox.IsChecked = (bool)localSettings.Values["metaboliteIdentificationMS2MinMatchedFrag_include_default"];
metaboliteIdentificationMS2MinMatchedFragNo_box.Text = localSettings.Values["metaboliteIdentificationMS2MinMatchedFragNo_default"].ToString();
metaboliteIdentificationRT_checkbox.IsChecked = (bool)localSettings.Values["metaboliteIdentificationRT_include_default"];
metaboliteIdentificationRTtol_box.Text = localSettings.Values["metaboliteIdentificationRTtol_default"].ToString();
loadedMS2DB_text.Text = "";
break;
case "element":
C_RangeSelector.RangeStart = (int)localSettings.Values["c_min_default"];
C_RangeSelector.RangeEnd = (int)localSettings.Values["c_max_default"];
ele_C_checkbox.IsChecked = (bool)localSettings.Values["c_include_default"];
H_RangeSelector.RangeStart = (int)localSettings.Values["h_min_default"];
H_RangeSelector.RangeEnd = (int)localSettings.Values["h_max_default"];
ele_H_checkbox.IsChecked = (bool)localSettings.Values["h_include_default"];
N_RangeSelector.RangeStart = (int)localSettings.Values["n_min_default"];
N_RangeSelector.RangeEnd = (int)localSettings.Values["n_max_default"];
ele_N_checkbox.IsChecked = (bool)localSettings.Values["n_include_default"];
O_RangeSelector.RangeStart = (int)localSettings.Values["o_min_default"];
O_RangeSelector.RangeEnd = (int)localSettings.Values["o_max_default"];
ele_O_checkbox.IsChecked = (bool)localSettings.Values["o_include_default"];
P_RangeSelector.RangeStart = (int)localSettings.Values["p_min_default"];
P_RangeSelector.RangeEnd = (int)localSettings.Values["p_max_default"];
ele_P_checkbox.IsChecked = (bool)localSettings.Values["p_include_default"];
S_RangeSelector.RangeStart = (int)localSettings.Values["s_min_default"];
S_RangeSelector.RangeEnd = (int)localSettings.Values["s_max_default"];
ele_S_checkbox.IsChecked = (bool)localSettings.Values["s_include_default"];
F_RangeSelector.RangeStart = (int)localSettings.Values["f_min_default"];
F_RangeSelector.RangeEnd = (int)localSettings.Values["f_max_default"];
ele_F_checkbox.IsChecked = (bool)localSettings.Values["f_include_default"];
Cl_RangeSelector.RangeStart = (int)localSettings.Values["cl_min_default"];
Cl_RangeSelector.RangeEnd = (int)localSettings.Values["cl_max_default"];
ele_Cl_checkbox.IsChecked = (bool)localSettings.Values["cl_include_default"];
Br_RangeSelector.RangeStart = (int)localSettings.Values["br_min_default"];
Br_RangeSelector.RangeEnd = (int)localSettings.Values["br_max_default"];
ele_Br_checkbox.IsChecked = (bool)localSettings.Values["br_include_default"];
I_RangeSelector.RangeStart = (int)localSettings.Values["i_min_default"];
I_RangeSelector.RangeEnd = (int)localSettings.Values["i_max_default"];
ele_I_checkbox.IsChecked = (bool)localSettings.Values["i_include_default"];
Si_RangeSelector.RangeStart = (int)localSettings.Values["si_min_default"];
Si_RangeSelector.RangeEnd = (int)localSettings.Values["si_max_default"];
ele_Si_checkbox.IsChecked = (bool)localSettings.Values["si_include_default"];
B_RangeSelector.RangeStart = (int)localSettings.Values["b_min_default"];
B_RangeSelector.RangeEnd = (int)localSettings.Values["b_max_default"];
ele_B_checkbox.IsChecked = (bool)localSettings.Values["b_include_default"];
Se_RangeSelector.RangeStart = (int)localSettings.Values["se_min_default"];
Se_RangeSelector.RangeEnd = (int)localSettings.Values["se_max_default"];
ele_Se_checkbox.IsChecked = (bool)localSettings.Values["se_include_default"];
break;
case "formulaDB":
//formula database
noResDB_checkbox.IsChecked = (bool)localSettings.Values["NoResDB_include_default"];
pubchem_checkbox.IsChecked = (bool)localSettings.Values["PubChem_include_default"];
mtb_lpd_checkbox.IsChecked = (bool)localSettings.Values["mtb_lpd_include_default"];
BMDB_checkbox.IsChecked = (bool)localSettings.Values["BMDB_include_default"];
ChEBI_checkbox.IsChecked = (bool)localSettings.Values["ChEBI_include_default"];
ECMDB_checkbox.IsChecked = (bool)localSettings.Values["ECMDB_include_default"];
FooDB_checkbox.IsChecked = (bool)localSettings.Values["FooDB_include_default"];
HMDB_checkbox.IsChecked = (bool)localSettings.Values["HMDB_include_default"];
KEGG_checkbox.IsChecked = (bool)localSettings.Values["KEGG_include_default"];
LMSD_checkbox.IsChecked = (bool)localSettings.Values["LMSD_include_default"];
MarkerDB_checkbox.IsChecked = (bool)localSettings.Values["MarkerDB_include_default"];
MCDB_checkbox.IsChecked = (bool)localSettings.Values["MCDB_include_default"];
PlantCyc_checkbox.IsChecked = (bool)localSettings.Values["PlantCyc_include_default"];
SMPDB_checkbox.IsChecked = (bool)localSettings.Values["SMPDB_include_default"];
YMDB_checkbox.IsChecked = (bool)localSettings.Values["YMDB_include_default"];
drug_txn_checkbox.IsChecked = (bool)localSettings.Values["drug_txn_include_default"];
DrugBank_checkbox.IsChecked = (bool)localSettings.Values["DrugBank_include_default"];
DSSTOX_checkbox.IsChecked = (bool)localSettings.Values["DSSTOX_include_default"];
HSDB_checkbox.IsChecked = (bool)localSettings.Values["HSDB_include_default"];
T3DB_checkbox.IsChecked = (bool)localSettings.Values["T3DB_include_default"];
TTD_checkbox.IsChecked = (bool)localSettings.Values["TTD_include_default"];
natProducts_checkbox.IsChecked = (bool)localSettings.Values["natProducts_include_default"];
ANPDB_checkbox.IsChecked = (bool)localSettings.Values["ANPDB_include_default"];
COCONUT_checkbox.IsChecked = (bool)localSettings.Values["COCONUT_include_default"];
NPASS_checkbox.IsChecked = (bool)localSettings.Values["NPASS_include_default"];
UNPD_checkbox.IsChecked = (bool)localSettings.Values["UNPD_include_default"];
xbiotics_checkbox.IsChecked = (bool)localSettings.Values["xbiotics_include_default"];
BLEXP_checkbox.IsChecked = (bool)localSettings.Values["BLEXP_include_default"];
NORMAN_checkbox.IsChecked = (bool)localSettings.Values["NORMAN_include_default"];
STF_IDENT_checkbox.IsChecked = (bool)localSettings.Values["STF_IDENT_include_default"];
contaminants_checkbox.IsChecked = (bool)localSettings.Values["contaminants_include_default"];
MaConDa_checkbox.IsChecked = (bool)localSettings.Values["MaConDa_include_default"];
break;
case "adduct":
List<Adduct> defaultPosList = new List<Adduct>();
using (Stream stream = File.Open(storageFolder.Path + @"\adductList_Pos_Default.bin", FileMode.Open))
{
var bformatter = new System.Runtime.Serialization.Formatters.Binary.BinaryFormatter();
defaultPosList = (List<Adduct>)bformatter.Deserialize(stream);
}
List<Adduct> defaultNegList = new List<Adduct>();
using (Stream stream = File.Open(storageFolder.Path + @"\adductList_Neg_Default.bin", FileMode.Open))
{
var bformatter = new System.Runtime.Serialization.Formatters.Binary.BinaryFormatter();
defaultNegList = (List<Adduct>)bformatter.Deserialize(stream);
}
adductList_Pos.Clear();
foreach (Adduct ad in defaultPosList)
{
adductList_Pos.Add(ad);
}
adductList_Neg.Clear();
foreach (Adduct ad in defaultNegList)
{
adductList_Neg.Add(ad);
}
break;
case "raw_data":
//isotopicPT_checkbox.IsChecked = (bool)localSettings.Values["isotopic_pattern_imp_default"];
featureClusterMsdial_checkbox.IsChecked = (bool)localSettings.Values["featureClusterMsdial_include_default"];
max_ispPeaks_box.Text = localSettings.Values["max_isotopic_peaks_default"].ToString();
ispAbundance_cut_box.Text = localSettings.Values["isotopic_abundance_cutoff_default"].ToString();
isp_group_masstol_box.Text = localSettings.Values["isotopologue_grp_masstol_default"].ToString();
ms2Group_checkbox.IsChecked = (bool)localSettings.Values["ms2_group_imp_default"];
cosSim_cut_box.Text = localSettings.Values["cos_similarity_cutoff_default"].ToString();
max_peakWidth_box.Text = localSettings.Values["max_peak_width_default"].ToString();
ms2Merge_checkbox.IsChecked = (bool)localSettings.Values["ms2_merging_default"];
break;
case "candidate_refinement":
topCandidates_box.Text = localSettings.Values["topCandidates_default"].ToString();
use_topCandidates_checkbox.IsChecked = (bool)localSettings.Values["use_topCandidates_default"];
use_allCandidates_checkbox.IsChecked = (bool)localSettings.Values["use_allCandidates_default"];
//expMS2fragNum_checkbox.IsChecked = (bool)localSettings.Values["expMS2fragNum_include_default"];
//expMS2fragNum_box.Text = localSettings.Values["expMS2fragNum_default"].ToString();
//expMS2fragInt_checkbox.IsChecked = (bool)localSettings.Values["expMS2fragInt_include_default"];
//expMS2fragInt_box.Text = localSettings.Values["expMS2fragInt_default"].ToString();
isp_sim_checkbox.IsChecked = (bool)localSettings.Values["ispPatternSim_include_default"];
isp_sim_box.Text = localSettings.Values["ispPatternSim_default"].ToString();
h_c_ratio_checkbox.IsChecked = (bool)localSettings.Values["h_c_ratio_include_default"];
h_c_ratio_box1.Text = localSettings.Values["h_c_ratio_box1_default"].ToString();
h_c_ratio_box2.Text = localSettings.Values["h_c_ratio_box2_default"].ToString();
o_c_ratio_checkbox.IsChecked = (bool)localSettings.Values["o_c_ratio_include_default"];
o_c_ratio_box1.Text = localSettings.Values["o_c_ratio_box1_default"].ToString();
o_c_ratio_box2.Text = localSettings.Values["o_c_ratio_box2_default"].ToString();
n_c_ratio_checkbox.IsChecked = (bool)localSettings.Values["n_c_ratio_include_default"];
n_c_ratio_box1.Text = localSettings.Values["n_c_ratio_box1_default"].ToString();
n_c_ratio_box2.Text = localSettings.Values["n_c_ratio_box2_default"].ToString();
p_c_ratio_checkbox.IsChecked = (bool)localSettings.Values["p_c_ratio_include_default"];
p_c_ratio_box1.Text = localSettings.Values["p_c_ratio_box1_default"].ToString();
p_c_ratio_box2.Text = localSettings.Values["p_c_ratio_box2_default"].ToString();
s_c_ratio_checkbox.IsChecked = (bool)localSettings.Values["s_c_ratio_include_default"];
s_c_ratio_box1.Text = localSettings.Values["s_c_ratio_box1_default"].ToString();
s_c_ratio_box2.Text = localSettings.Values["s_c_ratio_box2_default"].ToString();
f_c_ratio_checkbox.IsChecked = (bool)localSettings.Values["f_c_ratio_include_default"];
f_c_ratio_box1.Text = localSettings.Values["f_c_ratio_box1_default"].ToString();
f_c_ratio_box2.Text = localSettings.Values["f_c_ratio_box2_default"].ToString();
cl_c_ratio_checkbox.IsChecked = (bool)localSettings.Values["cl_c_ratio_include_default"];
cl_c_ratio_box1.Text = localSettings.Values["cl_c_ratio_box1_default"].ToString();
cl_c_ratio_box2.Text = localSettings.Values["cl_c_ratio_box2_default"].ToString();
br_c_ratio_checkbox.IsChecked = (bool)localSettings.Values["br_c_ratio_include_default"];
br_c_ratio_box1.Text = localSettings.Values["br_c_ratio_box1_default"].ToString();
br_c_ratio_box2.Text = localSettings.Values["br_c_ratio_box2_default"].ToString();
si_c_ratio_checkbox.IsChecked = (bool)localSettings.Values["si_c_ratio_include_default"];
si_c_ratio_box1.Text = localSettings.Values["si_c_ratio_box1_default"].ToString();
si_c_ratio_box2.Text = localSettings.Values["si_c_ratio_box2_default"].ToString();
o_p_ratio_checkbox.IsChecked = (bool)localSettings.Values["o_p_ratio_include_default"];
break;
case "others":
timeout_single_checkbox.IsChecked = (bool)localSettings.Values["timeout_single_include_default"];
timeout_single_box.Text = localSettings.Values["timeout_single_default"].ToString();
MS2FragReannotate_checkbox.IsChecked = (bool)localSettings.Values["MS2FragReannotate_include_default"];
//timeout_batch_checkbox.IsChecked = (bool)localSettings.Values["timeout_batch_include_default"];
//timeout_batch_box.Text = localSettings.Values["timeout_batch_default"].ToString();
break;
default:
break;
}
}
private void ADV_Apply(object sender, RoutedEventArgs e)
{
throwInvalidInputError = false;
//general panel
#region
localSettings.Values["selectedMSinstrument"] = ms_instrument_selection.SelectedIndex;
double ms1tol_adv;
if (double.TryParse(ms1tol_box.Text, out ms1tol_adv))
{
if (ms1tol_adv > 0)
{
localSettings.Values["ms1tol"] = ms1tol_adv;
}
else
{
throwInvalidInputError = true;
}
}
else
{
throwInvalidInputError = true;
}
double ms2tol_adv;
if (double.TryParse(ms2tol_box.Text, out ms2tol_adv))
{
if (ms2tol_adv > 0)
{
localSettings.Values["ms2tol"] = ms2tol_adv;
}
else
{
throwInvalidInputError = true;
}
}
else
{
throwInvalidInputError = true;
}
//localSettings.Values["ms1tol"] = Double.Parse(ms1tol_box.Text);
//localSettings.Values["ms2tol"] = Double.Parse(ms2tol_box.Text);
localSettings.Values["ms1tol_ppmON"] = ms1tol_switch.IsOn;
localSettings.Values["ms2tol_ppmON"] = ms2tol_switch.IsOn;
int topfrag_adv;
if (int.TryParse(topFrag_box.Text, out topfrag_adv))
{
if (topfrag_adv > 0)
{
localSettings.Values["topFrag"] = topfrag_adv;
}
else
{
throwInvalidInputError = true;
}
}
else
{
throwInvalidInputError = true;
}
//localSettings.Values["topFrag"] = int.Parse(topFrag_box.Text);
localSettings.Values["use_topFrag"] = use_topFrag_checkbox.IsChecked;
localSettings.Values["use_allFrag"] = use_allFrag_checkbox.IsChecked;
localSettings.Values["ms2Deisotope"] = ms2Deisotope_checkbox.IsChecked;
localSettings.Values["ms2Denoise"] = ms2Denoise_checkbox.IsChecked;
double maxNoiseInt_adv;
if (double.TryParse(maxNoiseInt_box.Text, out maxNoiseInt_adv))
{
if (maxNoiseInt_adv > 0)
{
localSettings.Values["maxNoiseInt"] = maxNoiseInt_adv;
}
else
{
throwInvalidInputError = true;
}
}
else
{
throwInvalidInputError = true;
}
double maxNoiseFragRatio_adv;
if (double.TryParse(maxNoiseFragRatio_box.Text, out maxNoiseFragRatio_adv))
{
if (maxNoiseFragRatio_adv > 0 && maxNoiseFragRatio_adv < 100)
{
localSettings.Values["maxNoiseFragRatio"] = maxNoiseFragRatio_adv;
}
else
{
throwInvalidInputError = true;
}
}
else
{
throwInvalidInputError = true;
}
double maxNoiseRSD_adv;
if (double.TryParse(maxNoiseRSD_box.Text, out maxNoiseRSD_adv))
{
if (maxNoiseRSD_adv > 0)
{
localSettings.Values["maxNoiseRSD"] = maxNoiseRSD_adv;
}
else
{
throwInvalidInputError = true;
}
}
else
{
throwInvalidInputError = true;
}
localSettings.Values["ExpSpecificGlobalAnnotation_include"] = ExpSpecificGlobalAnnotation_checkbox.IsChecked;
localSettings.Values["BUDDY_include"] = BUDDY_checkbox.IsChecked;
localSettings.Values["MS2LibrarySearch_include"] = MS2LibrarySearch_checkbox.IsChecked;
localSettings.Values["MetaScore_include"] = MetaScore_checkbox.IsChecked;
//localSettings.Values["maxNoiseInt"] = Double.Parse(maxNoiseInt_box.Text);
//localSettings.Values["maxNoiseFragRatio"] = Double.Parse(maxNoiseFragRatio_box.Text);
// ms2 library search
localSettings.Values["useCustomMS2DB_include"] = useCustomMS2DB_checkbox.IsChecked;
localSettings.Values["ms2MatchingAlgorithm"] = ms2MatchingAlgorithm_selection.SelectedIndex;
double metaboliteIdentificationMS2SimilarityScoreThreshold_adv;
if (double.TryParse(metaboliteIdentificationMS2SimilarityScoreThreshold_box.Text, out metaboliteIdentificationMS2SimilarityScoreThreshold_adv))
{
if (metaboliteIdentificationMS2SimilarityScoreThreshold_adv >= 0 && metaboliteIdentificationMS2SimilarityScoreThreshold_adv <= 1)
{
localSettings.Values["metaboliteIdentificationMS2SimilarityScoreThreshold"] = metaboliteIdentificationMS2SimilarityScoreThreshold_adv;
}
else
{
throwInvalidInputError = true;
}
}
else
{
throwInvalidInputError = true;
}
localSettings.Values["metaboliteIdentificationMS2MinMatchedFrag_include"] = metaboliteIdentificationMS2MinMatchedFrag_checkbox.IsChecked;
int metaboliteIdentificationMS2MinMatchedFragNo_adv;
if (int.TryParse(metaboliteIdentificationMS2MinMatchedFragNo_box.Text, out metaboliteIdentificationMS2MinMatchedFragNo_adv))
{
if (metaboliteIdentificationMS2MinMatchedFragNo_adv >= 0)
{
localSettings.Values["metaboliteIdentificationMS2MinMatchedFragNo"] = metaboliteIdentificationMS2MinMatchedFragNo_adv;
}
else
{
throwInvalidInputError = true;
}
}
else
{
throwInvalidInputError = true;
}
localSettings.Values["metaboliteIdentificationRT_include"] = metaboliteIdentificationRT_checkbox.IsChecked;
double metaboliteIdentificationRTtol_adv;
if (double.TryParse(metaboliteIdentificationRTtol_box.Text, out metaboliteIdentificationRTtol_adv))
{
if (metaboliteIdentificationRTtol_adv >= 0)
{
localSettings.Values["metaboliteIdentificationRTtol"] = metaboliteIdentificationRTtol_adv;
}
else
{
throwInvalidInputError = true;
}
}
else
{
throwInvalidInputError = true;
}
#endregion
if (customMS2DB != null && useCustomMS2DB_checkbox.IsChecked == true)
{
localSettings.Values["useCustomMS2DB_include"] = true;
localSettings.Values["customMS2DBName"] = customMS2DB.Path;
//await this.MainPage.LoadMS2Database(customMS2DB.Name);
}
//elements
if (currTab == "element")
{
C_RangeSelector.RangeStart = tryParsingIntHelper_non_neg(minC_box.Text);
C_RangeSelector.RangeEnd = tryParsingIntHelper_non_neg(maxC_box.Text);
H_RangeSelector.RangeStart = tryParsingIntHelper_non_neg(minH_box.Text);
H_RangeSelector.RangeEnd = tryParsingIntHelper_non_neg(maxH_box.Text);
N_RangeSelector.RangeStart = tryParsingIntHelper_non_neg(minN_box.Text);
N_RangeSelector.RangeEnd = tryParsingIntHelper_non_neg(maxN_box.Text);
O_RangeSelector.RangeStart = tryParsingIntHelper_non_neg(minO_box.Text);
O_RangeSelector.RangeEnd = tryParsingIntHelper_non_neg(maxO_box.Text);
P_RangeSelector.RangeStart = tryParsingIntHelper_non_neg(minP_box.Text);
P_RangeSelector.RangeEnd = tryParsingIntHelper_non_neg(maxP_box.Text);
S_RangeSelector.RangeStart = tryParsingIntHelper_non_neg(minS_box.Text);
S_RangeSelector.RangeEnd = tryParsingIntHelper_non_neg(maxS_box.Text);
F_RangeSelector.RangeStart = tryParsingIntHelper_non_neg(minF_box.Text);
F_RangeSelector.RangeEnd = tryParsingIntHelper_non_neg(maxF_box.Text);
Cl_RangeSelector.RangeStart = tryParsingIntHelper_non_neg(minCl_box.Text);
Cl_RangeSelector.RangeEnd = tryParsingIntHelper_non_neg(maxCl_box.Text);
Br_RangeSelector.RangeStart = tryParsingIntHelper_non_neg(minBr_box.Text);
Br_RangeSelector.RangeEnd = tryParsingIntHelper_non_neg(maxBr_box.Text);
I_RangeSelector.RangeStart = tryParsingIntHelper_non_neg(minI_box.Text);
I_RangeSelector.RangeEnd = tryParsingIntHelper_non_neg(maxI_box.Text);
Si_RangeSelector.RangeStart = tryParsingIntHelper_non_neg(minSi_box.Text);
Si_RangeSelector.RangeEnd = tryParsingIntHelper_non_neg(maxSi_box.Text);
B_RangeSelector.RangeStart = tryParsingIntHelper_non_neg(minB_box.Text);
B_RangeSelector.RangeEnd = tryParsingIntHelper_non_neg(maxB_box.Text);
Se_RangeSelector.RangeStart = tryParsingIntHelper_non_neg(minSe_box.Text);
Se_RangeSelector.RangeEnd = tryParsingIntHelper_non_neg(maxSe_box.Text);
}
localSettings.Values["c_min"] = Convert.ToInt32(C_RangeSelector.RangeStart);
localSettings.Values["c_max"] = Convert.ToInt32(C_RangeSelector.RangeEnd);
localSettings.Values["c_include"] = ele_C_checkbox.IsChecked;
localSettings.Values["h_min"] = Convert.ToInt32(H_RangeSelector.RangeStart);
localSettings.Values["h_max"] = Convert.ToInt32(H_RangeSelector.RangeEnd);
localSettings.Values["h_include"] = ele_H_checkbox.IsChecked;
localSettings.Values["n_min"] = Convert.ToInt32(N_RangeSelector.RangeStart);
localSettings.Values["n_max"] = Convert.ToInt32(N_RangeSelector.RangeEnd);
localSettings.Values["n_include"] = ele_N_checkbox.IsChecked;
localSettings.Values["o_min"] = Convert.ToInt32(O_RangeSelector.RangeStart);
localSettings.Values["o_max"] = Convert.ToInt32(O_RangeSelector.RangeEnd);
localSettings.Values["o_include"] = ele_O_checkbox.IsChecked;
localSettings.Values["p_min"] = Convert.ToInt32(P_RangeSelector.RangeStart);
localSettings.Values["p_max"] = Convert.ToInt32(P_RangeSelector.RangeEnd);
localSettings.Values["p_include"] = ele_P_checkbox.IsChecked;
localSettings.Values["s_min"] = Convert.ToInt32(S_RangeSelector.RangeStart);
localSettings.Values["s_max"] = Convert.ToInt32(S_RangeSelector.RangeEnd);
localSettings.Values["s_include"] = ele_S_checkbox.IsChecked;
localSettings.Values["f_min"] = Convert.ToInt32(F_RangeSelector.RangeStart);
localSettings.Values["f_max"] = Convert.ToInt32(F_RangeSelector.RangeEnd);
localSettings.Values["f_include"] = ele_F_checkbox.IsChecked;
localSettings.Values["cl_min"] = Convert.ToInt32(Cl_RangeSelector.RangeStart);
localSettings.Values["cl_max"] = Convert.ToInt32(Cl_RangeSelector.RangeEnd);
localSettings.Values["cl_include"] = ele_Cl_checkbox.IsChecked;
localSettings.Values["br_min"] = Convert.ToInt32(Br_RangeSelector.RangeStart);
localSettings.Values["br_max"] = Convert.ToInt32(Br_RangeSelector.RangeEnd);
localSettings.Values["br_include"] = ele_Br_checkbox.IsChecked;
localSettings.Values["i_min"] = Convert.ToInt32(I_RangeSelector.RangeStart);
localSettings.Values["i_max"] = Convert.ToInt32(I_RangeSelector.RangeEnd);
localSettings.Values["i_include"] = ele_I_checkbox.IsChecked;
localSettings.Values["si_min"] = Convert.ToInt32(Si_RangeSelector.RangeStart);
localSettings.Values["si_max"] = Convert.ToInt32(Si_RangeSelector.RangeEnd);
localSettings.Values["si_include"] = ele_Si_checkbox.IsChecked;
localSettings.Values["b_min"] = Convert.ToInt32(B_RangeSelector.RangeStart);
localSettings.Values["b_max"] = Convert.ToInt32(B_RangeSelector.RangeEnd);
localSettings.Values["b_include"] = ele_B_checkbox.IsChecked;
localSettings.Values["se_min"] = Convert.ToInt32(Se_RangeSelector.RangeStart);
localSettings.Values["se_max"] = Convert.ToInt32(Se_RangeSelector.RangeEnd);
localSettings.Values["se_include"] = ele_Se_checkbox.IsChecked;
//formula database
localSettings.Values["NoResDB_include"] = noResDB_checkbox.IsChecked;
localSettings.Values["PubChem_include"] = pubchem_checkbox.IsChecked;
localSettings.Values["mtb_lpd_include"] = mtb_lpd_checkbox.IsChecked;
localSettings.Values["BMDB_include"] = BMDB_checkbox.IsChecked;
localSettings.Values["ChEBI_include"] = ChEBI_checkbox.IsChecked;
localSettings.Values["ECMDB_include"] = ECMDB_checkbox.IsChecked;
localSettings.Values["FooDB_include"] = FooDB_checkbox.IsChecked;
localSettings.Values["HMDB_include"] = HMDB_checkbox.IsChecked;
localSettings.Values["KEGG_include"] = KEGG_checkbox.IsChecked;
localSettings.Values["LMSD_include"] = LMSD_checkbox.IsChecked;
localSettings.Values["MarkerDB_include"] = MarkerDB_checkbox.IsChecked;
localSettings.Values["MCDB_include"] = MCDB_checkbox.IsChecked;
localSettings.Values["PlantCyc_include"] = PlantCyc_checkbox.IsChecked;
localSettings.Values["SMPDB_include"] = SMPDB_checkbox.IsChecked;
localSettings.Values["YMDB_include"] = YMDB_checkbox.IsChecked;
localSettings.Values["drug_txn_include"] = drug_txn_checkbox.IsChecked;
localSettings.Values["DrugBank_include"] = DrugBank_checkbox.IsChecked;
localSettings.Values["DSSTOX_include"] = DSSTOX_checkbox.IsChecked;
localSettings.Values["HSDB_include"] = HSDB_checkbox.IsChecked;
localSettings.Values["T3DB_include"] = T3DB_checkbox.IsChecked;
localSettings.Values["TTD_include"] = TTD_checkbox.IsChecked;
localSettings.Values["natProducts_include"] = natProducts_checkbox.IsChecked;
localSettings.Values["ANPDB_include"] = ANPDB_checkbox.IsChecked;
localSettings.Values["COCONUT_include"] = COCONUT_checkbox.IsChecked;
localSettings.Values["NPASS_include"] = NPASS_checkbox.IsChecked;
localSettings.Values["UNPD_include"] = UNPD_checkbox.IsChecked;
localSettings.Values["xbiotics_include"] = xbiotics_checkbox.IsChecked;
localSettings.Values["BLEXP_include"] = BLEXP_checkbox.IsChecked;
localSettings.Values["NORMAN_include"] = NORMAN_checkbox.IsChecked;
localSettings.Values["STF_IDENT_include"] = STF_IDENT_checkbox.IsChecked;
localSettings.Values["contaminants_include"] = contaminants_checkbox.IsChecked;
localSettings.Values["MaConDa_include"] = MaConDa_checkbox.IsChecked;
if(noResDB_checkbox.IsChecked == false && pubchem_checkbox.IsChecked == false && BMDB_checkbox.IsChecked == false && ChEBI_checkbox.IsChecked == false &&
ECMDB_checkbox.IsChecked == false && FooDB_checkbox.IsChecked == false && HMDB_checkbox.IsChecked == false && KEGG_checkbox.IsChecked == false && LMSD_checkbox.IsChecked == false &&
MarkerDB_checkbox.IsChecked == false && MCDB_checkbox.IsChecked == false && PlantCyc_checkbox.IsChecked == false && SMPDB_checkbox.IsChecked == false && YMDB_checkbox.IsChecked == false &&
DrugBank_checkbox.IsChecked == false && DSSTOX_checkbox.IsChecked == false && HSDB_checkbox.IsChecked == false && T3DB_checkbox.IsChecked == false &&
TTD_checkbox.IsChecked == false && ANPDB_checkbox.IsChecked == false && COCONUT_checkbox.IsChecked == false && NPASS_checkbox.IsChecked == false &&
UNPD_checkbox.IsChecked == false && BLEXP_checkbox.IsChecked == false && NORMAN_checkbox.IsChecked == false && STF_IDENT_checkbox.IsChecked == false &&
MaConDa_checkbox.IsChecked == false)
{
throwInvalidInputError = true;
}
//adduct list
//serialize
using (Stream stream = File.Open(storageFolder.Path + @"\adductList_Pos.bin", FileMode.Create))
{