Added custom protease window in GUI #2352
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,84 @@ | ||
| <Window x:Class="MetaMorpheusGUI.Views.CustomProteaseWindow" | ||
| xmlns="http://schemas.microsoft.com/winfx/2006/xaml/presentation" | ||
| xmlns:x="http://schemas.microsoft.com/winfx/2006/xaml" | ||
| xmlns:d="http://schemas.microsoft.com/expression/blend/2008" | ||
| xmlns:mc="http://schemas.openxmlformats.org/markup-compatibility/2006" | ||
| xmlns:local="clr-namespace:MetaMorpheusGUI.Views" | ||
| mc:Ignorable="d" | ||
| Title="CustomProteaseWindow" Height="330" Width="380" ResizeMode="NoResize" WindowStartupLocation="CenterScreen"> | ||
| <Grid> | ||
| <StackPanel Orientation="Vertical" VerticalAlignment="Top" HorizontalAlignment="Center" Margin="0,5,0,0" Height="300"> | ||
| <!--protease name--> | ||
| <StackPanel Orientation="Horizontal" Height="40"> | ||
| <Label Content="Name" Width="135" Margin=" 10,5,5,5" FontSize="13"></Label> | ||
| <Label Content="*" Foreground="Red" FontWeight="Bold" /> | ||
| <TextBox x:Name="ProteaseNameTextBox" Width="155" Height="25"> | ||
| </TextBox> | ||
| </StackPanel> | ||
| <!--Cleavage specificity--> | ||
| <StackPanel Orientation="Horizontal" Height="40"> | ||
| <Label Content="Cleavage Specificity" Width="135" Margin=" 10,5,5,5" Height="33" FontSize="13"></Label> | ||
| <Label Content="*" Foreground="Red" FontWeight="Bold" /> | ||
| <ComboBox Name ="CleavageSpecComboBox" SelectionChanged ="CleavageSpecComboBox_SelectionChanged" Width="155" Height="25"> | ||
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| </ComboBox> | ||
| </StackPanel> | ||
| <!--Psi-MS Acession Number--> | ||
| <StackPanel Orientation="Horizontal" Height="40"> | ||
| <Label Content="Psi-MS Number" Width="145" Margin=" 10,5,10,10" Height="28" FontSize="13"></Label> | ||
| <TextBox Name="PsiMsAccessionNumTextBox" Width="155" Height="25"> | ||
| </TextBox> | ||
| </StackPanel> | ||
| <!--Psi-MS Name--> | ||
| <StackPanel Orientation="Horizontal" Height="40"> | ||
| <Label Content="Psi-MS Name" Width="145" Margin=" 10,5,10,10" FontSize="13"></Label> | ||
| <TextBox Name="PsiNameTextBox" Width="155" Height="25"> | ||
| </TextBox> | ||
| </StackPanel> | ||
| <!--Digestion motif--> | ||
| <StackPanel Orientation="Horizontal" Height="40"> | ||
| <Label Content="Digestion Motif" Width="135" Margin=" 10,5,5,5" Height="31" FontSize="13"></Label> | ||
| <Label Content="*" Foreground="Red" FontWeight="Bold" /> | ||
| <TextBox Name="DigestionMotifTextBox" Width="155" Height="25"> | ||
| <ToolTipService.ToolTip> | ||
| <ToolTip Content="Amino acid sequences or motifs recognized and cleaved by the protease"/> | ||
| </ToolTipService.ToolTip> | ||
| <TextBox.Style> | ||
| <Style TargetType="TextBox" xmlns:sys="clr-namespace:System;assembly=mscorlib"> | ||
| <Style.Resources> | ||
| <VisualBrush x:Key="CueBannerBrush" AlignmentX="Left" AlignmentY="Center" Stretch="None"> | ||
| <VisualBrush.Visual> | ||
| <Label Content="ex: 'A|', '|R', 'F[P]|'" Foreground="Gray" /> | ||
| </VisualBrush.Visual> | ||
| </VisualBrush> | ||
| </Style.Resources> | ||
| <Style.Triggers> | ||
| <Trigger Property="Text" Value="{x:Static sys:String.Empty}"> | ||
| <Setter Property="Background" Value="{StaticResource CueBannerBrush}" /> | ||
| </Trigger> | ||
| <Trigger Property="Text" Value="{x:Null}"> | ||
| <Setter Property="Background" Value="{StaticResource CueBannerBrush}" /> | ||
| </Trigger> | ||
| <Trigger Property="IsKeyboardFocused" Value="True"> | ||
| <Setter Property="Background" Value="White" /> | ||
| </Trigger> | ||
| </Style.Triggers> | ||
| </Style> | ||
| </TextBox.Style> | ||
| </TextBox> | ||
| </StackPanel> | ||
| <!--Cleavage Mod--> | ||
| <StackPanel Orientation="Horizontal" Height="40"> | ||
| <Label Content="Cleavage Mod" Width="145" Margin=" 10,5,10,10" Height="36" FontSize="13"></Label> | ||
| <TextBox Name="CleavageModTextBox" Width="155" Height="25"> | ||
| </TextBox> | ||
| </StackPanel> | ||
| <!--Save and cancel buttons--> | ||
| <StackPanel Orientation="Horizontal" Height="40" HorizontalAlignment="Center" Margin="8"> | ||
| <Button Name="SaveProtease" Content="Save protease" FontSize="13" Margin="5" Width="100" Click="SaveProteaseButton_Click" /> | ||
| <Button Name="CancelProtease" Content="Cancel" FontSize="13" Margin="5" Width="100" Click="CancelProteaseButton_Click" /> | ||
| </StackPanel> | ||
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| </StackPanel> | ||
| </Grid> | ||
| </Window> |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,127 @@ | ||
| using Proteomics.ProteolyticDigestion; | ||
| using System; | ||
| using System.Collections; | ||
| using System.Collections.Generic; | ||
| using System.Linq; | ||
| using System.Text; | ||
| using System.Threading.Tasks; | ||
| using System.Windows; | ||
| using System.Windows.Controls; | ||
| using System.Windows.Data; | ||
| using System.Windows.Documents; | ||
| using System.Windows.Input; | ||
| using System.Windows.Media; | ||
| using System.Windows.Media.Imaging; | ||
| using System.IO; | ||
| using EngineLayer; | ||
| using System.Xml; | ||
| using Easy.Common.Extensions; | ||
| using System.Linq; | ||
| using MassSpectrometry; | ||
| using Omics.Digestion; | ||
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| namespace MetaMorpheusGUI.Views | ||
| { | ||
| /// <summary> | ||
| /// Interaction logic for CustomProteaseWindow.xaml | ||
| /// </summary> | ||
| public partial class CustomProteaseWindow : Window | ||
| { | ||
| public CustomProteaseWindow() | ||
| { | ||
| InitializeComponent(); | ||
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| foreach (CleavageSpecificity c in Enum.GetValues(typeof(CleavageSpecificity))) | ||
| { | ||
| CleavageSpecComboBox.Items.Add(c); | ||
| } | ||
| } | ||
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| private void SaveProteaseButton_Click(object sender, RoutedEventArgs e) | ||
| { | ||
| if (ProteaseNameTextBox.Text.Length == 0) | ||
| { | ||
| MessageBox.Show("Please specify the name of the protease"); | ||
| return; | ||
| } | ||
| if (CleavageSpecComboBox.Text.Length == 0) | ||
| { | ||
| MessageBox.Show("Please specify the cleavage specificity of the protease"); | ||
| return; | ||
| } | ||
| if (DigestionMotifTextBox.Text.Length == 0) | ||
| { | ||
| MessageBox.Show("Please specify the digestion motif(s) of the protease"); | ||
|
There was a problem hiding this comment. Should we check to see if the digestion motiff is a valid amino acid? |
||
| return; | ||
| } | ||
| string proteaseName = ProteaseNameTextBox.Text; | ||
| string psiMsAccessionNum = PsiMsAccessionNumTextBox.Text; | ||
| string psiMsName = PsiNameTextBox.Text; | ||
| string motifString = DigestionMotifTextBox.Text; | ||
| Dictionary<string, CleavageSpecificity> CleavageSpecDic = new Dictionary<string, CleavageSpecificity>(); | ||
| foreach (CleavageSpecificity c in Enum.GetValues(typeof(CleavageSpecificity))) { | ||
| CleavageSpecDic.Add(c.ToString(), c); | ||
| } | ||
| CleavageSpecificity cleavageSpecificity = CleavageSpecDic[CleavageSpecComboBox.Text]; | ||
| List<DigestionMotif> digestionMotifs; | ||
|
There was a problem hiding this comment. Replace this dictionary creation with |
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| try | ||
| { | ||
| digestionMotifs = DigestionMotif.ParseDigestionMotifsFromString(motifString); | ||
| } | ||
| catch | ||
| { | ||
| MessageBox.Show("The motif(s) could not be parsed."); | ||
| return; | ||
| } | ||
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| //load the default ProteaseDictionary | ||
| //string folderPath = Environment.GetFolderPath(Environment.SpecialFolder.ProgramFiles); | ||
| //string path = ((!string.IsNullOrWhiteSpace(folderPath) && AppDomain.CurrentDomain.BaseDirectory.Contains(folderPath) && !AppDomain.CurrentDomain.BaseDirectory.Contains("Jenkins")) ? System.IO.Path.Combine(Environment.GetFolderPath(Environment.SpecialFolder.LocalApplicationData), "MetaMorpheus") : AppDomain.CurrentDomain.BaseDirectory); | ||
| //string path2 = System.IO.Path.Combine(path, "ProteolyticDigestion", "proteases.tsv"); | ||
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| //ProteaseDictionary.LoadProteaseDictionary(path2); | ||
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| //create a new Protease and add to ProteaseDictionary | ||
| Protease proteaseToAdd = new Protease(proteaseName, cleavageSpecificity, psiMsAccessionNum, psiMsName, digestionMotifs); | ||
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| if (ProteaseDictionary.Dictionary.ContainsKey(proteaseName)) | ||
| { | ||
| MessageBox.Show("This protease already exists"); | ||
| } | ||
| else | ||
| { | ||
| ProteaseDictionary.Dictionary.Add(proteaseName, proteaseToAdd); | ||
| } | ||
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| if (!ProteaseDictionary.Dictionary.TryAdd(proteaseName, proteaseToAdd)) | ||
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| { | ||
| MessageBox.Show("Success! Protease '" + proteaseName + "' has been added to the dictionary."); | ||
| } | ||
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| //customProtease file path | ||
| string ProtDirectory = Path.Combine(GlobalVariables.DataDir, @"ProteolyticDigestion"); | ||
| string customProteasePath = Path.Combine(ProtDirectory, @"CustomProtease.tsv"); | ||
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| //check if the customProtease file exists, create it if not | ||
| if (!File.Exists(customProteasePath)) | ||
| { | ||
| File.Create(customProteasePath); | ||
| } | ||
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| string lineToAdd = "\n" + proteaseName + "\t" + motifString + "\t\t\t" + CleavageSpecComboBox.Text + "\t" + psiMsAccessionNum + "\t" + psiMsName + "\t\t\t\t\t"; | ||
|
There was a problem hiding this comment. what pieces of information are being skipped over with all of the \t\t\t\t and is that information important here? |
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| var lines = new List<string> { lineToAdd }; | ||
| File.AppendAllLines(customProteasePath, lines); | ||
| DialogResult = true; | ||
| } | ||
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| private void CancelProteaseButton_Click(object sender, RoutedEventArgs e) | ||
| { | ||
| DialogResult = false; | ||
| } | ||
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| private void CleavageSpecComboBox_SelectionChanged(object sender, SelectionChangedEventArgs e) | ||
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| { | ||
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| } | ||
| } | ||
| } | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,35 @@ | ||
| using System; | ||
| using System.Collections.Generic; | ||
| using System.Linq; | ||
| using System.Text; | ||
| using System.Threading.Tasks; | ||
| using Proteomics.ProteolyticDigestion; | ||
| using System.IO; | ||
| using NUnit.Framework; | ||
| using EngineLayer; | ||
| using Omics.Digestion; | ||
| using MzLibUtil; | ||
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| namespace Test | ||
| { | ||
| public static class CustomProteaseTest | ||
| { | ||
| [Test] | ||
| public static void TestAddCustomProtease () | ||
| { | ||
| string ProtDirectory = Path.Combine(GlobalVariables.DataDir, @"ProteolyticDigestion"); | ||
| string customProteasePath = Path.Combine(ProtDirectory, @"CustomProtease.tsv"); | ||
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| string[] pString = new string[] { "p\tA|\t\t\tfull\tcusPsiNum\tcusPsiName\t\t\t\t\t" }; | ||
| File.WriteAllLines(customProteasePath, pString); | ||
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| GlobalVariables.LoadCustomProtease(); | ||
| var dictionary = ProteaseDictionary.Dictionary; | ||
| Assert.That(ProteaseDictionary.Dictionary.ContainsKey("p")); | ||
| Assert.That(ProteaseDictionary.Dictionary["p"].PsiMsName == "cusPsiName"); | ||
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| File.Delete(customProteasePath); | ||
| } | ||
| } | ||
| } |
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Are all of these new namespaces necessary?