Added custom protease window in GUI #2352
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… customProtease tsv to store all the customed proteases and then add to the dictionary
Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## master #2352 +/- ##
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+ Coverage 93.62% 93.64% +0.02%
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Files 140 140
Lines 21895 21923 +28
Branches 3005 3009 +4
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+ Hits 20499 20530 +31
+ Misses 937 936 -1
+ Partials 459 457 -2
|
nbollis
requested changes
Aug 15, 2024
| @@ -14,6 +15,9 @@ | |||
| using Omics.Modifications; | |||
| using TopDownProteomics; | |||
| using UsefulProteomicsDatabases; | |||
| using Omics.Digestion; | |||
| using static System.Net.Mime.MediaTypeNames; | |||
| using System.Collections; | |||
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Are all of these new namespaces necessary?
| } | ||
| if (DigestionMotifTextBox.Text.Length == 0) | ||
| { | ||
| MessageBox.Show("Please specify the digestion motif(s) of the protease"); |
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Should we check to see if the digestion motiff is a valid amino acid?
| //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"); |
| CleavageSpecDic.Add(c.ToString(), c); | ||
| } | ||
| CleavageSpecificity cleavageSpecificity = CleavageSpecDic[CleavageSpecComboBox.Text]; | ||
| List<DigestionMotif> digestionMotifs; |
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Replace this dictionary creation with
if (Enum.TryParse(CleavageSpecComboBox.Text, out _ cleaveageSpec)
{
set the value
}
else
{
message box error and return
}
| ProteaseDictionary.Dictionary.Add(proteaseName, proteaseToAdd); | ||
| } | ||
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| if (!ProteaseDictionary.Dictionary.TryAdd(proteaseName, proteaseToAdd)) |
| 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"; |
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what pieces of information are being skipped over with all of the \t\t\t\t and is that information important here?
| DialogResult = false; | ||
| } | ||
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| private void CleavageSpecComboBox_SelectionChanged(object sender, SelectionChangedEventArgs e) |
| { | ||
| string[] proteaseToAdd = File.ReadAllLines(customProteasePath); | ||
| for (int i = 0; i < proteaseToAdd.Length; i++) | ||
| { |
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Most likely need to start at i == 1 because the first row is the header
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