public List <string> Sequences(string sequence, FilterSequence filter)
{
List <string> pepList = new List <string>();
List <int> cutOffPosition = FindCutOffPosition(sequence);
//generate substring from sequences
int start, end;
for (int i = 0; i <= miss_cleavage_; i++)
{
for (int j = 0; j < cutOffPosition.Count - i - 1; j++)
{
start = cutOffPosition[j] + 1;
end = cutOffPosition[j + 1 + i];
if (end - start + 1 >= min_length_) // put minimum length in place
{
string sub = sequence.Substring(start, end - start + 1);
if (filter(sub))
{
pepList.Add(sub);
}
}
}
}
return(pepList);
}
public void IsAtEnd_Test()
{
var target = new FilterSequence <int>(
new ListSequence <int>(
new[] { 1, 2, 3 },
0
),
x => x % 2 == 0
);
target.IsAtEnd.Should().BeFalse();
target.GetNext().Should().Be(2);
target.IsAtEnd.Should().BeTrue();
}
public void GetNext_Test()
{
var target = new FilterSequence <int>(
new ListSequence <int>(
new[] { 1, 2, 3, 4, 5, 6 },
0
),
x => x % 2 == 0
);
target.GetNext().Should().Be(2);
target.GetNext().Should().Be(4);
target.GetNext().Should().Be(6);
target.GetNext().Should().Be(0);
}
public void Checkpoint_Test()
{
var target = new FilterSequence <char>(
"aBcDeFgH".ToCharacterSequence(),
x => char.IsUpper(x)
);
target.GetNext().Should().Be('B');
var cp = target.Checkpoint();
target.GetNext().Should().Be('D');
target.GetNext().Should().Be('F');
target.GetNext().Should().Be('H');
target.GetNext().Should().Be('\0');
cp.Rewind();
target.GetNext().Should().Be('D');
target.GetNext().Should().Be('F');
target.GetNext().Should().Be('H');
target.GetNext().Should().Be('\0');
}
public IEnumerable <object> Get(FilterSequence sequence)
{
switch (sequence)
{
case FilterSequence.Before:
{
return(_before);
}
case FilterSequence.After:
{
return(_after);
}
default:
{
return(_actual);
}
}
}
public static HashSet <string> DynamicModification(HashSet <string> peptides,
FilterSequence filter, bool oxidation = true, bool deamidation = true)
{
HashSet <string> peptideModifieds = new HashSet <string>();
if (oxidation)
{
peptides = Oxidation(peptides);
}
if (deamidation)
{
peptides = Deamidation(peptides);
}
foreach (string peptide in peptides)
{
if (filter(peptide))
{
peptideModifieds.Add(peptide);
}
}
return(peptideModifieds);
}
public MainViewModel()
{
ProgressBarValue = 0;
ProgressBarInfo = "";
FileManager.OnChange += FileMng_OnChange;
foreach (var filterName in GraphFilter.GetFilterNames())
{
FilterToAdd.Add(new ComboBoxItem()
{
Content = filterName
});
}
SelectAddFilter = FilterToAdd[0];
var bitmap = new Bitmap(@"Res\default.png");
SetImageSource(bitmap, "default.png");
LoadFilter = graphFilter.Add(FilterType.File, "MainFile");
FilterSequence.Add(LoadFilter);
bitmap.Dispose();
ExportButton = new SyncButtonViewModel()
{
Text = "Export",
Enabled = true,
PressCmd = async(SyncButtonViewModel button) =>
{
if (!m_exportInProgress)
{
button.Enabled = false;
ExportDlgView dlg = new ExportDlgView();
ExportDlgModel dlgModel = new ExportDlgModel(dlg, "export_settigs.xml");
dlg.DataContext = dlgModel;
var res = dlg.ShowDialog();
button.Enabled = true;
if (res == true)
{
m_exportInProgress = true;
button.Text = "Cancel";
ExportSettings exportSettings = dlgModel.Result;
await Task.Run(() =>
{
int totalCnt = FileManager.FileListInfo.Count;
for (int infoId = 0; m_exportInProgress && (infoId < totalCnt); infoId++)
{
string infoStr = FileManager.FileListInfo[infoId].Info;
App.Current.Dispatcher.Invoke(() =>
{
ProgressBarValue = (100 * infoId) / totalCnt;
ProgressBarInfo = infoStr;
});
ExportGraphFilterResult(infoId, infoStr, exportSettings);
}
});
ProgressBarValue = 0;
m_exportInProgress = false;
button.Text = "Export";
}
}
else
{
m_exportInProgress = false;
ProgressBarValue = 0;
}
}
};
}
