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Simplified UI for ad hoc spectrum extraction.
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Moved average spectrum from 5 decimal places to 6.
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@cjbaker
cjbaker committed Oct 28, 2011
1 parent 73a172d commit 61bf4e1
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Showing 11 changed files with 33 additions and 42 deletions.
8 changes: 4 additions & 4 deletions source/DataProviders/Test/ProteoWizard/AveragedSpectrumExtractorTest.cs
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Expand Up @@ -46,7 +46,7 @@ public void GetAveragedSpectrum()
timer.Stop();

XYDataHelper.AssertSpectrum(spectrum, 1.50005, 1.60005, 40383, timer, MinimumMillisecondsItShouldTakeToExtractSpectrum, MaximumMillisecondsItShouldTakeToExtractSpectrum);
XYDataHelper.AssertValue(spectrum, 300, 308.08392, 2);
XYDataHelper.AssertValue(spectrum, 300, 308.083923, 2);
}

[TestMethod]
Expand All @@ -60,7 +60,7 @@ public void GetAveragedSpectrumFromCache()
timer.Stop();

XYDataHelper.AssertSpectrum(spectrum, 1.50005, 1.60005, 40383, timer, MinimumMillisecondsItShouldTakeToPullSpectrumFromCache, MaximumMillisecondsItShouldTakeToPullSpectrumFromCache);
XYDataHelper.AssertValue(spectrum, 300, 308.08392, 2);
XYDataHelper.AssertValue(spectrum, 300, 308.083923, 2);
}

[TestMethod]
Expand All @@ -71,7 +71,7 @@ public void GetAveragedSpectrumForSpecificMassRange()
timer.Stop();

XYDataHelper.AssertSpectrum(spectrum, 1.50005, 1.60005, 24526, timer, MinimumMillisecondsItShouldTakeToExtractSpectrum, MaximumMillisecondsItShouldTakeToExtractSpectrum);
XYDataHelper.AssertValue(spectrum, 300, 308.08392, 2);
XYDataHelper.AssertValue(spectrum, 300, 308.083923, 2);
}

[TestMethod]
Expand All @@ -84,7 +84,7 @@ public void GetAveragedSpectrumForSpecificMassRangeFromCache()
timer.Stop();

XYDataHelper.AssertSpectrum(spectrum, 1.50005, 1.60005, 24526, timer, MinimumMillisecondsItShouldTakeToPullSpectrumFromCache, MaximumMillisecondsItShouldTakeToPullSpectrumFromCache);
XYDataHelper.AssertValue(spectrum, 300, 308.08392, 2);
XYDataHelper.AssertValue(spectrum, 300, 308.083923, 2);
}

[TestMethod]
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18 changes: 9 additions & 9 deletions source/Hydra/Core/Hydra.Core.csproj
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Expand Up @@ -105,17 +105,17 @@
</ProjectReference>
</ItemGroup>
<ItemGroup>
<Resource Include="Images\results.png" />
<Resource Include="Images\peptide.png" />
<Resource Include="Images\run.png" />
<Resource Include="Images\experiment.png" />
<Resource Include="Images\proteinState.png" />
<Resource Include="Images\network.png" />
<Resource Include="Images\labeling.png" />
<Resource Include="Images\project.png" />
<Resource Include="Events\Images\results.png" />
<Resource Include="Events\Images\peptide.png" />
<Resource Include="Events\Images\run.png" />
<Resource Include="Events\Images\experiment.png" />
<Resource Include="Events\Images\proteinState.png" />
<Resource Include="Events\Images\network.png" />
<Resource Include="Events\Images\labeling.png" />
<Resource Include="Events\Images\project.png" />
</ItemGroup>
<ItemGroup>
<Resource Include="Images\result.png" />
<Resource Include="Events\Images\result.png" />
</ItemGroup>
<Import Project="$(MSBuildToolsPath)\Microsoft.CSharp.targets" />
<Import Project="..\..\..\tools\Microsoft StyleCop 4.4.0.14\Microsoft.StyleCop.targets" />
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2 changes: 1 addition & 1 deletion source/Hydra/Run/Views/RunView.xaml
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Expand Up @@ -27,7 +27,7 @@
<ListView Name="listView">
<ListView.View>
<GridView>
<GridViewColumn Header="RT" DisplayMemberBinding="{Binding XValue, StringFormat=F3}"></GridViewColumn>
<GridViewColumn Header="RT" DisplayMemberBinding="{Binding XValue, StringFormat=F6}"></GridViewColumn>
<GridViewColumn Header="Intensity" DisplayMemberBinding="{Binding YValue}"></GridViewColumn>
</GridView>
</ListView.View>
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14 changes: 4 additions & 10 deletions source/Hydra/Run/Views/SpectrumSelectionDialog.xaml
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Expand Up @@ -16,16 +16,10 @@
<ColumnDefinition></ColumnDefinition>
<ColumnDefinition></ColumnDefinition>
</Grid.ColumnDefinitions>
<TextBlock Text="Start Mass:" VerticalAlignment="Center"></TextBlock>
<TextBlock Text="Stop Mass:" VerticalAlignment="Center" Grid.Row="1"></TextBlock>
<TextBlock Text="Monoisotopic Mass:" VerticalAlignment="Center" Grid.Row="2"></TextBlock>
<TextBlock Text="MZ Lower Offset:" VerticalAlignment="Center" Grid.Row="3"></TextBlock>
<TextBlock Text="MZ Upper Offset:" VerticalAlignment="Center" Grid.Row="4"></TextBlock>
<TextBox Text="{Binding StartMass}" Grid.Column="1" VerticalAlignment="Center"></TextBox>
<TextBox Text="{Binding StopMass}" Grid.Column="1" Grid.Row="1" VerticalAlignment="Center"></TextBox>
<TextBox Text="{Binding MonoisotopticMass}" Grid.Column="1" Grid.Row="2" VerticalAlignment="Center"></TextBox>
<TextBox Text="{Binding MZLowerOffset}" Grid.Column="1" Grid.Row="3" VerticalAlignment="Center"></TextBox>
<TextBox Text="{Binding MZUpperOffset}" Grid.Column="1" Grid.Row="4" VerticalAlignment="Center"></TextBox>
<TextBlock Text="Start RT:" VerticalAlignment="Center"></TextBlock>
<TextBlock Text="Stop RT:" VerticalAlignment="Center" Grid.Row="1"></TextBlock>
<TextBox Text="{Binding StartTime}" Grid.Column="1" VerticalAlignment="Center"></TextBox>
<TextBox Text="{Binding StopTime}" Grid.Column="1" Grid.Row="1" VerticalAlignment="Center"></TextBox>

<Button Content="Retrieve" Grid.Row="5" VerticalAlignment="Center" Width="80" Click="OnRetrieve"></Button>
<Button Content="Cancel" Grid.Row="5" Grid.Column="1" VerticalAlignment="Center" Width="80" Click="OnCancel"></Button>
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2 changes: 1 addition & 1 deletion source/Hydra/Run/Views/SpectrumSelectionDialog.xaml.cs
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Expand Up @@ -28,7 +28,7 @@ public SpectrumSelectionDialog(IEventAggregator eventAggregator, IRegionManager

private void OnRetrieve(object sender, RoutedEventArgs e)
{
RunViewModel viewModel = new RunViewModel(_run, _viewModel.StartMass, _viewModel.StopMass, _viewModel.MonoisotopicMass, _viewModel.MZLowerOffset, _viewModel.MZUpperOffset);
RunViewModel viewModel = new RunViewModel(_run, _viewModel.StartTime, _viewModel.StopTime, 0, 0, 1000000);
ManagedContent view = _regionManager.FindExistingView("DocumentRegion", typeof(RunView), viewModel.XYData.Title);
if (view == null)
{
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4 changes: 2 additions & 2 deletions source/Hydra/Run/Views/SpectrumSelectionDialogViewModel.cs
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Expand Up @@ -10,9 +10,9 @@ public SpectrumSelectionDialogViewModel()
MZUpperOffset = 5;
}

public double StartMass { get; set; }
public double StartTime { get; set; }

public double StopMass { get; set; }
public double StopTime { get; set; }

public double MonoisotopicMass { get; set; }

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2 changes: 1 addition & 1 deletion source/Hydra/Test/Hydra.Test.csproj
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Expand Up @@ -107,7 +107,7 @@
<Compile Include="Core\Domain\RunTest.cs" />
<Compile Include="DataProvider\CsvPeptideDataProviderTest.cs" />
<Compile Include="IntegrationTests\AlgorithmTestBase.cs" />
<Compile Include="IntegrationTests\MsMsFragmentAlgorithmTest.cs" />
<Compile Include="Modules\MsMsFragmentAlgorithmTest.cs" />
<Compile Include="Modules\Peptides\Views\IonViewModelTest.cs" />
<Compile Include="Modules\Peptides\Views\PeptidesViewModelTest.cs" />
<Compile Include="Modules\Peptides\Views\PeptideViewModelTest.cs" />
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8 changes: 4 additions & 4 deletions source/Hydra/Test/Modules/Runs/Views/SpectrumSelectionDialogViewModelTest.cs
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Expand Up @@ -27,14 +27,14 @@ public void Properties()
viewModel.MonoisotopicMass = 1;
viewModel.MZLowerOffset = 2;
viewModel.MZUpperOffset = 3;
viewModel.StartMass = 4;
viewModel.StopMass = 5;
viewModel.StartTime = 4;
viewModel.StopTime = 5;

Assert.AreEqual(1, viewModel.MonoisotopicMass);
Assert.AreEqual(2, viewModel.MZLowerOffset);
Assert.AreEqual(3, viewModel.MZUpperOffset);
Assert.AreEqual(4, viewModel.StartMass);
Assert.AreEqual(5, viewModel.StopMass);
Assert.AreEqual(4, viewModel.StartTime);
Assert.AreEqual(5, viewModel.StopTime);
}
}
}
9 changes: 3 additions & 6 deletions source/MassSpecStudio/Core/DataProvider/SpectrumHelper.cs
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Expand Up @@ -65,7 +65,7 @@ private static List<XYPoint> SumIntensities(List<Domain.ISpectrum> spectraToBeAv

private static void ApplyThreshold(XYPoint point)
{
point.XValue = Math.Truncate(point.XValue * 100000) / 100000;
point.XValue = Math.Truncate(point.XValue * 1000000) / 1000000;
}

private static bool IsOnlyOneSpectrumToBeAveraged(List<Domain.ISpectrum> spectraToBeAveraged)
Expand All @@ -82,15 +82,12 @@ private static void SortSumedXYData(List<XYPoint> sumedXYData)
});
}

private static List<XYPoint> CalculateAverageIntensities(List<XYPoint> sumedXYData)
private static List<XYPoint> CalculateAverageIntensities(List<XYPoint> sumedXYData, int numberOfSpectra)
{
List<XYPoint> averagedXYData = sumedXYData;
for (int i = 0; i < sumedXYData.Count; i++)
{
if (sumedXYData[i].NumberOfDuplicates > 0)
{
averagedXYData[i].YValue = sumedXYData[i].YValue / ((double)sumedXYData[i].NumberOfDuplicates);
}
averagedXYData[i].YValue = sumedXYData[i].YValue / (double)numberOfSpectra;
}
return averagedXYData;
}
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4 changes: 2 additions & 2 deletions source/MassSpecStudio/Processing/Steps/Views/SpectrumSelectionView.xaml
View file
Expand Up @@ -15,8 +15,8 @@
<ListView Name="listView">
<ListView.View>
<GridView>
<GridViewColumn Header="M/Z" DisplayMemberBinding="{Binding XValue, StringFormat=F5}"></GridViewColumn>
<GridViewColumn Header="Intensity" DisplayMemberBinding="{Binding YValue, StringFormat=F5}"></GridViewColumn>
<GridViewColumn Header="M/Z" DisplayMemberBinding="{Binding XValue, StringFormat=F6}"></GridViewColumn>
<GridViewColumn Header="Intensity" DisplayMemberBinding="{Binding YValue, StringFormat=F6}"></GridViewColumn>
<GridViewColumn Header="N" DisplayMemberBinding="{Binding NumberOfDuplicates}"></GridViewColumn>
</GridView>
</ListView.View>
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4 changes: 2 additions & 2 deletions source/MassSpecStudio/Processing/Steps/Views/XicSelectionView.xaml
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Expand Up @@ -16,8 +16,8 @@
<ListView Name="listView">
<ListView.View>
<GridView>
<GridViewColumn Header="RT" DisplayMemberBinding="{Binding XValue, StringFormat=F5}"></GridViewColumn>
<GridViewColumn Header="Intensity" DisplayMemberBinding="{Binding YValue, StringFormat=F5}"></GridViewColumn>
<GridViewColumn Header="RT" DisplayMemberBinding="{Binding XValue, StringFormat=F6}"></GridViewColumn>
<GridViewColumn Header="Intensity" DisplayMemberBinding="{Binding YValue, StringFormat=F6}"></GridViewColumn>
</GridView>
</ListView.View>
</ListView>
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