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Cystag #574

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c88258f
Functioning for perfect mock data
jgpavek Oct 22, 2020
a2874e4
Cysteine Count Tolerance Added
jgpavek Jun 25, 2021
52d3c9a
Merge branch 'Cystag' of https://github.com/jgpavek/ProteoformSuite i…
jgpavek Jun 25, 2021
a15cf0f
05092022
jgpavek May 9, 2022
df3c605
16052022
jgpavek May 16, 2022
d633eec
Cystag_05232022
jgpavek May 23, 2022
859f23c
CysTag_06162023
jgpavek Jun 16, 2023
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9 changes: 5 additions & 4 deletions ProteoWPFSuite/AggregatedProteoforms.xaml.cs
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -189,7 +189,7 @@ private void display_light_proteoforms()
selected_pf.lt_quant_components.ToList<IAggregatable>() :
selected_pf.hv_quant_components.ToList<IAggregatable>()));

if (Sweet.lollipop.neucode_labeled && (bool)ra)
if ((Sweet.lollipop.neucode_labeled || Sweet.lollipop.cystag_labeled) && (bool)ra)
{
DisplayUtility.FillDataGridView(dgv_AcceptNeuCdLtProteoforms, components.Select(c => new DisplayNeuCodePair(c as NeuCodePair)));
}
Expand All @@ -202,7 +202,7 @@ private void display_light_proteoforms()
DisplayUtility.FillDataGridView(dgv_AcceptNeuCdLtProteoforms, components.Select(c => new DisplayComponent(c as ProteoformSuiteInternal.Component)));
}

if (Sweet.lollipop.neucode_labeled && (bool)ra)
if ((Sweet.lollipop.neucode_labeled || Sweet.lollipop.cystag_labeled) && (bool)ra)
{
DisplayNeuCodePair.FormatNeuCodeTable(dgv_AcceptNeuCdLtProteoforms);
}
Expand Down Expand Up @@ -238,6 +238,7 @@ private void nUD_Missed_Monos_ValueChanged(object sender, EventArgs e)
private void nUD_Missed_Ks_ValueChanged(object sender, EventArgs e)
{
Sweet.lollipop.maximum_missed_lysines = Convert.ToInt32(nUD_Missed_Ks.Value);
Sweet.lollipop.maximum_missed_cysteines = Convert.ToInt32(nUD_Missed_Ks.Value);

@trishorts trishorts May 23, 2022

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missed ks?

}

private void bt_aggregate_Click(object sender, RoutedEventArgs e)
Expand Down Expand Up @@ -272,7 +273,7 @@ private void set_nud_minObs_maximum()
{
List<string> conditions = Sweet.lollipop.get_files(Sweet.lollipop.input_files, Purpose.Identification).Select(f => f.lt_condition).Distinct().ToList();

if (Sweet.lollipop.neucode_labeled)
if (Sweet.lollipop.neucode_labeled || Sweet.lollipop.cystag_labeled)
{
conditions.AddRange(Sweet.lollipop.get_files(Sweet.lollipop.input_files, Purpose.Identification).Select(f => f.hv_condition).Distinct());
}
Expand Down Expand Up @@ -304,7 +305,7 @@ private void nud_minObservations_ValueChanged(object sender, EventArgs e)
#region Public Methods
public bool ReadyToRunTheGamut()
{
return Sweet.lollipop.topdown_proteoforms.Count > 0 || (Sweet.lollipop.neucode_labeled && Sweet.lollipop.raw_neucode_pairs.Count > 0 || Sweet.lollipop.raw_experimental_components.Count > 0);
return Sweet.lollipop.topdown_proteoforms.Count > 0 || (Sweet.lollipop.neucode_labeled && Sweet.lollipop.raw_neucode_pairs.Count > 0 || Sweet.lollipop.cystag_labeled && Sweet.lollipop.raw_neucode_pairs.Count > 0 || Sweet.lollipop.raw_experimental_components.Count > 0);
}

public void RunTheGamut(bool full_run)
Expand Down
6 changes: 6 additions & 0 deletions ProteoWPFSuite/DisplayHelper/DisplayExperimentalProteoform.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -57,6 +57,10 @@ public double lysine_count
{
get { return e.lysine_count; }
}
public double cysteine_count
{
get { return e.cysteine_count; }
}

public bool mass_shifted
{
Expand Down Expand Up @@ -346,6 +350,7 @@ private static string header(string property_name)
if (property_name == nameof(agg_rt)) return "Aggregated RT";
if (property_name == nameof(observation_count)) return "Aggregated Component Count for Identification";
if (property_name == nameof(lysine_count)) return "Lysine Count";
if (property_name == nameof(cysteine_count)) return "Cysteine Count";
if (property_name == nameof(mass_shifted)) return "Manually Shifted Mass";
if (property_name == nameof(ptm_description)) return "PTM Description";
if (property_name == nameof(gene_name)) return "Gene Name";
Expand All @@ -368,6 +373,7 @@ private static string header(string property_name)
private static bool visible(string property_name, bool current)
{
if (property_name == nameof(lysine_count)) { return Sweet.lollipop.neucode_labeled; }
if(property_name == nameof(cysteine_count)) { return Sweet.lollipop.cystag_labeled; }
else return current;
}

Expand Down
9 changes: 8 additions & 1 deletion ProteoWPFSuite/DisplayHelper/DisplayNeuCodePair.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -39,7 +39,7 @@ public string id_heavy

public string overlapping_charge_states
{
get { return string.Join(",", c.charge_states.Select(x => x.charge_count.ToString())); }
get { return string.Join(",", c.overlappingChargeStates).ToString(); }
}

public double intensity_ratio
Expand All @@ -56,6 +56,10 @@ public int lysine_count
{
get { return c.lysine_count; }
}
public int cysteine_count
{
get { return c.cysteine_count; }
}

public double mass
{
Expand Down Expand Up @@ -148,6 +152,7 @@ private static string header(string property_name)
if (property_name == nameof(intensity_ratio)) { return "Intensity Ratio"; }
if (property_name == nameof(intensity_sum)) { return "Intensity Sum Overlapping Charge States"; }
if (property_name == nameof(lysine_count)) { return "Lysine Count"; }
if (property_name == nameof(cysteine_count)) { return "Cysteine Count"; }
if (property_name == nameof(input_file_filename)) { return "Input Filename"; }
if (property_name == nameof(input_file_purpose)) { return "Input File Purpose"; }
if (property_name == nameof(input_file_uniqueId)) { return "Input File Unique ID"; }
Expand All @@ -162,6 +167,8 @@ private static string header(string property_name)

private static bool visible(string property_name, bool current)
{
if(property_name == nameof(lysine_count)) { return Sweet.lollipop.neucode_labeled; }
if(property_name == nameof(cysteine_count)) { return Sweet.lollipop.cystag_labeled; }
return current;
}

Expand Down
11 changes: 11 additions & 0 deletions ProteoWPFSuite/DisplayHelper/DisplayProteoformRelation.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -76,6 +76,15 @@ public int LysineCount
}
}

public int CysteineCount
{
get
{
return ((ProteoformRelation)display_object).cysteine_count;
}
}


public int NearbyRelationCount
{
get
Expand Down Expand Up @@ -298,6 +307,7 @@ private static string header(string property_name, bool mask_experimental, bool
if (property_name == nameof(PeakCenterDeltaMass)) { return "Peak Center Delta Mass"; }
if (!raw_et_histogram && property_name == nameof(PeakCenterCount)) { return "Peak Center Count"; }
if (property_name == nameof(LysineCount)) { return "Lysine Count"; }
if(property_name == nameof(CysteineCount)) { return "Cysteine Count"; }
if (!raw_et_histogram && property_name == nameof(OutsideNoMansLand)) { return "Outside No Man's Land"; }

//ET formatting
Expand Down Expand Up @@ -374,6 +384,7 @@ private static bool visible(string property_name, bool current, bool mask_experi
if (property_name == nameof(TheoreticalDescription)) { return false; }
}
if (property_name == nameof(LysineCount)) return Sweet.lollipop.neucode_labeled;
if (property_name == nameof(CysteineCount)) return Sweet.lollipop.cystag_labeled;
return current;
}

Expand Down
4 changes: 2 additions & 2 deletions ProteoWPFSuite/ExperimentTheoreticalComparison.xaml.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -416,12 +416,12 @@ private void shift_masses()
foreach (DeltaMassPeak peak in peaks_to_shift)
{
int int_mass_shifter = Convert.ToInt32(peak.mass_shifter);
peak.shift_experimental_masses(int_mass_shifter, Sweet.lollipop.neucode_labeled);
peak.shift_experimental_masses(int_mass_shifter, Sweet.lollipop.neucode_labeled, Sweet.lollipop.cystag_labeled);
Sweet.shift_peak_action(peak);
}

((ProteoformSweet)this.MDIParent).rawExperimentalComponents.FillTablesAndCharts();
if (Sweet.lollipop.neucode_labeled)
if (Sweet.lollipop.neucode_labeled || Sweet.lollipop.cystag_labeled)
{
Sweet.lollipop.raw_neucode_pairs.Clear();
Sweet.lollipop.process_neucode_components(Sweet.lollipop.raw_neucode_pairs);
Expand Down
15 changes: 13 additions & 2 deletions ProteoWPFSuite/LoadResults.xaml
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Original file line number Diff line number Diff line change
Expand Up @@ -55,7 +55,7 @@
</GroupBox>

<!-- 2. Set Parameters -->
<GroupBox x:Name="box_parameters" Grid.Row="0" Grid.Column="1" HorizontalAlignment="Stretch" VerticalAlignment="Top" Height="150" FontSize="12" Padding="5 5 5 0">
<GroupBox x:Name="box_parameters" Grid.Row="0" Grid.Column="1" VerticalAlignment="Top" Height="157" FontSize="12" Padding="5 5 5 0" Grid.RowSpan="2">
<GroupBox.Header>
<TextBlock FontWeight="Bold">2. Set Parameters</TextBlock>
</GroupBox.Header>
Expand Down Expand Up @@ -84,9 +84,15 @@
Content="NeuCode Lysine" />
<RadioButton
x:Name="rb_unlabeled"
IsChecked="True"
IsChecked = "True"
HorizontalAlignment="Left"
Content="Unlabeled" />
<RadioButton
x:Name="rb_cystag"
IsChecked="{Binding Path=CK_rbcystag,UpdateSourceTrigger=PropertyChanged}"
HorizontalAlignment="Left"
Content="Cystag" />

</StackPanel>

<StackPanel x:Name="panel_fullrun" Grid.Column="0" Grid.Row="1" VerticalAlignment="Top" HorizontalAlignment="Left">
Expand Down Expand Up @@ -138,6 +144,11 @@
</Grid>
</StackPanel>

<StackPanel x:Name="panel_neucode_ratio" Grid.Column="1">
<CheckBox Content="Light Is More Abundant" x:Name="lightIsMoreAbundant_checkbox" Click="lightIsMoreAbundant_checkbox_Click"/>
<CheckBox Content="Heavy Is More Abundant" x:Name="heavyIsMoreAbundant_checkbox" Click="heavyIsMoreAbundant_checkbox_Click"/>
</StackPanel>

<StackPanel x:Name="panel_calibrate" Grid.Column="1">
<StackPanel.Resources>
<Style TargetType="{x:Type CheckBox}">
Expand Down
65 changes: 61 additions & 4 deletions ProteoWPFSuite/LoadResults.xaml.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -29,6 +29,7 @@ public LoadResults()
#region Private Fields
private String _labeltxt;
private bool ck_rbneucode;
private bool ck_rbcystag;
private int cb_select;
//private string[] cb_src;
#endregion Private Fields
Expand Down Expand Up @@ -71,7 +72,10 @@ public bool CK_rbneucode
return;
ck_rbneucode = value;
rb_neucode.IsChecked = (bool)ck_rbneucode;
rb_unlabeled.IsChecked = (bool)!ck_rbneucode;
if (!ck_rbcystag && !ck_rbneucode)
{
rb_unlabeled.IsChecked = true;
}
PropertyChanged?.Invoke(this, new PropertyChangedEventArgs("CK_rbneucode"));

this.MDIParent.enable_neuCodeProteoformPairsToolStripMenuItem((bool)ck_rbneucode);
Expand All @@ -87,7 +91,39 @@ public bool CK_rbneucode
populate_file_lists();
}
}


public bool CK_rbcystag
{
get
{
return ck_rbcystag;
}
set
{
if (ck_rbcystag == value)
return;
ck_rbcystag = value;
rb_cystag.IsChecked = (bool)ck_rbcystag;
if(!ck_rbcystag && !ck_rbneucode)
{
rb_unlabeled.IsChecked = true;
}
PropertyChanged?.Invoke(this, new PropertyChangedEventArgs("CK_rbcystag"));

this.MDIParent.enable_neuCodeProteoformPairsToolStripMenuItem((bool)ck_rbcystag);
Sweet.lollipop.cystag_labeled = (bool)ck_rbcystag;

foreach (InputFile f in Sweet.lollipop.input_files)
{
if ((bool)rb_cystag.IsChecked)
f.label = Labeling.Cystag;
if ((bool)rb_unlabeled.IsChecked)
f.label = Labeling.Unlabeled;
}
populate_file_lists();
}
}

public int CB_select
{
get
Expand All @@ -110,6 +146,7 @@ public void InitializeParameterSet()
{
// Initialize components in "2. Set Parameters"
CK_rbneucode = Sweet.lollipop.neucode_labeled;
CK_rbcystag = Sweet.lollipop.cystag_labeled;

// Initialize components in "2. Set Parameters" that fall under "1. Choose Analysis->Chemical Calibration"
cb_calibrate_raw_files.IsChecked = Sweet.lollipop.calibrate_raw_files;
Expand Down Expand Up @@ -227,31 +264,40 @@ private void populate_file_lists()
{
// In "2. Set Parameters"
panel_neucode_labeled_unlabled.Visibility = Visibility.Visible;
panel_neucode_ratio.Visibility = ck_rbcystag ? Visibility.Visible : Visibility.Collapsed;
panel_fullrun.Visibility = Visibility.Visible;
panel_calibrate.Visibility = Visibility.Collapsed;
panel_minmaxcharge.Visibility = Visibility.Collapsed;
panel_topdown_search.Visibility = Visibility.Collapsed;

//Set NeuCode light/heavy abundance ratio
if ((bool)lightIsMoreAbundant_checkbox.IsChecked == true && heavyIsMoreAbundant_checkbox.IsChecked == false)
Sweet.lollipop.neuCodeLightIsMoreAbundant = true;
else if ((bool)lightIsMoreAbundant_checkbox.IsChecked == false && heavyIsMoreAbundant_checkbox.IsChecked == true)
Sweet.lollipop.neuCodeLightIsMoreAbundant = false;

// In "3. Load Data Using Drop Down Menu"
cmb_loadTable1.IsEnabled = true;
for (int i = 0; i < 4; i++)
cmb_loadTable1.Items.Add(Lollipop.file_lists[i]);
cmb_loadTable1.Items.Add(Lollipop.file_lists[7]);
cmb_loadTable1.Items.Add(Lollipop.file_lists[8]);
cmb_loadTable1.SelectedIndex = 0;

// In "4. Start Analysis"
btn_stepthru.Visibility = Visibility.Visible;
btn_fullRun.Visibility = Visibility.Visible;
btn_calibrate.Visibility = Visibility.Collapsed;
btn_deconvolute.Visibility = Visibility.Collapsed;
btn_topdown_search.Visibility = Visibility.Collapsed;
btn_topdown_search.Visibility = Visibility.Collapsed;

}

else if (rb_chemicalCalibration.IsChecked == true)
{
// In "2. Set Parameters"
panel_neucode_labeled_unlabled.Visibility = Visibility.Visible;
panel_calibrate.Visibility = Visibility.Visible;
panel_calibrate.Visibility = Visibility.Visible;
panel_fullrun.Visibility = Visibility.Collapsed;
panel_minmaxcharge.Visibility = Visibility.Collapsed;
panel_topdown_search.Visibility = Visibility.Collapsed;
Expand Down Expand Up @@ -296,6 +342,7 @@ private void populate_file_lists()
{
// In "2. Set Parameters"
panel_topdown_search.Visibility = Visibility.Visible;
panel_neucode_ratio.Visibility = Visibility.Collapsed;
panel_minmaxcharge.Visibility = Visibility.Collapsed;
panel_neucode_labeled_unlabled.Visibility = Visibility.Collapsed;
panel_calibrate.Visibility = Visibility.Collapsed;
Expand Down Expand Up @@ -648,5 +695,15 @@ private void nud_cali_rt_tolerance_ValueChanged(object sender, EventArgs e)
Sweet.lollipop.cali_rt_tolerance = Convert.ToDouble(nud_cali_rt_tolerance.Value);
}
#endregion Chemical Calibration Private Methods

private void heavyIsMoreAbundant_checkbox_Click(object sender, RoutedEventArgs e)
{
populate_file_lists();
}

private void lightIsMoreAbundant_checkbox_Click(object sender, RoutedEventArgs e)
{
populate_file_lists();
}
}
}
8 changes: 4 additions & 4 deletions ProteoWPFSuite/NeuCodePairs.xaml
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Original file line number Diff line number Diff line change
Expand Up @@ -48,7 +48,7 @@
<!--Part of this control coded in backend .cs-->
<winformchart:Chart x:Name="ct_LysineCount" Palette="BrightPastel" Text="chart1" Dock="Fill" MouseClick="ct_LysineCount_MouseClick" Visible="True">
<winformchart:Chart.Series>
<winformchart:Series Name="lysineCount" ChartType="Line" ChartArea="ChartArea1" Legend="Legend1" MarkerBorderWidth="1" MarkerSize="5">
<winformchart:Series Name="lysineCount" ChartType="Line" MarkerBorderWidth="1" MarkerSize="5">
<winformchart:Series.SmartLabelStyle>
<winformchart:SmartLabelStyle/>
</winformchart:Series.SmartLabelStyle>
Expand Down Expand Up @@ -93,8 +93,8 @@
<ColumnDefinition Width="1*"></ColumnDefinition>
<ColumnDefinition Width="1.5*"></ColumnDefinition>
</Grid.ColumnDefinitions>
<Label Margin="0 0 0 0" Height="23" Grid.Column="0" Grid.Row="0" FontSize="11">K-Min</Label>
<Label Margin="0,0,0,0" Height="23" Grid.Column="0" Grid.Row="1" FontSize="11">K-Max</Label>
<TextBlock x:Name="AA_min_textblock" Text="K-Min" Margin="0 0 0 0" Height="23" Grid.Column="0" Grid.Row="0" FontSize="11" />

@trishorts trishorts May 23, 2022

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K?

<TextBlock x:Name="AA_max_textblock" Text="K-Min" Margin="0 0 0 0" Height="23" Grid.Column="0" Grid.Row="1" FontSize="11" />
<WindowsFormsHost Grid.Column="1" Height="20">
<winform:NumericUpDown x:Name="KMinAcceptable" Dock="Fill" Maximum="100" Minimum="-100" DecimalPlaces="2" Enabled="True" Visible="True" TabIndex="12" ValueChanged="KMinAcceptable_ValueChanged"/>
</WindowsFormsHost>
Expand Down Expand Up @@ -151,7 +151,7 @@
<WindowsFormsHost>
<winformchart:Chart x:Name="ct_IntensityRatio" Dock="Fill" MouseClick="ct_IntensityRatio_MouseClick" Margin="2, 2, 2, 2" TabIndex="1" Text="chart1">
<winformchart:Chart.Series>
<winformchart:Series ChartType="Line" ChartArea="ChartArea1" Name="intensityRatio" Legend="Legend1"/>
<winformchart:Series ChartType="Line" Name="intensityRatio"/>
</winformchart:Chart.Series>
<winformchart:Chart.Legends>
<winformchart:Legend Name="Legend1" Enabled="False"/>
Expand Down
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