Merge pull request #567 from lschaffer2/master

Added parameters

ProteoWPFSuite/RawExperimentalComponents.xaml

@@ -93,7 +93,16 @@
  <winform:NumericUpDown x:Name="nUD_mass_tolerance" Value="0" DecimalPlaces="0" Increment="1" Maximum="100" Minimum="0" ValueChanged="nUD_mass_tolerance_ValueChanged"></winform:NumericUpDown>
  </WindowsFormsHost>
  <Label Grid.Column="1" Grid.Row="0" Margin="5 10 5 0">Mass Tolerance for Merging Artifacts (ppm)</Label>
-
+ <WindowsFormsHost Margin="5 0 5 0" Grid.Column="0" Grid.Row="1">
+ <winform:NumericUpDown x:Name="nud_minCC" Value="0.70" DecimalPlaces="2" Increment=".01" Maximum="1" Minimum=".70" ValueChanged="nUD_minCC_ValueChanged"></winform:NumericUpDown>
+ </WindowsFormsHost>
+ <Label Grid.Column="1" Grid.Row="1" Margin="5 10 5 0">Cosine threshold between per-charge-intensities and fitted gaussian distribution</Label>
+ <WindowsFormsHost Margin="5 0 5 0" Grid.Column="0" Grid.Row="2">
+ <winform:NumericUpDown x:Name="nUD_minIC" Value="0.70" DecimalPlaces="2" Increment=".01" Maximum="1" Minimum="0.70" ValueChanged="nUD_minIC_ValueChanged"></winform:NumericUpDown>
+ </WindowsFormsHost>
+ <Label Grid.Column="1" Grid.Row="2" Margin="5 10 5 0">
+ Cosine threshold between averagine and observed isotope pattern
+ </Label>
  </Grid>
  <GridSplitter Grid.Row="1" Background="LightGray" HorizontalAlignment="Stretch" VerticalAlignment="Stretch" ResizeDirection="Rows" />
  <Grid Grid.Row="2">

ProteoWPFSuite/RawExperimentalComponents.xaml.cs

@@ -106,6 +106,8 @@ public void InitializeParameterSet()
  nUD_mass_tolerance.Value = (decimal)Sweet.lollipop.raw_component_mass_tolerance;
  CK_rb_displayIdentificationComponents = true;
  CK_rb_displayQuantificationComponents = false;
+ nud_minCC.Value = (decimal)Sweet.lollipop.minCC;
+ nUD_minIC.Value = (decimal)Sweet.lollipop.minIC;
  FillTablesAndCharts();
  }
 
@@ -210,7 +212,17 @@ private void nUD_mass_tolerance_ValueChanged(object sender, EventArgs e)
  Sweet.lollipop.raw_component_mass_tolerance = Convert.ToDouble(nUD_mass_tolerance.Value);
  }
 
+ private void nUD_minCC_ValueChanged(object sender, EventArgs e)
+ {
+ Sweet.lollipop.minCC = Convert.ToDouble(nud_minCC.Value);
+ }
+
+ private void nUD_minIC_ValueChanged(object sender, EventArgs e)
+ {
+ Sweet.lollipop.minIC = Convert.ToDouble(nUD_minIC.Value);
+ }
+
  #endregion Private Methods
- 
+
  }
 }

ProteoformSuiteInternal/Calibration.cs

@@ -620,6 +620,8 @@ public static void calibrate_td_hits_file(InputFile file)
  double corrected_RT;
  // key is filename, hit scan #, hit reported mass, value is corrected mass
  string[] row = old[i].Split('\t');
+ bool add_row_to_new_document = true;
+
  if (Sweet.lollipop.retention_time_calibration)
  {
  if (Sweet.lollipop.td_hit_RT_correction.TryGetValue(
@@ -628,7 +630,10 @@ public static void calibrate_td_hits_file(InputFile file)
  Convert.ToDouble(row[index_precursor_mass])), out corrected_RT))
  {
  row[index_retention_time] = corrected_RT.ToString();
- new_file.Add(String.Join("\t", row));
+ }
+ else
+ {
+ add_row_to_new_document = false;
  }
  }
 
@@ -640,10 +645,16 @@ public static void calibrate_td_hits_file(InputFile file)
  Convert.ToDouble(row[index_precursor_mass])), out corrected_mass))
  {
  row[index_precursor_mass] = corrected_mass.ToString();
- new_file.Add(String.Join("\t", row));
-
+ }
+ else
+ {
+ add_row_to_new_document = false;
  }
  }
+ if(add_row_to_new_document)
+ {
+ new_file.Add(String.Join("\t", row));
+ }
  }
  File.WriteAllLines(new_absolute_path, new_file);
  }
@@ -715,13 +726,13 @@ public static void calibrate_components_in_xlsx(InputFile file)
  if (Sweet.lollipop.component_mz_correction.TryGetValue(new Tuple<string, double, double>(file.filename, Math.Round(intensity, 0), Math.Round(mass, 2)), out value))
  {
  row[2] = value.ToString();
- new_file.Add(string.Join("\t", row));
  }
  if (Sweet.lollipop.component_RT_correction.TryGetValue(new Tuple<string, double, double>(file.filename, Math.Round(intensity, 0), Math.Round(mass, 2)), out value))
  {
  row[8] = (value*60).ToString();
- new_file.Add(string.Join("\t", row));
  }
+ new_file.Add(string.Join("\t", row));
+
  }
  else if (row.Length == 3 && Double.TryParse(row[0], out mass) &&
  Double.TryParse(row[1], out intensity))
@@ -730,13 +741,12 @@ public static void calibrate_components_in_xlsx(InputFile file)
  if (Sweet.lollipop.component_mz_correction.TryGetValue(new Tuple<string, double, double>(file.filename, Math.Round(intensity, 0), Math.Round(mass, 2)), out value))
  {
  row[0] = value.ToString();
- new_file.Add(string.Join("\t", row));
  }
  if (Sweet.lollipop.component_RT_correction.TryGetValue(new Tuple<string, double, double>(file.filename, Math.Round(intensity, 0), Math.Round(mass, 2)), out value))
  {
  row[2] = value.ToString();
- new_file.Add(string.Join("\t", row));
  }
+ new_file.Add(string.Join("\t", row));
  }
  }
  File.WriteAllLines(new_absolute_path, new_file);

ProteoformSuiteInternal/ComponentReader.cs

@@ -124,7 +124,7 @@ public List<Component> read_components_from_tsv(InputFile file, bool remove_miss
  add_component(c);
  }
  }
- else if(row.Length == 16)
+ else if (row.Length == 16)
  {
  List<string> cellStrings = new List<string>();
  cellStrings.Add(row[0]); //id
@@ -153,6 +153,13 @@ public List<Component> read_components_from_tsv(InputFile file, bool remove_miss
 
  if (acceptable_component(c))
  {
+ double IC = Convert.ToDouble(row[14]);
+ double CC = Convert.ToDouble(row[15]);
+ if (IC < Sweet.lollipop.minIC || CC < Sweet.lollipop.minCC)
+ {
+ continue;
+ }
+
  add_component(c);
  }
  }

ProteoformSuiteInternal/Lollipop.cs

@@ -144,6 +144,8 @@ public void enter_input_files(string[] files, IEnumerable<string> acceptable_ext
  public List<Component> raw_quantification_components = new List<Component>();
  public bool neucode_labeled = false;
  public double raw_component_mass_tolerance = 5;
+ public double minIC = 0.7;
+ public double minCC = 0.7;
 
  #endregion RAW EXPERIMENTAL COMPONENTS Public Fields
 
@@ -193,7 +195,11 @@ public string flash_deconv(int maxcharge, int mincharge, string directory)
 
  if(f.extension == ".raw")
  {
- return "Error: please convert .raw files to .mzML";
+ //var myMsDataFile = ThermoRawFileReaderData.LoadAllStaticData(f.complete_path);
+ //MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(myMsDataFile,
+ //f.directory + "\\" + f.filename + "PS.mzML", false);
+ //filelocation = f.directory + "\\" + f.filename + "PS";
+ return "Error: please convert .raw files to .mzML";
  }
 
  Process proc = new Process();

Test/Test.csproj

@@ -11,6 +11,10 @@
  <IsPackable>false</IsPackable>
  </PropertyGroup>
 
+ <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|AnyCPU'">
+ <PlatformTarget>x86</PlatformTarget>
+ </PropertyGroup>
+
  <ItemGroup>
  <PackageReference Include="mzLib" Version="1.0.472" />
  <PackageReference Include="nunit" Version="3.12.0" />

Test/TestFLASHDeconv.cs

@@ -29,7 +29,7 @@ public void testFLASHDeconv()
 
  List<Component> deconv_components = new List<Component>();
  Sweet.lollipop.process_raw_components(Sweet.lollipop.input_files.Where(f => f.purpose == Purpose.Identification).ToList(), deconv_components, Purpose.Identification, false);
- Assert.AreEqual(54, deconv_components.Count);
+ Assert.AreEqual(52, deconv_components.Count);
  Assert.AreEqual(6999.01, Math.Round(deconv_components.OrderBy(c => c.id).First().reported_monoisotopic_mass, 2));
  Assert.AreEqual(6999.01, Math.Round(deconv_components.OrderBy(c => c.id).First().weighted_monoisotopic_mass, 2));
  Assert.AreEqual(15184400000, Math.Round(deconv_components.OrderBy(c => c.id).First().intensity_reported, 2));