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));