Merge branch 'master' into Pep3

smith-chem-wisc · Aug 27, 2024 · 6359c3d · 6359c3d
2 parents 41f1011 + 30e73f0
commit 6359c3d
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Showing 2 changed files with 6 additions and 5 deletions.
diff --git a/MetaMorpheus/EngineLayer/PrecursorSearchModes/DotMassDiffAcceptor.cs b/MetaMorpheus/EngineLayer/PrecursorSearchModes/DotMassDiffAcceptor.cs
@@ -55,7 +55,7 @@ public override string ToString()
 
         public override string ToProseString()
         {
-            return (Tolerance.ToString() + " around " + String.Join(",", AcceptableSortedMassShifts) + " Da");
+            return (Tolerance.ToString() + " around " + String.Join(", ", AcceptableSortedMassShifts) + " Da");
         }
     }
-}
+}
diff --git a/MetaMorpheus/TaskLayer/MetaMorpheusTask.cs b/MetaMorpheus/TaskLayer/MetaMorpheusTask.cs
@@ -572,12 +572,13 @@ public MyTaskResults RunTask(string output_folder, List<DbForTask> currentProtei
                 using (StreamWriter file = new StreamWriter(proseFilePath))
                 {
                     file.WriteLine("The data analysis was performed using MetaMorpheus version " + GlobalVariables.MetaMorpheusVersion + ", available at " + "https://github.com/smith-chem-wisc/MetaMorpheus.");
+		    file.WriteLine();
                     file.Write(ProseCreatedWhileRunning.ToString());
                     file.WriteLine(SystemInfo.SystemProse().Replace(Environment.NewLine, "") + " ");
+		    file.WriteLine();
                     file.WriteLine("The total time to perform the " + TaskType + " task on " + currentRawDataFilepathList.Count + " spectra file(s) was " + String.Format("{0:0.00}", MyTaskResults.Time.TotalMinutes) + " minutes.");
                     file.WriteLine();
-                    file.WriteLine("Published works using MetaMorpheus software are encouraged to cite: Solntsev, S. K.; Shortreed, M. R.; Frey, B. L.; Smith, L. M. Enhanced Global Post-translational Modification Discovery with MetaMorpheus. Journal of Proteome Research. 2018, 17 (5), 1844-1851.");
-
+                    file.WriteLine("Published works using MetaMorpheus software are encouraged to cite the appropriate publications listed in the reference guide, found here: https://github.com/smith-chem-wisc/MetaMorpheus/blob/master/README.md.");
                     file.WriteLine();
                     file.WriteLine("Spectra files: ");
                     file.WriteLine(string.Join(Environment.NewLine, currentRawDataFilepathList.Select(b => '\t' + b)));
@@ -1224,4 +1225,4 @@ protected static void SanitizeProteinDatabase(List<Protein> proteins, TargetCont
             }
         }
     }
-}
+}