added std out parameter to the query parameters class

dominik-kopczynski · dominik-kopczynski · commit 9f69fe441d50 · 2020-01-16T14:30:36.000+01:00
diff --git a/MainClass.cs b/MainClass.cs
@@ -243,7 +243,7 @@ private static void SpectrumQueryParametersParsing(string[] args)
                 },
                 {
                     "s=|scans=",
-                    "The scan numbers. e.g. '1-5,20,25-30'",
+                    "The scan numbers. e.g. \"1-5, 20, 25-30\"",
                     v => parameters.scans = v
                 },
                 {
@@ -255,6 +255,11 @@ private static void SpectrumQueryParametersParsing(string[] args)
                     "p|noPeakPicking",
                     "Don't use the peak picking provided by the native Thermo library. By default peak picking is enabled.",
                     v => parameters.noPeakPicking = v != null
+                },
+                {
+                    "s|stdout",
+                    "Pipes the output into standard output. Logging is being turned off",
+                    v => parameters.stdout = v != null
                 }
             };
 
@@ -756,4 +761,4 @@ private static void ShowHelp(string message, OptionException optionException, Op
             Environment.Exit(-1);
         }
     }
-}
+}
diff --git a/Query/QueryParameters.cs b/Query/QueryParameters.cs
@@ -12,5 +12,30 @@ public class QueryParameters
         public string outputFile { get; set; }
         public bool noPeakPicking { get; set; }
         public HashSet<int> scanNumbers { get; set; }
+        public bool stdout { get; set; }
+        
+        
+        public QueryParameters()
+        {
+            help = false;
+            rawFilePath = "";
+            scans = "";
+            outputFile = "";
+            noPeakPicking = false;
+            scanNumbers = new HashSet<int>();
+            stdout = false;
+        }
+        
+        public QueryParameters(QueryParameters copy)
+        {
+            help = copy.help;
+            rawFilePath = copy.rawFilePath;
+            scans = copy.scans;
+            outputFile = copy.outputFile;
+            noPeakPicking = copy.noPeakPicking;
+            scanNumbers = new HashSet<int>();
+            foreach (int s in copy.scanNumbers) scanNumbers.Add(s);
+            stdout = copy.stdout;
+        }
     }
-}
+}
diff --git a/ThermoRawFileParserTest/xic_in.json b/ThermoRawFileParserTest/xic_in.json
@@ -1,18 +1,18 @@
 [
   {
     "mz":488.5384,
-    "tolerance":10,
-    "tolerance_unit":"ppm"
+    "tolerance": 2,
+    "tolerance_unit":"da"
   },
   {
-    "mz":575.2413,
-    "tolerance":10,
+    "mz":570.2413,
+    "tolerance":1000,
     "tolerance_unit":"ppm"
   },
   {
     "mz_start":749.7860,
-    "mz_end":749.8093,
-    "rt_start":10.5,
-    "rt_end":11
+    "mz_end":752.8093,
+    "rt_start":20,
+    "rt_end":80
   }
 ]

Original file line number	Diff line number	Diff line change
`@@ -243,7 +243,7 @@ private static void SpectrumQueryParametersParsing(string[] args)`
`243`	`243`	`},`
`244`	`244`	`{`
`245`	`245`	`"s=\|scans=",`
`246`		`- "The scan numbers. e.g. '1-5,20,25-30'",`
	`246`	`+ "The scan numbers. e.g. \"1-5, 20, 25-30\"",`
`247`	`247`	`v => parameters.scans = v`
`248`	`248`	`},`
`249`	`249`	`{`
`@@ -255,6 +255,11 @@ private static void SpectrumQueryParametersParsing(string[] args)`
`255`	`255`	`"p\|noPeakPicking",`
`256`	`256`	`"Don't use the peak picking provided by the native Thermo library. By default peak picking is enabled.",`
`257`	`257`	`v => parameters.noPeakPicking = v != null`
	`258`	`+ },`
	`259`	`+ {`
	`260`	`+ "s\|stdout",`
	`261`	`+ "Pipes the output into standard output. Logging is being turned off",`
	`262`	`+ v => parameters.stdout = v != null`
`258`	`263`	`}`
`259`	`264`	`};`
`260`	`265`
`@@ -756,4 +761,4 @@ private static void ShowHelp(string message, OptionException optionException, Op`
`756`	`761`	`Environment.Exit(-1);`
`757`	`762`	`}`
`758`	`763`	`}`
`759`		`-}`
	`764`	`+}`
Original file line number	Diff line number	Diff line change
`@@ -1,18 +1,18 @@`
`1`	`1`	`[`
`2`	`2`	`{`
`3`	`3`	`"mz":488.5384,`
`4`		`- "tolerance":10,`
`5`		`- "tolerance_unit":"ppm"`
	`4`	`+ "tolerance": 2,`
	`5`	`+ "tolerance_unit":"da"`
`6`	`6`	`},`
`7`	`7`	`{`
`8`		`- "mz":575.2413,`
`9`		`- "tolerance":10,`
	`8`	`+ "mz":570.2413,`
	`9`	`+ "tolerance":1000,`
`10`	`10`	`"tolerance_unit":"ppm"`
`11`	`11`	`},`
`12`	`12`	`{`
`13`	`13`	`"mz_start":749.7860,`
`14`		`- "mz_end":749.8093,`
`15`		`- "rt_start":10.5,`
`16`		`- "rt_end":11`
	`14`	`+ "mz_end":752.8093,`
	`15`	`+ "rt_start":20,`
	`16`	`+ "rt_end":80`
`17`	`17`	`}`
`18`	`18`	`]`