Merge pull request #170 from compomics/1.4.3

Release of v1.4.3
compomics · Sep 15, 2023 · 5e38f34 · 5e38f34
2 parents 45ed3df + 34656a8
commit 5e38f34
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Showing 26 changed files with 975 additions and 914 deletions.
diff --git a/MainClass.cs b/MainClass.cs
@@ -20,7 +20,7 @@ public static class MainClass
         private static readonly ILog Log =
             LogManager.GetLogger(System.Reflection.MethodBase.GetCurrentMethod().DeclaringType);
 
-        public const string Version = "1.4.2";
+        public const string Version = "1.4.3";
         public static void Main(string[] args)
         {
             // Set Invariant culture as default for all further processing

diff --git a/README.md b/README.md
@@ -192,7 +192,8 @@ Provide one of the following filters:
  * M/Z start and end
  * sequence and tolerance (tolerance unit optional, defaults to `ppm`)
 
-optionally one can define starting and ending retention times and thermo filter string (defaults to `ms`)
+optionally one can define starting and ending retention times, provide filter string (defaults to `ms`, i.e. only MS1 scans), and a comment (free text) field; any valid filter string is supported,
+however only basic validation is performed, see [issue #158](https://github.com/compomics/ThermoRawFileParser/issues/158) for details. Comment can contain any text and will be preserved in the output.
 
 An example input JSON file:
 
@@ -219,7 +220,17 @@ An example input JSON file:
         {
             "sequence":"TRANNEL",
             "tolerance":10
+        },
+        {
+            "mz":1014.5099732499732,
+            "rt_start":14.0600881872,
+            "rt_end":14.4167198290667,
+            "tolerance":5,
+            "tolerance_unit":"ppm",
+            "comment":"Only ion trap scans"
+            "scan_filter":"ITMS"
         }
+   }
 ]
 
 ```

diff --git a/RawFileParser.cs b/RawFileParser.cs
@@ -136,18 +136,23 @@ private static void ProcessFile(ParseInput parseInput)
 
                 // Get the number of instruments (controllers) present in the RAW file and set the 
                 // selected instrument to the MS instrument, first instance of it
-                rawFile.SelectInstrument(Device.MS, 1);
+                var firstScanNumber = -1;
+                var lastScanNumber = -1;
 
-                rawFile.IncludeReferenceAndExceptionData = !parseInput.ExData;
+                if (rawFile.GetInstrumentCountOfType(Device.MS) != 0)
+                {
+                    rawFile.SelectInstrument(Device.MS, 1);
+                    rawFile.IncludeReferenceAndExceptionData = !parseInput.ExData;
 
-                // Get the first and last scan from the RAW file
-                var firstScanNumber = rawFile.RunHeaderEx.FirstSpectrum;
-                var lastScanNumber = rawFile.RunHeaderEx.LastSpectrum;
+                    // Get the first and last scan from the RAW file
+                    firstScanNumber = rawFile.RunHeaderEx.FirstSpectrum;
+                    lastScanNumber = rawFile.RunHeaderEx.LastSpectrum;
 
-                // Check for empty file
-                if (lastScanNumber < 1)
-                {
-                    throw new RawFileParserException("Empty RAW file, no output will be produced");
+                    // Check for empty file
+                    if (lastScanNumber < 1)
+                    {
+                        throw new RawFileParserException("Empty RAW file, no output will be produced");
+                    }
                 }
 
                 if (parseInput.MetadataFormat != MetadataFormat.NONE)

diff --git a/ThermoRawFileParser.csproj b/ThermoRawFileParser.csproj
@@ -176,11 +176,11 @@
     <Reference Include="System.Data.DataSetExtensions" />
     <Reference Include="System.Data" />
     <Reference Include="System.Xml" />
-    <Reference Include="ThermoFisher.CommonCore.Data, Version=5.0.0.88, Culture=neutral, PublicKeyToken=1aef06afb5abd953, processorArchitecture=MSIL">
-      <HintPath>packages\ThermoFisher.CommonCore.Data.5.0.0.88\lib\ThermoFisher.CommonCore.Data.dll</HintPath>
+    <Reference Include="ThermoFisher.CommonCore.Data, Version=5.0.0.93, Culture=neutral, PublicKeyToken=1aef06afb5abd953, processorArchitecture=MSIL">
+      <HintPath>packages\ThermoFisher.CommonCore.Data.5.0.0.93\lib\netstandard2.0\ThermoFisher.CommonCore.Data.dll</HintPath>
     </Reference>
-    <Reference Include="ThermoFisher.CommonCore.RawFileReader, Version=5.0.0.88, Culture=neutral, PublicKeyToken=1aef06afb5abd953, processorArchitecture=MSIL">
-      <HintPath>packages\ThermoFisher.CommonCore.RawFileReader.5.0.0.88\lib\ThermoFisher.CommonCore.RawFileReader.dll</HintPath>
+    <Reference Include="ThermoFisher.CommonCore.RawFileReader, Version=5.0.0.93, Culture=neutral, PublicKeyToken=1aef06afb5abd953, processorArchitecture=MSIL">
+      <HintPath>packages\ThermoFisher.CommonCore.RawFileReader.5.0.0.93\lib\netstandard2.0\ThermoFisher.CommonCore.RawFileReader.dll</HintPath>
     </Reference>
     <Reference Include="zlib.net, Version=1.0.3.0, Culture=neutral, PublicKeyToken=47d7877cb3620160">
       <HintPath>packages\zlib.net.1.0.4.0\lib\zlib.net.dll</HintPath>
@@ -199,6 +199,7 @@
     <Compile Include="Query\ProxiSpectrumReader.cs" />
     <Compile Include="RawFileParserException.cs" />
     <Compile Include="RawFileParser.cs" />
+    <Compile Include="Util\CVHelpers.cs" />
     <Compile Include="Util\LimitedSizeDictionary.cs" />
     <Compile Include="Util\MZArray.cs" />
     <Compile Include="Util\NativeMethods.cs" />

diff --git a/ThermoRawFileParserTest/OntologyMappingTests.cs b/ThermoRawFileParserTest/OntologyMappingTests.cs
@@ -12,13 +12,13 @@ public class OntologyMappingTests
         public void TestGetInstrumentModel()
         {
             // exact match
-            var match = OntologyMapping.getInstrumentModel("LTQ Orbitrap");
+            var match = OntologyMapping.GetInstrumentModel("LTQ Orbitrap");
             Assert.AreEqual("MS:1000449", match.accession);
             // partial match, should return the longest partial match
-            var partialMatch = OntologyMapping.getInstrumentModel("LTQ Orbitrap XXL");
+            var partialMatch = OntologyMapping.GetInstrumentModel("LTQ Orbitrap XXL");
             Assert.AreEqual("MS:1000449", partialMatch.accession);
             // no match, should return the generic thermo instrument
-            var noMatch = OntologyMapping.getInstrumentModel("non existing model");
+            var noMatch = OntologyMapping.GetInstrumentModel("non existing model");
             Assert.AreEqual("MS:1000483", noMatch.accession);
         }
     }

diff --git a/ThermoRawFileParserTest/ThermoRawFileParserTest.csproj b/ThermoRawFileParserTest/ThermoRawFileParserTest.csproj
@@ -155,15 +155,15 @@
       <HintPath>..\packages\mzLib.1.0.450\lib\net471\ThermoFisher.CommonCore.BackgroundSubtraction.dll</HintPath>
       <Private>True</Private>
     </Reference>
-    <Reference Include="ThermoFisher.CommonCore.Data, Version=5.0.0.88, Culture=neutral, PublicKeyToken=1aef06afb5abd953, processorArchitecture=MSIL">
-      <HintPath>..\packages\ThermoFisher.CommonCore.Data.5.0.0.88\lib\ThermoFisher.CommonCore.Data.dll</HintPath>
+    <Reference Include="ThermoFisher.CommonCore.Data, Version=5.0.0.93, Culture=neutral, PublicKeyToken=1aef06afb5abd953, processorArchitecture=MSIL">
+      <HintPath>..\packages\ThermoFisher.CommonCore.Data.5.0.0.93\lib\netstandard2.0\ThermoFisher.CommonCore.Data.dll</HintPath>
     </Reference>
     <Reference Include="ThermoFisher.CommonCore.MassPrecisionEstimator, Version=1.0.0.0, Culture=neutral, PublicKeyToken=null">
       <HintPath>..\packages\mzLib.1.0.450\lib\net471\ThermoFisher.CommonCore.MassPrecisionEstimator.dll</HintPath>
       <Private>True</Private>
     </Reference>
-    <Reference Include="ThermoFisher.CommonCore.RawFileReader, Version=5.0.0.88, Culture=neutral, PublicKeyToken=1aef06afb5abd953, processorArchitecture=MSIL">
-      <HintPath>..\packages\ThermoFisher.CommonCore.RawFileReader.5.0.0.88\lib\ThermoFisher.CommonCore.RawFileReader.dll</HintPath>
+    <Reference Include="ThermoFisher.CommonCore.RawFileReader, Version=5.0.0.93, Culture=neutral, PublicKeyToken=1aef06afb5abd953, processorArchitecture=MSIL">
+      <HintPath>..\packages\ThermoFisher.CommonCore.RawFileReader.5.0.0.93\lib\netstandard2.0\ThermoFisher.CommonCore.RawFileReader.dll</HintPath>
     </Reference>
     <Reference Include="ThermoRawFileReader, Version=1.0.0.0, Culture=neutral, PublicKeyToken=null">
       <HintPath>..\packages\mzLib.1.0.450\lib\net471\ThermoRawFileReader.dll</HintPath>

diff --git a/ThermoRawFileParserTest/app.config b/ThermoRawFileParserTest/app.config
@@ -12,7 +12,7 @@
       </dependentAssembly>
       <dependentAssembly>
         <assemblyIdentity name="ThermoFisher.CommonCore.RawFileReader" publicKeyToken="1aef06afb5abd953" culture="neutral" />
-        <bindingRedirect oldVersion="0.0.0.0-5.0.0.88" newVersion="5.0.0.88" />
+        <bindingRedirect oldVersion="0.0.0.0-5.0.0.93" newVersion="5.0.0.93" />
       </dependentAssembly>
       <dependentAssembly>
         <assemblyIdentity name="System.Buffers" publicKeyToken="cc7b13ffcd2ddd51" culture="neutral" />
@@ -28,7 +28,7 @@
       </dependentAssembly>
       <dependentAssembly>
         <assemblyIdentity name="ThermoFisher.CommonCore.Data" publicKeyToken="1aef06afb5abd953" culture="neutral" />
-        <bindingRedirect oldVersion="0.0.0.0-5.0.0.88" newVersion="5.0.0.88" />
+        <bindingRedirect oldVersion="0.0.0.0-5.0.0.93" newVersion="5.0.0.93" />
       </dependentAssembly>
       <dependentAssembly>
         <assemblyIdentity name="System.IO.FileSystem.AccessControl" publicKeyToken="b03f5f7f11d50a3a" culture="neutral" />

diff --git a/ThermoRawFileParserTest/packages.config b/ThermoRawFileParserTest/packages.config
@@ -19,7 +19,7 @@
   <package id="System.IO.FileSystem.AccessControl" version="5.0.0" targetFramework="net472" />
   <package id="System.Security.AccessControl" version="5.0.0" targetFramework="net472" />
   <package id="System.Security.Principal.Windows" version="5.0.0" targetFramework="net472" />
-  <package id="ThermoFisher.CommonCore.Data" version="5.0.0.88" targetFramework="net472" />
-  <package id="ThermoFisher.CommonCore.RawFileReader" version="5.0.0.88" targetFramework="net472" />
+  <package id="ThermoFisher.CommonCore.Data" version="5.0.0.93" targetFramework="net472" />
+  <package id="ThermoFisher.CommonCore.RawFileReader" version="5.0.0.93" targetFramework="net472" />
   <package id="zlib.net" version="1.0.4.0" targetFramework="net471" />
 </packages>
diff --git a/Util/CVHelpers.cs b/Util/CVHelpers.cs
@@ -0,0 +1,21 @@
+using ThermoRawFileParser.Writer.MzML;
+
+namespace ThermoRawFileParser.Util
+{
+    public static class CVHelpers
+    {
+        public static CVParamType Copy (this CVParamType old)
+        {
+            return new CVParamType
+            {
+                accession = old.accession,
+                name = old.name,
+                cvRef = old.cvRef,
+                unitAccession = old.unitAccession,
+                unitCvRef = old.unitCvRef,
+                unitName = old.unitName,
+                value = old.value
+            };
+        }
+    }
+}