upload file

App.config

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+<?xml version="1.0" encoding="utf-8"?>
+<configuration>
+    <startup> 
+        <supportedRuntime version="v4.0" sku=".NETFramework,Version=v4.8" />
+    </startup>
+  <runtime>
+    <assemblyBinding xmlns="urn:schemas-microsoft-com:asm.v1">
+      <dependentAssembly>
+        <assemblyIdentity name="System.Runtime.CompilerServices.Unsafe" publicKeyToken="b03f5f7f11d50a3a" culture="neutral" />
+        <bindingRedirect oldVersion="0.0.0.0-6.0.0.0" newVersion="6.0.0.0" />
+      </dependentAssembly>
+    </assemblyBinding>
+  </runtime>
+</configuration>

FodyWeavers.xml

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+<Weavers xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="FodyWeavers.xsd">
+  <Costura />
+</Weavers>

FodyWeavers.xsd

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+<?xml version="1.0" encoding="utf-8"?>
+<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema">
+  <!-- This file was generated by Fody. Manual changes to this file will be lost when your project is rebuilt. -->
+  <xs:element name="Weavers">
+    <xs:complexType>
+      <xs:all>
+        <xs:element name="Costura" minOccurs="0" maxOccurs="1">
+          <xs:complexType>
+            <xs:all>
+              <xs:element minOccurs="0" maxOccurs="1" name="ExcludeAssemblies" type="xs:string">
+                <xs:annotation>
+                  <xs:documentation>A list of assembly names to exclude from the default action of "embed all Copy Local references", delimited with line breaks</xs:documentation>
+                </xs:annotation>
+              </xs:element>
+              <xs:element minOccurs="0" maxOccurs="1" name="IncludeAssemblies" type="xs:string">
+                <xs:annotation>
+                  <xs:documentation>A list of assembly names to include from the default action of "embed all Copy Local references", delimited with line breaks.</xs:documentation>
+                </xs:annotation>
+              </xs:element>
+              <xs:element minOccurs="0" maxOccurs="1" name="ExcludeRuntimeAssemblies" type="xs:string">
+                <xs:annotation>
+                  <xs:documentation>A list of runtime assembly names to exclude from the default action of "embed all Copy Local references", delimited with line breaks</xs:documentation>
+                </xs:annotation>
+              </xs:element>
+              <xs:element minOccurs="0" maxOccurs="1" name="IncludeRuntimeAssemblies" type="xs:string">
+                <xs:annotation>
+                  <xs:documentation>A list of runtime assembly names to include from the default action of "embed all Copy Local references", delimited with line breaks.</xs:documentation>
+                </xs:annotation>
+              </xs:element>
+              <xs:element minOccurs="0" maxOccurs="1" name="Unmanaged32Assemblies" type="xs:string">
+                <xs:annotation>
+                  <xs:documentation>A list of unmanaged 32 bit assembly names to include, delimited with line breaks.</xs:documentation>
+                </xs:annotation>
+              </xs:element>
+              <xs:element minOccurs="0" maxOccurs="1" name="Unmanaged64Assemblies" type="xs:string">
+                <xs:annotation>
+                  <xs:documentation>A list of unmanaged 64 bit assembly names to include, delimited with line breaks.</xs:documentation>
+                </xs:annotation>
+              </xs:element>
+              <xs:element minOccurs="0" maxOccurs="1" name="PreloadOrder" type="xs:string">
+                <xs:annotation>
+                  <xs:documentation>The order of preloaded assemblies, delimited with line breaks.</xs:documentation>
+                </xs:annotation>
+              </xs:element>
+            </xs:all>
+            <xs:attribute name="CreateTemporaryAssemblies" type="xs:boolean">
+              <xs:annotation>
+                <xs:documentation>This will copy embedded files to disk before loading them into memory. This is helpful for some scenarios that expected an assembly to be loaded from a physical file.</xs:documentation>
+              </xs:annotation>
+            </xs:attribute>
+            <xs:attribute name="IncludeDebugSymbols" type="xs:boolean">
+              <xs:annotation>
+                <xs:documentation>Controls if .pdbs for reference assemblies are also embedded.</xs:documentation>
+              </xs:annotation>
+            </xs:attribute>
+            <xs:attribute name="IncludeRuntimeReferences" type="xs:boolean">
+              <xs:annotation>
+                <xs:documentation>Controls if runtime assemblies are also embedded.</xs:documentation>
+              </xs:annotation>
+            </xs:attribute>
+            <xs:attribute name="UseRuntimeReferencePaths" type="xs:boolean">
+              <xs:annotation>
+                <xs:documentation>Controls whether the runtime assemblies are embedded with their full path or only with their assembly name.</xs:documentation>
+              </xs:annotation>
+            </xs:attribute>
+            <xs:attribute name="DisableCompression" type="xs:boolean">
+              <xs:annotation>
+                <xs:documentation>Embedded assemblies are compressed by default, and uncompressed when they are loaded. You can turn compression off with this option.</xs:documentation>
+              </xs:annotation>
+            </xs:attribute>
+            <xs:attribute name="DisableCleanup" type="xs:boolean">
+              <xs:annotation>
+                <xs:documentation>As part of Costura, embedded assemblies are no longer included as part of the build. This cleanup can be turned off.</xs:documentation>
+              </xs:annotation>
+            </xs:attribute>
+            <xs:attribute name="LoadAtModuleInit" type="xs:boolean">
+              <xs:annotation>
+                <xs:documentation>Costura by default will load as part of the module initialization. This flag disables that behavior. Make sure you call CosturaUtility.Initialize() somewhere in your code.</xs:documentation>
+              </xs:annotation>
+            </xs:attribute>
+            <xs:attribute name="IgnoreSatelliteAssemblies" type="xs:boolean">
+              <xs:annotation>
+                <xs:documentation>Costura will by default use assemblies with a name like 'resources.dll' as a satellite resource and prepend the output path. This flag disables that behavior.</xs:documentation>
+              </xs:annotation>
+            </xs:attribute>
+            <xs:attribute name="ExcludeAssemblies" type="xs:string">
+              <xs:annotation>
+                <xs:documentation>A list of assembly names to exclude from the default action of "embed all Copy Local references", delimited with |</xs:documentation>
+              </xs:annotation>
+            </xs:attribute>
+            <xs:attribute name="IncludeAssemblies" type="xs:string">
+              <xs:annotation>
+                <xs:documentation>A list of assembly names to include from the default action of "embed all Copy Local references", delimited with |.</xs:documentation>
+              </xs:annotation>
+            </xs:attribute>
+            <xs:attribute name="ExcludeRuntimeAssemblies" type="xs:string">
+              <xs:annotation>
+                <xs:documentation>A list of runtime assembly names to exclude from the default action of "embed all Copy Local references", delimited with |</xs:documentation>
+              </xs:annotation>
+            </xs:attribute>
+            <xs:attribute name="IncludeRuntimeAssemblies" type="xs:string">
+              <xs:annotation>
+                <xs:documentation>A list of runtime assembly names to include from the default action of "embed all Copy Local references", delimited with |.</xs:documentation>
+              </xs:annotation>
+            </xs:attribute>
+            <xs:attribute name="Unmanaged32Assemblies" type="xs:string">
+              <xs:annotation>
+                <xs:documentation>A list of unmanaged 32 bit assembly names to include, delimited with |.</xs:documentation>
+              </xs:annotation>
+            </xs:attribute>
+            <xs:attribute name="Unmanaged64Assemblies" type="xs:string">
+              <xs:annotation>
+                <xs:documentation>A list of unmanaged 64 bit assembly names to include, delimited with |.</xs:documentation>
+              </xs:annotation>
+            </xs:attribute>
+            <xs:attribute name="PreloadOrder" type="xs:string">
+              <xs:annotation>
+                <xs:documentation>The order of preloaded assemblies, delimited with |.</xs:documentation>
+              </xs:annotation>
+            </xs:attribute>
+          </xs:complexType>
+        </xs:element>
+      </xs:all>
+      <xs:attribute name="VerifyAssembly" type="xs:boolean">
+        <xs:annotation>
+          <xs:documentation>'true' to run assembly verification (PEVerify) on the target assembly after all weavers have been executed.</xs:documentation>
+        </xs:annotation>
+      </xs:attribute>
+      <xs:attribute name="VerifyIgnoreCodes" type="xs:string">
+        <xs:annotation>
+          <xs:documentation>A comma-separated list of error codes that can be safely ignored in assembly verification.</xs:documentation>
+        </xs:annotation>
+      </xs:attribute>
+      <xs:attribute name="GenerateXsd" type="xs:boolean">
+        <xs:annotation>
+          <xs:documentation>'false' to turn off automatic generation of the XML Schema file.</xs:documentation>
+        </xs:annotation>
+      </xs:attribute>
+    </xs:complexType>
+  </xs:element>
+</xs:schema>

Properties/AssemblyInfo.cs

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+using System.Reflection;
+using System.Runtime.CompilerServices;
+using System.Runtime.InteropServices;
+
+// 有关程序集的一般信息由以下
+// 控制。更改这些特性值可修改
+// 与程序集关联的信息。
+[assembly: AssemblyTitle("Raxport.net")]
+[assembly: AssemblyDescription("convert raw to ft")]
+[assembly: AssemblyConfiguration("")]
+[assembly: AssemblyCompany("XYZ")]
+[assembly: AssemblyProduct("Raxport.net")]
+[assembly: AssemblyCopyright("Copyright XYZ © 2022")]
+[assembly: AssemblyTrademark("")]
+[assembly: AssemblyCulture("")]
+
+// 将 ComVisible 设置为 false 会使此程序集中的类型
+//对 COM 组件不可见。如果需要从 COM 访问此程序集中的类型
+//请将此类型的 ComVisible 特性设置为 true。
+[assembly: ComVisible(false)]
+
+// 如果此项目向 COM 公开，则下列 GUID 用于类型库的 ID
+[assembly: Guid("52438da8-4c10-4edc-9b60-2c6d02a36a0b")]
+
+// 程序集的版本信息由下列四个值组成: 
+//
+//      主版本
+//      次版本
+//      生成号
+//      修订号
+//
+//可以指定所有这些值，也可以使用“生成号”和“修订号”的默认值
+//通过使用 "*"，如下所示:
+// [assembly: AssemblyVersion("1.0.*")]
+[assembly: AssemblyVersion("3.4.0.0")]
+[assembly: AssemblyFileVersion("3.4.0.0")]

README.md

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+### .Net version of Raxport
+
+Raxport is a simple program which extract scans from raw file generated by mass spectrum from ThermoFisher. It support orbitrap and iontrap scan both. But the generated .FT1 or .FT2 file will have charge information only if the scan is from orbitrap. And we only support MS1 and MS2 scan up to now.
+
+### Run it on Windows
+
+It need a .Net 4.8 environment while win10 and win11 have .Net installed. So, you can run it from terminal or CMD directly. Maybe you need to install .Net 4.8 if using win7.
+
+Download the released .exe file. CD to the file directory and run
+
+```bash
+.\Raxport.exe -i 'input path' -o 'output path -j 'threads number'
+```
+
+### Run it on Linux or MAC
+
+It need a mono environment on other OS. The simplest way to install mono is by conda. Run following code to install it.
+
+```bash
+conda install -c conda-forge mono
+```
+
+Download the released .exe file. CD to the file directory and run
+
+```bash
+mono Raxport.exe -i 'input path' -o 'output path' -j 'threads number'
+```
+
+### Scan in Genrated .FT1 file 
+
+The format of .FT1 is as following picture. All chunks are split by Tab. First "H" line is software information. Second "H" is column name for peaks. Third H is instrument model. Each scan has a scan header and peaks information table. "S" line in scan header is scan number and TIC (total ion current). First "I" is retention time. Second "I" is scan type. Third "I" is scan filter.
+
+![.FT1 Scan Demo](./FT1ScanDemo.png)
+
+### Scan in Genrated .FT2 file
+
+The format of .FT2 is as following picture. All chunks are split by Tab. First "H" line is software information. Second "H" is column name for peaks. Third H is instrument model. Each scan has a scan header and peaks information table. "S" line in scan header is scan number, precursor mz and TIC (total ion current). "Z" line is precursor charge and precursor mass. First "I" is retention time. Second "I" is scan type. Third "I" is scan filter."D" line is the scan number of precursor.
+
+![.FT2 Scan Demo](./FT2ScanDemo.png)
+
+### Compile it in Visual Studio
+
+Raxport.net is developed under .Net 4.8 and relies on ThermoFisher.CommonCore.RawFileReader.dll and ThermoFisher.CommonCore.Data.dll from FreeStyle of ThermoFisher. You can clone this project and compile it in Visual Studio. You may need to install Fody from NuGet to package all .dll files to make the output binary portable.