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v3.6.9
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@shengqh
shengqh committed Nov 12, 2014
1 parent 15f15aa commit 596d98e
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Showing 6 changed files with 106 additions and 50 deletions.
22 changes: 12 additions & 10 deletions MainForm.cs
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Expand Up @@ -18,7 +18,6 @@
using RCPA.Tools.Modification;
using RCPA.Tools.Quantification;
using RCPA.Tools.Quantification.Lipid;
using RCPA.Tools.Quantification.SmallMolecule;
using RCPA.Tools.Raw;
using RCPA.Tools.Sequest;
using RCPA.Tools.Summary;
Expand All @@ -39,6 +38,7 @@
using RCPA;
using RCPA.Proteomics.Quantification.IsobaricLabelling;
using RCPA.Proteomics.ProteomeDiscoverer;
using RCPA.Proteomics.Percolator;

namespace ProteomicsTools
{
Expand Down Expand Up @@ -123,6 +123,8 @@ public MainForm()
AddCommand(new SnpPeptideDistillerUI.Command());
AddCommand(new TargetPeptideDistillerUI.Command());

AddCommand(new MultiplePercolatorPeptideDistillerUI.Command());

AddCommand(new ToolCommandSeparator(MenuCommandType.Distiller));

AddCommand(new IdentifiedPeptidesDistillerUI.Command());
Expand Down Expand Up @@ -198,18 +200,18 @@ public MainForm()

AddCommand(new ToolCommandSeparator(MenuCommandType.Quantification));

AddCommand(new AgilentToMS1BuilderUI.Command());
//AddCommand(new AgilentToMS1BuilderUI.Command());

#if (!PublicVersion)
AddCommand(new ToolCommandSeparator(MenuCommandType.Quantification));

AddCommand(new SmallMoleculeDataPreparationProcessorUI.Command());
AddCommand(new SmallMoleculeDataMostIntensityBuilderUI.Command());
AddCommand(new SmallMoleculeSignificantPeakFinderUI.Command());
AddCommand(new SmallMoleculeQuantificationViewerUI.Command());
AddCommand(new SmallMoleculeDataImageBuilderUI.Command());
//AddCommand(new SmallMoleculeDataPreparationProcessorUI.Command());
//AddCommand(new SmallMoleculeDataMostIntensityBuilderUI.Command());
//AddCommand(new SmallMoleculeSignificantPeakFinderUI.Command());
//AddCommand(new SmallMoleculeQuantificationViewerUI.Command());
//AddCommand(new SmallMoleculeDataImageBuilderUI.Command());

AddCommand(new ToolCommandSeparator(MenuCommandType.Quantification));
//AddCommand(new ToolCommandSeparator(MenuCommandType.Quantification));
AddCommand(new ForwardReverseRatioCalibratorUI.Command());

AddCommand(new ProteinChromotographViewer.Command());
Expand Down Expand Up @@ -249,7 +251,7 @@ public MainForm()
//Sequest
AddCommand(new One2AllProcessorCommand());
AddCommand(new AtomCompositionIsotopicProfileBuilderCommand());
AddCommand(new NGlycanPeptideMassCalculatorCommand());
//AddCommand(new NGlycanPeptideMassCalculatorCommand());

//Database
AddCommand(new ReversedDatabaseBuilderCommand());
Expand All @@ -267,7 +269,7 @@ public MainForm()
AddCommand(new MassCalculatorUI.Command());
AddCommand(new IdentifiedPeptideSubtractorUI.Command());
AddCommand(new RawFileViewerUI.Command());
AddCommand(new AgilentFileViewerUI.Command());
//AddCommand(new AgilentFileViewerUI.Command());
AddCommand(new GenerateIsotopicFileUI.Command());

#if (!PublicVersion)
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2 changes: 1 addition & 1 deletion Properties/RcpaToolsAssembly.cs
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Expand Up @@ -15,6 +15,6 @@ static class RcpaToolsAssembly
internal const string Author = "Quanhu SHENG";
internal const string Company = "RCPA/CQS";
internal const string Copyright = "Copyright (C) 2006-2014 " + Company;
internal const string Version = "3.6.5";
internal const string Version = "3.6.9";
internal const string InformationalVersion = Version;
}
99 changes: 66 additions & 33 deletions RCPA.Tools.csproj
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Expand Up @@ -12,14 +12,10 @@
<AssemblyName>ProteomicsTools</AssemblyName>
<StartupObject>
</StartupObject>
<SccProjectName>
</SccProjectName>
<SccLocalPath>
</SccLocalPath>
<SccAuxPath>
</SccAuxPath>
<SccProvider>
</SccProvider>
<SccProjectName>Svn</SccProjectName>
<SccLocalPath>Svn</SccLocalPath>
<SccAuxPath>Svn</SccAuxPath>
<SccProvider>SubversionScc</SccProvider>
<IsWebBootstrapper>true</IsWebBootstrapper>
<FileUpgradeFlags>
</FileUpgradeFlags>
Expand All @@ -46,6 +42,8 @@
<ApplicationVersion>1.0.0.%2a</ApplicationVersion>
<UseApplicationTrust>false</UseApplicationTrust>
<BootstrapperEnabled>true</BootstrapperEnabled>
<SolutionDir Condition="$(SolutionDir) == '' Or $(SolutionDir) == '*Undefined*'">..\</SolutionDir>
<RestorePackages>true</RestorePackages>
</PropertyGroup>
<PropertyGroup Condition=" '$(Configuration)|$(Platform)' == 'Debug|AnyCPU' ">
<DebugSymbols>true</DebugSymbols>
Expand All @@ -65,47 +63,85 @@
<DebugType>pdbonly</DebugType>
<Optimize>true</Optimize>
<OutputPath>bin\Release\</OutputPath>
<DefineConstants>TRACE</DefineConstants>
<DefineConstants>
</DefineConstants>
<ErrorReport>prompt</ErrorReport>
<WarningLevel>4</WarningLevel>
<PlatformTarget>x64</PlatformTarget>
<CodeAnalysisRuleSet>AllRules.ruleset</CodeAnalysisRuleSet>
<AllowUnsafeBlocks>true</AllowUnsafeBlocks>
</PropertyGroup>
<PropertyGroup Condition="'$(Configuration)|$(Platform)' == 'Win32|AnyCPU'">
<OutputPath>bin\Win32\</OutputPath>
<DefineConstants>
</DefineConstants>
<Optimize>true</Optimize>
<DebugType>pdbonly</DebugType>
<PlatformTarget>AnyCPU</PlatformTarget>
<PlatformTarget>x86</PlatformTarget>
<ErrorReport>prompt</ErrorReport>
<CodeAnalysisRuleSet>AllRules.ruleset</CodeAnalysisRuleSet>
<AllowUnsafeBlocks>true</AllowUnsafeBlocks>
</PropertyGroup>
<PropertyGroup Condition="'$(Configuration)|$(Platform)' == 'Debug|x64'">
<DebugSymbols>true</DebugSymbols>
<OutputPath>bin\x64\Debug\</OutputPath>
<DefineConstants>DEBUG;TRACE</DefineConstants>
<DebugType>full</DebugType>
<PlatformTarget>x64</PlatformTarget>
<ErrorReport>prompt</ErrorReport>
<CodeAnalysisRuleSet>AllRules.ruleset</CodeAnalysisRuleSet>
</PropertyGroup>
<PropertyGroup Condition="'$(Configuration)|$(Platform)' == 'Release|x64'">
<OutputPath>bin\x64\Release\</OutputPath>
<DefineConstants>TRACE</DefineConstants>
<Optimize>true</Optimize>
<DebugType>pdbonly</DebugType>
<PlatformTarget>x64</PlatformTarget>
<ErrorReport>prompt</ErrorReport>
<CodeAnalysisRuleSet>AllRules.ruleset</CodeAnalysisRuleSet>
</PropertyGroup>
<PropertyGroup Condition="'$(Configuration)|$(Platform)' == 'Win32|x64'">
<OutputPath>bin\x64\Win32\</OutputPath>
<AllowUnsafeBlocks>true</AllowUnsafeBlocks>
<Optimize>true</Optimize>
<DebugType>pdbonly</DebugType>
<PlatformTarget>x64</PlatformTarget>
<ErrorReport>prompt</ErrorReport>
<CodeAnalysisRuleSet>AllRules.ruleset</CodeAnalysisRuleSet>
</PropertyGroup>
<PropertyGroup Condition="'$(Configuration)|$(Platform)' == 'Debug|x86'">
<DebugSymbols>true</DebugSymbols>
<OutputPath>bin\x86\Debug\</OutputPath>
<DefineConstants>DEBUG;TRACE</DefineConstants>
<DebugType>full</DebugType>
<PlatformTarget>x86</PlatformTarget>
<ErrorReport>prompt</ErrorReport>
<CodeAnalysisRuleSet>AllRules.ruleset</CodeAnalysisRuleSet>
</PropertyGroup>
<PropertyGroup Condition="'$(Configuration)|$(Platform)' == 'Release|x86'">
<OutputPath>bin\x86\Release\</OutputPath>
<DefineConstants>TRACE</DefineConstants>
<Optimize>true</Optimize>
<DebugType>pdbonly</DebugType>
<PlatformTarget>x86</PlatformTarget>
<ErrorReport>prompt</ErrorReport>
<CodeAnalysisRuleSet>AllRules.ruleset</CodeAnalysisRuleSet>
</PropertyGroup>
<PropertyGroup Condition="'$(Configuration)|$(Platform)' == 'Win32|x86'">
<OutputPath>bin\x86\Win32\</OutputPath>
<AllowUnsafeBlocks>true</AllowUnsafeBlocks>
<Optimize>true</Optimize>
<DebugType>pdbonly</DebugType>
<PlatformTarget>x86</PlatformTarget>
<ErrorReport>prompt</ErrorReport>
<CodeAnalysisRuleSet>AllRules.ruleset</CodeAnalysisRuleSet>
</PropertyGroup>
<ItemGroup>
<Reference Include="DigitalRune.Windows.Docking">
<HintPath>..\SQH.Lib\DigitalRune.Windows.Docking.dll</HintPath>
</Reference>
<Reference Include="MathNet.Numerics, Version=2.6.1.30, Culture=neutral, processorArchitecture=MSIL">
<SpecificVersion>False</SpecificVersion>
<HintPath>..\packages\MathNet.Numerics.2.6.2\lib\net40\MathNet.Numerics.dll</HintPath>
</Reference>
<Reference Include="MathNet.Numerics.IO">
<HintPath>..\packages\MathNet.Numerics.2.6.2\lib\net40\MathNet.Numerics.IO.dll</HintPath>
</Reference>
<Reference Include="nunit.framework">
<HintPath>..\packages\NUnit.2.5.7.10213\lib\nunit.framework.dll</HintPath>
</Reference>
<Reference Include="nunit.mocks">
<HintPath>..\packages\NUnit.2.5.7.10213\lib\nunit.mocks.dll</HintPath>
</Reference>
<Reference Include="pnunit.framework">
<HintPath>..\packages\NUnit.2.5.7.10213\lib\pnunit.framework.dll</HintPath>
</Reference>
<Reference Include="ProgressFormNET">
<HintPath>..\SQH.Lib\ProgressFormNET.dll</HintPath>
</Reference>
<Reference Include="System" />
<Reference Include="System.ComponentModel.DataAnnotations" />
<Reference Include="System.Configuration" />
<Reference Include="System.Core">
<RequiredTargetFramework>3.5</RequiredTargetFramework>
Expand All @@ -121,9 +157,6 @@
<Reference Include="System.Xml.Linq">
<RequiredTargetFramework>3.5</RequiredTargetFramework>
</Reference>
<Reference Include="ZedGraph">
<HintPath>..\SQH.Lib\ZedGraph.dll</HintPath>
</Reference>
</ItemGroup>
<ItemGroup>
<Compile Include="MainForm.cs">
Expand Down Expand Up @@ -188,7 +221,6 @@
<SubType>Designer</SubType>
<CopyToOutputDirectory>PreserveNewest</CopyToOutputDirectory>
</None>
<None Include="packages.config" />
<None Include="Properties\Settings.settings">
<Generator>SettingsSingleFileGenerator</Generator>
<LastGenOutput>Settings.Designer.cs</LastGenOutput>
Expand Down Expand Up @@ -295,4 +327,5 @@
<PreBuildEvent>copy "$(SolutionDir)RCPA.Tools.wiki\HOME.md" "$(ProjectDir)README.md"
</PreBuildEvent>
</PropertyGroup>
<Import Project="$(SolutionDir)\.nuget\nuget.targets" />
</Project>
12 changes: 12 additions & 0 deletions README.md
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Expand Up @@ -59,6 +59,18 @@ The c# source code is also provided at following repositories. Visual Studio 201
<a name="Changes"/>
#Changes

2014/11/12 Version 3.6.9
New feature: Extract peptide information from percolator input.xml and output.xml.

2014/10/16 Version 3.6.8
Bugfixed: Compatible with Mascot dat file with decoy searching.

2014/10/16 Version 3.6.7
Bugfixed: Modification parse error for mascot MSF file.

2014/10/15 Version 3.6.6
Bugfixed: Modification parse error for decoy entry in MSF file.

2014/10/14 Version 3.6.5
Bugfixed: Error "bad format" when parsing xtandem xml file.

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15 changes: 15 additions & 0 deletions app.config
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@@ -1,5 +1,9 @@
<?xml version="1.0" encoding="utf-8"?>
<configuration>
<configSections>
<!-- For more information on Entity Framework configuration, visit http://go.microsoft.com/fwlink/?LinkID=237468 -->
<section name="entityFramework" type="System.Data.Entity.Internal.ConfigFile.EntityFrameworkSection, EntityFramework, Version=6.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089" requirePermission="false" />
</configSections>
<runtime>
<assemblyBinding xmlns="urn:schemas-microsoft-com:asm.v1">
<dependentAssembly>
Expand All @@ -15,4 +19,15 @@
<startup>
<supportedRuntime version="v4.0" sku=".NETFramework,Version=v4.0" />
</startup>
<entityFramework>
<defaultConnectionFactory type="System.Data.Entity.Infrastructure.LocalDbConnectionFactory, EntityFramework">
<parameters>
<parameter value="v11.0" />
</parameters>
</defaultConnectionFactory>
<providers>
<provider invariantName="System.Data.SqlClient" type="System.Data.Entity.SqlServer.SqlProviderServices, EntityFramework.SqlServer" />
<provider invariantName="System.Data.SQLite.EF6" type="System.Data.SQLite.EF6.SQLiteProviderServices, System.Data.SQLite.EF6" />
</providers>
</entityFramework>
</configuration>
6 changes: 0 additions & 6 deletions packages.config
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