bio-velvet_underground 0.0.1
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- checksums.yaml +7 -0
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- data/ext/src/third-party/zlib-1.2.3/win32/Makefile.bor +107 -0
- data/ext/src/third-party/zlib-1.2.3/win32/Makefile.emx +69 -0
- data/ext/src/third-party/zlib-1.2.3/win32/Makefile.gcc +141 -0
- data/ext/src/third-party/zlib-1.2.3/win32/Makefile.msc +126 -0
- data/ext/src/third-party/zlib-1.2.3/win32/VisualC.txt +3 -0
- data/ext/src/third-party/zlib-1.2.3/win32/zlib.def +60 -0
- data/ext/src/third-party/zlib-1.2.3/win32/zlib1.rc +39 -0
- data/ext/src/third-party/zlib-1.2.3/zconf.h +332 -0
- data/ext/src/third-party/zlib-1.2.3/zconf.in.h +332 -0
- data/ext/src/third-party/zlib-1.2.3/zlib.3 +159 -0
- data/ext/src/third-party/zlib-1.2.3/zlib.h +1357 -0
- data/ext/src/third-party/zlib-1.2.3/zutil.c +318 -0
- data/ext/src/third-party/zlib-1.2.3/zutil.h +269 -0
- data/lib/bio-velvet_underground.rb +12 -0
- data/lib/bio-velvet_underground/external/VERSION +1 -0
- data/lib/bio-velvet_underground/velvet_underground.rb +72 -0
- data/spec/binary_sequence_store_spec.rb +27 -0
- data/spec/data/1/CnyUnifiedSeq +0 -0
- data/spec/spec_helper.rb +31 -0
- metadata +456 -0
@@ -0,0 +1,73 @@
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Building instructions for the DLL versions of Zlib 1.2.3
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========================================================
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This directory contains projects that build zlib and minizip using
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Microsoft Visual C++ 7.0/7.1, and Visual C++ .
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You don't need to build these projects yourself. You can download the
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binaries from:
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http://www.winimage.com/zLibDll
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More information can be found at this site.
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Build instructions for Visual Studio 7.x (32 bits)
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--------------------------------------------------
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- Uncompress current zlib, including all contrib/* files
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- Download the crtdll library from
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http://www.winimage.com/zLibDll/crtdll.zip
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Unzip crtdll.zip to extract crtdll.lib on contrib\vstudio\vc7.
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- Open contrib\vstudio\vc7\zlibvc.sln with Microsoft Visual C++ 7.x
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(Visual Studio .Net 2002 or 2003).
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Build instructions for Visual Studio 2005 (32 bits or 64 bits)
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--------------------------------------------------------------
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- Uncompress current zlib, including all contrib/* files
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- For 32 bits only: download the crtdll library from
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http://www.winimage.com/zLibDll/crtdll.zip
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Unzip crtdll.zip to extract crtdll.lib on contrib\vstudio\vc8.
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- Open contrib\vstudio\vc8\zlibvc.sln with Microsoft Visual C++ 8.0
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Build instructions for Visual Studio 2005 64 bits, PSDK compiler
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----------------------------------------------------------------
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at the time of writing this text file, Visual Studio 2005 (and
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Microsoft Visual C++ 8.0) is on the beta 2 stage.
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Using you can get the free 64 bits compiler from Platform SDK,
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which is NOT a beta, and compile using the Visual studio 2005 IDE
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see http://www.winimage.com/misc/sdk64onvs2005/ for instruction
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- Uncompress current zlib, including all contrib/* files
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- start Visual Studio 2005 from a platform SDK command prompt, using
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the /useenv switch
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- Open contrib\vstudio\vc8\zlibvc.sln with Microsoft Visual C++ 8.0
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Important
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---------
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- To use zlibwapi.dll in your application, you must define the
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macro ZLIB_WINAPI when compiling your application's source files.
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Additional notes
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----------------
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- This DLL, named zlibwapi.dll, is compatible to the old zlib.dll built
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by Gilles Vollant from the zlib 1.1.x sources, and distributed at
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http://www.winimage.com/zLibDll
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It uses the WINAPI calling convention for the exported functions, and
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includes the minizip functionality. If your application needs that
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particular build of zlib.dll, you can rename zlibwapi.dll to zlib.dll.
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- The new DLL was renamed because there exist several incompatible
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versions of zlib.dll on the Internet.
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- There is also an official DLL build of zlib, named zlib1.dll. This one
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is exporting the functions using the CDECL convention. See the file
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win32\DLL_FAQ.txt found in this zlib distribution.
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- There used to be a ZLIB_DLL macro in zlib 1.1.x, but now this symbol
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has a slightly different effect. To avoid compatibility problems, do
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not define it here.
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Gilles Vollant
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info@winimage.com
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<?xml version="1.0" encoding = "Windows-1252"?>
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<VisualStudioProject
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ProjectType="Visual C++"
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Version="7.00"
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Name="miniunz"
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ProjectGUID="{C52F9E7B-498A-42BE-8DB4-85A15694382A}"
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Keyword="Win32Proj">
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<Platforms>
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<Platform
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Name="Win32"/>
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</Platforms>
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<Configurations>
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<Configuration
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Name="Debug|Win32"
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OutputDirectory="Debug"
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IntermediateDirectory="Debug"
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ConfigurationType="1"
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CharacterSet="2">
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<Tool
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Name="VCCLCompilerTool"
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Optimization="0"
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AdditionalIncludeDirectories="..\..\..;..\..\minizip"
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PreprocessorDefinitions="WIN32;ZLIB_WINAPI;_DEBUG;_CONSOLE"
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MinimalRebuild="TRUE"
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BasicRuntimeChecks="3"
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RuntimeLibrary="5"
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UsePrecompiledHeader="0"
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WarningLevel="3"
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Detect64BitPortabilityProblems="TRUE"
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DebugInformationFormat="4"/>
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<Tool
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Name="VCCustomBuildTool"/>
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<Tool
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Name="VCLinkerTool"
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OutputFile="$(OutDir)/miniunz.exe"
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LinkIncremental="2"
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GenerateDebugInformation="TRUE"
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ProgramDatabaseFile="$(OutDir)/miniunz.pdb"
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SubSystem="1"
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TargetMachine="1"/>
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<Tool
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Name="VCMIDLTool"/>
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<Tool
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Name="VCPostBuildEventTool"/>
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<Tool
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Name="VCPreBuildEventTool"/>
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<Tool
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Name="VCPreLinkEventTool"/>
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<Tool
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Name="VCResourceCompilerTool"/>
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<Tool
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Name="VCWebServiceProxyGeneratorTool"/>
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<Tool
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Name="VCWebDeploymentTool"/>
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</Configuration>
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<Configuration
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Name="Release|Win32"
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OutputDirectory="Release"
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IntermediateDirectory="Release"
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ConfigurationType="1"
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CharacterSet="2">
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<Tool
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Name="VCCLCompilerTool"
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Optimization="2"
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InlineFunctionExpansion="1"
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OmitFramePointers="TRUE"
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AdditionalIncludeDirectories="..\..\..;..\..\minizip"
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PreprocessorDefinitions="WIN32;ZLIB_WINAPI;NDEBUG;_CONSOLE"
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StringPooling="TRUE"
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RuntimeLibrary="4"
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EnableFunctionLevelLinking="TRUE"
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UsePrecompiledHeader="0"
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WarningLevel="3"
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Detect64BitPortabilityProblems="TRUE"
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DebugInformationFormat="3"/>
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<Tool
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Name="VCCustomBuildTool"/>
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<Tool
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Name="VCLinkerTool"
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OutputFile="$(OutDir)/miniunz.exe"
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LinkIncremental="1"
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GenerateDebugInformation="TRUE"
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SubSystem="1"
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OptimizeReferences="2"
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EnableCOMDATFolding="2"
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OptimizeForWindows98="1"
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TargetMachine="1"/>
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<Tool
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Name="VCMIDLTool"/>
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<Tool
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Name="VCPostBuildEventTool"/>
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<Tool
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Name="VCPreBuildEventTool"/>
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<Tool
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Name="VCPreLinkEventTool"/>
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<Tool
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Name="VCResourceCompilerTool"/>
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<Tool
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Name="VCWebServiceProxyGeneratorTool"/>
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<Tool
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Name="VCWebDeploymentTool"/>
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</Configuration>
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</Configurations>
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<Files>
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<Filter
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Name="Source Files"
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Filter="cpp;c;cxx;def;odl;idl;hpj;bat;asm">
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<File
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RelativePath="..\..\minizip\miniunz.c">
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</File>
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</Filter>
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<Filter
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Filter="h;hpp;hxx;hm;inl;inc">
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</Filter>
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<Filter
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Name="Resource Files"
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Filter="rc;ico;cur;bmp;dlg;rc2;rct;bin;rgs;gif;jpg;jpeg;jpe">
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</Filter>
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<File
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RelativePath="ReleaseDll\zlibwapi.lib">
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</File>
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</Files>
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<Globals>
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</Globals>
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</VisualStudioProject>
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<?xml version="1.0" encoding = "Windows-1252"?>
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<VisualStudioProject
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ProjectType="Visual C++"
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Version="7.00"
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Name="minizip"
|
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ProjectGUID="{48CDD9DC-E09F-4135-9C0C-4FE50C3C654B}"
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Keyword="Win32Proj">
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<Platforms>
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<Platform
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Name="Win32"/>
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</Platforms>
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<Configurations>
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<Configuration
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Name="Debug|Win32"
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OutputDirectory="Debug"
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IntermediateDirectory="Debug"
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ConfigurationType="1"
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CharacterSet="2">
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<Tool
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Name="VCCLCompilerTool"
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Optimization="0"
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AdditionalIncludeDirectories="..\..\..;..\..\minizip"
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PreprocessorDefinitions="WIN32;ZLIB_WINAPI;_DEBUG;_CONSOLE"
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MinimalRebuild="TRUE"
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BasicRuntimeChecks="3"
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RuntimeLibrary="5"
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UsePrecompiledHeader="0"
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WarningLevel="3"
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Detect64BitPortabilityProblems="TRUE"
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DebugInformationFormat="4"/>
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<Tool
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Name="VCCustomBuildTool"/>
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<Tool
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Name="VCLinkerTool"
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OutputFile="$(OutDir)/minizip.exe"
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LinkIncremental="2"
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GenerateDebugInformation="TRUE"
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ProgramDatabaseFile="$(OutDir)/minizip.pdb"
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SubSystem="1"
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TargetMachine="1"/>
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<Tool
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Name="VCMIDLTool"/>
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<Tool
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Name="VCPostBuildEventTool"/>
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<Tool
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Name="VCPreBuildEventTool"/>
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<Tool
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Name="VCPreLinkEventTool"/>
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<Tool
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Name="VCResourceCompilerTool"/>
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<Tool
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Name="VCWebServiceProxyGeneratorTool"/>
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<Tool
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Name="VCWebDeploymentTool"/>
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</Configuration>
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<Configuration
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Name="Release|Win32"
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OutputDirectory="Release"
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IntermediateDirectory="Release"
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ConfigurationType="1"
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CharacterSet="2">
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<Tool
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Name="VCCLCompilerTool"
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Optimization="2"
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InlineFunctionExpansion="1"
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OmitFramePointers="TRUE"
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AdditionalIncludeDirectories="..\..\..;..\..\minizip"
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PreprocessorDefinitions="WIN32;ZLIB_WINAPI;NDEBUG;_CONSOLE"
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StringPooling="TRUE"
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RuntimeLibrary="4"
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EnableFunctionLevelLinking="TRUE"
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UsePrecompiledHeader="0"
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WarningLevel="3"
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Detect64BitPortabilityProblems="TRUE"
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DebugInformationFormat="3"/>
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<Tool
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Name="VCCustomBuildTool"/>
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<Tool
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Name="VCLinkerTool"
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OutputFile="$(OutDir)/minizip.exe"
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LinkIncremental="1"
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GenerateDebugInformation="TRUE"
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SubSystem="1"
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OptimizeReferences="2"
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EnableCOMDATFolding="2"
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OptimizeForWindows98="1"
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TargetMachine="1"/>
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<Tool
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Name="VCMIDLTool"/>
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<Tool
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Name="VCPostBuildEventTool"/>
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<Tool
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Name="VCPreBuildEventTool"/>
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<Tool
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Name="VCPreLinkEventTool"/>
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<Tool
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Name="VCResourceCompilerTool"/>
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<Tool
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Name="VCWebServiceProxyGeneratorTool"/>
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<Tool
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Name="VCWebDeploymentTool"/>
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</Configuration>
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</Configurations>
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<Files>
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<Filter
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Name="Source Files"
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Filter="cpp;c;cxx;def;odl;idl;hpj;bat;asm">
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<File
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RelativePath="..\..\minizip\minizip.c">
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</File>
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</Filter>
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<Filter
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Name="Header Files"
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Filter="h;hpp;hxx;hm;inl;inc">
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</Filter>
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<Filter
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Name="Resource Files"
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Filter="rc;ico;cur;bmp;dlg;rc2;rct;bin;rgs;gif;jpg;jpeg;jpe">
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</Filter>
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<File
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RelativePath="ReleaseDll\zlibwapi.lib">
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</File>
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</Files>
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<Globals>
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</Globals>
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</VisualStudioProject>
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<?xml version="1.0" encoding = "Windows-1252"?>
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<VisualStudioProject
|
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ProjectType="Visual C++"
|
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Version="7.00"
|
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Name="testZlibDll"
|
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ProjectGUID="{AA6666AA-E09F-4135-9C0C-4FE50C3C654C}"
|
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Keyword="Win32Proj">
|
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<Platforms>
|
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<Platform
|
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Name="Win32"/>
|
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</Platforms>
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<Configurations>
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<Configuration
|
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Name="Debug|Win32"
|
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OutputDirectory="Debug"
|
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IntermediateDirectory="Debug"
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ConfigurationType="1"
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CharacterSet="2">
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<Tool
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Name="VCCLCompilerTool"
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Optimization="0"
|
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AdditionalIncludeDirectories="..\..\.."
|
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PreprocessorDefinitions="WIN32;ZLIB_WINAPI;_DEBUG;_CONSOLE"
|
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MinimalRebuild="TRUE"
|
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BasicRuntimeChecks="3"
|
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RuntimeLibrary="5"
|
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UsePrecompiledHeader="0"
|
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WarningLevel="3"
|
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Detect64BitPortabilityProblems="TRUE"
|
30
|
+
DebugInformationFormat="4"/>
|
31
|
+
<Tool
|
32
|
+
Name="VCCustomBuildTool"/>
|
33
|
+
<Tool
|
34
|
+
Name="VCLinkerTool"
|
35
|
+
OutputFile="$(OutDir)/testzlib.exe"
|
36
|
+
LinkIncremental="2"
|
37
|
+
GenerateDebugInformation="TRUE"
|
38
|
+
ProgramDatabaseFile="$(OutDir)/testzlib.pdb"
|
39
|
+
SubSystem="1"
|
40
|
+
TargetMachine="1"/>
|
41
|
+
<Tool
|
42
|
+
Name="VCMIDLTool"/>
|
43
|
+
<Tool
|
44
|
+
Name="VCPostBuildEventTool"/>
|
45
|
+
<Tool
|
46
|
+
Name="VCPreBuildEventTool"/>
|
47
|
+
<Tool
|
48
|
+
Name="VCPreLinkEventTool"/>
|
49
|
+
<Tool
|
50
|
+
Name="VCResourceCompilerTool"/>
|
51
|
+
<Tool
|
52
|
+
Name="VCWebServiceProxyGeneratorTool"/>
|
53
|
+
<Tool
|
54
|
+
Name="VCWebDeploymentTool"/>
|
55
|
+
</Configuration>
|
56
|
+
<Configuration
|
57
|
+
Name="Release|Win32"
|
58
|
+
OutputDirectory="Release"
|
59
|
+
IntermediateDirectory="Release"
|
60
|
+
ConfigurationType="1"
|
61
|
+
CharacterSet="2">
|
62
|
+
<Tool
|
63
|
+
Name="VCCLCompilerTool"
|
64
|
+
Optimization="2"
|
65
|
+
InlineFunctionExpansion="1"
|
66
|
+
OmitFramePointers="TRUE"
|
67
|
+
AdditionalIncludeDirectories="..\..\.."
|
68
|
+
PreprocessorDefinitions="WIN32;ZLIB_WINAPI;NDEBUG;_CONSOLE"
|
69
|
+
StringPooling="TRUE"
|
70
|
+
RuntimeLibrary="4"
|
71
|
+
EnableFunctionLevelLinking="TRUE"
|
72
|
+
UsePrecompiledHeader="0"
|
73
|
+
WarningLevel="3"
|
74
|
+
Detect64BitPortabilityProblems="TRUE"
|
75
|
+
DebugInformationFormat="3"/>
|
76
|
+
<Tool
|
77
|
+
Name="VCCustomBuildTool"/>
|
78
|
+
<Tool
|
79
|
+
Name="VCLinkerTool"
|
80
|
+
OutputFile="$(OutDir)/testzlib.exe"
|
81
|
+
LinkIncremental="1"
|
82
|
+
GenerateDebugInformation="TRUE"
|
83
|
+
SubSystem="1"
|
84
|
+
OptimizeReferences="2"
|
85
|
+
EnableCOMDATFolding="2"
|
86
|
+
OptimizeForWindows98="1"
|
87
|
+
TargetMachine="1"/>
|
88
|
+
<Tool
|
89
|
+
Name="VCMIDLTool"/>
|
90
|
+
<Tool
|
91
|
+
Name="VCPostBuildEventTool"/>
|
92
|
+
<Tool
|
93
|
+
Name="VCPreBuildEventTool"/>
|
94
|
+
<Tool
|
95
|
+
Name="VCPreLinkEventTool"/>
|
96
|
+
<Tool
|
97
|
+
Name="VCResourceCompilerTool"/>
|
98
|
+
<Tool
|
99
|
+
Name="VCWebServiceProxyGeneratorTool"/>
|
100
|
+
<Tool
|
101
|
+
Name="VCWebDeploymentTool"/>
|
102
|
+
</Configuration>
|
103
|
+
</Configurations>
|
104
|
+
<Files>
|
105
|
+
<Filter
|
106
|
+
Name="Source Files"
|
107
|
+
Filter="cpp;c;cxx;def;odl;idl;hpj;bat;asm">
|
108
|
+
<File
|
109
|
+
RelativePath="..\..\testzlib\testzlib.c">
|
110
|
+
</File>
|
111
|
+
</Filter>
|
112
|
+
<Filter
|
113
|
+
Name="Header Files"
|
114
|
+
Filter="h;hpp;hxx;hm;inl;inc">
|
115
|
+
</Filter>
|
116
|
+
<Filter
|
117
|
+
Name="Resource Files"
|
118
|
+
Filter="rc;ico;cur;bmp;dlg;rc2;rct;bin;rgs;gif;jpg;jpeg;jpe">
|
119
|
+
</Filter>
|
120
|
+
<File
|
121
|
+
RelativePath="ReleaseDll\zlibwapi.lib">
|
122
|
+
</File>
|
123
|
+
</Files>
|
124
|
+
<Globals>
|
125
|
+
</Globals>
|
126
|
+
</VisualStudioProject>
|