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/uncompr.c +61 -0
- data/ext/src/third-party/zlib-1.2.3/win32/DLL_FAQ.txt +397 -0
- 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 +1,31 @@
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/* puff.h
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Copyright (C) 2002, 2003 Mark Adler, all rights reserved
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version 1.7, 3 Mar 2002
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This software is provided 'as-is', without any express or implied
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warranty. In no event will the author be held liable for any damages
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arising from the use of this software.
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Permission is granted to anyone to use this software for any purpose,
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including commercial applications, and to alter it and redistribute it
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freely, subject to the following restrictions:
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1. The origin of this software must not be misrepresented; you must not
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claim that you wrote the original software. If you use this software
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in a product, an acknowledgment in the product documentation would be
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appreciated but is not required.
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2. Altered source versions must be plainly marked as such, and must not be
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misrepresented as being the original software.
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3. This notice may not be removed or altered from any source distribution.
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Mark Adler madler@alumni.caltech.edu
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*/
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/*
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* See puff.c for purpose and usage.
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*/
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int puff(unsigned char *dest, /* pointer to destination pointer */
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unsigned long *destlen, /* amount of output space */
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unsigned char *source, /* pointer to source data pointer */
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unsigned long *sourcelen); /* amount of input available */
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Binary file
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@@ -0,0 +1,275 @@
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#include <stdio.h>
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#include <stdlib.h>
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#include <windows.h>
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#include "zlib.h"
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void MyDoMinus64(LARGE_INTEGER *R,LARGE_INTEGER A,LARGE_INTEGER B)
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{
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R->HighPart = A.HighPart - B.HighPart;
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if (A.LowPart >= B.LowPart)
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R->LowPart = A.LowPart - B.LowPart;
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else
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{
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R->LowPart = A.LowPart - B.LowPart;
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R->HighPart --;
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}
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}
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#ifdef _M_X64
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// see http://msdn2.microsoft.com/library/twchhe95(en-us,vs.80).aspx for __rdtsc
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unsigned __int64 __rdtsc(void);
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void BeginCountRdtsc(LARGE_INTEGER * pbeginTime64)
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{
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// printf("rdtsc = %I64x\n",__rdtsc());
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pbeginTime64->QuadPart=__rdtsc();
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}
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LARGE_INTEGER GetResRdtsc(LARGE_INTEGER beginTime64,BOOL fComputeTimeQueryPerf)
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{
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LARGE_INTEGER LIres;
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unsigned _int64 res=__rdtsc()-((unsigned _int64)(beginTime64.QuadPart));
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LIres.QuadPart=res;
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// printf("rdtsc = %I64x\n",__rdtsc());
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return LIres;
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}
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#else
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#ifdef _M_IX86
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void myGetRDTSC32(LARGE_INTEGER * pbeginTime64)
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{
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DWORD dwEdx,dwEax;
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_asm
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{
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rdtsc
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mov dwEax,eax
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mov dwEdx,edx
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}
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pbeginTime64->LowPart=dwEax;
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pbeginTime64->HighPart=dwEdx;
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}
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|
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void BeginCountRdtsc(LARGE_INTEGER * pbeginTime64)
|
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{
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myGetRDTSC32(pbeginTime64);
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}
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56
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LARGE_INTEGER GetResRdtsc(LARGE_INTEGER beginTime64,BOOL fComputeTimeQueryPerf)
|
58
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{
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59
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LARGE_INTEGER LIres,endTime64;
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60
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myGetRDTSC32(&endTime64);
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LIres.LowPart=LIres.HighPart=0;
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MyDoMinus64(&LIres,endTime64,beginTime64);
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return LIres;
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}
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#else
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void myGetRDTSC32(LARGE_INTEGER * pbeginTime64)
|
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{
|
69
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}
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void BeginCountRdtsc(LARGE_INTEGER * pbeginTime64)
|
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{
|
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}
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74
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|
75
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LARGE_INTEGER GetResRdtsc(LARGE_INTEGER beginTime64,BOOL fComputeTimeQueryPerf)
|
76
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{
|
77
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LARGE_INTEGER lr;
|
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lr.QuadPart=0;
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return lr;
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}
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#endif
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#endif
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void BeginCountPerfCounter(LARGE_INTEGER * pbeginTime64,BOOL fComputeTimeQueryPerf)
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85
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{
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86
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if ((!fComputeTimeQueryPerf) || (!QueryPerformanceCounter(pbeginTime64)))
|
87
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{
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88
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pbeginTime64->LowPart = GetTickCount();
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89
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pbeginTime64->HighPart = 0;
|
90
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}
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91
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}
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92
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|
93
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DWORD GetMsecSincePerfCounter(LARGE_INTEGER beginTime64,BOOL fComputeTimeQueryPerf)
|
94
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{
|
95
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LARGE_INTEGER endTime64,ticksPerSecond,ticks;
|
96
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DWORDLONG ticksShifted,tickSecShifted;
|
97
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DWORD dwLog=16+0;
|
98
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DWORD dwRet;
|
99
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if ((!fComputeTimeQueryPerf) || (!QueryPerformanceCounter(&endTime64)))
|
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dwRet = (GetTickCount() - beginTime64.LowPart)*1;
|
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else
|
102
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{
|
103
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MyDoMinus64(&ticks,endTime64,beginTime64);
|
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QueryPerformanceFrequency(&ticksPerSecond);
|
105
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+
|
106
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+
|
107
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{
|
108
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ticksShifted = Int64ShrlMod32(*(DWORDLONG*)&ticks,dwLog);
|
109
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tickSecShifted = Int64ShrlMod32(*(DWORDLONG*)&ticksPerSecond,dwLog);
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110
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+
|
111
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}
|
112
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+
|
113
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dwRet = (DWORD)((((DWORD)ticksShifted)*1000)/(DWORD)(tickSecShifted));
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dwRet *=1;
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115
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}
|
116
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return dwRet;
|
117
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}
|
118
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+
|
119
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int ReadFileMemory(const char* filename,long* plFileSize,void** pFilePtr)
|
120
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{
|
121
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FILE* stream;
|
122
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void* ptr;
|
123
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int retVal=1;
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stream=fopen(filename, "rb");
|
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if (stream==NULL)
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return 0;
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127
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+
|
128
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fseek(stream,0,SEEK_END);
|
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*plFileSize=ftell(stream);
|
131
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fseek(stream,0,SEEK_SET);
|
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ptr=malloc((*plFileSize)+1);
|
133
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if (ptr==NULL)
|
134
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retVal=0;
|
135
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+
else
|
136
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{
|
137
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if (fread(ptr, 1, *plFileSize,stream) != (*plFileSize))
|
138
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retVal=0;
|
139
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}
|
140
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fclose(stream);
|
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*pFilePtr=ptr;
|
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return retVal;
|
143
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+
}
|
144
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+
|
145
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+
int main(int argc, char *argv[])
|
146
|
+
{
|
147
|
+
int BlockSizeCompress=0x8000;
|
148
|
+
int BlockSizeUncompress=0x8000;
|
149
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+
int cprLevel=Z_DEFAULT_COMPRESSION ;
|
150
|
+
long lFileSize;
|
151
|
+
unsigned char* FilePtr;
|
152
|
+
long lBufferSizeCpr;
|
153
|
+
long lBufferSizeUncpr;
|
154
|
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long lCompressedSize=0;
|
155
|
+
unsigned char* CprPtr;
|
156
|
+
unsigned char* UncprPtr;
|
157
|
+
long lSizeCpr,lSizeUncpr;
|
158
|
+
DWORD dwGetTick,dwMsecQP;
|
159
|
+
LARGE_INTEGER li_qp,li_rdtsc,dwResRdtsc;
|
160
|
+
|
161
|
+
if (argc<=1)
|
162
|
+
{
|
163
|
+
printf("run TestZlib <File> [BlockSizeCompress] [BlockSizeUncompress] [compres. level]\n");
|
164
|
+
return 0;
|
165
|
+
}
|
166
|
+
|
167
|
+
if (ReadFileMemory(argv[1],&lFileSize,&FilePtr)==0)
|
168
|
+
{
|
169
|
+
printf("error reading %s\n",argv[1]);
|
170
|
+
return 1;
|
171
|
+
}
|
172
|
+
else printf("file %s read, %u bytes\n",argv[1],lFileSize);
|
173
|
+
|
174
|
+
if (argc>=3)
|
175
|
+
BlockSizeCompress=atol(argv[2]);
|
176
|
+
|
177
|
+
if (argc>=4)
|
178
|
+
BlockSizeUncompress=atol(argv[3]);
|
179
|
+
|
180
|
+
if (argc>=5)
|
181
|
+
cprLevel=(int)atol(argv[4]);
|
182
|
+
|
183
|
+
lBufferSizeCpr = lFileSize + (lFileSize/0x10) + 0x200;
|
184
|
+
lBufferSizeUncpr = lBufferSizeCpr;
|
185
|
+
|
186
|
+
CprPtr=(unsigned char*)malloc(lBufferSizeCpr + BlockSizeCompress);
|
187
|
+
|
188
|
+
BeginCountPerfCounter(&li_qp,TRUE);
|
189
|
+
dwGetTick=GetTickCount();
|
190
|
+
BeginCountRdtsc(&li_rdtsc);
|
191
|
+
{
|
192
|
+
z_stream zcpr;
|
193
|
+
int ret=Z_OK;
|
194
|
+
long lOrigToDo = lFileSize;
|
195
|
+
long lOrigDone = 0;
|
196
|
+
int step=0;
|
197
|
+
memset(&zcpr,0,sizeof(z_stream));
|
198
|
+
deflateInit(&zcpr,cprLevel);
|
199
|
+
|
200
|
+
zcpr.next_in = FilePtr;
|
201
|
+
zcpr.next_out = CprPtr;
|
202
|
+
|
203
|
+
|
204
|
+
do
|
205
|
+
{
|
206
|
+
long all_read_before = zcpr.total_in;
|
207
|
+
zcpr.avail_in = min(lOrigToDo,BlockSizeCompress);
|
208
|
+
zcpr.avail_out = BlockSizeCompress;
|
209
|
+
ret=deflate(&zcpr,(zcpr.avail_in==lOrigToDo) ? Z_FINISH : Z_SYNC_FLUSH);
|
210
|
+
lOrigDone += (zcpr.total_in-all_read_before);
|
211
|
+
lOrigToDo -= (zcpr.total_in-all_read_before);
|
212
|
+
step++;
|
213
|
+
} while (ret==Z_OK);
|
214
|
+
|
215
|
+
lSizeCpr=zcpr.total_out;
|
216
|
+
deflateEnd(&zcpr);
|
217
|
+
dwGetTick=GetTickCount()-dwGetTick;
|
218
|
+
dwMsecQP=GetMsecSincePerfCounter(li_qp,TRUE);
|
219
|
+
dwResRdtsc=GetResRdtsc(li_rdtsc,TRUE);
|
220
|
+
printf("total compress size = %u, in %u step\n",lSizeCpr,step);
|
221
|
+
printf("time = %u msec = %f sec\n",dwGetTick,dwGetTick/(double)1000.);
|
222
|
+
printf("defcpr time QP = %u msec = %f sec\n",dwMsecQP,dwMsecQP/(double)1000.);
|
223
|
+
printf("defcpr result rdtsc = %I64x\n\n",dwResRdtsc.QuadPart);
|
224
|
+
}
|
225
|
+
|
226
|
+
CprPtr=(unsigned char*)realloc(CprPtr,lSizeCpr);
|
227
|
+
UncprPtr=(unsigned char*)malloc(lBufferSizeUncpr + BlockSizeUncompress);
|
228
|
+
|
229
|
+
BeginCountPerfCounter(&li_qp,TRUE);
|
230
|
+
dwGetTick=GetTickCount();
|
231
|
+
BeginCountRdtsc(&li_rdtsc);
|
232
|
+
{
|
233
|
+
z_stream zcpr;
|
234
|
+
int ret=Z_OK;
|
235
|
+
long lOrigToDo = lSizeCpr;
|
236
|
+
long lOrigDone = 0;
|
237
|
+
int step=0;
|
238
|
+
memset(&zcpr,0,sizeof(z_stream));
|
239
|
+
inflateInit(&zcpr);
|
240
|
+
|
241
|
+
zcpr.next_in = CprPtr;
|
242
|
+
zcpr.next_out = UncprPtr;
|
243
|
+
|
244
|
+
|
245
|
+
do
|
246
|
+
{
|
247
|
+
long all_read_before = zcpr.total_in;
|
248
|
+
zcpr.avail_in = min(lOrigToDo,BlockSizeUncompress);
|
249
|
+
zcpr.avail_out = BlockSizeUncompress;
|
250
|
+
ret=inflate(&zcpr,Z_SYNC_FLUSH);
|
251
|
+
lOrigDone += (zcpr.total_in-all_read_before);
|
252
|
+
lOrigToDo -= (zcpr.total_in-all_read_before);
|
253
|
+
step++;
|
254
|
+
} while (ret==Z_OK);
|
255
|
+
|
256
|
+
lSizeUncpr=zcpr.total_out;
|
257
|
+
inflateEnd(&zcpr);
|
258
|
+
dwGetTick=GetTickCount()-dwGetTick;
|
259
|
+
dwMsecQP=GetMsecSincePerfCounter(li_qp,TRUE);
|
260
|
+
dwResRdtsc=GetResRdtsc(li_rdtsc,TRUE);
|
261
|
+
printf("total uncompress size = %u, in %u step\n",lSizeUncpr,step);
|
262
|
+
printf("time = %u msec = %f sec\n",dwGetTick,dwGetTick/(double)1000.);
|
263
|
+
printf("uncpr time QP = %u msec = %f sec\n",dwMsecQP,dwMsecQP/(double)1000.);
|
264
|
+
printf("uncpr result rdtsc = %I64x\n\n",dwResRdtsc.QuadPart);
|
265
|
+
}
|
266
|
+
|
267
|
+
if (lSizeUncpr==lFileSize)
|
268
|
+
{
|
269
|
+
if (memcmp(FilePtr,UncprPtr,lFileSize)==0)
|
270
|
+
printf("compare ok\n");
|
271
|
+
|
272
|
+
}
|
273
|
+
|
274
|
+
return 0;
|
275
|
+
}
|
@@ -0,0 +1,14 @@
|
|
1
|
+
CC=cc
|
2
|
+
CFLAGS=-g
|
3
|
+
|
4
|
+
untgz: untgz.o ../../libz.a
|
5
|
+
$(CC) $(CFLAGS) -o untgz untgz.o -L../.. -lz
|
6
|
+
|
7
|
+
untgz.o: untgz.c ../../zlib.h
|
8
|
+
$(CC) $(CFLAGS) -c -I../.. untgz.c
|
9
|
+
|
10
|
+
../../libz.a:
|
11
|
+
cd ../..; ./configure; make
|
12
|
+
|
13
|
+
clean:
|
14
|
+
rm -f untgz untgz.o *~
|
@@ -0,0 +1,17 @@
|
|
1
|
+
CC=cl
|
2
|
+
CFLAGS=-MD
|
3
|
+
|
4
|
+
untgz.exe: untgz.obj ..\..\zlib.lib
|
5
|
+
$(CC) $(CFLAGS) untgz.obj ..\..\zlib.lib
|
6
|
+
|
7
|
+
untgz.obj: untgz.c ..\..\zlib.h
|
8
|
+
$(CC) $(CFLAGS) -c -I..\.. untgz.c
|
9
|
+
|
10
|
+
..\..\zlib.lib:
|
11
|
+
cd ..\..
|
12
|
+
$(MAKE) -f win32\makefile.msc
|
13
|
+
cd contrib\untgz
|
14
|
+
|
15
|
+
clean:
|
16
|
+
-del untgz.obj
|
17
|
+
-del untgz.exe
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@@ -0,0 +1,674 @@
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1
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+
/*
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2
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+
* untgz.c -- Display contents and extract files from a gzip'd TAR file
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3
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*
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4
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* written by Pedro A. Aranda Gutierrez <paag@tid.es>
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5
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* adaptation to Unix by Jean-loup Gailly <jloup@gzip.org>
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6
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* various fixes by Cosmin Truta <cosmint@cs.ubbcluj.ro>
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*/
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8
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+
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9
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#include <stdio.h>
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10
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#include <stdlib.h>
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11
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#include <string.h>
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12
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#include <time.h>
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13
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#include <errno.h>
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14
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15
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#include "zlib.h"
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#ifdef unix
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# include <unistd.h>
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#else
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# include <direct.h>
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# include <io.h>
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#endif
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#ifdef WIN32
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#include <windows.h>
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# ifndef F_OK
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# define F_OK 0
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# endif
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# define mkdir(dirname,mode) _mkdir(dirname)
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# ifdef _MSC_VER
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# define access(path,mode) _access(path,mode)
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# define chmod(path,mode) _chmod(path,mode)
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# define strdup(str) _strdup(str)
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# endif
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#else
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# include <utime.h>
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#endif
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38
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+
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39
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+
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40
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/* values used in typeflag field */
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41
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+
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42
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#define REGTYPE '0' /* regular file */
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43
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#define AREGTYPE '\0' /* regular file */
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44
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#define LNKTYPE '1' /* link */
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45
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#define SYMTYPE '2' /* reserved */
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46
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#define CHRTYPE '3' /* character special */
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#define BLKTYPE '4' /* block special */
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48
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#define DIRTYPE '5' /* directory */
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49
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#define FIFOTYPE '6' /* FIFO special */
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50
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#define CONTTYPE '7' /* reserved */
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51
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+
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52
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/* GNU tar extensions */
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53
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+
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54
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#define GNUTYPE_DUMPDIR 'D' /* file names from dumped directory */
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55
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#define GNUTYPE_LONGLINK 'K' /* long link name */
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56
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#define GNUTYPE_LONGNAME 'L' /* long file name */
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#define GNUTYPE_MULTIVOL 'M' /* continuation of file from another volume */
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#define GNUTYPE_NAMES 'N' /* file name that does not fit into main hdr */
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59
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#define GNUTYPE_SPARSE 'S' /* sparse file */
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60
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#define GNUTYPE_VOLHDR 'V' /* tape/volume header */
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61
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+
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+
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/* tar header */
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#define BLOCKSIZE 512
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#define SHORTNAMESIZE 100
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+
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struct tar_header
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{ /* byte offset */
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70
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char name[100]; /* 0 */
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71
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char mode[8]; /* 100 */
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72
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char uid[8]; /* 108 */
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73
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char gid[8]; /* 116 */
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74
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char size[12]; /* 124 */
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75
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char mtime[12]; /* 136 */
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76
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char chksum[8]; /* 148 */
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77
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char typeflag; /* 156 */
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78
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char linkname[100]; /* 157 */
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79
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char magic[6]; /* 257 */
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80
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char version[2]; /* 263 */
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81
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char uname[32]; /* 265 */
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82
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char gname[32]; /* 297 */
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83
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char devmajor[8]; /* 329 */
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84
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char devminor[8]; /* 337 */
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85
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char prefix[155]; /* 345 */
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86
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/* 500 */
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};
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88
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+
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union tar_buffer
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90
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{
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91
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char buffer[BLOCKSIZE];
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struct tar_header header;
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};
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94
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95
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struct attr_item
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96
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{
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struct attr_item *next;
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98
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char *fname;
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int mode;
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100
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time_t time;
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};
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102
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103
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enum { TGZ_EXTRACT, TGZ_LIST, TGZ_INVALID };
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104
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+
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105
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char *TGZfname OF((const char *));
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106
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void TGZnotfound OF((const char *));
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107
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108
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int getoct OF((char *, int));
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109
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char *strtime OF((time_t *));
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110
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int setfiletime OF((char *, time_t));
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111
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void push_attr OF((struct attr_item **, char *, int, time_t));
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112
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void restore_attr OF((struct attr_item **));
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113
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+
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114
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int ExprMatch OF((char *, char *));
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115
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+
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116
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int makedir OF((char *));
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117
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int matchname OF((int, int, char **, char *));
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118
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void error OF((const char *));
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120
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int tar OF((gzFile, int, int, int, char **));
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121
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+
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122
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void help OF((int));
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123
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int main OF((int, char **));
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124
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125
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char *prog;
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126
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127
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const char *TGZsuffix[] = { "\0", ".tar", ".tar.gz", ".taz", ".tgz", NULL };
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128
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129
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/* return the file name of the TGZ archive */
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130
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/* or NULL if it does not exist */
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131
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132
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char *TGZfname (const char *arcname)
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133
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{
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134
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static char buffer[1024];
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135
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int origlen,i;
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136
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strcpy(buffer,arcname);
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origlen = strlen(buffer);
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139
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for (i=0; TGZsuffix[i]; i++)
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{
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142
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strcpy(buffer+origlen,TGZsuffix[i]);
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if (access(buffer,F_OK) == 0)
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return buffer;
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145
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}
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return NULL;
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147
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}
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148
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+
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149
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+
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150
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/* error message for the filename */
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151
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+
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152
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void TGZnotfound (const char *arcname)
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153
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{
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154
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int i;
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155
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156
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fprintf(stderr,"%s: Couldn't find ",prog);
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157
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for (i=0;TGZsuffix[i];i++)
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fprintf(stderr,(TGZsuffix[i+1]) ? "%s%s, " : "or %s%s\n",
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arcname,
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TGZsuffix[i]);
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exit(1);
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162
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}
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163
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+
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164
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+
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165
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/* convert octal digits to int */
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166
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/* on error return -1 */
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167
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+
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168
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int getoct (char *p,int width)
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169
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{
|
170
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int result = 0;
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171
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char c;
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172
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+
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173
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while (width--)
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174
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{
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175
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c = *p++;
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if (c == 0)
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break;
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178
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if (c == ' ')
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continue;
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180
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if (c < '0' || c > '7')
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return -1;
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result = result * 8 + (c - '0');
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183
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}
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return result;
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}
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186
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+
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187
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+
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188
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/* convert time_t to string */
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189
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/* use the "YYYY/MM/DD hh:mm:ss" format */
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190
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+
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191
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char *strtime (time_t *t)
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192
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{
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193
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struct tm *local;
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194
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static char result[32];
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195
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+
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196
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local = localtime(t);
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197
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sprintf(result,"%4d/%02d/%02d %02d:%02d:%02d",
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local->tm_year+1900, local->tm_mon+1, local->tm_mday,
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local->tm_hour, local->tm_min, local->tm_sec);
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200
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return result;
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201
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}
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202
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+
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203
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+
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204
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/* set file time */
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205
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206
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int setfiletime (char *fname,time_t ftime)
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{
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208
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#ifdef WIN32
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static int isWinNT = -1;
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SYSTEMTIME st;
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FILETIME locft, modft;
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struct tm *loctm;
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HANDLE hFile;
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int result;
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215
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+
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loctm = localtime(&ftime);
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if (loctm == NULL)
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return -1;
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219
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+
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220
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st.wYear = (WORD)loctm->tm_year + 1900;
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st.wMonth = (WORD)loctm->tm_mon + 1;
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st.wDayOfWeek = (WORD)loctm->tm_wday;
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st.wDay = (WORD)loctm->tm_mday;
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224
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st.wHour = (WORD)loctm->tm_hour;
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225
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st.wMinute = (WORD)loctm->tm_min;
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226
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st.wSecond = (WORD)loctm->tm_sec;
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227
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st.wMilliseconds = 0;
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228
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if (!SystemTimeToFileTime(&st, &locft) ||
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229
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!LocalFileTimeToFileTime(&locft, &modft))
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230
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return -1;
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231
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+
|
232
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if (isWinNT < 0)
|
233
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+
isWinNT = (GetVersion() < 0x80000000) ? 1 : 0;
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234
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hFile = CreateFile(fname, GENERIC_WRITE, 0, NULL, OPEN_EXISTING,
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235
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(isWinNT ? FILE_FLAG_BACKUP_SEMANTICS : 0),
|
236
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NULL);
|
237
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if (hFile == INVALID_HANDLE_VALUE)
|
238
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return -1;
|
239
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+
result = SetFileTime(hFile, NULL, NULL, &modft) ? 0 : -1;
|
240
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+
CloseHandle(hFile);
|
241
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+
return result;
|
242
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+
#else
|
243
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+
struct utimbuf settime;
|
244
|
+
|
245
|
+
settime.actime = settime.modtime = ftime;
|
246
|
+
return utime(fname,&settime);
|
247
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+
#endif
|
248
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+
}
|
249
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+
|
250
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+
|
251
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+
/* push file attributes */
|
252
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+
|
253
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+
void push_attr(struct attr_item **list,char *fname,int mode,time_t time)
|
254
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+
{
|
255
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+
struct attr_item *item;
|
256
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+
|
257
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+
item = (struct attr_item *)malloc(sizeof(struct attr_item));
|
258
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+
if (item == NULL)
|
259
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+
error("Out of memory");
|
260
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+
item->fname = strdup(fname);
|
261
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+
item->mode = mode;
|
262
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+
item->time = time;
|
263
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+
item->next = *list;
|
264
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+
*list = item;
|
265
|
+
}
|
266
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+
|
267
|
+
|
268
|
+
/* restore file attributes */
|
269
|
+
|
270
|
+
void restore_attr(struct attr_item **list)
|
271
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+
{
|
272
|
+
struct attr_item *item, *prev;
|
273
|
+
|
274
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+
for (item = *list; item != NULL; )
|
275
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+
{
|
276
|
+
setfiletime(item->fname,item->time);
|
277
|
+
chmod(item->fname,item->mode);
|
278
|
+
prev = item;
|
279
|
+
item = item->next;
|
280
|
+
free(prev);
|
281
|
+
}
|
282
|
+
*list = NULL;
|
283
|
+
}
|
284
|
+
|
285
|
+
|
286
|
+
/* match regular expression */
|
287
|
+
|
288
|
+
#define ISSPECIAL(c) (((c) == '*') || ((c) == '/'))
|
289
|
+
|
290
|
+
int ExprMatch (char *string,char *expr)
|
291
|
+
{
|
292
|
+
while (1)
|
293
|
+
{
|
294
|
+
if (ISSPECIAL(*expr))
|
295
|
+
{
|
296
|
+
if (*expr == '/')
|
297
|
+
{
|
298
|
+
if (*string != '\\' && *string != '/')
|
299
|
+
return 0;
|
300
|
+
string ++; expr++;
|
301
|
+
}
|
302
|
+
else if (*expr == '*')
|
303
|
+
{
|
304
|
+
if (*expr ++ == 0)
|
305
|
+
return 1;
|
306
|
+
while (*++string != *expr)
|
307
|
+
if (*string == 0)
|
308
|
+
return 0;
|
309
|
+
}
|
310
|
+
}
|
311
|
+
else
|
312
|
+
{
|
313
|
+
if (*string != *expr)
|
314
|
+
return 0;
|
315
|
+
if (*expr++ == 0)
|
316
|
+
return 1;
|
317
|
+
string++;
|
318
|
+
}
|
319
|
+
}
|
320
|
+
}
|
321
|
+
|
322
|
+
|
323
|
+
/* recursive mkdir */
|
324
|
+
/* abort on ENOENT; ignore other errors like "directory already exists" */
|
325
|
+
/* return 1 if OK */
|
326
|
+
/* 0 on error */
|
327
|
+
|
328
|
+
int makedir (char *newdir)
|
329
|
+
{
|
330
|
+
char *buffer = strdup(newdir);
|
331
|
+
char *p;
|
332
|
+
int len = strlen(buffer);
|
333
|
+
|
334
|
+
if (len <= 0) {
|
335
|
+
free(buffer);
|
336
|
+
return 0;
|
337
|
+
}
|
338
|
+
if (buffer[len-1] == '/') {
|
339
|
+
buffer[len-1] = '\0';
|
340
|
+
}
|
341
|
+
if (mkdir(buffer, 0755) == 0)
|
342
|
+
{
|
343
|
+
free(buffer);
|
344
|
+
return 1;
|
345
|
+
}
|
346
|
+
|
347
|
+
p = buffer+1;
|
348
|
+
while (1)
|
349
|
+
{
|
350
|
+
char hold;
|
351
|
+
|
352
|
+
while(*p && *p != '\\' && *p != '/')
|
353
|
+
p++;
|
354
|
+
hold = *p;
|
355
|
+
*p = 0;
|
356
|
+
if ((mkdir(buffer, 0755) == -1) && (errno == ENOENT))
|
357
|
+
{
|
358
|
+
fprintf(stderr,"%s: Couldn't create directory %s\n",prog,buffer);
|
359
|
+
free(buffer);
|
360
|
+
return 0;
|
361
|
+
}
|
362
|
+
if (hold == 0)
|
363
|
+
break;
|
364
|
+
*p++ = hold;
|
365
|
+
}
|
366
|
+
free(buffer);
|
367
|
+
return 1;
|
368
|
+
}
|
369
|
+
|
370
|
+
|
371
|
+
int matchname (int arg,int argc,char **argv,char *fname)
|
372
|
+
{
|
373
|
+
if (arg == argc) /* no arguments given (untgz tgzarchive) */
|
374
|
+
return 1;
|
375
|
+
|
376
|
+
while (arg < argc)
|
377
|
+
if (ExprMatch(fname,argv[arg++]))
|
378
|
+
return 1;
|
379
|
+
|
380
|
+
return 0; /* ignore this for the moment being */
|
381
|
+
}
|
382
|
+
|
383
|
+
|
384
|
+
/* tar file list or extract */
|
385
|
+
|
386
|
+
int tar (gzFile in,int action,int arg,int argc,char **argv)
|
387
|
+
{
|
388
|
+
union tar_buffer buffer;
|
389
|
+
int len;
|
390
|
+
int err;
|
391
|
+
int getheader = 1;
|
392
|
+
int remaining = 0;
|
393
|
+
FILE *outfile = NULL;
|
394
|
+
char fname[BLOCKSIZE];
|
395
|
+
int tarmode;
|
396
|
+
time_t tartime;
|
397
|
+
struct attr_item *attributes = NULL;
|
398
|
+
|
399
|
+
if (action == TGZ_LIST)
|
400
|
+
printf(" date time size file\n"
|
401
|
+
" ---------- -------- --------- -------------------------------------\n");
|
402
|
+
while (1)
|
403
|
+
{
|
404
|
+
len = gzread(in, &buffer, BLOCKSIZE);
|
405
|
+
if (len < 0)
|
406
|
+
error(gzerror(in, &err));
|
407
|
+
/*
|
408
|
+
* Always expect complete blocks to process
|
409
|
+
* the tar information.
|
410
|
+
*/
|
411
|
+
if (len != BLOCKSIZE)
|
412
|
+
{
|
413
|
+
action = TGZ_INVALID; /* force error exit */
|
414
|
+
remaining = 0; /* force I/O cleanup */
|
415
|
+
}
|
416
|
+
|
417
|
+
/*
|
418
|
+
* If we have to get a tar header
|
419
|
+
*/
|
420
|
+
if (getheader >= 1)
|
421
|
+
{
|
422
|
+
/*
|
423
|
+
* if we met the end of the tar
|
424
|
+
* or the end-of-tar block,
|
425
|
+
* we are done
|
426
|
+
*/
|
427
|
+
if (len == 0 || buffer.header.name[0] == 0)
|
428
|
+
break;
|
429
|
+
|
430
|
+
tarmode = getoct(buffer.header.mode,8);
|
431
|
+
tartime = (time_t)getoct(buffer.header.mtime,12);
|
432
|
+
if (tarmode == -1 || tartime == (time_t)-1)
|
433
|
+
{
|
434
|
+
buffer.header.name[0] = 0;
|
435
|
+
action = TGZ_INVALID;
|
436
|
+
}
|
437
|
+
|
438
|
+
if (getheader == 1)
|
439
|
+
{
|
440
|
+
strncpy(fname,buffer.header.name,SHORTNAMESIZE);
|
441
|
+
if (fname[SHORTNAMESIZE-1] != 0)
|
442
|
+
fname[SHORTNAMESIZE] = 0;
|
443
|
+
}
|
444
|
+
else
|
445
|
+
{
|
446
|
+
/*
|
447
|
+
* The file name is longer than SHORTNAMESIZE
|
448
|
+
*/
|
449
|
+
if (strncmp(fname,buffer.header.name,SHORTNAMESIZE-1) != 0)
|
450
|
+
error("bad long name");
|
451
|
+
getheader = 1;
|
452
|
+
}
|
453
|
+
|
454
|
+
/*
|
455
|
+
* Act according to the type flag
|
456
|
+
*/
|
457
|
+
switch (buffer.header.typeflag)
|
458
|
+
{
|
459
|
+
case DIRTYPE:
|
460
|
+
if (action == TGZ_LIST)
|
461
|
+
printf(" %s <dir> %s\n",strtime(&tartime),fname);
|
462
|
+
if (action == TGZ_EXTRACT)
|
463
|
+
{
|
464
|
+
makedir(fname);
|
465
|
+
push_attr(&attributes,fname,tarmode,tartime);
|
466
|
+
}
|
467
|
+
break;
|
468
|
+
case REGTYPE:
|
469
|
+
case AREGTYPE:
|
470
|
+
remaining = getoct(buffer.header.size,12);
|
471
|
+
if (remaining == -1)
|
472
|
+
{
|
473
|
+
action = TGZ_INVALID;
|
474
|
+
break;
|
475
|
+
}
|
476
|
+
if (action == TGZ_LIST)
|
477
|
+
printf(" %s %9d %s\n",strtime(&tartime),remaining,fname);
|
478
|
+
else if (action == TGZ_EXTRACT)
|
479
|
+
{
|
480
|
+
if (matchname(arg,argc,argv,fname))
|
481
|
+
{
|
482
|
+
outfile = fopen(fname,"wb");
|
483
|
+
if (outfile == NULL) {
|
484
|
+
/* try creating directory */
|
485
|
+
char *p = strrchr(fname, '/');
|
486
|
+
if (p != NULL) {
|
487
|
+
*p = '\0';
|
488
|
+
makedir(fname);
|
489
|
+
*p = '/';
|
490
|
+
outfile = fopen(fname,"wb");
|
491
|
+
}
|
492
|
+
}
|
493
|
+
if (outfile != NULL)
|
494
|
+
printf("Extracting %s\n",fname);
|
495
|
+
else
|
496
|
+
fprintf(stderr, "%s: Couldn't create %s",prog,fname);
|
497
|
+
}
|
498
|
+
else
|
499
|
+
outfile = NULL;
|
500
|
+
}
|
501
|
+
getheader = 0;
|
502
|
+
break;
|
503
|
+
case GNUTYPE_LONGLINK:
|
504
|
+
case GNUTYPE_LONGNAME:
|
505
|
+
remaining = getoct(buffer.header.size,12);
|
506
|
+
if (remaining < 0 || remaining >= BLOCKSIZE)
|
507
|
+
{
|
508
|
+
action = TGZ_INVALID;
|
509
|
+
break;
|
510
|
+
}
|
511
|
+
len = gzread(in, fname, BLOCKSIZE);
|
512
|
+
if (len < 0)
|
513
|
+
error(gzerror(in, &err));
|
514
|
+
if (fname[BLOCKSIZE-1] != 0 || (int)strlen(fname) > remaining)
|
515
|
+
{
|
516
|
+
action = TGZ_INVALID;
|
517
|
+
break;
|
518
|
+
}
|
519
|
+
getheader = 2;
|
520
|
+
break;
|
521
|
+
default:
|
522
|
+
if (action == TGZ_LIST)
|
523
|
+
printf(" %s <---> %s\n",strtime(&tartime),fname);
|
524
|
+
break;
|
525
|
+
}
|
526
|
+
}
|
527
|
+
else
|
528
|
+
{
|
529
|
+
unsigned int bytes = (remaining > BLOCKSIZE) ? BLOCKSIZE : remaining;
|
530
|
+
|
531
|
+
if (outfile != NULL)
|
532
|
+
{
|
533
|
+
if (fwrite(&buffer,sizeof(char),bytes,outfile) != bytes)
|
534
|
+
{
|
535
|
+
fprintf(stderr,
|
536
|
+
"%s: Error writing %s -- skipping\n",prog,fname);
|
537
|
+
fclose(outfile);
|
538
|
+
outfile = NULL;
|
539
|
+
remove(fname);
|
540
|
+
}
|
541
|
+
}
|
542
|
+
remaining -= bytes;
|
543
|
+
}
|
544
|
+
|
545
|
+
if (remaining == 0)
|
546
|
+
{
|
547
|
+
getheader = 1;
|
548
|
+
if (outfile != NULL)
|
549
|
+
{
|
550
|
+
fclose(outfile);
|
551
|
+
outfile = NULL;
|
552
|
+
if (action != TGZ_INVALID)
|
553
|
+
push_attr(&attributes,fname,tarmode,tartime);
|
554
|
+
}
|
555
|
+
}
|
556
|
+
|
557
|
+
/*
|
558
|
+
* Abandon if errors are found
|
559
|
+
*/
|
560
|
+
if (action == TGZ_INVALID)
|
561
|
+
{
|
562
|
+
error("broken archive");
|
563
|
+
break;
|
564
|
+
}
|
565
|
+
}
|
566
|
+
|
567
|
+
/*
|
568
|
+
* Restore file modes and time stamps
|
569
|
+
*/
|
570
|
+
restore_attr(&attributes);
|
571
|
+
|
572
|
+
if (gzclose(in) != Z_OK)
|
573
|
+
error("failed gzclose");
|
574
|
+
|
575
|
+
return 0;
|
576
|
+
}
|
577
|
+
|
578
|
+
|
579
|
+
/* ============================================================ */
|
580
|
+
|
581
|
+
void help(int exitval)
|
582
|
+
{
|
583
|
+
printf("untgz version 0.2.1\n"
|
584
|
+
" using zlib version %s\n\n",
|
585
|
+
zlibVersion());
|
586
|
+
printf("Usage: untgz file.tgz extract all files\n"
|
587
|
+
" untgz file.tgz fname ... extract selected files\n"
|
588
|
+
" untgz -l file.tgz list archive contents\n"
|
589
|
+
" untgz -h display this help\n");
|
590
|
+
exit(exitval);
|
591
|
+
}
|
592
|
+
|
593
|
+
void error(const char *msg)
|
594
|
+
{
|
595
|
+
fprintf(stderr, "%s: %s\n", prog, msg);
|
596
|
+
exit(1);
|
597
|
+
}
|
598
|
+
|
599
|
+
|
600
|
+
/* ============================================================ */
|
601
|
+
|
602
|
+
#if defined(WIN32) && defined(__GNUC__)
|
603
|
+
int _CRT_glob = 0; /* disable argument globbing in MinGW */
|
604
|
+
#endif
|
605
|
+
|
606
|
+
int main(int argc,char **argv)
|
607
|
+
{
|
608
|
+
int action = TGZ_EXTRACT;
|
609
|
+
int arg = 1;
|
610
|
+
char *TGZfile;
|
611
|
+
gzFile *f;
|
612
|
+
|
613
|
+
prog = strrchr(argv[0],'\\');
|
614
|
+
if (prog == NULL)
|
615
|
+
{
|
616
|
+
prog = strrchr(argv[0],'/');
|
617
|
+
if (prog == NULL)
|
618
|
+
{
|
619
|
+
prog = strrchr(argv[0],':');
|
620
|
+
if (prog == NULL)
|
621
|
+
prog = argv[0];
|
622
|
+
else
|
623
|
+
prog++;
|
624
|
+
}
|
625
|
+
else
|
626
|
+
prog++;
|
627
|
+
}
|
628
|
+
else
|
629
|
+
prog++;
|
630
|
+
|
631
|
+
if (argc == 1)
|
632
|
+
help(0);
|
633
|
+
|
634
|
+
if (strcmp(argv[arg],"-l") == 0)
|
635
|
+
{
|
636
|
+
action = TGZ_LIST;
|
637
|
+
if (argc == ++arg)
|
638
|
+
help(0);
|
639
|
+
}
|
640
|
+
else if (strcmp(argv[arg],"-h") == 0)
|
641
|
+
{
|
642
|
+
help(0);
|
643
|
+
}
|
644
|
+
|
645
|
+
if ((TGZfile = TGZfname(argv[arg])) == NULL)
|
646
|
+
TGZnotfound(argv[arg]);
|
647
|
+
|
648
|
+
++arg;
|
649
|
+
if ((action == TGZ_LIST) && (arg != argc))
|
650
|
+
help(1);
|
651
|
+
|
652
|
+
/*
|
653
|
+
* Process the TGZ file
|
654
|
+
*/
|
655
|
+
switch(action)
|
656
|
+
{
|
657
|
+
case TGZ_LIST:
|
658
|
+
case TGZ_EXTRACT:
|
659
|
+
f = gzopen(TGZfile,"rb");
|
660
|
+
if (f == NULL)
|
661
|
+
{
|
662
|
+
fprintf(stderr,"%s: Couldn't gzopen %s\n",prog,TGZfile);
|
663
|
+
return 1;
|
664
|
+
}
|
665
|
+
exit(tar(f, action, arg, argc, argv));
|
666
|
+
break;
|
667
|
+
|
668
|
+
default:
|
669
|
+
error("Unknown option");
|
670
|
+
exit(1);
|
671
|
+
}
|
672
|
+
|
673
|
+
return 0;
|
674
|
+
}
|