bio-velvet_underground 0.0.1
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +7 -0
- data/.document +5 -0
- data/.gitmodules +3 -0
- data/.travis.yml +13 -0
- data/Gemfile +19 -0
- data/LICENSE.txt +20 -0
- data/README.md +53 -0
- data/Rakefile +51 -0
- data/VERSION +1 -0
- data/ext/bioruby.patch +60 -0
- data/ext/mkrf_conf.rb +50 -0
- data/ext/src/Makefile +125 -0
- data/ext/src/src/allocArray.c +305 -0
- data/ext/src/src/allocArray.h +86 -0
- data/ext/src/src/autoOpen.c +107 -0
- data/ext/src/src/autoOpen.h +18 -0
- data/ext/src/src/binarySequences.c +813 -0
- data/ext/src/src/binarySequences.h +125 -0
- data/ext/src/src/concatenatedGraph.c +233 -0
- data/ext/src/src/concatenatedGraph.h +30 -0
- data/ext/src/src/concatenatedPreGraph.c +262 -0
- data/ext/src/src/concatenatedPreGraph.h +29 -0
- data/ext/src/src/correctedGraph.c +2642 -0
- data/ext/src/src/correctedGraph.h +32 -0
- data/ext/src/src/dfib.c +509 -0
- data/ext/src/src/dfib.h +69 -0
- data/ext/src/src/dfibHeap.c +89 -0
- data/ext/src/src/dfibHeap.h +39 -0
- data/ext/src/src/dfibpriv.h +105 -0
- data/ext/src/src/fib.c +628 -0
- data/ext/src/src/fib.h +78 -0
- data/ext/src/src/fibHeap.c +79 -0
- data/ext/src/src/fibHeap.h +41 -0
- data/ext/src/src/fibpriv.h +110 -0
- data/ext/src/src/globals.h +153 -0
- data/ext/src/src/graph.c +3983 -0
- data/ext/src/src/graph.h +233 -0
- data/ext/src/src/graphReConstruction.c +1472 -0
- data/ext/src/src/graphReConstruction.h +30 -0
- data/ext/src/src/graphStats.c +2167 -0
- data/ext/src/src/graphStats.h +72 -0
- data/ext/src/src/kmer.c +652 -0
- data/ext/src/src/kmer.h +73 -0
- data/ext/src/src/kmerOccurenceTable.c +236 -0
- data/ext/src/src/kmerOccurenceTable.h +44 -0
- data/ext/src/src/kseq.h +223 -0
- data/ext/src/src/locallyCorrectedGraph.c +557 -0
- data/ext/src/src/locallyCorrectedGraph.h +40 -0
- data/ext/src/src/passageMarker.c +677 -0
- data/ext/src/src/passageMarker.h +137 -0
- data/ext/src/src/preGraph.c +1717 -0
- data/ext/src/src/preGraph.h +106 -0
- data/ext/src/src/preGraphConstruction.c +990 -0
- data/ext/src/src/preGraphConstruction.h +26 -0
- data/ext/src/src/readCoherentGraph.c +557 -0
- data/ext/src/src/readCoherentGraph.h +30 -0
- data/ext/src/src/readSet.c +1734 -0
- data/ext/src/src/readSet.h +67 -0
- data/ext/src/src/recycleBin.c +199 -0
- data/ext/src/src/recycleBin.h +58 -0
- data/ext/src/src/roadMap.c +342 -0
- data/ext/src/src/roadMap.h +65 -0
- data/ext/src/src/run.c +318 -0
- data/ext/src/src/run.h +52 -0
- data/ext/src/src/run2.c +712 -0
- data/ext/src/src/scaffold.c +1876 -0
- data/ext/src/src/scaffold.h +64 -0
- data/ext/src/src/shortReadPairs.c +1243 -0
- data/ext/src/src/shortReadPairs.h +32 -0
- data/ext/src/src/splay.c +259 -0
- data/ext/src/src/splay.h +43 -0
- data/ext/src/src/splayTable.c +1315 -0
- data/ext/src/src/splayTable.h +31 -0
- data/ext/src/src/tightString.c +362 -0
- data/ext/src/src/tightString.h +82 -0
- data/ext/src/src/utility.c +199 -0
- data/ext/src/src/utility.h +98 -0
- data/ext/src/third-party/zlib-1.2.3/ChangeLog +855 -0
- data/ext/src/third-party/zlib-1.2.3/FAQ +339 -0
- data/ext/src/third-party/zlib-1.2.3/INDEX +51 -0
- data/ext/src/third-party/zlib-1.2.3/Makefile +154 -0
- data/ext/src/third-party/zlib-1.2.3/Makefile.in +154 -0
- data/ext/src/third-party/zlib-1.2.3/README +125 -0
- data/ext/src/third-party/zlib-1.2.3/adler32.c +149 -0
- data/ext/src/third-party/zlib-1.2.3/algorithm.txt +209 -0
- data/ext/src/third-party/zlib-1.2.3/amiga/Makefile.pup +66 -0
- data/ext/src/third-party/zlib-1.2.3/amiga/Makefile.sas +65 -0
- data/ext/src/third-party/zlib-1.2.3/as400/bndsrc +132 -0
- data/ext/src/third-party/zlib-1.2.3/as400/compile.clp +123 -0
- data/ext/src/third-party/zlib-1.2.3/as400/readme.txt +111 -0
- data/ext/src/third-party/zlib-1.2.3/as400/zlib.inc +331 -0
- data/ext/src/third-party/zlib-1.2.3/compress.c +79 -0
- data/ext/src/third-party/zlib-1.2.3/configure +459 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/README.contrib +71 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/ada/buffer_demo.adb +106 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/ada/mtest.adb +156 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/ada/read.adb +156 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/ada/readme.txt +65 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/ada/test.adb +463 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/ada/zlib-streams.adb +225 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/ada/zlib-streams.ads +114 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/ada/zlib-thin.adb +141 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/ada/zlib-thin.ads +450 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/ada/zlib.adb +701 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/ada/zlib.ads +328 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/ada/zlib.gpr +20 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/asm586/README.586 +43 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/asm586/match.S +364 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/asm686/README.686 +34 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/asm686/match.S +329 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/blast/Makefile +8 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/blast/README +4 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/blast/blast.c +444 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/blast/blast.h +71 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/blast/test.pk +0 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/blast/test.txt +1 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/delphi/ZLib.pas +557 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/delphi/ZLibConst.pas +11 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/delphi/readme.txt +76 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/delphi/zlibd32.mak +93 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib.build +33 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib.chm +0 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib.sln +21 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/AssemblyInfo.cs +58 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/ChecksumImpl.cs +202 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/CircularBuffer.cs +83 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/CodecBase.cs +198 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/Deflater.cs +106 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/DotZLib.cs +288 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/DotZLib.csproj +141 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/GZipStream.cs +301 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/Inflater.cs +105 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/UnitTests.cs +274 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/LICENSE_1_0.txt +23 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/readme.txt +58 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/infback9/README +1 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/infback9/infback9.c +608 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/infback9/infback9.h +37 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/infback9/inffix9.h +107 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/infback9/inflate9.h +47 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/infback9/inftree9.c +323 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/infback9/inftree9.h +55 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/inflate86/inffas86.c +1157 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/inflate86/inffast.S +1368 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/iostream/test.cpp +24 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/iostream/zfstream.cpp +329 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/iostream/zfstream.h +128 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/iostream2/zstream.h +307 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/iostream2/zstream_test.cpp +25 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/iostream3/README +35 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/iostream3/TODO +17 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/iostream3/test.cc +50 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/iostream3/zfstream.cc +479 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/iostream3/zfstream.h +466 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/masm686/match.asm +413 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/masmx64/bld_ml64.bat +2 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/masmx64/gvmat64.asm +513 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/masmx64/gvmat64.obj +0 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/masmx64/inffas8664.c +186 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/masmx64/inffasx64.asm +392 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/masmx64/inffasx64.obj +0 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/masmx64/readme.txt +28 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/bld_ml32.bat +2 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/gvmat32.asm +972 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/gvmat32.obj +0 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/gvmat32c.c +62 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/inffas32.asm +1083 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/inffas32.obj +0 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/mkasm.bat +3 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/readme.txt +21 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/minizip/ChangeLogUnzip +67 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/minizip/Makefile +25 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/minizip/crypt.h +132 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/minizip/ioapi.c +177 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/minizip/ioapi.h +75 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/minizip/iowin32.c +270 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/minizip/iowin32.h +21 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/minizip/miniunz.c +585 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/minizip/minizip.c +420 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/minizip/mztools.c +281 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/minizip/mztools.h +31 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/minizip/unzip.c +1598 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/minizip/unzip.h +354 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/minizip/zip.c +1219 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/minizip/zip.h +235 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/pascal/example.pas +599 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/pascal/readme.txt +76 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/pascal/zlibd32.mak +93 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/pascal/zlibpas.pas +236 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/puff/Makefile +8 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/puff/README +63 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/puff/puff.c +837 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/puff/puff.h +31 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/puff/zeros.raw +0 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/testzlib/testzlib.c +275 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/testzlib/testzlib.txt +10 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/untgz/Makefile +14 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/untgz/Makefile.msc +17 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/untgz/untgz.c +674 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/readme.txt +73 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/miniunz.vcproj +126 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/minizip.vcproj +126 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/testzlib.vcproj +126 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/zlib.rc +32 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/zlibstat.vcproj +246 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/zlibvc.def +92 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/zlibvc.sln +78 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/zlibvc.vcproj +445 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/miniunz.vcproj +566 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/minizip.vcproj +563 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/testzlib.vcproj +948 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/testzlibdll.vcproj +567 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/zlib.rc +32 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/zlibstat.vcproj +870 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/zlibvc.def +92 -0
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- data/ext/src/third-party/zlib-1.2.3/crc32.c +423 -0
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- data/ext/src/third-party/zlib-1.2.3/deflate.c +1736 -0
- data/ext/src/third-party/zlib-1.2.3/deflate.h +331 -0
- data/ext/src/third-party/zlib-1.2.3/example.c +565 -0
- data/ext/src/third-party/zlib-1.2.3/examples/README.examples +42 -0
- data/ext/src/third-party/zlib-1.2.3/examples/fitblk.c +233 -0
- data/ext/src/third-party/zlib-1.2.3/examples/gun.c +693 -0
- data/ext/src/third-party/zlib-1.2.3/examples/gzappend.c +500 -0
- data/ext/src/third-party/zlib-1.2.3/examples/gzjoin.c +448 -0
- data/ext/src/third-party/zlib-1.2.3/examples/gzlog.c +413 -0
- data/ext/src/third-party/zlib-1.2.3/examples/gzlog.h +58 -0
- data/ext/src/third-party/zlib-1.2.3/examples/zlib_how.html +523 -0
- data/ext/src/third-party/zlib-1.2.3/examples/zpipe.c +191 -0
- data/ext/src/third-party/zlib-1.2.3/examples/zran.c +404 -0
- data/ext/src/third-party/zlib-1.2.3/gzio.c +1026 -0
- data/ext/src/third-party/zlib-1.2.3/infback.c +623 -0
- data/ext/src/third-party/zlib-1.2.3/inffast.c +318 -0
- data/ext/src/third-party/zlib-1.2.3/inffast.h +11 -0
- data/ext/src/third-party/zlib-1.2.3/inffixed.h +94 -0
- data/ext/src/third-party/zlib-1.2.3/inflate.c +1368 -0
- data/ext/src/third-party/zlib-1.2.3/inflate.h +115 -0
- data/ext/src/third-party/zlib-1.2.3/inftrees.c +329 -0
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- data/ext/src/third-party/zlib-1.2.3/minigzip.c +322 -0
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- data/ext/src/third-party/zlib-1.2.3/msdos/Makefile.dj2 +104 -0
- data/ext/src/third-party/zlib-1.2.3/msdos/Makefile.emx +69 -0
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- data/ext/src/third-party/zlib-1.2.3/msdos/Makefile.tc +94 -0
- data/ext/src/third-party/zlib-1.2.3/old/Makefile.riscos +151 -0
- data/ext/src/third-party/zlib-1.2.3/old/README +3 -0
- data/ext/src/third-party/zlib-1.2.3/old/descrip.mms +48 -0
- data/ext/src/third-party/zlib-1.2.3/old/os2/Makefile.os2 +136 -0
- data/ext/src/third-party/zlib-1.2.3/old/os2/zlib.def +51 -0
- data/ext/src/third-party/zlib-1.2.3/old/visual-basic.txt +160 -0
- data/ext/src/third-party/zlib-1.2.3/old/zlib.html +971 -0
- data/ext/src/third-party/zlib-1.2.3/projects/README.projects +41 -0
- data/ext/src/third-party/zlib-1.2.3/projects/visualc6/README.txt +73 -0
- data/ext/src/third-party/zlib-1.2.3/projects/visualc6/example.dsp +278 -0
- data/ext/src/third-party/zlib-1.2.3/projects/visualc6/minigzip.dsp +278 -0
- data/ext/src/third-party/zlib-1.2.3/projects/visualc6/zlib.dsp +609 -0
- data/ext/src/third-party/zlib-1.2.3/projects/visualc6/zlib.dsw +59 -0
- data/ext/src/third-party/zlib-1.2.3/qnx/package.qpg +141 -0
- data/ext/src/third-party/zlib-1.2.3/trees.c +1219 -0
- data/ext/src/third-party/zlib-1.2.3/trees.h +128 -0
- 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
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//
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// � Copyright Henrik Ravn 2004
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//
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// Use, modification and distribution are subject to the Boost Software License, Version 1.0.
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// (See accompanying file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
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//
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using System;
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using System.IO;
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using System.Runtime.InteropServices;
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namespace DotZLib
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{
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/// <summary>
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/// Implements a compressed <see cref="Stream"/>, in GZip (.gz) format.
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/// </summary>
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public class GZipStream : Stream, IDisposable
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{
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#region Dll Imports
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[DllImport("ZLIB1.dll", CallingConvention=CallingConvention.Cdecl, CharSet=CharSet.Ansi)]
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private static extern IntPtr gzopen(string name, string mode);
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[DllImport("ZLIB1.dll", CallingConvention=CallingConvention.Cdecl)]
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private static extern int gzclose(IntPtr gzFile);
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[DllImport("ZLIB1.dll", CallingConvention=CallingConvention.Cdecl)]
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private static extern int gzwrite(IntPtr gzFile, int data, int length);
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[DllImport("ZLIB1.dll", CallingConvention=CallingConvention.Cdecl)]
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private static extern int gzread(IntPtr gzFile, int data, int length);
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[DllImport("ZLIB1.dll", CallingConvention=CallingConvention.Cdecl)]
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private static extern int gzgetc(IntPtr gzFile);
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[DllImport("ZLIB1.dll", CallingConvention=CallingConvention.Cdecl)]
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private static extern int gzputc(IntPtr gzFile, int c);
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#endregion
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#region Private data
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private IntPtr _gzFile;
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private bool _isDisposed = false;
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private bool _isWriting;
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#endregion
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#region Constructors
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/// <summary>
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/// Creates a new file as a writeable GZipStream
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/// </summary>
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/// <param name="fileName">The name of the compressed file to create</param>
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/// <param name="level">The compression level to use when adding data</param>
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/// <exception cref="ZLibException">If an error occurred in the internal zlib function</exception>
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public GZipStream(string fileName, CompressLevel level)
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{
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_isWriting = true;
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_gzFile = gzopen(fileName, String.Format("wb{0}", (int)level));
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if (_gzFile == IntPtr.Zero)
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throw new ZLibException(-1, "Could not open " + fileName);
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}
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/// <summary>
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/// Opens an existing file as a readable GZipStream
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/// </summary>
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/// <param name="fileName">The name of the file to open</param>
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/// <exception cref="ZLibException">If an error occurred in the internal zlib function</exception>
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public GZipStream(string fileName)
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{
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_isWriting = false;
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_gzFile = gzopen(fileName, "rb");
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if (_gzFile == IntPtr.Zero)
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throw new ZLibException(-1, "Could not open " + fileName);
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}
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#endregion
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#region Access properties
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/// <summary>
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/// Returns true of this stream can be read from, false otherwise
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/// </summary>
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public override bool CanRead
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{
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get
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return !_isWriting;
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}
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}
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/// <summary>
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/// Returns false.
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/// </summary>
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public override bool CanSeek
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{
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get
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{
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return false;
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}
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}
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/// <summary>
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/// Returns true if this tsream is writeable, false otherwise
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/// </summary>
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public override bool CanWrite
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{
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get
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{
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return _isWriting;
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}
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}
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#endregion
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#region Destructor & IDispose stuff
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/// <summary>
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/// Destroys this instance
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/// </summary>
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~GZipStream()
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{
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cleanUp(false);
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}
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/// <summary>
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/// Closes the external file handle
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/// </summary>
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public void Dispose()
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{
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cleanUp(true);
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}
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// Does the actual closing of the file handle.
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private void cleanUp(bool isDisposing)
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{
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if (!_isDisposed)
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{
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gzclose(_gzFile);
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_isDisposed = true;
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}
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}
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#endregion
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#region Basic reading and writing
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/// <summary>
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/// Attempts to read a number of bytes from the stream.
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/// </summary>
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/// <param name="buffer">The destination data buffer</param>
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/// <param name="offset">The index of the first destination byte in <c>buffer</c></param>
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/// <param name="count">The number of bytes requested</param>
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/// <returns>The number of bytes read</returns>
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/// <exception cref="ArgumentNullException">If <c>buffer</c> is null</exception>
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/// <exception cref="ArgumentOutOfRangeException">If <c>count</c> or <c>offset</c> are negative</exception>
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/// <exception cref="ArgumentException">If <c>offset</c> + <c>count</c> is > buffer.Length</exception>
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/// <exception cref="NotSupportedException">If this stream is not readable.</exception>
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/// <exception cref="ObjectDisposedException">If this stream has been disposed.</exception>
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public override int Read(byte[] buffer, int offset, int count)
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{
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if (!CanRead) throw new NotSupportedException();
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if (buffer == null) throw new ArgumentNullException();
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if (offset < 0 || count < 0) throw new ArgumentOutOfRangeException();
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if ((offset+count) > buffer.Length) throw new ArgumentException();
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if (_isDisposed) throw new ObjectDisposedException("GZipStream");
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GCHandle h = GCHandle.Alloc(buffer, GCHandleType.Pinned);
|
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int result;
|
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try
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{
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result = gzread(_gzFile, h.AddrOfPinnedObject().ToInt32() + offset, count);
|
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if (result < 0)
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throw new IOException();
|
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}
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finally
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{
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h.Free();
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}
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return result;
|
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}
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/// <summary>
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/// Attempts to read a single byte from the stream.
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/// </summary>
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/// <returns>The byte that was read, or -1 in case of error or End-Of-File</returns>
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public override int ReadByte()
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{
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if (!CanRead) throw new NotSupportedException();
|
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if (_isDisposed) throw new ObjectDisposedException("GZipStream");
|
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return gzgetc(_gzFile);
|
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}
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/// <summary>
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/// Writes a number of bytes to the stream
|
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/// </summary>
|
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/// <param name="buffer"></param>
|
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/// <param name="offset"></param>
|
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/// <param name="count"></param>
|
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/// <exception cref="ArgumentNullException">If <c>buffer</c> is null</exception>
|
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/// <exception cref="ArgumentOutOfRangeException">If <c>count</c> or <c>offset</c> are negative</exception>
|
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/// <exception cref="ArgumentException">If <c>offset</c> + <c>count</c> is > buffer.Length</exception>
|
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/// <exception cref="NotSupportedException">If this stream is not writeable.</exception>
|
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/// <exception cref="ObjectDisposedException">If this stream has been disposed.</exception>
|
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public override void Write(byte[] buffer, int offset, int count)
|
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{
|
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if (!CanWrite) throw new NotSupportedException();
|
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if (buffer == null) throw new ArgumentNullException();
|
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if (offset < 0 || count < 0) throw new ArgumentOutOfRangeException();
|
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if ((offset+count) > buffer.Length) throw new ArgumentException();
|
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if (_isDisposed) throw new ObjectDisposedException("GZipStream");
|
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|
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GCHandle h = GCHandle.Alloc(buffer, GCHandleType.Pinned);
|
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try
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{
|
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int result = gzwrite(_gzFile, h.AddrOfPinnedObject().ToInt32() + offset, count);
|
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if (result < 0)
|
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throw new IOException();
|
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}
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|
+
finally
|
215
|
+
{
|
216
|
+
h.Free();
|
217
|
+
}
|
218
|
+
}
|
219
|
+
|
220
|
+
/// <summary>
|
221
|
+
/// Writes a single byte to the stream
|
222
|
+
/// </summary>
|
223
|
+
/// <param name="value">The byte to add to the stream.</param>
|
224
|
+
/// <exception cref="NotSupportedException">If this stream is not writeable.</exception>
|
225
|
+
/// <exception cref="ObjectDisposedException">If this stream has been disposed.</exception>
|
226
|
+
public override void WriteByte(byte value)
|
227
|
+
{
|
228
|
+
if (!CanWrite) throw new NotSupportedException();
|
229
|
+
if (_isDisposed) throw new ObjectDisposedException("GZipStream");
|
230
|
+
|
231
|
+
int result = gzputc(_gzFile, (int)value);
|
232
|
+
if (result < 0)
|
233
|
+
throw new IOException();
|
234
|
+
}
|
235
|
+
#endregion
|
236
|
+
|
237
|
+
#region Position & length stuff
|
238
|
+
/// <summary>
|
239
|
+
/// Not supported.
|
240
|
+
/// </summary>
|
241
|
+
/// <param name="value"></param>
|
242
|
+
/// <exception cref="NotSupportedException">Always thrown</exception>
|
243
|
+
public override void SetLength(long value)
|
244
|
+
{
|
245
|
+
throw new NotSupportedException();
|
246
|
+
}
|
247
|
+
|
248
|
+
/// <summary>
|
249
|
+
/// Not suppported.
|
250
|
+
/// </summary>
|
251
|
+
/// <param name="offset"></param>
|
252
|
+
/// <param name="origin"></param>
|
253
|
+
/// <returns></returns>
|
254
|
+
/// <exception cref="NotSupportedException">Always thrown</exception>
|
255
|
+
public override long Seek(long offset, SeekOrigin origin)
|
256
|
+
{
|
257
|
+
throw new NotSupportedException();
|
258
|
+
}
|
259
|
+
|
260
|
+
/// <summary>
|
261
|
+
/// Flushes the <c>GZipStream</c>.
|
262
|
+
/// </summary>
|
263
|
+
/// <remarks>In this implementation, this method does nothing. This is because excessive
|
264
|
+
/// flushing may degrade the achievable compression rates.</remarks>
|
265
|
+
public override void Flush()
|
266
|
+
{
|
267
|
+
// left empty on purpose
|
268
|
+
}
|
269
|
+
|
270
|
+
/// <summary>
|
271
|
+
/// Gets/sets the current position in the <c>GZipStream</c>. Not suppported.
|
272
|
+
/// </summary>
|
273
|
+
/// <remarks>In this implementation this property is not supported</remarks>
|
274
|
+
/// <exception cref="NotSupportedException">Always thrown</exception>
|
275
|
+
public override long Position
|
276
|
+
{
|
277
|
+
get
|
278
|
+
{
|
279
|
+
throw new NotSupportedException();
|
280
|
+
}
|
281
|
+
set
|
282
|
+
{
|
283
|
+
throw new NotSupportedException();
|
284
|
+
}
|
285
|
+
}
|
286
|
+
|
287
|
+
/// <summary>
|
288
|
+
/// Gets the size of the stream. Not suppported.
|
289
|
+
/// </summary>
|
290
|
+
/// <remarks>In this implementation this property is not supported</remarks>
|
291
|
+
/// <exception cref="NotSupportedException">Always thrown</exception>
|
292
|
+
public override long Length
|
293
|
+
{
|
294
|
+
get
|
295
|
+
{
|
296
|
+
throw new NotSupportedException();
|
297
|
+
}
|
298
|
+
}
|
299
|
+
#endregion
|
300
|
+
}
|
301
|
+
}
|
@@ -0,0 +1,105 @@
|
|
1
|
+
//
|
2
|
+
// � Copyright Henrik Ravn 2004
|
3
|
+
//
|
4
|
+
// Use, modification and distribution are subject to the Boost Software License, Version 1.0.
|
5
|
+
// (See accompanying file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
|
6
|
+
//
|
7
|
+
|
8
|
+
using System;
|
9
|
+
using System.Diagnostics;
|
10
|
+
using System.Runtime.InteropServices;
|
11
|
+
|
12
|
+
namespace DotZLib
|
13
|
+
{
|
14
|
+
|
15
|
+
/// <summary>
|
16
|
+
/// Implements a data decompressor, using the inflate algorithm in the ZLib dll
|
17
|
+
/// </summary>
|
18
|
+
public class Inflater : CodecBase
|
19
|
+
{
|
20
|
+
#region Dll imports
|
21
|
+
[DllImport("ZLIB1.dll", CallingConvention=CallingConvention.Cdecl, CharSet=CharSet.Ansi)]
|
22
|
+
private static extern int inflateInit_(ref ZStream sz, string vs, int size);
|
23
|
+
|
24
|
+
[DllImport("ZLIB1.dll", CallingConvention=CallingConvention.Cdecl)]
|
25
|
+
private static extern int inflate(ref ZStream sz, int flush);
|
26
|
+
|
27
|
+
[DllImport("ZLIB1.dll", CallingConvention=CallingConvention.Cdecl)]
|
28
|
+
private static extern int inflateReset(ref ZStream sz);
|
29
|
+
|
30
|
+
[DllImport("ZLIB1.dll", CallingConvention=CallingConvention.Cdecl)]
|
31
|
+
private static extern int inflateEnd(ref ZStream sz);
|
32
|
+
#endregion
|
33
|
+
|
34
|
+
/// <summary>
|
35
|
+
/// Constructs an new instance of the <c>Inflater</c>
|
36
|
+
/// </summary>
|
37
|
+
public Inflater() : base()
|
38
|
+
{
|
39
|
+
int retval = inflateInit_(ref _ztream, Info.Version, Marshal.SizeOf(_ztream));
|
40
|
+
if (retval != 0)
|
41
|
+
throw new ZLibException(retval, "Could not initialize inflater");
|
42
|
+
|
43
|
+
resetOutput();
|
44
|
+
}
|
45
|
+
|
46
|
+
|
47
|
+
/// <summary>
|
48
|
+
/// Adds more data to the codec to be processed.
|
49
|
+
/// </summary>
|
50
|
+
/// <param name="data">Byte array containing the data to be added to the codec</param>
|
51
|
+
/// <param name="offset">The index of the first byte to add from <c>data</c></param>
|
52
|
+
/// <param name="count">The number of bytes to add</param>
|
53
|
+
/// <remarks>Adding data may, or may not, raise the <c>DataAvailable</c> event</remarks>
|
54
|
+
public override void Add(byte[] data, int offset, int count)
|
55
|
+
{
|
56
|
+
if (data == null) throw new ArgumentNullException();
|
57
|
+
if (offset < 0 || count < 0) throw new ArgumentOutOfRangeException();
|
58
|
+
if ((offset+count) > data.Length) throw new ArgumentException();
|
59
|
+
|
60
|
+
int total = count;
|
61
|
+
int inputIndex = offset;
|
62
|
+
int err = 0;
|
63
|
+
|
64
|
+
while (err >= 0 && inputIndex < total)
|
65
|
+
{
|
66
|
+
copyInput(data, inputIndex, Math.Min(total - inputIndex, kBufferSize));
|
67
|
+
err = inflate(ref _ztream, (int)FlushTypes.None);
|
68
|
+
if (err == 0)
|
69
|
+
while (_ztream.avail_out == 0)
|
70
|
+
{
|
71
|
+
OnDataAvailable();
|
72
|
+
err = inflate(ref _ztream, (int)FlushTypes.None);
|
73
|
+
}
|
74
|
+
|
75
|
+
inputIndex += (int)_ztream.total_in;
|
76
|
+
}
|
77
|
+
setChecksum( _ztream.adler );
|
78
|
+
}
|
79
|
+
|
80
|
+
|
81
|
+
/// <summary>
|
82
|
+
/// Finishes up any pending data that needs to be processed and handled.
|
83
|
+
/// </summary>
|
84
|
+
public override void Finish()
|
85
|
+
{
|
86
|
+
int err;
|
87
|
+
do
|
88
|
+
{
|
89
|
+
err = inflate(ref _ztream, (int)FlushTypes.Finish);
|
90
|
+
OnDataAvailable();
|
91
|
+
}
|
92
|
+
while (err == 0);
|
93
|
+
setChecksum( _ztream.adler );
|
94
|
+
inflateReset(ref _ztream);
|
95
|
+
resetOutput();
|
96
|
+
}
|
97
|
+
|
98
|
+
/// <summary>
|
99
|
+
/// Closes the internal zlib inflate stream
|
100
|
+
/// </summary>
|
101
|
+
protected override void CleanUp() { inflateEnd(ref _ztream); }
|
102
|
+
|
103
|
+
|
104
|
+
}
|
105
|
+
}
|