bio-velvet_underground 0.0.1
Sign up to get free protection for your applications and to get access to all the features.
- 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
- data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/zlibvc.sln +144 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/zlibvc.vcproj +1219 -0
- data/ext/src/third-party/zlib-1.2.3/crc32.c +423 -0
- data/ext/src/third-party/zlib-1.2.3/crc32.h +441 -0
- 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
- data/ext/src/third-party/zlib-1.2.3/inftrees.h +55 -0
- data/ext/src/third-party/zlib-1.2.3/make_vms.com +461 -0
- data/ext/src/third-party/zlib-1.2.3/minigzip.c +322 -0
- data/ext/src/third-party/zlib-1.2.3/msdos/Makefile.bor +109 -0
- 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
- data/ext/src/third-party/zlib-1.2.3/msdos/Makefile.msc +106 -0
- 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
@@ -0,0 +1,34 @@
|
|
1
|
+
This is a patched version of zlib, modified to use
|
2
|
+
Pentium-Pro-optimized assembly code in the deflation algorithm. The
|
3
|
+
files changed/added by this patch are:
|
4
|
+
|
5
|
+
README.686
|
6
|
+
match.S
|
7
|
+
|
8
|
+
The speedup that this patch provides varies, depending on whether the
|
9
|
+
compiler used to build the original version of zlib falls afoul of the
|
10
|
+
PPro's speed traps. My own tests show a speedup of around 10-20% at
|
11
|
+
the default compression level, and 20-30% using -9, against a version
|
12
|
+
compiled using gcc 2.7.2.3. Your mileage may vary.
|
13
|
+
|
14
|
+
Note that this code has been tailored for the PPro/PII in particular,
|
15
|
+
and will not perform particuarly well on a Pentium.
|
16
|
+
|
17
|
+
If you are using an assembler other than GNU as, you will have to
|
18
|
+
translate match.S to use your assembler's syntax. (Have fun.)
|
19
|
+
|
20
|
+
Brian Raiter
|
21
|
+
breadbox@muppetlabs.com
|
22
|
+
April, 1998
|
23
|
+
|
24
|
+
|
25
|
+
Added for zlib 1.1.3:
|
26
|
+
|
27
|
+
The patches come from
|
28
|
+
http://www.muppetlabs.com/~breadbox/software/assembly.html
|
29
|
+
|
30
|
+
To compile zlib with this asm file, copy match.S to the zlib directory
|
31
|
+
then do:
|
32
|
+
|
33
|
+
CFLAGS="-O3 -DASMV" ./configure
|
34
|
+
make OBJA=match.o
|
@@ -0,0 +1,329 @@
|
|
1
|
+
/* match.s -- Pentium-Pro-optimized version of longest_match()
|
2
|
+
* Written for zlib 1.1.2
|
3
|
+
* Copyright (C) 1998 Brian Raiter <breadbox@muppetlabs.com>
|
4
|
+
*
|
5
|
+
* This is free software; you can redistribute it and/or modify it
|
6
|
+
* under the terms of the GNU General Public License.
|
7
|
+
*/
|
8
|
+
|
9
|
+
#ifndef NO_UNDERLINE
|
10
|
+
#define match_init _match_init
|
11
|
+
#define longest_match _longest_match
|
12
|
+
#endif
|
13
|
+
|
14
|
+
#define MAX_MATCH (258)
|
15
|
+
#define MIN_MATCH (3)
|
16
|
+
#define MIN_LOOKAHEAD (MAX_MATCH + MIN_MATCH + 1)
|
17
|
+
#define MAX_MATCH_8 ((MAX_MATCH + 7) & ~7)
|
18
|
+
|
19
|
+
/* stack frame offsets */
|
20
|
+
|
21
|
+
#define chainlenwmask 0 /* high word: current chain len */
|
22
|
+
/* low word: s->wmask */
|
23
|
+
#define window 4 /* local copy of s->window */
|
24
|
+
#define windowbestlen 8 /* s->window + bestlen */
|
25
|
+
#define scanstart 16 /* first two bytes of string */
|
26
|
+
#define scanend 12 /* last two bytes of string */
|
27
|
+
#define scanalign 20 /* dword-misalignment of string */
|
28
|
+
#define nicematch 24 /* a good enough match size */
|
29
|
+
#define bestlen 28 /* size of best match so far */
|
30
|
+
#define scan 32 /* ptr to string wanting match */
|
31
|
+
|
32
|
+
#define LocalVarsSize (36)
|
33
|
+
/* saved ebx 36 */
|
34
|
+
/* saved edi 40 */
|
35
|
+
/* saved esi 44 */
|
36
|
+
/* saved ebp 48 */
|
37
|
+
/* return address 52 */
|
38
|
+
#define deflatestate 56 /* the function arguments */
|
39
|
+
#define curmatch 60
|
40
|
+
|
41
|
+
/* All the +zlib1222add offsets are due to the addition of fields
|
42
|
+
* in zlib in the deflate_state structure since the asm code was first written
|
43
|
+
* (if you compile with zlib 1.0.4 or older, use "zlib1222add equ (-4)").
|
44
|
+
* (if you compile with zlib between 1.0.5 and 1.2.2.1, use "zlib1222add equ 0").
|
45
|
+
* if you compile with zlib 1.2.2.2 or later , use "zlib1222add equ 8").
|
46
|
+
*/
|
47
|
+
|
48
|
+
#define zlib1222add (8)
|
49
|
+
|
50
|
+
#define dsWSize (36+zlib1222add)
|
51
|
+
#define dsWMask (44+zlib1222add)
|
52
|
+
#define dsWindow (48+zlib1222add)
|
53
|
+
#define dsPrev (56+zlib1222add)
|
54
|
+
#define dsMatchLen (88+zlib1222add)
|
55
|
+
#define dsPrevMatch (92+zlib1222add)
|
56
|
+
#define dsStrStart (100+zlib1222add)
|
57
|
+
#define dsMatchStart (104+zlib1222add)
|
58
|
+
#define dsLookahead (108+zlib1222add)
|
59
|
+
#define dsPrevLen (112+zlib1222add)
|
60
|
+
#define dsMaxChainLen (116+zlib1222add)
|
61
|
+
#define dsGoodMatch (132+zlib1222add)
|
62
|
+
#define dsNiceMatch (136+zlib1222add)
|
63
|
+
|
64
|
+
|
65
|
+
.file "match.S"
|
66
|
+
|
67
|
+
.globl match_init, longest_match
|
68
|
+
|
69
|
+
.text
|
70
|
+
|
71
|
+
/* uInt longest_match(deflate_state *deflatestate, IPos curmatch) */
|
72
|
+
|
73
|
+
longest_match:
|
74
|
+
|
75
|
+
/* Save registers that the compiler may be using, and adjust %esp to */
|
76
|
+
/* make room for our stack frame. */
|
77
|
+
|
78
|
+
pushl %ebp
|
79
|
+
pushl %edi
|
80
|
+
pushl %esi
|
81
|
+
pushl %ebx
|
82
|
+
subl $LocalVarsSize, %esp
|
83
|
+
|
84
|
+
/* Retrieve the function arguments. %ecx will hold cur_match */
|
85
|
+
/* throughout the entire function. %edx will hold the pointer to the */
|
86
|
+
/* deflate_state structure during the function's setup (before */
|
87
|
+
/* entering the main loop). */
|
88
|
+
|
89
|
+
movl deflatestate(%esp), %edx
|
90
|
+
movl curmatch(%esp), %ecx
|
91
|
+
|
92
|
+
/* uInt wmask = s->w_mask; */
|
93
|
+
/* unsigned chain_length = s->max_chain_length; */
|
94
|
+
/* if (s->prev_length >= s->good_match) { */
|
95
|
+
/* chain_length >>= 2; */
|
96
|
+
/* } */
|
97
|
+
|
98
|
+
movl dsPrevLen(%edx), %eax
|
99
|
+
movl dsGoodMatch(%edx), %ebx
|
100
|
+
cmpl %ebx, %eax
|
101
|
+
movl dsWMask(%edx), %eax
|
102
|
+
movl dsMaxChainLen(%edx), %ebx
|
103
|
+
jl LastMatchGood
|
104
|
+
shrl $2, %ebx
|
105
|
+
LastMatchGood:
|
106
|
+
|
107
|
+
/* chainlen is decremented once beforehand so that the function can */
|
108
|
+
/* use the sign flag instead of the zero flag for the exit test. */
|
109
|
+
/* It is then shifted into the high word, to make room for the wmask */
|
110
|
+
/* value, which it will always accompany. */
|
111
|
+
|
112
|
+
decl %ebx
|
113
|
+
shll $16, %ebx
|
114
|
+
orl %eax, %ebx
|
115
|
+
movl %ebx, chainlenwmask(%esp)
|
116
|
+
|
117
|
+
/* if ((uInt)nice_match > s->lookahead) nice_match = s->lookahead; */
|
118
|
+
|
119
|
+
movl dsNiceMatch(%edx), %eax
|
120
|
+
movl dsLookahead(%edx), %ebx
|
121
|
+
cmpl %eax, %ebx
|
122
|
+
jl LookaheadLess
|
123
|
+
movl %eax, %ebx
|
124
|
+
LookaheadLess: movl %ebx, nicematch(%esp)
|
125
|
+
|
126
|
+
/* register Bytef *scan = s->window + s->strstart; */
|
127
|
+
|
128
|
+
movl dsWindow(%edx), %esi
|
129
|
+
movl %esi, window(%esp)
|
130
|
+
movl dsStrStart(%edx), %ebp
|
131
|
+
lea (%esi,%ebp), %edi
|
132
|
+
movl %edi, scan(%esp)
|
133
|
+
|
134
|
+
/* Determine how many bytes the scan ptr is off from being */
|
135
|
+
/* dword-aligned. */
|
136
|
+
|
137
|
+
movl %edi, %eax
|
138
|
+
negl %eax
|
139
|
+
andl $3, %eax
|
140
|
+
movl %eax, scanalign(%esp)
|
141
|
+
|
142
|
+
/* IPos limit = s->strstart > (IPos)MAX_DIST(s) ? */
|
143
|
+
/* s->strstart - (IPos)MAX_DIST(s) : NIL; */
|
144
|
+
|
145
|
+
movl dsWSize(%edx), %eax
|
146
|
+
subl $MIN_LOOKAHEAD, %eax
|
147
|
+
subl %eax, %ebp
|
148
|
+
jg LimitPositive
|
149
|
+
xorl %ebp, %ebp
|
150
|
+
LimitPositive:
|
151
|
+
|
152
|
+
/* int best_len = s->prev_length; */
|
153
|
+
|
154
|
+
movl dsPrevLen(%edx), %eax
|
155
|
+
movl %eax, bestlen(%esp)
|
156
|
+
|
157
|
+
/* Store the sum of s->window + best_len in %esi locally, and in %esi. */
|
158
|
+
|
159
|
+
addl %eax, %esi
|
160
|
+
movl %esi, windowbestlen(%esp)
|
161
|
+
|
162
|
+
/* register ush scan_start = *(ushf*)scan; */
|
163
|
+
/* register ush scan_end = *(ushf*)(scan+best_len-1); */
|
164
|
+
/* Posf *prev = s->prev; */
|
165
|
+
|
166
|
+
movzwl (%edi), %ebx
|
167
|
+
movl %ebx, scanstart(%esp)
|
168
|
+
movzwl -1(%edi,%eax), %ebx
|
169
|
+
movl %ebx, scanend(%esp)
|
170
|
+
movl dsPrev(%edx), %edi
|
171
|
+
|
172
|
+
/* Jump into the main loop. */
|
173
|
+
|
174
|
+
movl chainlenwmask(%esp), %edx
|
175
|
+
jmp LoopEntry
|
176
|
+
|
177
|
+
.balign 16
|
178
|
+
|
179
|
+
/* do {
|
180
|
+
* match = s->window + cur_match;
|
181
|
+
* if (*(ushf*)(match+best_len-1) != scan_end ||
|
182
|
+
* *(ushf*)match != scan_start) continue;
|
183
|
+
* [...]
|
184
|
+
* } while ((cur_match = prev[cur_match & wmask]) > limit
|
185
|
+
* && --chain_length != 0);
|
186
|
+
*
|
187
|
+
* Here is the inner loop of the function. The function will spend the
|
188
|
+
* majority of its time in this loop, and majority of that time will
|
189
|
+
* be spent in the first ten instructions.
|
190
|
+
*
|
191
|
+
* Within this loop:
|
192
|
+
* %ebx = scanend
|
193
|
+
* %ecx = curmatch
|
194
|
+
* %edx = chainlenwmask - i.e., ((chainlen << 16) | wmask)
|
195
|
+
* %esi = windowbestlen - i.e., (window + bestlen)
|
196
|
+
* %edi = prev
|
197
|
+
* %ebp = limit
|
198
|
+
*/
|
199
|
+
LookupLoop:
|
200
|
+
andl %edx, %ecx
|
201
|
+
movzwl (%edi,%ecx,2), %ecx
|
202
|
+
cmpl %ebp, %ecx
|
203
|
+
jbe LeaveNow
|
204
|
+
subl $0x00010000, %edx
|
205
|
+
js LeaveNow
|
206
|
+
LoopEntry: movzwl -1(%esi,%ecx), %eax
|
207
|
+
cmpl %ebx, %eax
|
208
|
+
jnz LookupLoop
|
209
|
+
movl window(%esp), %eax
|
210
|
+
movzwl (%eax,%ecx), %eax
|
211
|
+
cmpl scanstart(%esp), %eax
|
212
|
+
jnz LookupLoop
|
213
|
+
|
214
|
+
/* Store the current value of chainlen. */
|
215
|
+
|
216
|
+
movl %edx, chainlenwmask(%esp)
|
217
|
+
|
218
|
+
/* Point %edi to the string under scrutiny, and %esi to the string we */
|
219
|
+
/* are hoping to match it up with. In actuality, %esi and %edi are */
|
220
|
+
/* both pointed (MAX_MATCH_8 - scanalign) bytes ahead, and %edx is */
|
221
|
+
/* initialized to -(MAX_MATCH_8 - scanalign). */
|
222
|
+
|
223
|
+
movl window(%esp), %esi
|
224
|
+
movl scan(%esp), %edi
|
225
|
+
addl %ecx, %esi
|
226
|
+
movl scanalign(%esp), %eax
|
227
|
+
movl $(-MAX_MATCH_8), %edx
|
228
|
+
lea MAX_MATCH_8(%edi,%eax), %edi
|
229
|
+
lea MAX_MATCH_8(%esi,%eax), %esi
|
230
|
+
|
231
|
+
/* Test the strings for equality, 8 bytes at a time. At the end,
|
232
|
+
* adjust %edx so that it is offset to the exact byte that mismatched.
|
233
|
+
*
|
234
|
+
* We already know at this point that the first three bytes of the
|
235
|
+
* strings match each other, and they can be safely passed over before
|
236
|
+
* starting the compare loop. So what this code does is skip over 0-3
|
237
|
+
* bytes, as much as necessary in order to dword-align the %edi
|
238
|
+
* pointer. (%esi will still be misaligned three times out of four.)
|
239
|
+
*
|
240
|
+
* It should be confessed that this loop usually does not represent
|
241
|
+
* much of the total running time. Replacing it with a more
|
242
|
+
* straightforward "rep cmpsb" would not drastically degrade
|
243
|
+
* performance.
|
244
|
+
*/
|
245
|
+
LoopCmps:
|
246
|
+
movl (%esi,%edx), %eax
|
247
|
+
xorl (%edi,%edx), %eax
|
248
|
+
jnz LeaveLoopCmps
|
249
|
+
movl 4(%esi,%edx), %eax
|
250
|
+
xorl 4(%edi,%edx), %eax
|
251
|
+
jnz LeaveLoopCmps4
|
252
|
+
addl $8, %edx
|
253
|
+
jnz LoopCmps
|
254
|
+
jmp LenMaximum
|
255
|
+
LeaveLoopCmps4: addl $4, %edx
|
256
|
+
LeaveLoopCmps: testl $0x0000FFFF, %eax
|
257
|
+
jnz LenLower
|
258
|
+
addl $2, %edx
|
259
|
+
shrl $16, %eax
|
260
|
+
LenLower: subb $1, %al
|
261
|
+
adcl $0, %edx
|
262
|
+
|
263
|
+
/* Calculate the length of the match. If it is longer than MAX_MATCH, */
|
264
|
+
/* then automatically accept it as the best possible match and leave. */
|
265
|
+
|
266
|
+
lea (%edi,%edx), %eax
|
267
|
+
movl scan(%esp), %edi
|
268
|
+
subl %edi, %eax
|
269
|
+
cmpl $MAX_MATCH, %eax
|
270
|
+
jge LenMaximum
|
271
|
+
|
272
|
+
/* If the length of the match is not longer than the best match we */
|
273
|
+
/* have so far, then forget it and return to the lookup loop. */
|
274
|
+
|
275
|
+
movl deflatestate(%esp), %edx
|
276
|
+
movl bestlen(%esp), %ebx
|
277
|
+
cmpl %ebx, %eax
|
278
|
+
jg LongerMatch
|
279
|
+
movl windowbestlen(%esp), %esi
|
280
|
+
movl dsPrev(%edx), %edi
|
281
|
+
movl scanend(%esp), %ebx
|
282
|
+
movl chainlenwmask(%esp), %edx
|
283
|
+
jmp LookupLoop
|
284
|
+
|
285
|
+
/* s->match_start = cur_match; */
|
286
|
+
/* best_len = len; */
|
287
|
+
/* if (len >= nice_match) break; */
|
288
|
+
/* scan_end = *(ushf*)(scan+best_len-1); */
|
289
|
+
|
290
|
+
LongerMatch: movl nicematch(%esp), %ebx
|
291
|
+
movl %eax, bestlen(%esp)
|
292
|
+
movl %ecx, dsMatchStart(%edx)
|
293
|
+
cmpl %ebx, %eax
|
294
|
+
jge LeaveNow
|
295
|
+
movl window(%esp), %esi
|
296
|
+
addl %eax, %esi
|
297
|
+
movl %esi, windowbestlen(%esp)
|
298
|
+
movzwl -1(%edi,%eax), %ebx
|
299
|
+
movl dsPrev(%edx), %edi
|
300
|
+
movl %ebx, scanend(%esp)
|
301
|
+
movl chainlenwmask(%esp), %edx
|
302
|
+
jmp LookupLoop
|
303
|
+
|
304
|
+
/* Accept the current string, with the maximum possible length. */
|
305
|
+
|
306
|
+
LenMaximum: movl deflatestate(%esp), %edx
|
307
|
+
movl $MAX_MATCH, bestlen(%esp)
|
308
|
+
movl %ecx, dsMatchStart(%edx)
|
309
|
+
|
310
|
+
/* if ((uInt)best_len <= s->lookahead) return (uInt)best_len; */
|
311
|
+
/* return s->lookahead; */
|
312
|
+
|
313
|
+
LeaveNow:
|
314
|
+
movl deflatestate(%esp), %edx
|
315
|
+
movl bestlen(%esp), %ebx
|
316
|
+
movl dsLookahead(%edx), %eax
|
317
|
+
cmpl %eax, %ebx
|
318
|
+
jg LookaheadRet
|
319
|
+
movl %ebx, %eax
|
320
|
+
LookaheadRet:
|
321
|
+
|
322
|
+
/* Restore the stack and return from whence we came. */
|
323
|
+
|
324
|
+
addl $LocalVarsSize, %esp
|
325
|
+
popl %ebx
|
326
|
+
popl %esi
|
327
|
+
popl %edi
|
328
|
+
popl %ebp
|
329
|
+
match_init: ret
|
@@ -0,0 +1,444 @@
|
|
1
|
+
/* blast.c
|
2
|
+
* Copyright (C) 2003 Mark Adler
|
3
|
+
* For conditions of distribution and use, see copyright notice in blast.h
|
4
|
+
* version 1.1, 16 Feb 2003
|
5
|
+
*
|
6
|
+
* blast.c decompresses data compressed by the PKWare Compression Library.
|
7
|
+
* This function provides functionality similar to the explode() function of
|
8
|
+
* the PKWare library, hence the name "blast".
|
9
|
+
*
|
10
|
+
* This decompressor is based on the excellent format description provided by
|
11
|
+
* Ben Rudiak-Gould in comp.compression on August 13, 2001. Interestingly, the
|
12
|
+
* example Ben provided in the post is incorrect. The distance 110001 should
|
13
|
+
* instead be 111000. When corrected, the example byte stream becomes:
|
14
|
+
*
|
15
|
+
* 00 04 82 24 25 8f 80 7f
|
16
|
+
*
|
17
|
+
* which decompresses to "AIAIAIAIAIAIA" (without the quotes).
|
18
|
+
*/
|
19
|
+
|
20
|
+
/*
|
21
|
+
* Change history:
|
22
|
+
*
|
23
|
+
* 1.0 12 Feb 2003 - First version
|
24
|
+
* 1.1 16 Feb 2003 - Fixed distance check for > 4 GB uncompressed data
|
25
|
+
*/
|
26
|
+
|
27
|
+
#include <setjmp.h> /* for setjmp(), longjmp(), and jmp_buf */
|
28
|
+
#include "blast.h" /* prototype for blast() */
|
29
|
+
|
30
|
+
#define local static /* for local function definitions */
|
31
|
+
#define MAXBITS 13 /* maximum code length */
|
32
|
+
#define MAXWIN 4096 /* maximum window size */
|
33
|
+
|
34
|
+
/* input and output state */
|
35
|
+
struct state {
|
36
|
+
/* input state */
|
37
|
+
blast_in infun; /* input function provided by user */
|
38
|
+
void *inhow; /* opaque information passed to infun() */
|
39
|
+
unsigned char *in; /* next input location */
|
40
|
+
unsigned left; /* available input at in */
|
41
|
+
int bitbuf; /* bit buffer */
|
42
|
+
int bitcnt; /* number of bits in bit buffer */
|
43
|
+
|
44
|
+
/* input limit error return state for bits() and decode() */
|
45
|
+
jmp_buf env;
|
46
|
+
|
47
|
+
/* output state */
|
48
|
+
blast_out outfun; /* output function provided by user */
|
49
|
+
void *outhow; /* opaque information passed to outfun() */
|
50
|
+
unsigned next; /* index of next write location in out[] */
|
51
|
+
int first; /* true to check distances (for first 4K) */
|
52
|
+
unsigned char out[MAXWIN]; /* output buffer and sliding window */
|
53
|
+
};
|
54
|
+
|
55
|
+
/*
|
56
|
+
* Return need bits from the input stream. This always leaves less than
|
57
|
+
* eight bits in the buffer. bits() works properly for need == 0.
|
58
|
+
*
|
59
|
+
* Format notes:
|
60
|
+
*
|
61
|
+
* - Bits are stored in bytes from the least significant bit to the most
|
62
|
+
* significant bit. Therefore bits are dropped from the bottom of the bit
|
63
|
+
* buffer, using shift right, and new bytes are appended to the top of the
|
64
|
+
* bit buffer, using shift left.
|
65
|
+
*/
|
66
|
+
local int bits(struct state *s, int need)
|
67
|
+
{
|
68
|
+
int val; /* bit accumulator */
|
69
|
+
|
70
|
+
/* load at least need bits into val */
|
71
|
+
val = s->bitbuf;
|
72
|
+
while (s->bitcnt < need) {
|
73
|
+
if (s->left == 0) {
|
74
|
+
s->left = s->infun(s->inhow, &(s->in));
|
75
|
+
if (s->left == 0) longjmp(s->env, 1); /* out of input */
|
76
|
+
}
|
77
|
+
val |= (int)(*(s->in)++) << s->bitcnt; /* load eight bits */
|
78
|
+
s->left--;
|
79
|
+
s->bitcnt += 8;
|
80
|
+
}
|
81
|
+
|
82
|
+
/* drop need bits and update buffer, always zero to seven bits left */
|
83
|
+
s->bitbuf = val >> need;
|
84
|
+
s->bitcnt -= need;
|
85
|
+
|
86
|
+
/* return need bits, zeroing the bits above that */
|
87
|
+
return val & ((1 << need) - 1);
|
88
|
+
}
|
89
|
+
|
90
|
+
/*
|
91
|
+
* Huffman code decoding tables. count[1..MAXBITS] is the number of symbols of
|
92
|
+
* each length, which for a canonical code are stepped through in order.
|
93
|
+
* symbol[] are the symbol values in canonical order, where the number of
|
94
|
+
* entries is the sum of the counts in count[]. The decoding process can be
|
95
|
+
* seen in the function decode() below.
|
96
|
+
*/
|
97
|
+
struct huffman {
|
98
|
+
short *count; /* number of symbols of each length */
|
99
|
+
short *symbol; /* canonically ordered symbols */
|
100
|
+
};
|
101
|
+
|
102
|
+
/*
|
103
|
+
* Decode a code from the stream s using huffman table h. Return the symbol or
|
104
|
+
* a negative value if there is an error. If all of the lengths are zero, i.e.
|
105
|
+
* an empty code, or if the code is incomplete and an invalid code is received,
|
106
|
+
* then -9 is returned after reading MAXBITS bits.
|
107
|
+
*
|
108
|
+
* Format notes:
|
109
|
+
*
|
110
|
+
* - The codes as stored in the compressed data are bit-reversed relative to
|
111
|
+
* a simple integer ordering of codes of the same lengths. Hence below the
|
112
|
+
* bits are pulled from the compressed data one at a time and used to
|
113
|
+
* build the code value reversed from what is in the stream in order to
|
114
|
+
* permit simple integer comparisons for decoding.
|
115
|
+
*
|
116
|
+
* - The first code for the shortest length is all ones. Subsequent codes of
|
117
|
+
* the same length are simply integer decrements of the previous code. When
|
118
|
+
* moving up a length, a one bit is appended to the code. For a complete
|
119
|
+
* code, the last code of the longest length will be all zeros. To support
|
120
|
+
* this ordering, the bits pulled during decoding are inverted to apply the
|
121
|
+
* more "natural" ordering starting with all zeros and incrementing.
|
122
|
+
*/
|
123
|
+
local int decode(struct state *s, struct huffman *h)
|
124
|
+
{
|
125
|
+
int len; /* current number of bits in code */
|
126
|
+
int code; /* len bits being decoded */
|
127
|
+
int first; /* first code of length len */
|
128
|
+
int count; /* number of codes of length len */
|
129
|
+
int index; /* index of first code of length len in symbol table */
|
130
|
+
int bitbuf; /* bits from stream */
|
131
|
+
int left; /* bits left in next or left to process */
|
132
|
+
short *next; /* next number of codes */
|
133
|
+
|
134
|
+
bitbuf = s->bitbuf;
|
135
|
+
left = s->bitcnt;
|
136
|
+
code = first = index = 0;
|
137
|
+
len = 1;
|
138
|
+
next = h->count + 1;
|
139
|
+
while (1) {
|
140
|
+
while (left--) {
|
141
|
+
code |= (bitbuf & 1) ^ 1; /* invert code */
|
142
|
+
bitbuf >>= 1;
|
143
|
+
count = *next++;
|
144
|
+
if (code < first + count) { /* if length len, return symbol */
|
145
|
+
s->bitbuf = bitbuf;
|
146
|
+
s->bitcnt = (s->bitcnt - len) & 7;
|
147
|
+
return h->symbol[index + (code - first)];
|
148
|
+
}
|
149
|
+
index += count; /* else update for next length */
|
150
|
+
first += count;
|
151
|
+
first <<= 1;
|
152
|
+
code <<= 1;
|
153
|
+
len++;
|
154
|
+
}
|
155
|
+
left = (MAXBITS+1) - len;
|
156
|
+
if (left == 0) break;
|
157
|
+
if (s->left == 0) {
|
158
|
+
s->left = s->infun(s->inhow, &(s->in));
|
159
|
+
if (s->left == 0) longjmp(s->env, 1); /* out of input */
|
160
|
+
}
|
161
|
+
bitbuf = *(s->in)++;
|
162
|
+
s->left--;
|
163
|
+
if (left > 8) left = 8;
|
164
|
+
}
|
165
|
+
return -9; /* ran out of codes */
|
166
|
+
}
|
167
|
+
|
168
|
+
/*
|
169
|
+
* Given a list of repeated code lengths rep[0..n-1], where each byte is a
|
170
|
+
* count (high four bits + 1) and a code length (low four bits), generate the
|
171
|
+
* list of code lengths. This compaction reduces the size of the object code.
|
172
|
+
* Then given the list of code lengths length[0..n-1] representing a canonical
|
173
|
+
* Huffman code for n symbols, construct the tables required to decode those
|
174
|
+
* codes. Those tables are the number of codes of each length, and the symbols
|
175
|
+
* sorted by length, retaining their original order within each length. The
|
176
|
+
* return value is zero for a complete code set, negative for an over-
|
177
|
+
* subscribed code set, and positive for an incomplete code set. The tables
|
178
|
+
* can be used if the return value is zero or positive, but they cannot be used
|
179
|
+
* if the return value is negative. If the return value is zero, it is not
|
180
|
+
* possible for decode() using that table to return an error--any stream of
|
181
|
+
* enough bits will resolve to a symbol. If the return value is positive, then
|
182
|
+
* it is possible for decode() using that table to return an error for received
|
183
|
+
* codes past the end of the incomplete lengths.
|
184
|
+
*/
|
185
|
+
local int construct(struct huffman *h, const unsigned char *rep, int n)
|
186
|
+
{
|
187
|
+
int symbol; /* current symbol when stepping through length[] */
|
188
|
+
int len; /* current length when stepping through h->count[] */
|
189
|
+
int left; /* number of possible codes left of current length */
|
190
|
+
short offs[MAXBITS+1]; /* offsets in symbol table for each length */
|
191
|
+
short length[256]; /* code lengths */
|
192
|
+
|
193
|
+
/* convert compact repeat counts into symbol bit length list */
|
194
|
+
symbol = 0;
|
195
|
+
do {
|
196
|
+
len = *rep++;
|
197
|
+
left = (len >> 4) + 1;
|
198
|
+
len &= 15;
|
199
|
+
do {
|
200
|
+
length[symbol++] = len;
|
201
|
+
} while (--left);
|
202
|
+
} while (--n);
|
203
|
+
n = symbol;
|
204
|
+
|
205
|
+
/* count number of codes of each length */
|
206
|
+
for (len = 0; len <= MAXBITS; len++)
|
207
|
+
h->count[len] = 0;
|
208
|
+
for (symbol = 0; symbol < n; symbol++)
|
209
|
+
(h->count[length[symbol]])++; /* assumes lengths are within bounds */
|
210
|
+
if (h->count[0] == n) /* no codes! */
|
211
|
+
return 0; /* complete, but decode() will fail */
|
212
|
+
|
213
|
+
/* check for an over-subscribed or incomplete set of lengths */
|
214
|
+
left = 1; /* one possible code of zero length */
|
215
|
+
for (len = 1; len <= MAXBITS; len++) {
|
216
|
+
left <<= 1; /* one more bit, double codes left */
|
217
|
+
left -= h->count[len]; /* deduct count from possible codes */
|
218
|
+
if (left < 0) return left; /* over-subscribed--return negative */
|
219
|
+
} /* left > 0 means incomplete */
|
220
|
+
|
221
|
+
/* generate offsets into symbol table for each length for sorting */
|
222
|
+
offs[1] = 0;
|
223
|
+
for (len = 1; len < MAXBITS; len++)
|
224
|
+
offs[len + 1] = offs[len] + h->count[len];
|
225
|
+
|
226
|
+
/*
|
227
|
+
* put symbols in table sorted by length, by symbol order within each
|
228
|
+
* length
|
229
|
+
*/
|
230
|
+
for (symbol = 0; symbol < n; symbol++)
|
231
|
+
if (length[symbol] != 0)
|
232
|
+
h->symbol[offs[length[symbol]]++] = symbol;
|
233
|
+
|
234
|
+
/* return zero for complete set, positive for incomplete set */
|
235
|
+
return left;
|
236
|
+
}
|
237
|
+
|
238
|
+
/*
|
239
|
+
* Decode PKWare Compression Library stream.
|
240
|
+
*
|
241
|
+
* Format notes:
|
242
|
+
*
|
243
|
+
* - First byte is 0 if literals are uncoded or 1 if they are coded. Second
|
244
|
+
* byte is 4, 5, or 6 for the number of extra bits in the distance code.
|
245
|
+
* This is the base-2 logarithm of the dictionary size minus six.
|
246
|
+
*
|
247
|
+
* - Compressed data is a combination of literals and length/distance pairs
|
248
|
+
* terminated by an end code. Literals are either Huffman coded or
|
249
|
+
* uncoded bytes. A length/distance pair is a coded length followed by a
|
250
|
+
* coded distance to represent a string that occurs earlier in the
|
251
|
+
* uncompressed data that occurs again at the current location.
|
252
|
+
*
|
253
|
+
* - A bit preceding a literal or length/distance pair indicates which comes
|
254
|
+
* next, 0 for literals, 1 for length/distance.
|
255
|
+
*
|
256
|
+
* - If literals are uncoded, then the next eight bits are the literal, in the
|
257
|
+
* normal bit order in th stream, i.e. no bit-reversal is needed. Similarly,
|
258
|
+
* no bit reversal is needed for either the length extra bits or the distance
|
259
|
+
* extra bits.
|
260
|
+
*
|
261
|
+
* - Literal bytes are simply written to the output. A length/distance pair is
|
262
|
+
* an instruction to copy previously uncompressed bytes to the output. The
|
263
|
+
* copy is from distance bytes back in the output stream, copying for length
|
264
|
+
* bytes.
|
265
|
+
*
|
266
|
+
* - Distances pointing before the beginning of the output data are not
|
267
|
+
* permitted.
|
268
|
+
*
|
269
|
+
* - Overlapped copies, where the length is greater than the distance, are
|
270
|
+
* allowed and common. For example, a distance of one and a length of 518
|
271
|
+
* simply copies the last byte 518 times. A distance of four and a length of
|
272
|
+
* twelve copies the last four bytes three times. A simple forward copy
|
273
|
+
* ignoring whether the length is greater than the distance or not implements
|
274
|
+
* this correctly.
|
275
|
+
*/
|
276
|
+
local int decomp(struct state *s)
|
277
|
+
{
|
278
|
+
int lit; /* true if literals are coded */
|
279
|
+
int dict; /* log2(dictionary size) - 6 */
|
280
|
+
int symbol; /* decoded symbol, extra bits for distance */
|
281
|
+
int len; /* length for copy */
|
282
|
+
int dist; /* distance for copy */
|
283
|
+
int copy; /* copy counter */
|
284
|
+
unsigned char *from, *to; /* copy pointers */
|
285
|
+
static int virgin = 1; /* build tables once */
|
286
|
+
static short litcnt[MAXBITS+1], litsym[256]; /* litcode memory */
|
287
|
+
static short lencnt[MAXBITS+1], lensym[16]; /* lencode memory */
|
288
|
+
static short distcnt[MAXBITS+1], distsym[64]; /* distcode memory */
|
289
|
+
static struct huffman litcode = {litcnt, litsym}; /* length code */
|
290
|
+
static struct huffman lencode = {lencnt, lensym}; /* length code */
|
291
|
+
static struct huffman distcode = {distcnt, distsym};/* distance code */
|
292
|
+
/* bit lengths of literal codes */
|
293
|
+
static const unsigned char litlen[] = {
|
294
|
+
11, 124, 8, 7, 28, 7, 188, 13, 76, 4, 10, 8, 12, 10, 12, 10, 8, 23, 8,
|
295
|
+
9, 7, 6, 7, 8, 7, 6, 55, 8, 23, 24, 12, 11, 7, 9, 11, 12, 6, 7, 22, 5,
|
296
|
+
7, 24, 6, 11, 9, 6, 7, 22, 7, 11, 38, 7, 9, 8, 25, 11, 8, 11, 9, 12,
|
297
|
+
8, 12, 5, 38, 5, 38, 5, 11, 7, 5, 6, 21, 6, 10, 53, 8, 7, 24, 10, 27,
|
298
|
+
44, 253, 253, 253, 252, 252, 252, 13, 12, 45, 12, 45, 12, 61, 12, 45,
|
299
|
+
44, 173};
|
300
|
+
/* bit lengths of length codes 0..15 */
|
301
|
+
static const unsigned char lenlen[] = {2, 35, 36, 53, 38, 23};
|
302
|
+
/* bit lengths of distance codes 0..63 */
|
303
|
+
static const unsigned char distlen[] = {2, 20, 53, 230, 247, 151, 248};
|
304
|
+
static const short base[16] = { /* base for length codes */
|
305
|
+
3, 2, 4, 5, 6, 7, 8, 9, 10, 12, 16, 24, 40, 72, 136, 264};
|
306
|
+
static const char extra[16] = { /* extra bits for length codes */
|
307
|
+
0, 0, 0, 0, 0, 0, 0, 0, 1, 2, 3, 4, 5, 6, 7, 8};
|
308
|
+
|
309
|
+
/* set up decoding tables (once--might not be thread-safe) */
|
310
|
+
if (virgin) {
|
311
|
+
construct(&litcode, litlen, sizeof(litlen));
|
312
|
+
construct(&lencode, lenlen, sizeof(lenlen));
|
313
|
+
construct(&distcode, distlen, sizeof(distlen));
|
314
|
+
virgin = 0;
|
315
|
+
}
|
316
|
+
|
317
|
+
/* read header */
|
318
|
+
lit = bits(s, 8);
|
319
|
+
if (lit > 1) return -1;
|
320
|
+
dict = bits(s, 8);
|
321
|
+
if (dict < 4 || dict > 6) return -2;
|
322
|
+
|
323
|
+
/* decode literals and length/distance pairs */
|
324
|
+
do {
|
325
|
+
if (bits(s, 1)) {
|
326
|
+
/* get length */
|
327
|
+
symbol = decode(s, &lencode);
|
328
|
+
len = base[symbol] + bits(s, extra[symbol]);
|
329
|
+
if (len == 519) break; /* end code */
|
330
|
+
|
331
|
+
/* get distance */
|
332
|
+
symbol = len == 2 ? 2 : dict;
|
333
|
+
dist = decode(s, &distcode) << symbol;
|
334
|
+
dist += bits(s, symbol);
|
335
|
+
dist++;
|
336
|
+
if (s->first && dist > s->next)
|
337
|
+
return -3; /* distance too far back */
|
338
|
+
|
339
|
+
/* copy length bytes from distance bytes back */
|
340
|
+
do {
|
341
|
+
to = s->out + s->next;
|
342
|
+
from = to - dist;
|
343
|
+
copy = MAXWIN;
|
344
|
+
if (s->next < dist) {
|
345
|
+
from += copy;
|
346
|
+
copy = dist;
|
347
|
+
}
|
348
|
+
copy -= s->next;
|
349
|
+
if (copy > len) copy = len;
|
350
|
+
len -= copy;
|
351
|
+
s->next += copy;
|
352
|
+
do {
|
353
|
+
*to++ = *from++;
|
354
|
+
} while (--copy);
|
355
|
+
if (s->next == MAXWIN) {
|
356
|
+
if (s->outfun(s->outhow, s->out, s->next)) return 1;
|
357
|
+
s->next = 0;
|
358
|
+
s->first = 0;
|
359
|
+
}
|
360
|
+
} while (len != 0);
|
361
|
+
}
|
362
|
+
else {
|
363
|
+
/* get literal and write it */
|
364
|
+
symbol = lit ? decode(s, &litcode) : bits(s, 8);
|
365
|
+
s->out[s->next++] = symbol;
|
366
|
+
if (s->next == MAXWIN) {
|
367
|
+
if (s->outfun(s->outhow, s->out, s->next)) return 1;
|
368
|
+
s->next = 0;
|
369
|
+
s->first = 0;
|
370
|
+
}
|
371
|
+
}
|
372
|
+
} while (1);
|
373
|
+
return 0;
|
374
|
+
}
|
375
|
+
|
376
|
+
/* See comments in blast.h */
|
377
|
+
int blast(blast_in infun, void *inhow, blast_out outfun, void *outhow)
|
378
|
+
{
|
379
|
+
struct state s; /* input/output state */
|
380
|
+
int err; /* return value */
|
381
|
+
|
382
|
+
/* initialize input state */
|
383
|
+
s.infun = infun;
|
384
|
+
s.inhow = inhow;
|
385
|
+
s.left = 0;
|
386
|
+
s.bitbuf = 0;
|
387
|
+
s.bitcnt = 0;
|
388
|
+
|
389
|
+
/* initialize output state */
|
390
|
+
s.outfun = outfun;
|
391
|
+
s.outhow = outhow;
|
392
|
+
s.next = 0;
|
393
|
+
s.first = 1;
|
394
|
+
|
395
|
+
/* return if bits() or decode() tries to read past available input */
|
396
|
+
if (setjmp(s.env) != 0) /* if came back here via longjmp(), */
|
397
|
+
err = 2; /* then skip decomp(), return error */
|
398
|
+
else
|
399
|
+
err = decomp(&s); /* decompress */
|
400
|
+
|
401
|
+
/* write any leftover output and update the error code if needed */
|
402
|
+
if (err != 1 && s.next && s.outfun(s.outhow, s.out, s.next) && err == 0)
|
403
|
+
err = 1;
|
404
|
+
return err;
|
405
|
+
}
|
406
|
+
|
407
|
+
#ifdef TEST
|
408
|
+
/* Example of how to use blast() */
|
409
|
+
#include <stdio.h>
|
410
|
+
#include <stdlib.h>
|
411
|
+
|
412
|
+
#define CHUNK 16384
|
413
|
+
|
414
|
+
local unsigned inf(void *how, unsigned char **buf)
|
415
|
+
{
|
416
|
+
static unsigned char hold[CHUNK];
|
417
|
+
|
418
|
+
*buf = hold;
|
419
|
+
return fread(hold, 1, CHUNK, (FILE *)how);
|
420
|
+
}
|
421
|
+
|
422
|
+
local int outf(void *how, unsigned char *buf, unsigned len)
|
423
|
+
{
|
424
|
+
return fwrite(buf, 1, len, (FILE *)how) != len;
|
425
|
+
}
|
426
|
+
|
427
|
+
/* Decompress a PKWare Compression Library stream from stdin to stdout */
|
428
|
+
int main(void)
|
429
|
+
{
|
430
|
+
int ret, n;
|
431
|
+
|
432
|
+
/* decompress to stdout */
|
433
|
+
ret = blast(inf, stdin, outf, stdout);
|
434
|
+
if (ret != 0) fprintf(stderr, "blast error: %d\n", ret);
|
435
|
+
|
436
|
+
/* see if there are any leftover bytes */
|
437
|
+
n = 0;
|
438
|
+
while (getchar() != EOF) n++;
|
439
|
+
if (n) fprintf(stderr, "blast warning: %d unused bytes of input\n", n);
|
440
|
+
|
441
|
+
/* return blast() error code */
|
442
|
+
return ret;
|
443
|
+
}
|
444
|
+
#endif
|