minimap2 0.2.22.0 → 0.2.24.1
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- checksums.yaml +4 -4
- data/README.md +60 -76
- data/ext/Rakefile +55 -0
- data/ext/cmappy/cmappy.c +129 -0
- data/ext/cmappy/cmappy.h +44 -0
- data/ext/minimap2/FAQ.md +46 -0
- data/ext/minimap2/LICENSE.txt +24 -0
- data/ext/minimap2/MANIFEST.in +10 -0
- data/ext/minimap2/Makefile +132 -0
- data/ext/minimap2/Makefile.simde +97 -0
- data/ext/minimap2/NEWS.md +821 -0
- data/ext/minimap2/README.md +403 -0
- data/ext/minimap2/align.c +1020 -0
- data/ext/minimap2/bseq.c +169 -0
- data/ext/minimap2/bseq.h +64 -0
- data/ext/minimap2/code_of_conduct.md +30 -0
- data/ext/minimap2/cookbook.md +243 -0
- data/ext/minimap2/esterr.c +64 -0
- data/ext/minimap2/example.c +63 -0
- data/ext/minimap2/format.c +559 -0
- data/ext/minimap2/hit.c +466 -0
- data/ext/minimap2/index.c +775 -0
- data/ext/minimap2/kalloc.c +205 -0
- data/ext/minimap2/kalloc.h +76 -0
- data/ext/minimap2/kdq.h +132 -0
- data/ext/minimap2/ketopt.h +120 -0
- data/ext/minimap2/khash.h +615 -0
- data/ext/minimap2/krmq.h +474 -0
- data/ext/minimap2/kseq.h +256 -0
- data/ext/minimap2/ksort.h +153 -0
- data/ext/minimap2/ksw2.h +184 -0
- data/ext/minimap2/ksw2_dispatch.c +96 -0
- data/ext/minimap2/ksw2_extd2_sse.c +402 -0
- data/ext/minimap2/ksw2_exts2_sse.c +416 -0
- data/ext/minimap2/ksw2_extz2_sse.c +313 -0
- data/ext/minimap2/ksw2_ll_sse.c +152 -0
- data/ext/minimap2/kthread.c +159 -0
- data/ext/minimap2/kthread.h +15 -0
- data/ext/minimap2/kvec.h +105 -0
- data/ext/minimap2/lchain.c +369 -0
- data/ext/minimap2/main.c +459 -0
- data/ext/minimap2/map.c +714 -0
- data/ext/minimap2/minimap.h +410 -0
- data/ext/minimap2/minimap2.1 +725 -0
- data/ext/minimap2/misc/README.md +179 -0
- data/ext/minimap2/misc/mmphase.js +335 -0
- data/ext/minimap2/misc/paftools.js +3149 -0
- data/ext/minimap2/misc.c +162 -0
- data/ext/minimap2/mmpriv.h +132 -0
- data/ext/minimap2/options.c +234 -0
- data/ext/minimap2/pe.c +177 -0
- data/ext/minimap2/python/README.rst +196 -0
- data/ext/minimap2/python/cmappy.h +152 -0
- data/ext/minimap2/python/cmappy.pxd +153 -0
- data/ext/minimap2/python/mappy.pyx +273 -0
- data/ext/minimap2/python/minimap2.py +39 -0
- data/ext/minimap2/sdust.c +213 -0
- data/ext/minimap2/sdust.h +25 -0
- data/ext/minimap2/seed.c +131 -0
- data/ext/minimap2/setup.py +55 -0
- data/ext/minimap2/sketch.c +143 -0
- data/ext/minimap2/splitidx.c +84 -0
- data/ext/minimap2/sse2neon/emmintrin.h +1689 -0
- data/ext/minimap2/test/MT-human.fa +278 -0
- data/ext/minimap2/test/MT-orang.fa +276 -0
- data/ext/minimap2/test/q-inv.fa +4 -0
- data/ext/minimap2/test/q2.fa +2 -0
- data/ext/minimap2/test/t-inv.fa +127 -0
- data/ext/minimap2/test/t2.fa +2 -0
- data/ext/minimap2/tex/Makefile +21 -0
- data/ext/minimap2/tex/bioinfo.cls +930 -0
- data/ext/minimap2/tex/blasr-mc.eval +17 -0
- data/ext/minimap2/tex/bowtie2-s3.sam.eval +28 -0
- data/ext/minimap2/tex/bwa-s3.sam.eval +52 -0
- data/ext/minimap2/tex/bwa.eval +55 -0
- data/ext/minimap2/tex/eval2roc.pl +33 -0
- data/ext/minimap2/tex/graphmap.eval +4 -0
- data/ext/minimap2/tex/hs38-simu.sh +10 -0
- data/ext/minimap2/tex/minialign.eval +49 -0
- data/ext/minimap2/tex/minimap2.bib +460 -0
- data/ext/minimap2/tex/minimap2.tex +724 -0
- data/ext/minimap2/tex/mm2-s3.sam.eval +62 -0
- data/ext/minimap2/tex/mm2-update.tex +240 -0
- data/ext/minimap2/tex/mm2.approx.eval +12 -0
- data/ext/minimap2/tex/mm2.eval +13 -0
- data/ext/minimap2/tex/natbib.bst +1288 -0
- data/ext/minimap2/tex/natbib.sty +803 -0
- data/ext/minimap2/tex/ngmlr.eval +38 -0
- data/ext/minimap2/tex/roc.gp +60 -0
- data/ext/minimap2/tex/snap-s3.sam.eval +62 -0
- data/ext/minimap2.patch +19 -0
- data/lib/minimap2/aligner.rb +4 -4
- data/lib/minimap2/alignment.rb +11 -11
- data/lib/minimap2/ffi/constants.rb +20 -16
- data/lib/minimap2/ffi/functions.rb +5 -0
- data/lib/minimap2/ffi.rb +4 -5
- data/lib/minimap2/version.rb +2 -2
- data/lib/minimap2.rb +51 -15
- metadata +97 -79
- data/lib/minimap2/ffi_helper.rb +0 -53
- data/vendor/libminimap2.so +0 -0
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%% NOTICE:
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%% It may not be distributed in exchange for money,
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%% The author provides it `as is' and does not guarantee it in any way.
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%% Copyright (C) 1994 Patrick W. Daly
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% Such a package is natbib.sty by Patrick W. Daly
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% of the author names, as they should appear in the citation, with the year
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% \cite[chap. 2]{key} ==>> (Jones et al., 1990, chap. 2)
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% \cite[e.g.][p. 32]{key} ==>> (e.g. Jones et al., p. 32)
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%%---------------------------------------------------------------------
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ENTRY
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{ address
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author
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booktitle
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chapter
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edition
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editor
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howpublished
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institution
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journal
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key
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month
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note
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number
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organization
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pages
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publisher
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school
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series
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title
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type
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volume
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year
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}
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{}
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{ label extra.label sort.label }
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INTEGERS { output.state before.all mid.sentence after.sentence after.block }
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FUNCTION {init.state.consts}
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{ #0 'before.all :=
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#1 'mid.sentence :=
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#2 'after.sentence :=
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#3 'after.block :=
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}
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STRINGS { s t }
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FUNCTION {output.nonnull}
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{ 's :=
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output.state mid.sentence =
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{ ", " * write$ }
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{ output.state after.block =
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{ add.period$ write$
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newline$
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"\newblock " write$
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}
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{ output.state before.all =
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'write$
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{ add.period$ " " * write$ }
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if$
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}
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if$
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mid.sentence 'output.state :=
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}
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if$
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s
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}
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FUNCTION {output}
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{ duplicate$ empty$
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'pop$
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'output.nonnull
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if$
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}
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FUNCTION {output.check}
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{ 't :=
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duplicate$ empty$
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{ pop$ "empty " t * " in " * cite$ * warning$ }
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'output.nonnull
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if$
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}
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FUNCTION {fin.entry}
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{ add.period$
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write$
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newline$
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}
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FUNCTION {new.block}
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{ output.state before.all =
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'skip$
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{ after.block 'output.state := }
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if$
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}
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FUNCTION {new.sentence}
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{ output.state after.block =
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'skip$
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{ output.state before.all =
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'skip$
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{ after.sentence 'output.state := }
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if$
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}
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if$
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}
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FUNCTION {not}
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{ { #0 }
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{ #1 }
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if$
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}
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FUNCTION {and}
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{ 'skip$
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{ pop$ #0 }
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if$
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}
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FUNCTION {or}
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{ { pop$ #1 }
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'skip$
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if$
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}
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FUNCTION {non.stop}
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{ duplicate$
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"}" * add.period$
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#-1 #1 substring$ "." =
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}
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FUNCTION {new.block.checkb}
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{ empty$
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swap$ empty$
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and
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'skip$
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'new.block
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if$
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}
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FUNCTION {field.or.null}
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{ duplicate$ empty$
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{ pop$ "" }
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'skip$
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if$
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}
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FUNCTION {emphasize}
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{ duplicate$ empty$
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{ pop$ "" }
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{ "{\em " swap$ * non.stop
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{ "\/}" * }
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{ "}" * }
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if$
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}
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if$
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}
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FUNCTION {bolden}
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{ duplicate$ empty$
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{ pop$ "" }
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{ "{\bf " swap$ * "}" * }
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if$
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}
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INTEGERS { nameptr namesleft numnames }
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FUNCTION {format.names}
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{ 's :=
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#1 'nameptr :=
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s num.names$ 'numnames :=
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numnames 'namesleft :=
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{ namesleft #0 > }
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{ s nameptr
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"{vv~}{ll}{, jj}{, f.}" format.name$ 't :=
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nameptr #1 >
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{
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namesleft #1 >
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{ ", " * t * }
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{
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numnames #2 >
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{ "," * }
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'skip$
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if$
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t "others" =
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{ " " * "et~al." emphasize * }
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{ " and " * t * }
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if$
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}
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if$
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}
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't
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if$
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nameptr #1 + 'nameptr :=
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namesleft #1 - 'namesleft :=
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}
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while$
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}
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FUNCTION {format.names.ed}
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{ 's :=
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#1 'nameptr :=
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s num.names$ 'numnames :=
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numnames 'namesleft :=
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{ namesleft #0 > }
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{ s nameptr
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"{f.~}{vv~}{ll}{, jj}"
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format.name$ 't :=
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nameptr #1 >
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{
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namesleft #1 >
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{ ", " * t * }
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{
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numnames #2 >
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{ "," * }
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'skip$
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if$
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t "others" =
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{ " " * "et~al." emphasize * }
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{ " and " * t * }
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if$
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}
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if$
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}
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't
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if$
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nameptr #1 + 'nameptr :=
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namesleft #1 - 'namesleft :=
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}
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while$
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}
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FUNCTION {format.key}
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{ empty$
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{ key field.or.null }
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+
{ "" }
|
302
|
+
if$
|
303
|
+
}
|
304
|
+
|
305
|
+
FUNCTION {format.authors}
|
306
|
+
{ author empty$
|
307
|
+
{ "" }
|
308
|
+
{ author format.names }
|
309
|
+
if$
|
310
|
+
}
|
311
|
+
|
312
|
+
FUNCTION {format.editors}
|
313
|
+
{ editor empty$
|
314
|
+
{ "" }
|
315
|
+
{ editor format.names
|
316
|
+
editor num.names$ #1 >
|
317
|
+
{ ", editors" * }
|
318
|
+
{ ", editor" * }
|
319
|
+
if$
|
320
|
+
}
|
321
|
+
if$
|
322
|
+
}
|
323
|
+
|
324
|
+
FUNCTION {format.in.editors}
|
325
|
+
{ editor empty$
|
326
|
+
{ "" }
|
327
|
+
{ editor format.names.ed
|
328
|
+
editor num.names$ #1 >
|
329
|
+
{ ", editors" * }
|
330
|
+
{ ", editor" * }
|
331
|
+
if$
|
332
|
+
}
|
333
|
+
if$
|
334
|
+
}
|
335
|
+
|
336
|
+
FUNCTION {format.title}
|
337
|
+
{ title empty$
|
338
|
+
{ "" }
|
339
|
+
{ title "t" change.case$
|
340
|
+
}
|
341
|
+
if$
|
342
|
+
}
|
343
|
+
|
344
|
+
FUNCTION {format.full.names}
|
345
|
+
{'s :=
|
346
|
+
#1 'nameptr :=
|
347
|
+
s num.names$ 'numnames :=
|
348
|
+
numnames 'namesleft :=
|
349
|
+
{ namesleft #0 > }
|
350
|
+
{ s nameptr
|
351
|
+
"{vv~}{ll}" format.name$ 't :=
|
352
|
+
nameptr #1 >
|
353
|
+
{
|
354
|
+
namesleft #1 >
|
355
|
+
{ ", " * t * }
|
356
|
+
{
|
357
|
+
numnames #2 >
|
358
|
+
{ "," * }
|
359
|
+
'skip$
|
360
|
+
if$
|
361
|
+
t "others" =
|
362
|
+
{ " " * "et~al." emphasize * }
|
363
|
+
{ " and " * t * }
|
364
|
+
if$
|
365
|
+
}
|
366
|
+
if$
|
367
|
+
}
|
368
|
+
't
|
369
|
+
if$
|
370
|
+
nameptr #1 + 'nameptr :=
|
371
|
+
namesleft #1 - 'namesleft :=
|
372
|
+
}
|
373
|
+
while$
|
374
|
+
}
|
375
|
+
|
376
|
+
FUNCTION {author.editor.key.full}
|
377
|
+
{ author empty$
|
378
|
+
{ editor empty$
|
379
|
+
{ key empty$
|
380
|
+
{ cite$ #1 #3 substring$ }
|
381
|
+
'key
|
382
|
+
if$
|
383
|
+
}
|
384
|
+
{ editor format.full.names }
|
385
|
+
if$
|
386
|
+
}
|
387
|
+
{ author format.full.names }
|
388
|
+
if$
|
389
|
+
}
|
390
|
+
|
391
|
+
FUNCTION {author.key.full}
|
392
|
+
{ author empty$
|
393
|
+
{ key empty$
|
394
|
+
{ cite$ #1 #3 substring$ }
|
395
|
+
'key
|
396
|
+
if$
|
397
|
+
}
|
398
|
+
{ author format.full.names }
|
399
|
+
if$
|
400
|
+
}
|
401
|
+
|
402
|
+
FUNCTION {editor.key.full}
|
403
|
+
{ editor empty$
|
404
|
+
{ key empty$
|
405
|
+
{ cite$ #1 #3 substring$ }
|
406
|
+
'key
|
407
|
+
if$
|
408
|
+
}
|
409
|
+
{ editor format.full.names }
|
410
|
+
if$
|
411
|
+
}
|
412
|
+
|
413
|
+
FUNCTION {make.full.names}
|
414
|
+
{ type$ "book" =
|
415
|
+
type$ "inbook" =
|
416
|
+
or
|
417
|
+
'author.editor.key.full
|
418
|
+
{ type$ "proceedings" =
|
419
|
+
'editor.key.full
|
420
|
+
'author.key.full
|
421
|
+
if$
|
422
|
+
}
|
423
|
+
if$
|
424
|
+
}
|
425
|
+
|
426
|
+
FUNCTION {output.bibitem}
|
427
|
+
{ newline$
|
428
|
+
"\bibitem[" write$
|
429
|
+
label write$
|
430
|
+
")" make.full.names * "]{" * write$
|
431
|
+
cite$ write$
|
432
|
+
"}" write$
|
433
|
+
newline$
|
434
|
+
""
|
435
|
+
before.all 'output.state :=
|
436
|
+
}
|
437
|
+
|
438
|
+
FUNCTION {n.dashify}
|
439
|
+
{ 't :=
|
440
|
+
""
|
441
|
+
{ t empty$ not }
|
442
|
+
{ t #1 #1 substring$ "-" =
|
443
|
+
{ t #1 #2 substring$ "--" = not
|
444
|
+
{ "--" *
|
445
|
+
t #2 global.max$ substring$ 't :=
|
446
|
+
}
|
447
|
+
{ { t #1 #1 substring$ "-" = }
|
448
|
+
{ "-" *
|
449
|
+
t #2 global.max$ substring$ 't :=
|
450
|
+
}
|
451
|
+
while$
|
452
|
+
}
|
453
|
+
if$
|
454
|
+
}
|
455
|
+
{ t #1 #1 substring$ *
|
456
|
+
t #2 global.max$ substring$ 't :=
|
457
|
+
}
|
458
|
+
if$
|
459
|
+
}
|
460
|
+
while$
|
461
|
+
}
|
462
|
+
|
463
|
+
FUNCTION {word.in}
|
464
|
+
{ "In " }
|
465
|
+
|
466
|
+
FUNCTION {format.date}
|
467
|
+
{ year duplicate$ empty$
|
468
|
+
{ "empty year in " cite$ * "; set to ????" * warning$
|
469
|
+
pop$ "????" }
|
470
|
+
'skip$
|
471
|
+
if$
|
472
|
+
before.all 'output.state :=
|
473
|
+
" (" swap$ * extra.label * ")" *
|
474
|
+
}
|
475
|
+
|
476
|
+
FUNCTION {format.btitle}
|
477
|
+
{ title emphasize
|
478
|
+
}
|
479
|
+
|
480
|
+
FUNCTION {tie.or.space.connect}
|
481
|
+
{ duplicate$ text.length$ #3 <
|
482
|
+
{ "~" }
|
483
|
+
{ " " }
|
484
|
+
if$
|
485
|
+
swap$ * *
|
486
|
+
}
|
487
|
+
|
488
|
+
FUNCTION {either.or.check}
|
489
|
+
{ empty$
|
490
|
+
'pop$
|
491
|
+
{ "can't use both " swap$ * " fields in " * cite$ * warning$ }
|
492
|
+
if$
|
493
|
+
}
|
494
|
+
|
495
|
+
FUNCTION {format.bvolume}
|
496
|
+
{ volume empty$
|
497
|
+
{ "" }
|
498
|
+
{ "volume" volume tie.or.space.connect
|
499
|
+
series empty$
|
500
|
+
'skip$
|
501
|
+
{ " of " * series emphasize * }
|
502
|
+
if$
|
503
|
+
"volume and number" number either.or.check
|
504
|
+
}
|
505
|
+
if$
|
506
|
+
}
|
507
|
+
|
508
|
+
FUNCTION {format.number.series}
|
509
|
+
{ volume empty$
|
510
|
+
{ number empty$
|
511
|
+
{ series field.or.null }
|
512
|
+
{ output.state mid.sentence =
|
513
|
+
{ "number" }
|
514
|
+
{ "Number" }
|
515
|
+
if$
|
516
|
+
number tie.or.space.connect
|
517
|
+
series empty$
|
518
|
+
{ "there's a number but no series in " cite$ * warning$ }
|
519
|
+
{ " in " * series * }
|
520
|
+
if$
|
521
|
+
}
|
522
|
+
if$
|
523
|
+
}
|
524
|
+
{ "" }
|
525
|
+
if$
|
526
|
+
}
|
527
|
+
|
528
|
+
FUNCTION {format.edition}
|
529
|
+
{ edition empty$
|
530
|
+
{ "" }
|
531
|
+
{ output.state mid.sentence =
|
532
|
+
{ edition "l" change.case$ " edition" * }
|
533
|
+
{ edition "t" change.case$ " edition" * }
|
534
|
+
if$
|
535
|
+
}
|
536
|
+
if$
|
537
|
+
}
|
538
|
+
|
539
|
+
INTEGERS { multiresult }
|
540
|
+
|
541
|
+
FUNCTION {multi.page.check}
|
542
|
+
{ 't :=
|
543
|
+
#0 'multiresult :=
|
544
|
+
{ multiresult not
|
545
|
+
t empty$ not
|
546
|
+
and
|
547
|
+
}
|
548
|
+
{ t #1 #1 substring$
|
549
|
+
duplicate$ "-" =
|
550
|
+
swap$ duplicate$ "," =
|
551
|
+
swap$ "+" =
|
552
|
+
or or
|
553
|
+
{ #1 'multiresult := }
|
554
|
+
{ t #2 global.max$ substring$ 't := }
|
555
|
+
if$
|
556
|
+
}
|
557
|
+
while$
|
558
|
+
multiresult
|
559
|
+
}
|
560
|
+
|
561
|
+
FUNCTION {format.pages}
|
562
|
+
{ pages empty$
|
563
|
+
{ "" }
|
564
|
+
{ pages multi.page.check
|
565
|
+
{ "pages" pages n.dashify tie.or.space.connect }
|
566
|
+
{ "page" pages tie.or.space.connect }
|
567
|
+
if$
|
568
|
+
}
|
569
|
+
if$
|
570
|
+
}
|
571
|
+
|
572
|
+
FUNCTION {format.vol.num.pages}
|
573
|
+
{ volume field.or.null
|
574
|
+
bolden
|
575
|
+
number empty$
|
576
|
+
'skip$
|
577
|
+
{ "(" number * ")" * *
|
578
|
+
volume empty$
|
579
|
+
{ "there's a number but no volume in " cite$ * warning$ }
|
580
|
+
'skip$
|
581
|
+
if$
|
582
|
+
}
|
583
|
+
if$
|
584
|
+
pages empty$
|
585
|
+
'skip$
|
586
|
+
{ duplicate$ empty$
|
587
|
+
{ pop$ format.pages }
|
588
|
+
{ ", " * pages n.dashify * }
|
589
|
+
if$
|
590
|
+
}
|
591
|
+
if$
|
592
|
+
}
|
593
|
+
|
594
|
+
FUNCTION {format.chapter.pages}
|
595
|
+
{ chapter empty$
|
596
|
+
'format.pages
|
597
|
+
{ type empty$
|
598
|
+
{ "chapter" }
|
599
|
+
{ type "l" change.case$ }
|
600
|
+
if$
|
601
|
+
chapter tie.or.space.connect
|
602
|
+
pages empty$
|
603
|
+
'skip$
|
604
|
+
{ ", " * format.pages * }
|
605
|
+
if$
|
606
|
+
}
|
607
|
+
if$
|
608
|
+
}
|
609
|
+
|
610
|
+
FUNCTION {format.in.ed.booktitle}
|
611
|
+
{ booktitle empty$
|
612
|
+
{ "" }
|
613
|
+
{ editor empty$
|
614
|
+
{ word.in booktitle emphasize * }
|
615
|
+
{ word.in format.in.editors * ", " * booktitle emphasize * }
|
616
|
+
if$
|
617
|
+
}
|
618
|
+
if$
|
619
|
+
}
|
620
|
+
|
621
|
+
FUNCTION {format.thesis.type}
|
622
|
+
{ type empty$
|
623
|
+
'skip$
|
624
|
+
{ pop$
|
625
|
+
type "t" change.case$
|
626
|
+
}
|
627
|
+
if$
|
628
|
+
}
|
629
|
+
|
630
|
+
FUNCTION {format.tr.number}
|
631
|
+
{ type empty$
|
632
|
+
{ "Technical Report" }
|
633
|
+
'type
|
634
|
+
if$
|
635
|
+
number empty$
|
636
|
+
{ "t" change.case$ }
|
637
|
+
{ number tie.or.space.connect }
|
638
|
+
if$
|
639
|
+
}
|
640
|
+
|
641
|
+
FUNCTION {format.article.crossref}
|
642
|
+
{
|
643
|
+
word.in
|
644
|
+
"\cite{" * crossref * "}" *
|
645
|
+
}
|
646
|
+
|
647
|
+
FUNCTION {format.book.crossref}
|
648
|
+
{ volume empty$
|
649
|
+
{ "empty volume in " cite$ * "'s crossref of " * crossref * warning$
|
650
|
+
word.in
|
651
|
+
}
|
652
|
+
{ "Volume" volume tie.or.space.connect
|
653
|
+
" of " *
|
654
|
+
}
|
655
|
+
if$
|
656
|
+
"\cite{" * crossref * "}" *
|
657
|
+
}
|
658
|
+
|
659
|
+
FUNCTION {format.incoll.inproc.crossref}
|
660
|
+
{
|
661
|
+
word.in
|
662
|
+
"\cite{" * crossref * "}" *
|
663
|
+
}
|
664
|
+
|
665
|
+
FUNCTION {article}
|
666
|
+
{ output.bibitem
|
667
|
+
format.authors "author" output.check
|
668
|
+
author format.key output
|
669
|
+
format.date "year" output.check
|
670
|
+
new.block
|
671
|
+
format.title "title" output.check
|
672
|
+
new.block
|
673
|
+
crossref missing$
|
674
|
+
{ journal emphasize "journal" output.check
|
675
|
+
format.vol.num.pages output
|
676
|
+
}
|
677
|
+
{ format.article.crossref output.nonnull
|
678
|
+
format.pages output
|
679
|
+
}
|
680
|
+
if$
|
681
|
+
new.block
|
682
|
+
note output
|
683
|
+
fin.entry
|
684
|
+
}
|
685
|
+
|
686
|
+
FUNCTION {book}
|
687
|
+
{ output.bibitem
|
688
|
+
author empty$
|
689
|
+
{ format.editors "author and editor" output.check
|
690
|
+
editor format.key output
|
691
|
+
}
|
692
|
+
{ format.authors output.nonnull
|
693
|
+
crossref missing$
|
694
|
+
{ "author and editor" editor either.or.check }
|
695
|
+
'skip$
|
696
|
+
if$
|
697
|
+
}
|
698
|
+
if$
|
699
|
+
format.date "year" output.check
|
700
|
+
new.block
|
701
|
+
format.btitle "title" output.check
|
702
|
+
crossref missing$
|
703
|
+
{ format.bvolume output
|
704
|
+
new.block
|
705
|
+
format.number.series output
|
706
|
+
new.sentence
|
707
|
+
publisher "publisher" output.check
|
708
|
+
address output
|
709
|
+
}
|
710
|
+
{
|
711
|
+
new.block
|
712
|
+
format.book.crossref output.nonnull
|
713
|
+
}
|
714
|
+
if$
|
715
|
+
format.edition output
|
716
|
+
new.block
|
717
|
+
note output
|
718
|
+
fin.entry
|
719
|
+
}
|
720
|
+
|
721
|
+
FUNCTION {booklet}
|
722
|
+
{ output.bibitem
|
723
|
+
format.authors output
|
724
|
+
author format.key output
|
725
|
+
format.date "year" output.check
|
726
|
+
new.block
|
727
|
+
format.title "title" output.check
|
728
|
+
new.block
|
729
|
+
howpublished output
|
730
|
+
address output
|
731
|
+
new.block
|
732
|
+
note output
|
733
|
+
fin.entry
|
734
|
+
}
|
735
|
+
|
736
|
+
FUNCTION {inbook}
|
737
|
+
{ output.bibitem
|
738
|
+
author empty$
|
739
|
+
{ format.editors "author and editor" output.check
|
740
|
+
editor format.key output
|
741
|
+
}
|
742
|
+
{ format.authors output.nonnull
|
743
|
+
crossref missing$
|
744
|
+
{ "author and editor" editor either.or.check }
|
745
|
+
'skip$
|
746
|
+
if$
|
747
|
+
}
|
748
|
+
if$
|
749
|
+
format.date "year" output.check
|
750
|
+
new.block
|
751
|
+
format.btitle "title" output.check
|
752
|
+
crossref missing$
|
753
|
+
{ format.bvolume output
|
754
|
+
format.chapter.pages "chapter and pages" output.check
|
755
|
+
new.block
|
756
|
+
format.number.series output
|
757
|
+
new.sentence
|
758
|
+
publisher "publisher" output.check
|
759
|
+
address output
|
760
|
+
}
|
761
|
+
{ format.chapter.pages "chapter and pages" output.check
|
762
|
+
new.block
|
763
|
+
format.book.crossref output.nonnull
|
764
|
+
}
|
765
|
+
if$
|
766
|
+
format.edition output
|
767
|
+
new.block
|
768
|
+
note output
|
769
|
+
fin.entry
|
770
|
+
}
|
771
|
+
|
772
|
+
FUNCTION {incollection}
|
773
|
+
{ output.bibitem
|
774
|
+
format.authors "author" output.check
|
775
|
+
author format.key output
|
776
|
+
format.date "year" output.check
|
777
|
+
new.block
|
778
|
+
format.title "title" output.check
|
779
|
+
new.block
|
780
|
+
crossref missing$
|
781
|
+
{ format.in.ed.booktitle "booktitle" output.check
|
782
|
+
format.bvolume output
|
783
|
+
format.number.series output
|
784
|
+
format.chapter.pages output
|
785
|
+
new.sentence
|
786
|
+
publisher "publisher" output.check
|
787
|
+
address output
|
788
|
+
format.edition output
|
789
|
+
}
|
790
|
+
{ format.incoll.inproc.crossref output.nonnull
|
791
|
+
format.chapter.pages output
|
792
|
+
}
|
793
|
+
if$
|
794
|
+
new.block
|
795
|
+
note output
|
796
|
+
fin.entry
|
797
|
+
}
|
798
|
+
|
799
|
+
FUNCTION {inproceedings}
|
800
|
+
{ output.bibitem
|
801
|
+
format.authors "author" output.check
|
802
|
+
author format.key output
|
803
|
+
format.date "year" output.check
|
804
|
+
new.block
|
805
|
+
format.title "title" output.check
|
806
|
+
new.block
|
807
|
+
crossref missing$
|
808
|
+
{ format.in.ed.booktitle "booktitle" output.check
|
809
|
+
format.bvolume output
|
810
|
+
format.number.series output
|
811
|
+
format.pages output
|
812
|
+
address output
|
813
|
+
new.sentence
|
814
|
+
organization output
|
815
|
+
publisher output
|
816
|
+
}
|
817
|
+
{ format.incoll.inproc.crossref output.nonnull
|
818
|
+
format.pages output
|
819
|
+
}
|
820
|
+
if$
|
821
|
+
new.block
|
822
|
+
note output
|
823
|
+
fin.entry
|
824
|
+
}
|
825
|
+
|
826
|
+
FUNCTION {conference} { inproceedings }
|
827
|
+
|
828
|
+
FUNCTION {manual}
|
829
|
+
{ output.bibitem
|
830
|
+
format.authors output
|
831
|
+
author format.key output
|
832
|
+
format.date "year" output.check
|
833
|
+
new.block
|
834
|
+
format.btitle "title" output.check
|
835
|
+
organization address new.block.checkb
|
836
|
+
organization output
|
837
|
+
address output
|
838
|
+
format.edition output
|
839
|
+
new.block
|
840
|
+
note output
|
841
|
+
fin.entry
|
842
|
+
}
|
843
|
+
|
844
|
+
FUNCTION {mastersthesis}
|
845
|
+
{ output.bibitem
|
846
|
+
format.authors "author" output.check
|
847
|
+
author format.key output
|
848
|
+
format.date "year" output.check
|
849
|
+
new.block
|
850
|
+
format.btitle "title" output.check
|
851
|
+
new.block
|
852
|
+
"Master's thesis" format.thesis.type output.nonnull
|
853
|
+
school "school" output.check
|
854
|
+
address output
|
855
|
+
new.block
|
856
|
+
note output
|
857
|
+
fin.entry
|
858
|
+
}
|
859
|
+
|
860
|
+
FUNCTION {misc}
|
861
|
+
{ output.bibitem
|
862
|
+
format.authors output
|
863
|
+
author format.key output
|
864
|
+
format.date "year" output.check
|
865
|
+
new.block
|
866
|
+
format.title output
|
867
|
+
new.block
|
868
|
+
howpublished output
|
869
|
+
new.block
|
870
|
+
note output
|
871
|
+
fin.entry
|
872
|
+
}
|
873
|
+
|
874
|
+
FUNCTION {phdthesis}
|
875
|
+
{ output.bibitem
|
876
|
+
format.authors "author" output.check
|
877
|
+
author format.key output
|
878
|
+
format.date "year" output.check
|
879
|
+
new.block
|
880
|
+
format.btitle "title" output.check
|
881
|
+
new.block
|
882
|
+
"Ph.D. thesis" format.thesis.type output.nonnull
|
883
|
+
school "school" output.check
|
884
|
+
address output
|
885
|
+
new.block
|
886
|
+
note output
|
887
|
+
fin.entry
|
888
|
+
}
|
889
|
+
|
890
|
+
FUNCTION {proceedings}
|
891
|
+
{ output.bibitem
|
892
|
+
format.editors output
|
893
|
+
editor format.key output
|
894
|
+
format.date "year" output.check
|
895
|
+
new.block
|
896
|
+
format.btitle "title" output.check
|
897
|
+
format.bvolume output
|
898
|
+
format.number.series output
|
899
|
+
address output
|
900
|
+
new.sentence
|
901
|
+
organization output
|
902
|
+
publisher output
|
903
|
+
new.block
|
904
|
+
note output
|
905
|
+
fin.entry
|
906
|
+
}
|
907
|
+
|
908
|
+
FUNCTION {techreport}
|
909
|
+
{ output.bibitem
|
910
|
+
format.authors "author" output.check
|
911
|
+
author format.key output
|
912
|
+
format.date "year" output.check
|
913
|
+
new.block
|
914
|
+
format.title "title" output.check
|
915
|
+
new.block
|
916
|
+
format.tr.number output.nonnull
|
917
|
+
institution "institution" output.check
|
918
|
+
address output
|
919
|
+
new.block
|
920
|
+
note output
|
921
|
+
fin.entry
|
922
|
+
}
|
923
|
+
|
924
|
+
FUNCTION {unpublished}
|
925
|
+
{ output.bibitem
|
926
|
+
format.authors "author" output.check
|
927
|
+
author format.key output
|
928
|
+
format.date "year" output.check
|
929
|
+
new.block
|
930
|
+
format.title "title" output.check
|
931
|
+
new.block
|
932
|
+
note "note" output.check
|
933
|
+
fin.entry
|
934
|
+
}
|
935
|
+
|
936
|
+
FUNCTION {default.type} { misc }
|
937
|
+
|
938
|
+
MACRO {jan} {"January"}
|
939
|
+
|
940
|
+
MACRO {feb} {"February"}
|
941
|
+
|
942
|
+
MACRO {mar} {"March"}
|
943
|
+
|
944
|
+
MACRO {apr} {"April"}
|
945
|
+
|
946
|
+
MACRO {may} {"May"}
|
947
|
+
|
948
|
+
MACRO {jun} {"June"}
|
949
|
+
|
950
|
+
MACRO {jul} {"July"}
|
951
|
+
|
952
|
+
MACRO {aug} {"August"}
|
953
|
+
|
954
|
+
MACRO {sep} {"September"}
|
955
|
+
|
956
|
+
MACRO {oct} {"October"}
|
957
|
+
|
958
|
+
MACRO {nov} {"November"}
|
959
|
+
|
960
|
+
MACRO {dec} {"December"}
|
961
|
+
|
962
|
+
MACRO {acmcs} {"ACM Computing Surveys"}
|
963
|
+
|
964
|
+
MACRO {acta} {"Acta Informatica"}
|
965
|
+
|
966
|
+
MACRO {cacm} {"Communications of the ACM"}
|
967
|
+
|
968
|
+
MACRO {ibmjrd} {"IBM Journal of Research and Development"}
|
969
|
+
|
970
|
+
MACRO {ibmsj} {"IBM Systems Journal"}
|
971
|
+
|
972
|
+
MACRO {ieeese} {"IEEE Transactions on Software Engineering"}
|
973
|
+
|
974
|
+
MACRO {ieeetc} {"IEEE Transactions on Computers"}
|
975
|
+
|
976
|
+
MACRO {ieeetcad}
|
977
|
+
{"IEEE Transactions on Computer-Aided Design of Integrated Circuits"}
|
978
|
+
|
979
|
+
MACRO {ipl} {"Information Processing Letters"}
|
980
|
+
|
981
|
+
MACRO {jacm} {"Journal of the ACM"}
|
982
|
+
|
983
|
+
MACRO {jcss} {"Journal of Computer and System Sciences"}
|
984
|
+
|
985
|
+
MACRO {scp} {"Science of Computer Programming"}
|
986
|
+
|
987
|
+
MACRO {sicomp} {"SIAM Journal on Computing"}
|
988
|
+
|
989
|
+
MACRO {tocs} {"ACM Transactions on Computer Systems"}
|
990
|
+
|
991
|
+
MACRO {tods} {"ACM Transactions on Database Systems"}
|
992
|
+
|
993
|
+
MACRO {tog} {"ACM Transactions on Graphics"}
|
994
|
+
|
995
|
+
MACRO {toms} {"ACM Transactions on Mathematical Software"}
|
996
|
+
|
997
|
+
MACRO {toois} {"ACM Transactions on Office Information Systems"}
|
998
|
+
|
999
|
+
MACRO {toplas} {"ACM Transactions on Programming Languages and Systems"}
|
1000
|
+
|
1001
|
+
MACRO {tcs} {"Theoretical Computer Science"}
|
1002
|
+
|
1003
|
+
READ
|
1004
|
+
|
1005
|
+
FUNCTION {sortify}
|
1006
|
+
{ purify$
|
1007
|
+
"l" change.case$
|
1008
|
+
}
|
1009
|
+
|
1010
|
+
INTEGERS { len }
|
1011
|
+
|
1012
|
+
FUNCTION {chop.word}
|
1013
|
+
{ 's :=
|
1014
|
+
'len :=
|
1015
|
+
s #1 len substring$ =
|
1016
|
+
{ s len #1 + global.max$ substring$ }
|
1017
|
+
's
|
1018
|
+
if$
|
1019
|
+
}
|
1020
|
+
|
1021
|
+
FUNCTION {format.lab.names}
|
1022
|
+
{ 's :=
|
1023
|
+
s #1 "{vv~}{ll}" format.name$
|
1024
|
+
s num.names$ duplicate$
|
1025
|
+
#2 >
|
1026
|
+
{ pop$ " " * "et~al." emphasize * }
|
1027
|
+
{ #2 <
|
1028
|
+
'skip$
|
1029
|
+
{ s #2 "{ff }{vv }{ll}{ jj}" format.name$ "others" =
|
1030
|
+
{ " " * "et~al." emphasize * }
|
1031
|
+
{ " and " * s #2 "{vv~}{ll}" format.name$ * }
|
1032
|
+
if$
|
1033
|
+
}
|
1034
|
+
if$
|
1035
|
+
}
|
1036
|
+
if$
|
1037
|
+
}
|
1038
|
+
|
1039
|
+
FUNCTION {author.key.label}
|
1040
|
+
{ author empty$
|
1041
|
+
{ key empty$
|
1042
|
+
{ cite$ #1 #3 substring$ }
|
1043
|
+
'key
|
1044
|
+
if$
|
1045
|
+
}
|
1046
|
+
{ author format.lab.names }
|
1047
|
+
if$
|
1048
|
+
}
|
1049
|
+
|
1050
|
+
FUNCTION {author.editor.key.label}
|
1051
|
+
{ author empty$
|
1052
|
+
{ editor empty$
|
1053
|
+
{ key empty$
|
1054
|
+
{ cite$ #1 #3 substring$ }
|
1055
|
+
'key
|
1056
|
+
if$
|
1057
|
+
}
|
1058
|
+
{ editor format.lab.names }
|
1059
|
+
if$
|
1060
|
+
}
|
1061
|
+
{ author format.lab.names }
|
1062
|
+
if$
|
1063
|
+
}
|
1064
|
+
|
1065
|
+
FUNCTION {editor.key.label}
|
1066
|
+
{ editor empty$
|
1067
|
+
{ key empty$
|
1068
|
+
{ cite$ #1 #3 substring$ }
|
1069
|
+
'key
|
1070
|
+
if$
|
1071
|
+
}
|
1072
|
+
{ editor format.lab.names }
|
1073
|
+
if$
|
1074
|
+
}
|
1075
|
+
|
1076
|
+
FUNCTION {calc.label}
|
1077
|
+
{ type$ "book" =
|
1078
|
+
type$ "inbook" =
|
1079
|
+
or
|
1080
|
+
'author.editor.key.label
|
1081
|
+
{ type$ "proceedings" =
|
1082
|
+
'editor.key.label
|
1083
|
+
'author.key.label
|
1084
|
+
if$
|
1085
|
+
}
|
1086
|
+
if$
|
1087
|
+
"("
|
1088
|
+
*
|
1089
|
+
year duplicate$ empty$
|
1090
|
+
{ pop$ "????" }
|
1091
|
+
{ purify$ #-1 #4 substring$ }
|
1092
|
+
if$
|
1093
|
+
*
|
1094
|
+
'label :=
|
1095
|
+
}
|
1096
|
+
|
1097
|
+
FUNCTION {sort.format.names}
|
1098
|
+
{ 's :=
|
1099
|
+
#1 'nameptr :=
|
1100
|
+
""
|
1101
|
+
s num.names$ 'numnames :=
|
1102
|
+
numnames 'namesleft :=
|
1103
|
+
{ namesleft #0 > }
|
1104
|
+
{ nameptr #1 >
|
1105
|
+
{ " " * }
|
1106
|
+
'skip$
|
1107
|
+
if$
|
1108
|
+
s nameptr
|
1109
|
+
"{vv{ } }{ll{ }}{ f{ }}{ jj{ }}"
|
1110
|
+
format.name$ 't :=
|
1111
|
+
nameptr numnames = t "others" = and
|
1112
|
+
{ "et al" * }
|
1113
|
+
{ numnames #2 > nameptr #2 = and
|
1114
|
+
{ "zzzzzz" * #1 'namesleft := }
|
1115
|
+
{ t sortify * }
|
1116
|
+
if$
|
1117
|
+
}
|
1118
|
+
if$
|
1119
|
+
nameptr #1 + 'nameptr :=
|
1120
|
+
namesleft #1 - 'namesleft :=
|
1121
|
+
}
|
1122
|
+
while$
|
1123
|
+
}
|
1124
|
+
|
1125
|
+
FUNCTION {sort.format.title}
|
1126
|
+
{ 't :=
|
1127
|
+
"A " #2
|
1128
|
+
"An " #3
|
1129
|
+
"The " #4 t chop.word
|
1130
|
+
chop.word
|
1131
|
+
chop.word
|
1132
|
+
sortify
|
1133
|
+
#1 global.max$ substring$
|
1134
|
+
}
|
1135
|
+
|
1136
|
+
FUNCTION {author.sort}
|
1137
|
+
{ author empty$
|
1138
|
+
{ key empty$
|
1139
|
+
{ "to sort, need author or key in " cite$ * warning$
|
1140
|
+
""
|
1141
|
+
}
|
1142
|
+
{ key sortify }
|
1143
|
+
if$
|
1144
|
+
}
|
1145
|
+
{ author sort.format.names }
|
1146
|
+
if$
|
1147
|
+
}
|
1148
|
+
|
1149
|
+
FUNCTION {author.editor.sort}
|
1150
|
+
{ author empty$
|
1151
|
+
{ editor empty$
|
1152
|
+
{ key empty$
|
1153
|
+
{ "to sort, need author, editor, or key in " cite$ * warning$
|
1154
|
+
""
|
1155
|
+
}
|
1156
|
+
{ key sortify }
|
1157
|
+
if$
|
1158
|
+
}
|
1159
|
+
{ editor sort.format.names }
|
1160
|
+
if$
|
1161
|
+
}
|
1162
|
+
{ author sort.format.names }
|
1163
|
+
if$
|
1164
|
+
}
|
1165
|
+
|
1166
|
+
FUNCTION {editor.sort}
|
1167
|
+
{ editor empty$
|
1168
|
+
{ key empty$
|
1169
|
+
{ "to sort, need editor or key in " cite$ * warning$
|
1170
|
+
""
|
1171
|
+
}
|
1172
|
+
{ key sortify }
|
1173
|
+
if$
|
1174
|
+
}
|
1175
|
+
{ editor sort.format.names }
|
1176
|
+
if$
|
1177
|
+
}
|
1178
|
+
|
1179
|
+
FUNCTION {presort}
|
1180
|
+
{ calc.label
|
1181
|
+
label sortify
|
1182
|
+
" "
|
1183
|
+
*
|
1184
|
+
type$ "book" =
|
1185
|
+
type$ "inbook" =
|
1186
|
+
or
|
1187
|
+
'author.editor.sort
|
1188
|
+
{ type$ "proceedings" =
|
1189
|
+
'editor.sort
|
1190
|
+
'author.sort
|
1191
|
+
if$
|
1192
|
+
}
|
1193
|
+
if$
|
1194
|
+
#1 entry.max$ substring$
|
1195
|
+
'sort.label :=
|
1196
|
+
sort.label
|
1197
|
+
*
|
1198
|
+
" "
|
1199
|
+
*
|
1200
|
+
title field.or.null
|
1201
|
+
sort.format.title
|
1202
|
+
*
|
1203
|
+
#1 entry.max$ substring$
|
1204
|
+
'sort.key$ :=
|
1205
|
+
}
|
1206
|
+
|
1207
|
+
ITERATE {presort}
|
1208
|
+
|
1209
|
+
SORT
|
1210
|
+
|
1211
|
+
STRINGS { last.label next.extra }
|
1212
|
+
|
1213
|
+
INTEGERS { last.extra.num }
|
1214
|
+
|
1215
|
+
FUNCTION {initialize.extra.label.stuff}
|
1216
|
+
{ #0 int.to.chr$ 'last.label :=
|
1217
|
+
"" 'next.extra :=
|
1218
|
+
#0 'last.extra.num :=
|
1219
|
+
}
|
1220
|
+
|
1221
|
+
FUNCTION {forward.pass}
|
1222
|
+
{ last.label label =
|
1223
|
+
{ last.extra.num #1 + 'last.extra.num :=
|
1224
|
+
last.extra.num int.to.chr$ 'extra.label :=
|
1225
|
+
}
|
1226
|
+
{ "a" chr.to.int$ 'last.extra.num :=
|
1227
|
+
"" 'extra.label :=
|
1228
|
+
label 'last.label :=
|
1229
|
+
}
|
1230
|
+
if$
|
1231
|
+
}
|
1232
|
+
|
1233
|
+
FUNCTION {reverse.pass}
|
1234
|
+
{ next.extra "b" =
|
1235
|
+
{ "a" 'extra.label := }
|
1236
|
+
'skip$
|
1237
|
+
if$
|
1238
|
+
extra.label 'next.extra :=
|
1239
|
+
label extra.label * 'label :=
|
1240
|
+
}
|
1241
|
+
|
1242
|
+
EXECUTE {initialize.extra.label.stuff}
|
1243
|
+
|
1244
|
+
ITERATE {forward.pass}
|
1245
|
+
|
1246
|
+
REVERSE {reverse.pass}
|
1247
|
+
|
1248
|
+
FUNCTION {bib.sort.order}
|
1249
|
+
{ sort.label
|
1250
|
+
" "
|
1251
|
+
*
|
1252
|
+
year field.or.null sortify
|
1253
|
+
*
|
1254
|
+
" "
|
1255
|
+
*
|
1256
|
+
title field.or.null
|
1257
|
+
sort.format.title
|
1258
|
+
*
|
1259
|
+
#1 entry.max$ substring$
|
1260
|
+
'sort.key$ :=
|
1261
|
+
}
|
1262
|
+
|
1263
|
+
ITERATE {bib.sort.order}
|
1264
|
+
|
1265
|
+
SORT
|
1266
|
+
|
1267
|
+
FUNCTION {begin.bib}
|
1268
|
+
{ preamble$ empty$
|
1269
|
+
'skip$
|
1270
|
+
{ preamble$ write$ newline$ }
|
1271
|
+
if$
|
1272
|
+
"\begin{thebibliography}{}" write$ newline$
|
1273
|
+
}
|
1274
|
+
|
1275
|
+
EXECUTE {begin.bib}
|
1276
|
+
|
1277
|
+
EXECUTE {init.state.consts}
|
1278
|
+
|
1279
|
+
ITERATE {call.type$}
|
1280
|
+
|
1281
|
+
FUNCTION {end.bib}
|
1282
|
+
{ newline$
|
1283
|
+
"\end{thebibliography}" write$ newline$
|
1284
|
+
}
|
1285
|
+
|
1286
|
+
EXECUTE {end.bib}
|
1287
|
+
%% End of customized bst file
|
1288
|
+
|