RubyGems - rbbt - Versions diffs - 1.2.5 → 2.0.0 - Mend

rbbt 1.2.5 → 2.0.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (88) hide show

checksums.yaml +7 -0
data/README.rdoc +2 -138
metadata +69 -214
data/LICENSE +0 -20
data/bin/rbbt_config +0 -245
data/install_scripts/classifier/R/classify.R +0 -36
data/install_scripts/classifier/Rakefile +0 -140
data/install_scripts/get_abner.sh +0 -2
data/install_scripts/get_banner.sh +0 -25
data/install_scripts/get_biocreative.sh +0 -72
data/install_scripts/get_crf++.sh +0 -26
data/install_scripts/get_entrez.sh +0 -4
data/install_scripts/get_go.sh +0 -4
data/install_scripts/get_polysearch.sh +0 -8
data/install_scripts/ner/Rakefile +0 -206
data/install_scripts/ner/config/default.rb +0 -52
data/install_scripts/norm/Rakefile +0 -219
data/install_scripts/norm/config/cue_default.rb +0 -10
data/install_scripts/norm/config/tokens_default.rb +0 -86
data/install_scripts/norm/functions.sh +0 -23
data/install_scripts/organisms/Ath.Rakefile +0 -55
data/install_scripts/organisms/Cal.Rakefile +0 -84
data/install_scripts/organisms/Cel.Rakefile +0 -109
data/install_scripts/organisms/Hsa.Rakefile +0 -140
data/install_scripts/organisms/Mmu.Rakefile +0 -77
data/install_scripts/organisms/Rakefile +0 -43
data/install_scripts/organisms/Rno.Rakefile +0 -88
data/install_scripts/organisms/Sce.Rakefile +0 -66
data/install_scripts/organisms/Spo.Rakefile +0 -40
data/install_scripts/organisms/rake-include.rb +0 -252
data/install_scripts/wordlists/consonants +0 -897
data/install_scripts/wordlists/stopwords +0 -1
data/lib/rbbt.rb +0 -83
data/lib/rbbt/bow/bow.rb +0 -88
data/lib/rbbt/bow/classifier.rb +0 -116
data/lib/rbbt/bow/dictionary.rb +0 -187
data/lib/rbbt/ner/abner.rb +0 -34
data/lib/rbbt/ner/banner.rb +0 -73
data/lib/rbbt/ner/dictionaryNER.rb +0 -98
data/lib/rbbt/ner/regexpNER.rb +0 -70
data/lib/rbbt/ner/rner.rb +0 -227
data/lib/rbbt/ner/rnorm.rb +0 -143
data/lib/rbbt/ner/rnorm/cue_index.rb +0 -80
data/lib/rbbt/ner/rnorm/tokens.rb +0 -217
data/lib/rbbt/sources/biocreative.rb +0 -75
data/lib/rbbt/sources/biomart.rb +0 -105
data/lib/rbbt/sources/entrez.rb +0 -211
data/lib/rbbt/sources/go.rb +0 -85
data/lib/rbbt/sources/gscholar.rb +0 -74
data/lib/rbbt/sources/organism.rb +0 -241
data/lib/rbbt/sources/polysearch.rb +0 -117
data/lib/rbbt/sources/pubmed.rb +0 -248
data/lib/rbbt/util/arrayHash.rb +0 -266
data/lib/rbbt/util/filecache.rb +0 -72
data/lib/rbbt/util/index.rb +0 -47
data/lib/rbbt/util/misc.rb +0 -106
data/lib/rbbt/util/open.rb +0 -251
data/lib/rbbt/util/rake.rb +0 -183
data/lib/rbbt/util/simpleDSL.rb +0 -87
data/lib/rbbt/util/tmpfile.rb +0 -35
data/tasks/install.rake +0 -124
data/test/rbbt/bow/test_bow.rb +0 -33
data/test/rbbt/bow/test_classifier.rb +0 -72
data/test/rbbt/bow/test_dictionary.rb +0 -91
data/test/rbbt/ner/rnorm/test_cue_index.rb +0 -57
data/test/rbbt/ner/rnorm/test_tokens.rb +0 -70
data/test/rbbt/ner/test_abner.rb +0 -17
data/test/rbbt/ner/test_banner.rb +0 -17
data/test/rbbt/ner/test_dictionaryNER.rb +0 -122
data/test/rbbt/ner/test_regexpNER.rb +0 -33
data/test/rbbt/ner/test_rner.rb +0 -126
data/test/rbbt/ner/test_rnorm.rb +0 -47
data/test/rbbt/sources/test_biocreative.rb +0 -38
data/test/rbbt/sources/test_biomart.rb +0 -31
data/test/rbbt/sources/test_entrez.rb +0 -49
data/test/rbbt/sources/test_go.rb +0 -24
data/test/rbbt/sources/test_organism.rb +0 -59
data/test/rbbt/sources/test_polysearch.rb +0 -27
data/test/rbbt/sources/test_pubmed.rb +0 -39
data/test/rbbt/util/test_arrayHash.rb +0 -257
data/test/rbbt/util/test_filecache.rb +0 -37
data/test/rbbt/util/test_index.rb +0 -31
data/test/rbbt/util/test_misc.rb +0 -20
data/test/rbbt/util/test_open.rb +0 -110
data/test/rbbt/util/test_simpleDSL.rb +0 -57
data/test/rbbt/util/test_tmpfile.rb +0 -21
data/test/test_helper.rb +0 -4
data/test/test_rbbt.rb +0 -11

data/install_scripts/wordlists/consonants DELETED

@@ -1,897 +0,0 @@
-bbr
-sts
-nds
-dgm
-ptl
-ptn
-bsc
-ntl
-nth
-ntm
-rbs
-rpt
-bst
-rdl
-nts
-nsh
-pts
-ccl
-rns
-mpl
-ngl
-rds
-ccr
-rst
-ckn
-ctr
-cts
-nct
-cch
-ndr
-dbl
-dcr
-dgr
-dsh
-dsm
-rth
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-rkb
-rkd
-rkh
-ngm
-ngs
-rkm
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-rkr
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-rld
-rmh
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-rmw
-rsh
-ldb
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-thf
-ths
-nch
-stl
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-ggl
-ght
-nkl
-stb
-stw
-ngd
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-cht
-nks
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-tst
-chs
-lst
-rsn
-rlp
-rlw
-ttl
-rls
-spr
-dth
-ldc
-ldf
-ldl
-lfr
-llf
-msb
-ngn
-llp
-lls
-ndb
-ndf
-ndj
-ndl
-ndm
-ndw
-ngb
-nst
-rgr
-ntr
-shb
-shf
-sps
-stf
-thd
-thh
-rdr
-bbl
-lfg
-lfh
-rbl
-rml
-rmt
-rts
-shc
-shd
-ngt
-shr
-shs
-rcr
-rfr
-rpr
-rsk
-rsp
-rwh
-lth
-ghs
-llb
-llk
-lsh
-lts
-stc
-ngh
-stm
-lch
-lwr
-ntn
-lks
-ltm
-ddl
-ffl
-nsc
-lkw
-ltz
-rch
-thr
-ssl
-ssn
-cks
-btr
-npl
-npr
-str
-shl
-nsk
-nsl
-nsm
-nsp
-ssf
-nwh
-pgr
-nwr
-pbr
-rcl
-psh
-pst
-psw
-rpl
-rsc
-rwr
-scl
-ntf
-nfl
-xpl
-ldm
-nfr
-ngr
-mpr
-rnk
-mpt
-nkn
-rnc
-rnp
-rnt
-rtl
-sks
-lft
-scr
-ltr
-mbr
-ggr
-nsw
-ppr
-ttr
-wns
-nbl
-nbr
-ckl
-ncl
-ncr
-rbr
-rfl
-nsv
-nss
-mbl
-chr
-mph
-mps
-fts
-thb
-thc
-thl
-thp
-pkn
-ppl
-chd
-ghn
-nsd
-nsf
-nsg
-ghb
-ghf
-ghg
-ghl
-ndt
-mbn
-mbs
-mbt
-rsd
-thw
-dst
-llg
-llh
-llt
-xtb
-xts
-nkf
-ckh
-ckw
-ctf
-ctl
-lsp
-ffs
-skm
-Tch
-mst
-chn
-rfb
-tsh
-tbr
-ftl
-ftn
-zzl
-rdf
-bgr
-bpl
-bsp
-btl
-ffr
-lph
-ghw
-ckb
-ckc
-ckm
-ckp
-ckr
-rmb
-rnl
-rnn
-ndp
-rkl
-msh
-rsm
-pch
-ffn
-lln
-chl
-sph
-llw
-spl
-Spr
-shn
-wsh
-wst
-ffb
-ftb
-fth
-ftw
-mnl
-rgh
-ndn
-sms
-gns
-gnt
-ntw
-thn
-pdr
-wbl
-wdr
-wfl
-wpl
-gfr
-gnp
-nkh
-xth
-llc
-rpn
-rps
-wls
-psk
-pwr
-rtf
-rtt
-rtw
-rtb
-rtc
-rtn
-phs
-lfl
-rfd
-rfs
-sch
-ptr
-Sch
-rnf
-tsm
-tsw
-ffm
-lpt
-lsk
-lcl
-lpl
-ltb
-ltc
-ltl
-ltp
-ltw
-ndc
-pph
-stn
-ftr
-ghc
-ghh
-ghr
-shm
-stp
-thm
-chm
-tts
-ngw
-phr
-chf
-dbr
-dsk
-psc
-spb
-ddr
-gnm
-lms
-llm
-mpk
-rrh
-nsb
-rtz
-sth
-ssm
-rtr
-std
-stg
-mpn
-tkn
-rph
-phl
-gsk
-gst
-lgr
-ngp
-psq
-nkt
-nns
-rkw
-rsl
-ssb
-ssk
-ssp
-ssw
-wnb
-ntb
-gms
-tcl
-tcr
-tdr
-tfl
-tgr
-tpl
-tsc
-tsk
-tsp
-ddb
-dds
-ffh
-pht
-pth
-rdn
-msk
-ckt
-wsb
-wsc
-wsf
-wsl
-wsm
-wsp
-wsr
-wss
-wsv
-wsw
-wts
-tzs
-dfl
-dsl
-skr
-shv
-ntg
-ntp
-rtg
-lkm
-sbr
-ssh
-sst
-swr
-lsm
-rlb
-tth
-McC
-lpr
-ckj
-dsp
-wbr
-wdl
-mpp
-pfr
-ftf
-Khm
-llj
-ckd
-lbr
-hnn
-hns
-rgl
-rnm
-shw
-nkb
-nkp
-nkw
-nnk
-rtm
-ctm
-ctn
-rct
-xpr
-xtr
-mpb
-mns
-rnb
-mdr
-lpf
-lpm
-ldr
-nck
-ndq
-gsh
-ndg
-ndk
-rdb
-rdc
-rdh
-rdt
-rdw
-rmf
-wks
-dch
-dph
-msm
-wth
-ldh
-lfb
-lfp
-lfw
-ndd
-ssr
-ngk
-nkg
-rlf
-rlh
-ssc
-lcr
-gwr
-tsb
-rsw
-rsq
-xgl
-ncs
-wch
-lkl
-lkt
-tpr
-ldw
-lmd
-rmn
-shp
-dgl
-lkn
-rrs
-xch
-xcl
-xcr
-lfs
-nsn
-lmm
-nkm
-mpm
-mbb
-mbw
-sdr
-bbs
-cst
-ggb
-ggc
-ggh
-ggn
-ggp
-ggs
-msd
-rkn
-vsk
-btf
-bts
-wnc
-wnf
-wng
-wnh
-wnp
-wnr
-wnt
-wnw
-ctw
-gtr
-scs
-sgr
-skw
-phn
-wsk
-xsw
-spn
-wds
-rnw
-ntd
-chw
-ckf
-gwh
-Chr
-mfl
-msc
-msp
-mpd
-bdr
-lml
-lmn
-mpf
-mpg
-skl
-skn
-dcl
-dsw
-ddh
-lbs
-lkh
-lld
-llr
-kcl
-ksh
-kst
-hms
-dfr
-kth
-tht
-bsl
-rdm
-mbp
-wgr
-rck
-nkr
-chc
-chh
-fst
-wkw
-ckg
-sht
-rcs
-rmc
-rmp
-fghbstr
-rdpl
-rdsw
-rksh
-rldl
-rlds
-rldw
-rthl
-rthw
-chts
-rdst
-ngst
-dths
-ndbr
-ndsc
-ndsh
-ndsl
-ndst
-ndsw
-ngsp
-tchc
-tchd
-thdr
-thst
-rmth
-shcl
-shst
-tchb
-tchf
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-tchs
-tcht
-ngth
-rstr
-ghtl
-ghts
-llkn
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-stch
-lksw
-llfl
-nstr
-nsch
-nscr
-pstr
-rnst
-lfth
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-nchr
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-nssh
-ckst
-mphs
-thbr
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-chst
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-nsgr
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-tchg
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-llsh
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-ptwr
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-nskr
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-ckcl
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-ghth
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-llst
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-tchw
-wnbr
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-rchm
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-tspr
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-ffsp
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-ldsm
-phth
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-tzsc
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-ghtd
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-ghtm
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-nthl
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-lksh
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-rshm
-tchl
-ncht
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-mbsk
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-tchk
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-mphr
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-ntsm
-lmsm
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-ghsc
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-tchh
-ndcl
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-rdsc
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-rshn
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-rlfr
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-ngpl
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-cksb
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-rpts
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-rspl
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-ggpl
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-ghtp
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-wstr
-nctl
-rtsp
-tsch
-pths
-thbl
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-chsh
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-ftsm
-nksh
-wlsp
-sscr
-ssbr
-ssch
-rksc
-rnbr
-rnfl
-lths
-cksc
-rchw
-mscr
-rtwh
-shwh
-lfsk
-mpgr
-nksm
-cksk
-ckwh
-llfr
-kthr
-stpl
-stst
-mbpr
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-rthp
-rthd
-dspr
-schw
-ckdr
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-cksl
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-cktr
-llpl
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-rchb
-rchd
-rcht
-rmchrldsh
-rthwh
-chtsm
-ndscr
-ngspr
-tchcr
-tchst
-ngths
-llspr
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-tchbl
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-rtswr
-stscr
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-rdstr
-tzsch
-ghtcl
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-ghtst
-ngthw
-ckstr
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-rdscr
-rtstr
-rtthr
-lmstr
-rthsh
-wnstr
-tschm
-rkscr
-tchph
-rscht
-ststr
-rthpl
-ckscr
-rmstrtchstr
-tchphr