[med-svn] [Git][med-team/vmatch][master] 7 commits: include SELECT data
Sascha Steinbiss
gitlab at salsa.debian.org
Thu Jan 2 12:17:38 GMT 2020
Sascha Steinbiss pushed to branch master at Debian Med / vmatch
Commits:
0c4331df by Sascha Steinbiss at 2020-01-02T12:12:56+01:00
include SELECT data
- - - - -
380dfdc9 by Sascha Steinbiss at 2020-01-02T12:13:09+01:00
update excluded files
- - - - -
03c2142d by Sascha Steinbiss at 2020-01-02T12:13:39+01:00
New upstream version 2.3.0+dfsg
- - - - -
4281a9a4 by Sascha Steinbiss at 2020-01-02T12:13:47+01:00
Update upstream source from tag 'upstream/2.3.0+dfsg'
Update to upstream version '2.3.0+dfsg'
with Debian dir ba0e392cc577ac0a5e4a1f511a3f47c1d9abf886
- - - - -
f9f56f3f by Sascha Steinbiss at 2020-01-02T12:39:33+01:00
finish d/copyright
- - - - -
2987723f by Sascha Steinbiss at 2020-01-02T13:16:40+01:00
use up-to-date license texts
- - - - -
fe111553 by Sascha Steinbiss at 2020-01-02T13:16:52+01:00
enable building on 32bit
- - - - -
24 changed files:
- debian/copyright
- debian/libvmatch-dev.install
- debian/rules
- debian/vmatch.install
- − src/doc/WWW/.gitignore
- − src/doc/WWW/.ispell_american
- − src/doc/WWW/Dataflowfig.tex
- − src/doc/WWW/Makefile
- − src/doc/WWW/PUSH-cmd.txt
- − src/doc/WWW/download.html
- − src/doc/WWW/extractpart.pl
- − src/doc/WWW/index.html
- − src/doc/WWW/introexclude
- − src/doc/WWW/matchgraph.gif
- − src/doc/WWW/remove-html.rb
- − src/doc/WWW/replace-header.rb
- − src/doc/WWW/replace-par.rb
- − src/doc/WWW/vmweb.css
- − src/doc/WWW/vmweb.tex
- − src/doc/WWW/xhtml-lat1.ent
- − src/doc/WWW/xhtml-special.ent
- − src/doc/WWW/xhtml-symbol.ent
- − src/doc/WWW/xhtml1-transitional.dtd
- − src/testdata/swissSmall
Changes:
=====================================
debian/copyright
=====================================
@@ -4,13 +4,101 @@ Source: https://github.com/genometools/vstree
Files-Excluded: src/lib-homann
src/include/libpssm.h
src/Makedef
- src/doc/WWW/distributions
+ src/doc/WWW
src/doc/*.so.*
+ src/testdata/swissSmall
Files: *
-Copyright: © 2000-2006 Stefan Kurtz <kurtz at zbh.uni-hamburg.de>
+Copyright: (C) 2000-2006 Stefan Kurtz <kurtz at zbh.uni-hamburg.de>
+ (C) 2000-2016 LScSA-Software GmbH
License: ISC
+Files: src/include/functrace.h
+Copyright: (C) 2003-2004 Gordon Gremme <gremme at zbh.uni-hamburg.de>
+License: ISC
+
+Files: src/include/genfile.h
+Copyright: (C) 2005 Gordon Gremme <gremme at zbh.uni-hamburg.de>
+License: ISC
+
+Files: src/include/xmlindent.h
+Copyright: (C) 2004-2005 Gordon Gremme <gremme at zbh.uni-hamburg.de>
+License: ISC
+
+Files: src/kurtz-basic/redblack.c
+Copyright: 1995, 1996, 1997, 2000 Free Software Foundation, Inc.
+License: LGPL-2.1+
+ The GNU C Library is free software; you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation; either version 2.1, or (at your option)
+ any later version.
+ .
+ The GNU C Library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU Lesser General Public License for more details.
+ .
+ You should have received a copy of the GNU Lesser General Public License along
+ with this program; if not, write to the Free Software Foundation,
+ Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+ .
+ On Debian systems, the complete text of the GNU Lesser General Public
+ License version 2.1 can be found in ‘/usr/share/common-licenses/LGPL-2.1’.
+Comment: With modifications by Vmatch authors.
+
+Files: src/bin/config-guess.sh
+Copyright: (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999,
+ 2000, 2001, 2002, 2003 Free Software Foundation, Inc.
+License: GPL-2+
+ This program is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+ .
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License along
+ with this program; if not, write to the Free Software Foundation, Inc.,
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ .
+ As a special exception to the GNU General Public License, if you
+ distribute this file as part of a program that contains a
+ configuration script generated by Autoconf, you may include it under
+ the same distribution terms that you use for the rest of that program.
+ .
+ On Debian systems, the complete text of the GNU General Public
+ License version 2 can be found in `/usr/share/common-licenses/GPL-2'.
+
+Files: src/bin/install.sh
+Copyright: (C) 1994 X Consortium
+License: X11
+ Permission is hereby granted, free of charge, to any person obtaining a copy
+ of this software and associated documentation files (the "Software"), to
+ deal in the Software without restriction, including without limitation the
+ rights to use, copy, modify, merge, publish, distribute, sublicense, and/or
+ sell copies of the Software, and to permit persons to whom the Software is
+ furnished to do so, subject to the following conditions:
+ .
+ The above copyright notice and this permission notice shall be included in
+ all copies or substantial portions of the Software.
+ .
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ X CONSORTIUM BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN
+ AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNEC-
+ TION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+ .
+ Except as contained in this notice, the name of the X Consortium shall not
+ be used in advertising or otherwise to promote the sale, use or other deal-
+ ings in this Software without prior written authorization from the X Consor-
+ tium.
+ .
+ FSF changes to this file are in the public domain.
+
License: ISC
Permission to use, copy, modify, and distribute this software for any
purpose with or without fee is hereby granted, provided that the above
=====================================
debian/libvmatch-dev.install
=====================================
@@ -2,4 +2,8 @@ src/lib/libfiles/*.a /usr/lib
src/include/*.h /usr/include/vmatch
src/include/*.pr /usr/include/vmatch
src/Vmatch/*.pr /usr/include/vmatch
-src/Vmatch/SELECT /usr/share/vmatch
+src/Vmatch/SELECT/*.c /usr/share/vmatch/SELECT
+src/Vmatch/SELECT/*.h /usr/share/vmatch/SELECT
+src/Vmatch/SELECT/Shareddef /usr/share/vmatch/SELECT
+src/Vmatch/SELECT/*akefile* /usr/share/vmatch/SELECT
+src/Vmatch/SELECT/Mk* /usr/share/vmatch/SELECT
=====================================
debian/rules
=====================================
@@ -1,5 +1,15 @@
#!/usr/bin/make -f
+include /usr/share/dpkg/default.mk
+
+BITS:=$(shell dpkg-architecture | fgrep DEB_TARGET_ARCH_BITS= | cut -f 2 -d'=')
+
+ifeq ($(BITS),64)
+ VSTREE_ARCH:=linux-gcc-64
+else
+ VSTREE_ARCH:=linux-gcc
+endif
+
DH_VERBOSE := 1
export LC_ALL=C.UTF-8
export DEB_BUILD_MAINT_OPTIONS=hardening=+all
@@ -13,7 +23,7 @@ override_dh_auto_clean:
rm -rf debian/man
override_dh_auto_build:
- cd src && mklink.sh linux-gcc-64
+ cd src && mklink.sh $(VSTREE_ARCH)
cd src && make licensemanager=no $*
override_dh_auto_install:
=====================================
debian/vmatch.install
=====================================
@@ -12,3 +12,4 @@ src/dist/vmatch/vseqselect /usr/bin
src/dist/vmatch/vstree2tex /usr/bin
src/dist/vmatch/vsubseqselect /usr/bin
src/dist/vmatch/TRANS /usr/share/vmatch
+src/Vmatch/SELECT/*.so /usr/lib/vmatch/SELECT
=====================================
src/doc/WWW/.gitignore deleted
=====================================
@@ -1 +0,0 @@
-vmweb.pdf
=====================================
src/doc/WWW/.ispell_american deleted
=====================================
@@ -1,660 +0,0 @@
-EMBL
-Fasta
-Genbank
-Gzipped
-Kurtz
-SWISSPROT
-Vmatch
-postprocessing
-pt
-AtGDB
-barleypop
-biophys
-cDNA
-dataflow
-Dataflowfig
-DJ
-duesseldorf
-edu
-Fernandes
-Gbp
-GCB
-genalyzer
-GeneChip
-genomic
-gif
-GL
-html
-hypa
-iastate
-img
-matchgraph
-mga
-oligo
-patternsearch
-PatternSearch
-pdf
-PDF
-php
-PlantGDB
-possumsearch
-PossumSearch
-RescueMu
-RSA
-rsat
-splicenest
-transposons
-virtman
-vmatchlic
-vmweb
-vrac
-Walbot
-Xenopus
-zmdb
-ac
-AMD
-Arabidopsis
-BarleyBase
-bibiserv
-bielefeld
-Bioinformatics
-biotools
-cgi
-commolbio
-Debian
-ESTs
-GenBank
-hamburg
-Helden
-http
-HyPa
-KPATH
-kurtz
-latexonly
-mkvtree
-molgen
-mpg
-Multimat
-oligos
-org
-OSX
-pl
-plantgdb
-PowerPC
-Promide
-Rahmann
-Redhat
-reputer
-REPuter
-Sparc
-SpliceNest
-src
-SuSe
-Sven
-techfak
-thaliana
-ulb
-vmatch
-www
-zbh
-Zea
-ASRP
-GSSanalysis
-laevis
-meningioma
-microarray
-micromatches
-miRNA
-mRNA
-mutransposon
-Transposon
-ABR
-AKA
-ALI
-ALT
-ALV
-AME
-ANG
-AQU
-ARN
-Affymetrix
-Agave
-Apr
-Aureobasidium
-Azadirachta
-BAI
-BAL
-BEC
-BEH
-BEI
-BEL
-BER
-BLA
-BLI
-BLO
-BOD
-BOH
-BOR
-BOU
-BOV
-BRE
-BRI
-BRO
-BRU
-BUC
-BUE
-BioExtract
-Biopieces
-BlastP
-CAS
-CAV
-CEV
-CHA
-CHAU
-CHE
-CHI
-CHO
-CHOU
-CHU
-CLA
-CLO
-COH
-COL
-CRISPRFinder
-CRISPRdatabase
-CRISPRfinder
-CRISPRs
-CRO
-CUL
-Chlorophyceae
-Chs
-CrossLink
-Cscript
-CurrentUsage
-DAR
-DAS
-DAV
-DEA
-DEE
-DES
-DEZ
-DHA
-DIBO
-DIC
-DIJ
-DNAVis
-DOL
-DOO
-DOR
-DUC
-DUM
-DUR
-EBR
-EIS
-ELD
-ELL
-ENG
-ERI
-EST
-Ecoli
-FANTOM
-FAU
-FER
-FESCH
-FIC
-FIE
-FLE
-FOF
-FOS
-FRE
-Floydiella
-Frankia
-GAE
-GAO
-GAR
-GAU
-GEN
-GEO
-GER
-GES
-GEY
-GIE
-GLA
-GLAE
-GNF
-GNI
-GOL
-GOM
-GON
-GOS
-GRAE
-GRE
-GRI
-GRO
-GRU
-GU
-GUA
-Genome
-GenomeThreader
-Gepard
-GmbH
-Graminella
-HAA
-HAB
-HAC
-HAK
-HAN
-HAR
-HAU
-HAZ
-HEA
-HED
-HEL
-HEP
-HES
-HIL
-HIN
-HLE
-HOEH
-HOF
-HOL
-HOM
-HOR
-HRI
-HRV
-HUL
-HUR
-HUS
-HYS
-HYT
-Heliothis
-IKE
-IMM
-Illumina
-JAC
-JAI
-JEN
-JI
-JOH
-JOR
-JOU
-KAE
-KAM
-KAN
-KAR
-KAT
-KAW
-KEM
-KER
-KEV
-KHA
-KLE
-KNA
-KOE
-KOEN
-KOG
-KOL
-KON
-KOP
-KOS
-KOU
-KOZ
-KRI
-KRO
-KRU
-KRUE
-KUB
-KUC
-KUD
-KUG
-KUM
-KUR
-LAL
-LAM
-LAR
-LAU
-LAZ
-LBNL
-LEA
-LEM
-LER
-LI
-LIA
-LIN
-LIU
-LOEW
-LOM
-LOR
-LScSA
-LU
-LUO
-LUS
-Leptosira
-MAA
-MAL
-MCC
-MCL
-MCM
-MEH
-MER
-MEY
-MIC
-MIN
-MIPSPlantsDB
-MOC
-MOE
-MOH
-MOL
-MOR
-MUL
-MYE
-Macronuclear
-Maize
-MicroRNAs
-Mu
-Myotis
-NAI
-NAO
-NAR
-NEL
-NIC
-NOU
-NOV
-NUR
-NUS
-NYG
-Neochloris
-OHL
-OKA
-OSS
-OTI
-OTT
-PAU
-PAV
-PEC
-PEE
-PEL
-PFE
-PLE
-PLEXdb
-POB
-POM
-POU
-PRI
-Piwik
-PriMUX
-ProbeMatch
-QPALMA
-RAD
-RAH
-REE
-REH
-REI
-REN
-RIN
-RIS
-RIV
-RNA
-RNAi
-RNAseq
-ROS
-RT
-RefSeq
-Rnnotator
-SAF
-SAK
-SAR
-SCHAA
-SCHAEF
-SCHAR
-SCHAT
-SCHEL
-SCHIJ
-SCHIL
-SCHLE
-SCHLU
-SCHLUE
-SCHMU
-SCHNE
-SCHOE
-SCHOF
-SCHOL
-SCHOO
-SCHRO
-SCHUL
-SCHWA
-SCHWE
-SCO
-SCZ
-SEG
-SEI
-SEK
-SEV
-SHA
-SHI
-SHU
-SIE
-SIM
-SIMAP
-SLE
-SLO
-SMA
-SMI
-SMY
-SNY
-SOE
-SOU
-SPA
-SPI
-STE
-STEI
-STEU
-STO
-STR
-STU
-SU
-SUL
-SZY
-Schwab
-Seidel
-Shewanella
-Silva
-Slezak
-Spirodela
-Stefan
-Streptococcaceae
-TAC
-TAF
-TAK
-TAL
-TAY
-TEM
-THA
-THI
-TIK
-TIR
-TIS
-TOL
-TOR
-TOU
-TRI
-TRO
-TRU
-TSA
-TSU
-TT
-TUR
-Tembe
-Tetrahymena
-Thellungiella
-UDE
-UPA
-URA
-UST
-Univ
-VAI
-VAL
-VAS
-VAU
-VEL
-VER
-VHA
-VIN
-VIT
-VIV
-VLA
-VMatchForArabidopsis
-VOI
-VOS
-VOSS
-VRA
-WAL
-WEI
-WES
-WHA
-WHE
-WIC
-WIE
-WIL
-WIS
-WOD
-WOL
-WOR
-WRE
-WU
-XU
-Xanthomonas
-YAN
-YU
-YUN
-ZAJ
-ZAL
-ZAV
-ZEM
-ZHA
-ZHE
-ZHO
-ZHU
-ZIM
-ZIN
-aRNH
-ab
-al
-alt
-articlerender
-artid
-biomoby
-biopieces
-bp
-budworm
-cand
-chromosomal
-chromosome
-chromosomes
-colorlinks
-com
-contigs
-crispr
-crosslink
-daytrial
-de
-div
-dnavis
-doc
-enableLinkTracking
-endophytes
-epichloid
-exome
-exon
-fcgi
-fescue
-fr
-genmome
-genome
-genomes
-genomethreader
-getTracker
-goltsman
-gov
-gsf
-href
-ht
-https
-idsite
-indels
-indica
-informatik
-interspaced
-isotigs
-javascript
-jgi
-js
-li
-linkcolor
-llnl
-lscsa
-ltr
-lucifugus
-mailto
-maize
-meliloti
-mer
-mers
-metagenome
-metagenomes
-miRNAs
-microalgae
-mips
-mircoRNA
-mitochondrial
-ncRNAs
-nigrifrons
-nih
-nl
-noscript
-novo
-oleoabundans
-oneidensis
-oryzae
-parvula
-pesticidal
-pigeonpea
-piwik
-piwikTracker
-pkBaseURL
-plastid
-polyrhiza
-preprocess
-prj
-probeBase
-proteome
-psud
-pubmedcentral
-pullulans
-retroviruses
-rnafolding
-seq
-siRNA
-simap
-sp
-str
-subfamilies
-terrestris
-tex
-thermophila
-tigr
-trackPageView
-transcriptional
-transcriptome
-trialbox
-tue
-tuebingen
-ul
-unescape
-uni
-var
-virescens
-weigelworld
-wiki
-wmd
-zenlicensemanager
=====================================
src/doc/WWW/Dataflowfig.tex deleted
=====================================
@@ -1,19 +0,0 @@
-\documentclass[11pt]{article}
-\usepackage{a4wide}
-\pagestyle{empty}
-\begin{document}
-\input{Dataflow.inc}
-
-\noindent The dataflow in \emph{Vmatch}.
-The programs
-are shown in ellipses. The inputs are the database
-and the query sequences and the alphabet transformation,
-represented by rectangles. At the center of all
-computations the persistent index is shown. All other
-rectangles represent the different kinds of output.
-
-\begin{center}
-\centerline{\box\graph}
-\end{center}
-
-\end{document}
=====================================
src/doc/WWW/Makefile deleted
=====================================
@@ -1,99 +0,0 @@
-vmwebfiles=Dataflowfig.pdf\
- AboKurOhl2004.pdf\
- AboKurOhl2002.pdf\
- BreKurWal2002.pdf\
- ChoSchleKurGie2004.pdf\
- FitGarKucKurMyeOttSleVitZemMcc2002.pdf\
- KurChoOhlSchleStoGie2001.pdf\
- HoehKurOhl2002.pdf\
- GraeStrKurSte2001.pdf\
- BecStroHomGieKur2004.pdf\
- KrueSczKurGie2004.pdf\
- virtman.pdf
-
-PAPERS=${WORK}/archive-etc/own-papers
-
-SERVER=vmatchserver
-WWWBASEDIR=/var/www/html
-
-all:vmweb.pdf vmweb.tgz
-
-vmweb.pdf:vmweb.tex introduction.inc
- latexmk vmweb
-
-introduction.inc:../virtman.tex introexclude
- extractpart.pl introduction ../virtman.tex |\
- grep -v -f introexclude |\
- sed -e 's/\\subsection\*{The parts/\\section*{The parts/' | \
- perl -pe 's/\\cite{ABO:KUR:OHL:2004}\.\%\%second/(Abouelhoda, Kurtz, Ohlebusch 2004)./' | \
- perl -pe 's/\\cite{(.*)}[\.,]?/\n\\bibentry{\1}\n/' > $@
-
-Dataflow.inc:../Dataflow.pic
- pic -t ../Dataflow.pic > $@
-
-index.html:vmweb.tex vmweb.pdf introduction.inc replace-header.rb replace-par.rb
- htlatex vmweb.tex "xhtml, charset=utf-8" " -cunihtf -utf8"
- cat vmweb.html | replace-header.rb | \
- replace-par.rb | \
- sed -e 's/CONTENT=/content=/' \
- -e 's/ALT=/alt=/' > $@
-
-validate:index.html xhtml-lat1.ent xhtml-symbol.ent xhtml-special.ent xhtml1-transitional.dtd
- cat index.html | sed -e 's/\"http:\/\/www.w3.org\/TR\/xhtml1\/DTD\//\"/' > .tmp.html
- xmllint --valid --noout .tmp.html
- rm -f .tmp.html
-
-# also run validation on https://validator.w3.org/
-
-Dataflowfig.dvi:Dataflowfig.tex Dataflow.inc
- latex Dataflowfig.tex
-
-Dataflowfig.pdf:Dataflowfig.dvi
- dvipdf $<
-
-vmweb.tgz:matchgraph.gif ${vmwebfiles} index.html vmweb.pdf
- tar -cvzf $@ matchgraph.gif ${vmwebfiles} index.html vmweb.pdf
-
-virtman.pdf:
- cp ../virtman.pdf .
-
-AboKurOhl2004.pdf:
- cp ${PAPERS}/$@ .
-
-AboKurOhl2002.pdf:
- cp ${PAPERS}/$@ .
-
-BreKurWal2002.pdf:
- cp ${PAPERS}/$@ .
-
-ChoSchleKurGie2004.pdf:
- cp ${PAPERS}/$@ .
-
-FitGarKucKurMyeOttSleVitZemMcc2002.pdf:
- cp ${PAPERS}/$@ .
-
-KurChoOhlSchleStoGie2001.pdf:
- cp ${PAPERS}/$@ .
-
-HoehKurOhl2002.pdf:
- cp ${PAPERS}/$@ .
-
-GraeStrKurSte2001.pdf:
- cp ${PAPERS}/$@ .
-
-KrueSczKurGie2004.pdf:
- cp ${PAPERS}/$@ .
-
-BecStroHomGieKur2004.pdf:
- cp ${PAPERS}/$@ .
-
-installwww:
- rsync -rv index.html vmweb.css download.html virtman.pdf vmweb.pdf matchgraph.gif distributions $(SERVER):$(WWWBASEDIR)
-
-clean:
- rm -f *.toc *.ilg *.out *.idx *.ind *.dvi *.ps *.log *.aux
- rm -f *.bbl *.blg
- rm -f vmweb.4ct vmweb.xref vmweb.tmp vmweb.lg vmweb.idv vmweb.html vmweb.4tc vmweb.fls vmweb.fdb_latexmk
- rm -f comment.cut introduction.inc
- rm -f Dataflow.inc
- rm -f ${vmwebfiles}
=====================================
src/doc/WWW/PUSH-cmd.txt deleted
=====================================
@@ -1 +0,0 @@
-git push kurtz at genometools.org:/home/kurtz/lscsa/vstree.git sk
=====================================
src/doc/WWW/download.html deleted
=====================================
@@ -1,53 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN" "http://www.w3.org/TR/html4/strict.dtd">
-<html>
-
-<head>
- <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
- <title>Download Vmatch</title>
- <link rel="stylesheet" type="text/css" href="vmweb.css">
-</head>
-
-<body>
-
-<h1>Download <i>Vmatch</i></h1>
-
-<p>
-By downloading Vmatch you agree to the following:
-</p>
-
-<p>
-<code>
- Vmatch is provided on an <strong>AS IS</strong> basis. The developers do not warrant its validity
-of performance, efficiency, or suitability, nor do they warrant that Vmatch is
-free from errors. All warranties, including without limitation, any warranty or
-merchantability or fitness for a particular purpose, are hereby excluded.
-</code>
-</p>
-
-<h2>Linux</h2>
-<a href="distributions/vmatch-2.3.0-Linux_x86_64-64bit.tar.gz">vmatch-2.3.0-Linux_x86_64-64bit.tar.gz</a> (2017-06-12)<br/>
-<a href="distributions/vmatch-2.3.0-Linux_i386-32bit.tar.gz">vmatch-2.3.0-Linux_i386-32bit.tar.gz</a> (2017-06-12)<br/>
-
-<h2>Mac OS</h2>
-<a href="distributions/vmatch-2.3.0-Darwin_i386-64bit.tar.gz">vmatch-2.3.0-Darwin_i386-64bit.tar.gz</a> (2017-06-12)<br/>
-<a href="distributions/vmatch-2.3.0-Darwin_i386-32bit.tar.gz">vmatch-2.3.0-Darwin_i386-32bit.tar.gz</a> (2017-06-12)<br/>
-
-<h2>Windows</h2>
-<a href="distributions/vmatch-2.3.0-Windows_i686-64bit.zip">vmatch-2.3.0-Windows_i686-64bit.zip</a> (2017-06-12)<br/>
-<a href="distributions/vmatch-2.3.0-Windows_i686-32bit.zip">vmatch-2.3.0-Windows_i686-32bit.zip</a> (2017-06-12)<br/>
-
-<!-- Piwik -->
-<script type="text/javascript">
-var pkBaseURL = "https://zenlicensemanager.com/piwik/";
-document.write(unescape("%3Cscript src='" + pkBaseURL + "piwik.js' type='text/javascript'%3E%3C/script%3E"));
-</script><script type="text/javascript">
-try {
-var piwikTracker = Piwik.getTracker(pkBaseURL + "piwik.php", 3);
-piwikTracker.trackPageView();
-piwikTracker.enableLinkTracking();
-} catch( err ) {}
-</script><noscript><p><img src="https://zenlicensemanager.com/piwik/piwik.php?idsite=3" style="border:0" alt="" /></p></noscript>
-<!-- End Piwik Tracking Tag -->
-
-</body>
-</html>
=====================================
src/doc/WWW/extractpart.pl deleted
=====================================
@@ -1,85 +0,0 @@
-#!/usr/bin/env perl
-
-# select a list of options from a documentation
-
-use strict;
-use warnings;
-
-my $numofargs = scalar @ARGV;
-
-if($numofargs le 1)
-{
- print STDERR "Usage: $0 <tags to be selected> <filename>\n";
- exit 1;
-}
-
-my(%tagtab) = ();
-
-my $filename = $ARGV[$numofargs-1];
-
-for(my $i=0; $i<$numofargs-1; $i++)
-{
- my $key = $ARGV[$i];
- $tagtab{$key} = 1;
-}
-
-# Get file data
-
-my @filecontents = get_file_data($filename);
-
-my $currenttagtext = '';
-my $currenttag = '';
-my $intag = 0; # inside an option (which can be multiline)
-
-for my $line (@filecontents)
-{
- if($intag)
- {
- if($line =~ /^\%\%\%END{([a-z]+)/)
- {
- if($1 ne $currenttag)
- {
- print STDERR "$0: BEGIN{$currenttag} ends with END{$1}\n";
- exit 1;
- }
- print STDERR "\%\%\%matched END with \"$currenttag\"\n";
- $intag = 0;
- print $currenttagtext, "\n";
- $currenttagtext = '';
- $currenttag = '';
- } else
- {
- $currenttagtext .= $line;
- }
- } else
- {
- if($line =~ /^\%\%\%BEGIN{([a-z]+)}/)
- {
- print STDERR "\%\%\%matched BEGIN with \"$1\"\n";
- if(exists $tagtab{$1})
- {
- $intag = 1;
- $currenttag = $1;
- }
- }
- }
-}
-
-exit 0;
-
-# check if the number of arguments is as expected
-# get last argument
-
-sub get_file_data
-{
- my($filename) = @_;
-
- unless(open(GET_FILE_DATA, $filename))
- {
- print STDERR "$0: Cannot open file $filename\n";
- exit 1;
- }
- my @filedata = <GET_FILE_DATA>;
- close GET_FILE_DATA;
- return @filedata;
-}
=====================================
src/doc/WWW/index.html deleted
=====================================
The diff for this file was not included because it is too large.
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@@ -1,2 +0,0 @@
-\\begin{AboutVmatch}
-\\end{AboutVmatch}
=====================================
src/doc/WWW/matchgraph.gif deleted
=====================================
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=====================================
src/doc/WWW/remove-html.rb deleted
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@@ -1,12 +0,0 @@
-#!/usr/bin/env ruby
-
-def remove_html_tags(s)
- re = /<("[^"]*"|'[^']*'|[^'">])*>/
- return s.gsub(re, "")
-end
-
-ARGV.each do |filename|
- file = File.open(filename, "rb")
- contents = file.read
- print remove_html_tags(contents)
-end
=====================================
src/doc/WWW/replace-header.rb deleted
=====================================
@@ -1,20 +0,0 @@
-#!/usr/bin/env ruby
-
-STDIN.each_line do |line|
- if line.match(/<meta name=\"src\" content="vmweb.tex"/)
- print "#{line}"
- puts <<'HEADER'
-<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"/>
-<meta name="description" CONTENT="The Vmatch large scale sequence analysis
-software is a versatile software tool for efficiently solving large scale sequence matching tasks."/>
-<meta name="keywords" CONTENT="sequence analysis, sequence mapping, BLAST, bioinformatics, computational biology"/>
-<meta http-equiv="Content-Style-Type" content="text/css"/>
-HEADER
- elsif line.match(/class=\"titleHead|author|date\"/)
- print line.gsub(/class=/,"align=\"center\" class=").gsub(/h2/,"h1")
- elsif line.match(/\/h2/)
- print line.gsub(/\/h2/,"\/h1")
- else
- print line
- end
-end
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src/doc/WWW/replace-par.rb deleted
=====================================
@@ -1,3 +0,0 @@
-#!/usr/bin/env ruby
-
-puts STDIN.read.gsub!(/<p class=\"noindent\" > <!--delete paragraph-->(.*)\n?<\/p\>/,"\\1\n")
=====================================
src/doc/WWW/vmweb.css deleted
=====================================
@@ -1,44 +0,0 @@
-body {
- font-family: Verdana, Geneva, Arial, sans-serif;
-}
-h1, h2, h3, h4, h5, h6 {
- color:black;
-}
-#w3checklogo {
- float: right;
- clear: right;
-}
-#downloadbox {
- float: right;
- clear: right;
- width: 280px;
- padding-right: 20px;
-}
-#downloadbox li {
- list-style-type: none;
-}
-#downloadbox li a {
- list-style-type: none;
- border : 1px solid black;
- display: block;
- padding: 4px 15px 4px 15px;
- text-decoration: none;
-}
-#downloadbox li a:link {
- color: black;
- background: rgb(90%, 90%, 20%);
-}
-#downloadbox li a:visited {
- color: gray;
- background: rgb(90%, 90%, 20%);
-}
-#downloadbox li a:hover {
- color: white;
- background: rgb(60%, 60%, 90%);
-}
-#footer {
- font-size: 66%;
- text-align: center;
- margin-top: 20px;
- background-color: #DDDDDD;
-}
=====================================
src/doc/WWW/vmweb.tex deleted
=====================================
@@ -1,840 +0,0 @@
-\documentclass[12pt]{article}
-\usepackage{ifpdf}
-\usepackage{graphicx}
-\usepackage{mathptmx}
-\usepackage{natbib}
-\usepackage{numprint}
-\usepackage{bibentry}
-\usepackage{xspace}
-\usepackage[latin1]{inputenc}
-\usepackage{hyperref}
-\hypersetup{%
- colorlinks=true,
- linkcolor=blue
-}
-
-\newcommand{\Vmatch}[0]{\textit{Vmatch}\xspace}
-\newcommand{\Mybibentry}[2]{\item \bibentry{#1} \par%
-In this work \Vmatch was used \xspace #2\xspace}
-%\newcommand{\href}[2]{#2}
-%\nobibliography*
-\newcounter{Allusages}
-\newcommand{\Updateusages}{\addtocounter{Allusages}{\theenumi}}
-\newcommand{\PrintVol}[1]{#1}
-\newcommand{\Includegraphics}[2]{%
-\includegraphics[#1]{#2.pdf}
-}
-
-\makeatletter
-\edef\texforht{TT\noexpand\fi
- \@ifpackageloaded{tex4ht}
- {\noexpand\iftrue}
- {\noexpand\iffalse}}
-\makeatother
-\ifpdf
-\newcommand{\HCode}[1]{}
-\fi
-
-\title{The \Vmatch large scale sequence analysis software}
-\author{Stefan Kurtz}
-\date{\today}
-\parskip5pt
-\parindent0pt
-\begin{document}
-\maketitle
-
-\bibliographystyle{plain}
-\nobibliography{defines,ltr,assembly,algorithms,rnafolding,commolbio,biotools,kurtz,genomes,strings,genetics,metagenomes}
-
-\HCode{
-<!--delete paragraph-->
-<br/>
-<center>
-<img src="matchgraph.gif"
- alt="show matches of different sizes in a matchgraph"/>
-</center>
-<div id="downloadbox">
-<ul>
- <li><a href="download.html">Download <i>Vmatch</i>!</a></li>
-</ul>
-</div>
-}
-
-This is the web-site for \Vmatch,
-a versatile software tool for efficiently
-solving large scale se\-quence matching tasks.
-\Vmatch subsumes the software tool
-\href{http://bibiserv.techfak.uni-bielefeld.de/reputer}{REPuter},
-but is much more general, with a very flexible user interface,
-and improved space and time requirements.
-\HCode{
-<a href="vmweb.pdf">Here</a> is a printable version of this
-HTML-page in PDF.
-}
-
-\section*{Features of \Vmatch}
-The \href{virtman.pdf}{\Vmatch-manual}
-gives many examples on how to use \Vmatch. Here are the program's most
-important features.
-
-\input{introduction.inc}
-
-\HCode{
-<a href="Dataflowfig.pdf">Here</a> is an overview of the dataflow
-in <i>Vmatch</i>.
-}
-
-\section*{Related tools}
-There are several tools which are
-based on the persistent index of \Vmatch:
-
-\begin{description}
-\item[Genalyzer]
-is a graphical user interface
-to visualize the output of \Vmatch in form of a match graph.
-For details see
-
-\bibentry{CHO:SCHLE:KUR:GIE:2004}
-
-Genalyzer is not available any more.
-\item[\href{http://bibiserv.techfak.uni-bielefeld.de/mga/}{MGA}]
-is a program to compute multiple alignments of complete
-genomes. For details see
-
-\bibentry{HOEH:KUR:OHL:2002}
-\item[Multimat] is a program to compute multiple exact matches between
-three or more genome size sequences. For details see
-
-\bibentry{OHL:KUR:2008}
-
-Please contact
-\href{http://www.zbh.uni-hamburg.de/kurtz}{Stefan Kurtz} if you are interested
-in using Multimat.
-
-\item[\href{http://bibiserv.techfak.uni-bielefeld.de/possumsearch/}{PossumSearch}]
-Is a program to search for position specific scoring matrices.
-For details, see
-
-\bibentry{BEC:HOM:GIE:KUR:2006}
-\item
-\item[\href{http://www.genomethreader.org/}{GenomeThreader}]
-is a software tool to compute gene structure predictions. The gene structure
-predictions are calculated using a similarity-based approach where additional
-cDNA/EST and/or protein sequences are used to predict gene structures via
-spliced alignments. \textit{GenomeThreader} uses the matching capabilities
-of \Vmatch to efficiently map the reference sequence to a genomic
-sequence. For details, see
-
-\bibentry{GRE:BRE:SPA:KUR:2005}
-\item
-\item[\href{http://www.biopieces.org/}{Biopieces}]
-is a collection of bioinformatics tools that can be pieced together in a
-very easy and flexible manner to perform both simple and complex tasks.
-Some Biopieces depend on \Vmatch. For details see
-\url{http://www.biopieces.org/}.
-\end{description}
-
-\HCode{
-<a name="CurrentUsage"/>
-}
-\section*{Previous and Current Usages}
-
-We provide an annotated bibliography listing papers which applied \Vmatch
-and shortly describe the tasks for which \Vmatch was used. We omit our own
-papers. The references were collected by a
-\href{https://scholar.google.de/scholar?q=Vmatch+AND+Kurtz+OR+www.vmatch.de}%
- {search in Google scholar}
-(which, as of Jan 2, 2016 retrieved 397 results.)
-
-\subsection*{Usages in Plant Genome Research}
-\begin{enumerate}
-\Mybibentry{BRE:KUR:WAL:2002}{
-to a compute a non-redundant set from a large collection of protein sequences
-from Zea-Maize.}
-
-Similar applications are described in
-
-\bibentry{DON:ROY:FRE:WAL:BRE:2003}.
-%\item
-%For the development of the
-%\href{http://barleypop.vrac.iastate.edu/BarleyBase/content.php}{Barley1 GeneChip} \Vmatch is used to search
-%against probes.
-\item
-PLEXdb is a database for gene expression resources for plants and plant
-pathogens, see
-
-\bibentry{DAS:VAN:HON:WIS:DIC:2012}
-
-PLEXdb provides a \Vmatch-based
-\href{http://www.plantgdb.org/cgi-bin/prj/PLEXdb/ProbeMatch.pl}{web-service}
-to match PLEXdb probes.
-
-\item
-The assembly of the Arabidopsis thaliana genome from 2004
-(GenBank entries of 2/19/04) contained vector sequence contaminations.
-For example, region \numprint{3617880} to \numprint{3625027} of
-chromosome II contained
-a cloning vector. \Vmatch was used to detect the vector contamination,
-see \href{http://www.plantgdb.org/AtGDB/Annotation/vector.php}{here}
-
-\item
-\bibentry{DON:LAW:SCHLUE:WIL:KUR:LUS:BRE:2005}
-
-This work describes PlantGDB, which
-provides a service called
-\href{http://www.plantgdb.org/PlantGDB-cgi/vmatch/patternsearch.pl}{PatternSearch at PlantGDB}
-for genome wide pattern searches in plant sequences. The service is based
-on \Vmatch.
-\Mybibentry{LIN:KRO:2005}{
-for three different tasks:
-\begin{itemize}
-\item
-Searching spliced mRNA in the Arabidopsis genome to detect
-micromatches of length at least 20 with maximum 2 mismatches.
-\item
-Finding matches of length at least 15 long with at most one mismatch
-between predicted mature miRNA-sequences and a set of ESTs as well
-as sequences from the Arabidopsis Small RNA Project (ASRP).
-\item
-Aligning and performing single linkage clustering
-of the predicted mature miRNA sequences. Candidate pairs aligning over at least
-17 bases, allowing an edit distance of 1 were grouped in the same family.
-\end{itemize}}
-
-\item
-\bibentry{POM:LEM:TUR:2006}
-
-\bibentry{TUR:OTI:LEM:2006}
-
-In these papers \Vmatch was used to search
-and compare repeated elements in different chloroplast DNA.
-
-\item
-\bibentry{SPA:NOU:HAA:YAN:GUN:HIN:KLE:HAB:SCHOO:MAY:2007}
-In this work about the \textit{MIPSPlantsDB} database
-\Vmatch was used to cluster large sequence sets.
-
-\Mybibentry{SCHIJ:VOS:MAR:JON:ROS:MOL:TIK:ANG:TUN:BOV:2007}{
-to compare target genes of the tomato Chs RNAi to a tomato gene index.}
-
-\Mybibentry{LIN:JAC:NYG:MAN:KRO:2007}{
-to search different
-plant genomes for matches of length at least 20 with maximum of 2 mismatches.
-Here the fact that \Vmatch is an exhaustive search tool is important.}
-
-\Mybibentry{DEC:OTI:THU:LEM:2007}{
-to determine the presence of shared repeated elements of minimum length
-30, with up to 10\% mismatches using in different sequence sets from
-the green alga \textit{Leptosira terrestris}.}
-
-\Mybibentry{OSS:SCHNE:CLA:LAN:WAR:WEI:2008}{
-to map millions of short sequence reads to the \textit{A.~Thaliana} genome.
-Up to four mismatches and up to three indels were allowed in the matching
-process. The seed size was chosen to be 0. The reads were aligned using the
-best match strategy by iteratively increasing the the allowed number of
-mismatches and gaps at each round.}
-
-\Mybibentry{DIBO:OSS:SCHNE:RAT:2008}{
-to map millions of short sequence reads to the \textit{A.~Thaliana} genome.
-\Vmatch was part of a multi-step pipeline, combining a fast
-matching algorithm (\Vmatch) for initial read mapping and
-an optimal alignment algorithm based on dynamic programming (QPALMA)
-for high quality detection of splice sites.}
-
-\Mybibentry{ASS:HER:LIN:HUE:TAL:SMA:IMM:ELD:FIE:SCHAT:2010}{
-for motif searching in different plant genomes.}
-
-\Mybibentry{EVE:SAT:GOL:MEY:BET:SAK:WAR:JAC:2010}{
-to map unique consensus sequence tags to the maize reference genome.}
-
-\Mybibentry{BRO:OTI:LEM:TUR:2010}{
-to identify and cluster repeated sequences in \textit{Floydiella} chloroplast
-genome.}
-
-\Mybibentry{REH:AQU:GRU:HEN:HIL:LAU:NAO:PAT:ROM:SHU:2010}{
-to calculate direct and reverse complementary matches of length {17} bp or
-greater with edit distance {1} or less between five nuclear chromosomes
-and mitochondrial and chloroplast genome sequences.}
-
-\Mybibentry{SEK:LIN:CHI:HAN:BUE:LEO:KAE:2011}{
-to search probe sequences against the maize genome
-the cDNA sequences of the official maize gene models.}
-
-\Mybibentry{DAS:OH:HAA:HER:HON:ALI:YUN:BRE:ZHU:BOH:2011}{
-for clustering sequences assembled from 454-reads of
-\textit{Thellungiella parvula}, a model for the evolution of plant
-adaptation to extreme environments.}
-
-\Mybibentry{WIL:HOF:KLE:WEI:2011}{
-for grouping short reads into
-pools representing the same RAD tag.}
-
-\Mybibentry{GAO:ZHO:WAN:SU:WAN:2011}{
-for detecting and
-clustering repetitive sequences in diverse fern plastid genomes.}
-
-\Mybibentry{SLO:ALV:CHU:WU:MCC:PAL:TAY:2012}{
-to precisely
-define the boundaries of all repeats with 100\% sequence identity.}
-
-\Mybibentry{DUB:FAR:SCHLU:CAN:ABE:TUT:WOO:SHA:MUL:KUD:2011}{
-cluster sequences based on their six-frame translation.}
-
-\Mybibentry{SAX:PEN:UPA:KUM:CAR:SCHLU:FAR:WHA:SAR:MAY:2012}{
-to identify reciprocal best matches between the pigeonpea sequences and
-other legume sequences.}
-
-\Mybibentry{HAZ:REE:RIS:PEC:2012}{
-for assembly clustering and
-optimization of contigs for
-\textit{Neochloris oleoabundans} (a Chlorophyceae class green microalgae).}
-
-\Mybibentry{MAR:KLE:BAN:BLA:MAC:SCHMU:SCHOL:GUN:WIC:SIM:2012}{
-to match reads against a repeat library to
-identity the content of the repetitive DNA per sequence read.}
-
-\Mybibentry{CHI:DAV:BUE:2011}{
-to align individual probes to representative gene models.}
-
-\Mybibentry{SEV:DIJ:HAM:2011}{
-for performing exact searches with
-peptides against the filtered proteome of \textit{A. thaliana}.}
-
-\Mybibentry{WOL:WEI:SEG:ROS:BEI:DON:SPI:NOR:REH:KOE:2011}{
-to map RNAseq reads,
-allowing up to two mismatches (option \texttt{-h 2})
-and generating maximal substring matches
-that are unique in some reference dataset (option \texttt{-mum cand}).}
-
-\Mybibentry{FLE:KHA:JOH:YOU:MIT:WRE:HES:FOS:SCHAR:SCO:2011}{
-to identify terminal inverted repeats of length range {10-65} bp,
-$\geq 80\%$ identity, maximum inter-TIR distance 650~bp in in genomes of
-epichloid fungal endophytes of grasses.}
-
-\Mybibentry{CHI:KON:BUE:2012}{
-to match putative unique transcript sequence assemblies.}
-
-\Mybibentry{CHE:CAS:BAI:RED:MIC:2012}{
-for refining assemblies of Illumina reads in the context of a transcriptome
-project for plant virus vector \textit{Graminella nigrifrons}.}
-
-\Mybibentry{KRI:PAT:JAI:GAU:CHOU:VAI:DEE:HAR:KRI:NAI:2012}{
-for clustering repeats and for building a consensus repeat library in the
-context of genome and transcriptome projects for \textit{Azadirachta indica}, a
-medicinal and pesticidal angiosperm.}
-
-\Mybibentry{LIU:KUM:ZHA:ZHE:WAR:2012}{
-to map unique consensus sequences tags to the maize reference
-genome and to predict targets of novel miRNAs.}
-
-\Mybibentry{BOU:KOU:PAV:MIN:TSA:DAR:2012}{
-for masking Long Terminal Repeats in the Maize Genome Sequence.}
-
-\item In the papers
-
-\bibentry{HER:MAR:DOR:PFE:GAL:SCHAA:JOU:SIM:VAL:DOL:2012}
-
-\bibentry{PHI:PAU:BER:SOU:CHO:LAU:SIM:SAF:BEL:VAU:2013}
-
-\Vmatch was used to mask repetitive DNA.
-
-\Mybibentry{HOW:YU:KNA:CRO:KOL:DOL:LOR:DEA:2013}{
-to cluster \numprint{40010} assembled isotigs.}
-
-\Mybibentry{KAR:HAA:MAL:GEE:BOV:LAM:ANG:MAA:2013}{
-to preprocess short reads in the context of identifying mircoRNA targets in
-tomato fruit development.}
-
-\Mybibentry{GRO:MAR:SIM:ABR:WAN:VIS:2013}{
-in an all-vs-all comparison to bin contigs into
-loci based on a minimum of 200~bp sequence overlap in the context of
-transcriptome assembly for two Agave-species.}
-
-\Mybibentry{KAN:HEL:DUR:WIN:ENG:BEH:HOL:BRA:HAU:FER:2013}{
-to align 454-reads to assembled isotigs for Ragweed pollen.}
-
-\Mybibentry{KUG:SIE:NUS:AME:SPAN:STEI:LEM:MAY:BUE:SCHWE:2013}{
-for comparing gene sets.}
-
-\Mybibentry{MAR:ZHO:HAS:SCHMU:VRA:KUB:KOEN:KUG:SCHOL:HAC:2013}{
-to detect repetitive DNA content of chromosomal survey
-sequences from the Rye genome.}
-
-\item
-In the papers
-
-\bibentry{KOP:MAR:VHA:HRV:VRA:BAR:KOP:CAT:STO:NOV:2013}
-
-\bibentry{KOP:MAR:CHA:HRI:VRA:BAR:2013}
-
-\Vmatch was used for
-identifying repetitive DNA content in contigs of meadow fescue chromosome 4F
-assembled from Illumina short reads.
-
-\item
-In the papers
-
-\bibentry{JAY:WAN:YU:TAC:PEL:COL:REN:VOI:2011}
-
-\bibentry{WAN:WEI:SMI:2013}
-
-\Vmatch was used for mapping siRNA sequences to the
-\textit{Arabidopsis thaliana} genome.
-
-\Mybibentry{HEN:VIV:DES:CHAU:PAY:GUT:CAS:2014}{
-for the identification of binding motifs.}
-
-\Mybibentry{WAN:HAB:GUN:GLAE:NUS:LUO:LOM:BOR:KER:SHA:2014}{
-for masking one sequence set with another and for
-mapping miRNA sequences of all plant species present in a reference database
-to whole-genome assembly of \textit{Spirodela polyrhiza}.}
-
-\Mybibentry{LOG:SCHEL:NUR:SAM:PEN:2014}{
-for repeat detection.}
-
-\Mybibentry{WAN:SHI:RIN:2015}{
-to eliminate redundancies in assemblies of Illumina reads in
-the context of studying plant defense mechanisms.}
-
-\Mybibentry{ASH:HUL:WAN:YAN:GUA:JON:MAT:MOC:CHE:STE:2015}{
-for clustering to determine a non-redundant set of assembled contigs.}
-
-\Mybibentry{UST:NOV:BLI:SMY:2015}{
-for clustering sequences based on their RT and aRNH domain.}
-
-\Mybibentry{HLE:RIV:CLA:MAR:VAN:GON:GAR:LER:SIM:VAL:2015}{
-for identifying repeats in contigs assembled from 454-reads.}
-
-\Mybibentry{SHE:YAN:LU:WAN:SON:2015}{
-for identifying inverted repeats in chloroplast genomes.}
-
-\Mybibentry{PAN:MOH:KHA:MEH:EBR:2015}{
-to identify contaminations and repetitive elements by
-comparison of mRNA sequences to vector, bacterial and repeat databases.}
-
-\Mybibentry{WOL:TWO:GAD:KNA:GRU:GEN:2015}{
-to cluster contigs of different assemblies into groups of homologous sequences.}
-
-\Mybibentry{YAN:LU:SHE:YAN:XU:SON:2015}{
-to identify inverted repeats in chloroplast genomes.}
-
-\Updateusages
-\end{enumerate}
-
-\subsection*{Usages in the Microbial Genome Research}
-\begin{enumerate}
-\item
-The
-\href{http://www.llnl.gov/str/April04/Slezak.html}{KPATH system},
-developed at the Lawrence Livermore National Laboratories, and
-described in
-
-\bibentry{FIT:GAR:KUC:KUR:MYE:OTT:SLE:VIT:ZEM:MCC:2002}
-
-\bibentry{SLE:KUC:OTT:TOR:MED:SMI:TRU:MUL:LAM:VIT:ZEM:ZHO:GAR:2003}
-
-used \Vmatch to detect unique substrings in large
-collection of DNA sequences. These unique substrings serve as
-signatures allowing for rapid and accurate diagnostics
-to identify pathogen bacteria and viruses. A similar application
-is reported in \bibentry{GAR:KUC:VIT:SLE:2003}.
-
-\Mybibentry{POB:WET:SZY:SCHIL:KUR:MEY:NAT:BECK:2006}{
-to map signature tags to the genome
-of \textit{S.~meliloti}.}
-
-\item
-The
-\href{http://crispr.u-psud.fr/Server/CRISPRfinder.php}{CRISPRFinder}-program
-and the
-\href{http://crispr.u-psud.fr/crispr/CRISPRdatabase.php}{CRISPRdatabase}, described in
-
-\bibentry{GRI:VER:POU:2007A}
-
-\bibentry{GRI:VER:POU:2007B}
-
-used \Vmatch to
-efficiently find maximal repeats, as a first step in localizing
-Clustered regularly interspaced short palindromic repeats (CRISPRs).
-
-\Mybibentry{VOSS:GEO:SCHOE:UDE:HES:2009}{
-to map predicted sequences to
-information about Rho-independent terminators provided by a specific database.}
-
-\Mybibentry{SCHMU:CAN:SCHLU:MA:MIT:NEL:HYT:SON:THE:CHE:2010}{
-to cluster DNA-sequences into families based on their
-six-frame translation.}
-
-\Mybibentry{ZIM:GES:CHE:LOR:SCHRO:2010}{
-to align 454-sequences to the Ecoli-genome and to cluster the sequences.}
-
-\Mybibentry{TOU:DEN:MED:BAR:ELK:PET:2010}{
-for detecting repeats in three bacterial species.}
-
-\Mybibentry{MAY:MAR:HED:SIM:LIU:MOR:STEU:TAU:ROE:GUN:2011}{
-for masking repeats in 454-reads.}
-
-\Mybibentry{PUS:MAN:JI:LI:EVA:CRA:MOR:MEA:SIN:SAX:2011}{
-to identify distal primers.}
-
-\Mybibentry{BRE:SHE:POP:2011}{
-for removing redundant transcripts assembled in an RNA-seq study based on
-Illumina reads for \textit{Heliothis virescens} (tobacco budworm), infected
-with a virus.}
-
-\Mybibentry{TRI:HAM:BUE:TIS:VER:ZIN:LEA:2011}{
-to search unassembled Illumina reads of US and African strains of
-\textit{Xanthomonas oryzae} for evidence of transcriptional activator-like
-effector sequences.}
-
-\item
-\Vmatch is used as an integral part of the PriMUX software package described in
-
-\bibentry{HYS:NAR:ELS:CAR:WIL:GAR:2012}
-
-In this context \Vmatch used for selecting multiplex compatible,
-degenerate primers and probes to detect diverse targets such as viruses.
-
-\Mybibentry{SHE:POP:2012}{
-to identify redundant contigs from de novo exome assemblies.}
-
-\Mybibentry{HUR:SUL:2013}{
-to identify reads which have no common 20-mers with other
-reads in a context of a marine viral metagenome project.}
-
-\Mybibentry{ZHU:RHO:FESCH:2013}{
-for clustering potential complete
-Endogenous retroviruses of the bat \textit{Myotis lucifugus} into subfamilies.}
-
-\item In the three papers
-
-\bibentry{HUR:WES:BRU:SUL:2014}
-
-\bibentry{HUR:DEN:POU:SUL:2013}
-
-\bibentry{BRU:HUR:SCHOF:DUC:SUL:2015}
-
-\Vmatch was used for $k$-mer analysis in the context of different marine
-metagenome projects.
-
-\Mybibentry{DEC:PAR:2014}{
-for $k$-mer analysis in the context of microbial communities.}
-
-\Mybibentry{BEN:BOU:FIC:KRI:LAR:2014}{
-in an iterative scheme to construct contigs from reads associated with
-resistance genes in the context of a shotgun metagenome project.}
-
-\Mybibentry{NIC:THI:GAR:MCL:FOF:KOS:ELL:BRE:JAC:JAI:2013}{
-to match probe candidate sequences against viral sequences and the human
-genmome sequence.}
-
-\Mybibentry{HEN:RUM:SCZ:VEL:DIE:GER:GOM:RAH:STO:BOR:2014}{
-to identify the species of the Streptococcaceae
-by comparing with Silva 115 release 16S reference sequence database.}
-\Updateusages
-\end{enumerate}
-
-\subsection*{Usages in General Web-Servers or Sequence Analysis Software}
-\begin{enumerate}
-\item
-Since 2000,
-the \href{http://rsat.ulb.ac.be/rsat/}{RSA-tools}, described in
-
-\bibentry{HEL:RIO:COL:2000}
-
-and developed by Jacques van Helden
-use \Vmatch to \href{http://rsat.ulb.ac.be/rsat/purge-sequence_form.cgi}{purge}
-sequences before computing sequence statistics. Similar applications are
-reported in the following papers:
-
-\bibentry{HUL:WEE:CRO:GER:HEP:HEL:2003}
-
-\bibentry{SIM:WOD:COH:HEL:2004}
-
-\bibentry{SIM:HEL:COH:WOD:2004}.
-
-\item
-The program \href{http://splicenest.molgen.mpg.de/}{SpliceNest}, described in
-
-\bibentry{COW:HAA:VIN:2002}
-
-computes gene indices and uses \Vmatch to
-\href{http://splicenest.molgen.mpg.de/doc/help.html\#mapping}{map} clustered
-sequences to large genomes.
-%\item
-%The oligo design program
-%\href{http://oligos.molgen.mpg.de/}{Promide}
-%\bibentry{RAH:2002} developed by
-%Sven Rahmann is based on the persistent index structure of \Vmatch.
-%Promide uses \textit{mkvtree} for generating the index.
-\item
-\href{http://bibiserv.techfak.uni-bielefeld.de/e2g/}{e2g}
-is a web-based server which efficiently maps large
-EST and cDNA data sets to genomic DNA. The use of \Vmatch
-allows to significantly extend the size of data that can be mapped in
-reasonable time. e2g is available as a web service and hosts
-large collections of EST sequences (e.g.\ 4.1 million mouse ESTs
-of 1.87 Gbp) in a precomputed persistent index. For details see
-
-\bibentry{KRUE:SCZ:KUR:GIE:2004}.
-
-\item
-The \href{http://bibiserv.techfak.uni-bielefeld.de/}{Bielefeld Bioinformatics Server} provides the
-\href{http://bibiserv.techfak.uni-bielefeld.de/reputer/}{REPuter}
-web-service to compute repeats in complete genomes. The service is based on
-\Vmatch.
-
-\Mybibentry{FER:DON:SCHNE:MOR:NAN:BRE:WAL:2004}{
-to (1) match \numprint{130861} vector-trimmed sequences against the maize
-repeat database, and (2) to cluster near-identical sequences. }
-%The \href{http://www.mutransposon.org/project/RescueMu/research/GSSanalysis}%
- %{Mu Transposon Information Resource},
-\item
-\href{http://www-ab.informatik.uni-tuebingen.de/software/crosslink/welcome.html}{CrossLink}, described in
-
-\bibentry{DEZ:SCHAEF:WIE:WEI:HUS:2006}
-
-is a versatile computational tool which aids in visualizing
-relationships between RNA sequences (particularly between ncRNAs and
-their putative target transcripts) in an intuitive and accessible way.
-Besides BLAST, CrossLink uses \Vmatch to reveal the sequence
-relationships to be visualized.
-
-\item
-The early version of the web-service \href{http://mips.gsf.de/simap/}%
- {Similarity matrix of Proteins (SIMAP)}, see
-
-\bibentry{ARN:RAT:TIS:TRU:STU:MEW:2005}
-
-used \Vmatch to locate
-the sequences in SIMAP which are similar to a given query. This is much
-faster than running BLAST.
-
-\Mybibentry{FIE:VAN:PEE:VAN:NAP:2005}{
-to compute similarities between genomes, which are then visualized by the
-program \href{http://www.win.tue.nl/dnavis/}{DNAVis}.}
-
-\item In the paper
-
-\bibentry{SEI:KRUE:HAR:SCHWA:LOEW:MER:DAN:GIE:2006}
-
-Seidel et.\ al.\ describe
-methods for creating web-services and give examples which, among other tools,
-also integrate \Vmatch.
-
-\item
-The program \textit{Gepard}
-
-\bibentry{KRU:ARN:RAT:2007}
-
-uses \textit{mkvtree} to compute enhanced suffix arrays.
-
-\item
-\Vmatch is used a part of the transcriptome assembler software Rnnotator,
-described in
-
-\bibentry{MAR:BRU:FAN:MEN:BLO:ZHA:SHE:SNY:WAN:2010}
-\item
-The BioExtract-Server described in
-
-\bibentry{LUS:JEN:BRE:2011}
-
-uses \Vmatch to remove duplicated sequences.
-
-\Mybibentry{LUS:GNI:DOO:2015}{
-for removing duplicates in BlastP results. This use is
-part of a workflow in
-\href{http://www.myexperiment.org/workflows/3131.html}{myexperiment}.
-}
-
-\Mybibentry{GRE:LOY:HOR:RAT:2015}{
-for probe/primer search functionality in the probeBase database.}
-\Updateusages
-\end{enumerate}
-
-\subsection*{Current Usages in Human Genome Research}
-\begin{enumerate}
-\Mybibentry{BUC:JAR:MEN:MAT:SCO:GRE:LAN:DUM:2005}{
-to reveal long repeats inside human chromosome 1 and long similar regions
-between human chromosome 1 and all other human chromosomes.}
-
-\Mybibentry{LIA:WAN:LIU:JI:LIU:CHE:WEB:REE:DEA:2007}{
-for Vector screening.}
-
-\Mybibentry{NYG:JAC:LIN:ERI:BAL:FLY:TOL:MOE:SOE:KRO:LIT:2009}{
-for mapping short reads.}
-
-\Mybibentry{COL:SOB:LU:THA:BOW:BRO:GRE:BAR:HUT:2009}{
-for matching reads to sets of RNA sequences and the Human genome.}
-
-\Mybibentry{CLO:WAN:XU:GU:LEA:HEA:BAR:STE:MAR:NOU:2011}{
-to uniquely map miRNAs against the human genome.}
-
-\Mybibentry{TAK:TSU:KAT:OKA:HOR:IKE:URA:KAW:HAS:IKE:2011}{
-to determine the positions of CAGE tags on the human genome.}
-
-\Mybibentry{KEV:LAL:LI:CAV:NAR:KAM:MIT:HAK:KOZ:GEN:2011}{
-to align sections of reads against RefSeq mRNA exon sequences.}
-
-\Mybibentry{KID:CHE:WAN:JAC:ZHA:BOY:FIR:TAN:GAE:COL:2012}{
-to align sets of genes.}
-
-\Mybibentry{YAM:IKE:BOE:HOR:TAK:URA:KAI:CAR:KAW:HAY:2014}{
-to determine the positions of CAGE tags on the human genome.}
-
-\Updateusages
-\end{enumerate}
-
-\subsection*{Current Usages for different Model Organisms}
-\begin{enumerate}
-\Mybibentry{SCZ:BECK:BRI:GIE:ALT:2005}{
-to cluster \numprint{317242} EST and cDNA sequences from
-\textit{Xenopus laevis}. \Vmatch was chosen for the following reasons:
-\begin{itemize}
-\item
-At first, there was no clustering tool available which could handle
-large data sets efficiently, and which was documented well enough to
-allow a detailed b replication and evaluation of existing clusters.
-\item
-Second, \Vmatch identifies similarities between sequences rapidly,
-and it provides additional options to cluster a set of sequences
-based on these matches. Furthermore, the \Vmatch output provides
-information about how the clusters were derived. Due to the
-efficiency of \Vmatch, it was possible to perform the clustering for a
-wide variety of parameters on the complete sequence set.
-This allows to study the effect of the parameter choice on the clustering.
-\end{itemize}}
-
-\Mybibentry{SPIT:LOR:CUL:SCZ:FUEL:2006}{
-to cluster EST-sequences of \textit{Xenopus laevis}.}
-
-\Mybibentry{EIS:COY:WU:WU:THI:WOR:BAD:REN:AME:JON:2006}{
-to search exact repeats in the Macronuclear Genome Sequence of the Ciliate
-\textit{Tetrahymena thermophila}.}
-%\item
-%\href{http://www.plantgdb.org/}{PlantGDB} provides a Web Service
-%named \href{https://biomoby.tigr.org/wiki/index.php/Code_Examples_-_Java}{VMatchForArabidopsis}%
-%
-%based on \Vmatch. It allows to search sequences
-%from \textit{Arabidopsis Thaliana}.
-%\item
-%The \href{http://www.jgi.doe.gov/science/posters/LBNL-59860goltsman.pdf}{DOE Joint Genome Institute}%
-%
-%used \Vmatch to
-%identify and mask all continuous non-unique sequence fragments over
-%500~bp in \textit{Frankia sp.} and \textit{Shewanella oneidensis}.
-
-\Mybibentry{FAU:FOR:CHA:SCHRO:HAY:CAR:HUM:GRI:2008}{
-for mapping
-\begin{itemize}
-\item
-\numprint{11567973} FANTOM3 mouse CAGE tags to the mouse genome
-with minimum match length of {18} bp, a single internal mismatch allowed,
-and multiple mismatches allowed at tag ends.
-\item
-Affymetrix GNF probe sequences to transcripts without allowing for mismatches.
-\end{itemize}}
-
-
-\Mybibentry{PRI:JOR:2008}{
-to search small RNA signatures in entire miRNA gene sequences for
-Arabidopsis and rice.}
-
-\Mybibentry{TAF:GLA:LASS:HAY:CAR:MAT:2009}{
-to map small RNA data sets onto the corresponding reference
-genomes for different model organisms.}
-
-\Mybibentry{PLE:PAS:BER:AKA:CAR:VAS:LAZ:SEV:VLA:SIM:2012}{
-for mapping Illumina reads to the mouse genome.}
-
-\Mybibentry{KEN:SHI:2012}{
-for redundancy removal in the context of transcriptome assembly of
-a keelworm species.}
-
-\Mybibentry{GOS:OHM:KOG:SON:TUR:ZAJ:ZAL:GRU:SUN:HAN:2014}{
-to remove redundant contigs in a genome project of four
-\textit{Aureobasidium pullulans} varieties.}
-
-\Mybibentry{MCM:GAR:BAI:KEM:WAR:CEV:ROB:SCHUL:BAL:HOL:2015}{
-for merging assemblies of Illumina sequenced cDNA.}
-
-% add applications at Bioinformatics Center Copenhagen Univ., see E-mails from
-% Feb 2007, this may be the Biopieces.
-
-% the following paper cites \Vmatch, but does not use it.
-% http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1868776
-% \bibentry{TEM:ZAV:BOD:CHA:GEY:WAS:BEN:REI:2007}, Tembe et et.\ al.\
-
-%Add "Highly Specific Gene Silencing by Artificial MicroRNAs in Arabidopsis"
-%of Schwab et al, 2006, and implemented on wmd2.weigelworld.org.
-%refers to Hypa and not really to \Vmatch.
-
-\Mybibentry{MOR:DHA:PAV:TRO:WHE:HEL:2015}{
-to combine and scaffold contigs.}
-
-\Updateusages
-\end{enumerate}
-
-Total number of usages: \arabic{Allusages}
-
-\section*{Availability}
-\Vmatch is available for
-\href{http://www.vmatch.de/download.html}{download}
-in executable form for the following platforms:
-
-\begin{itemize}
-\item
-Linux
-\item
-Mac OS X
-\item
-MS Windows
-\end{itemize}
-
-\section*{Developer}
-\Vmatch was developed since May 2000 by
-\href{http://www.zbh.uni-hamburg.de/kurtz}{Stefan Kurtz},
-a professor of
-Computer Science at the Center for Bioinformatics, University of Hamburg,
-Germany.
-
-\HCode{
-<!--delete paragraph-->
-<b>Important Documents</b>
-<ul>
-<li>
-The <a href="virtman.pdf"><i>Vmatch</i>-manual</a>
-</li>
-</ul>
-}
-
-\HCode{
-<!--delete paragraph-->
-<div id="footer">
-Copyright © 2000-2017 <a href="mailto:kurtz at zbh.uni-hamburg.de">
-Stefan Kurtz</a>. Last update: 2017-06-15
-</div>
-}
-
-\HCode{
-<!--delete paragraph-->
-<!-- Piwik -->
-<div id="piwik">
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-var pkBaseURL = "https://zenlicensemanager.com/piwik/";
-document.write(unescape("%3Cscript src='" + pkBaseURL + "piwik.js' type='text/javascript'%3E%3C/script%3E"));
-</script><script type="text/javascript">
-try {
-var piwikTracker = Piwik.getTracker(pkBaseURL + "piwik.php", 3);
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-</noscript>
-<!-- End Piwik Tracking Tag -->
-</div>
-}
-\end{document}
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- conforming SGML systems and applications as defined in
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-<!-- Character entity set. Typical invocation:
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-<!ENTITY otilde "õ"> <!-- latin small letter o with tilde,
- U+00F5 ISOlat1 -->
-<!ENTITY ouml "ö"> <!-- latin small letter o with diaeresis,
- U+00F6 ISOlat1 -->
-<!ENTITY divide "÷"> <!-- division sign, U+00F7 ISOnum -->
-<!ENTITY oslash "ø"> <!-- latin small letter o with stroke,
- = latin small letter o slash,
- U+00F8 ISOlat1 -->
-<!ENTITY ugrave "ù"> <!-- latin small letter u with grave,
- U+00F9 ISOlat1 -->
-<!ENTITY uacute "ú"> <!-- latin small letter u with acute,
- U+00FA ISOlat1 -->
-<!ENTITY ucirc "û"> <!-- latin small letter u with circumflex,
- U+00FB ISOlat1 -->
-<!ENTITY uuml "ü"> <!-- latin small letter u with diaeresis,
- U+00FC ISOlat1 -->
-<!ENTITY yacute "ý"> <!-- latin small letter y with acute,
- U+00FD ISOlat1 -->
-<!ENTITY thorn "þ"> <!-- latin small letter thorn,
- U+00FE ISOlat1 -->
-<!ENTITY yuml "ÿ"> <!-- latin small letter y with diaeresis,
- U+00FF ISOlat1 -->
=====================================
src/doc/WWW/xhtml-special.ent deleted
=====================================
@@ -1,80 +0,0 @@
-<!-- Special characters for XHTML -->
-
-<!-- Character entity set. Typical invocation:
- <!ENTITY % HTMLspecial PUBLIC
- "-//W3C//ENTITIES Special for XHTML//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml-special.ent">
- %HTMLspecial;
--->
-
-<!-- Portions (C) International Organization for Standardization 1986:
- Permission to copy in any form is granted for use with
- conforming SGML systems and applications as defined in
- ISO 8879, provided this notice is included in all copies.
--->
-
-<!-- Relevant ISO entity set is given unless names are newly introduced.
- New names (i.e., not in ISO 8879 list) do not clash with any
- existing ISO 8879 entity names. ISO 10646 character numbers
- are given for each character, in hex. values are decimal
- conversions of the ISO 10646 values and refer to the document
- character set. Names are Unicode names.
--->
-
-<!-- C0 Controls and Basic Latin -->
-<!ENTITY quot """> <!-- quotation mark, U+0022 ISOnum -->
-<!ENTITY amp "&"> <!-- ampersand, U+0026 ISOnum -->
-<!ENTITY lt "<"> <!-- less-than sign, U+003C ISOnum -->
-<!ENTITY gt ">"> <!-- greater-than sign, U+003E ISOnum -->
-<!ENTITY apos "'"> <!-- apostrophe = APL quote, U+0027 ISOnum -->
-
-<!-- Latin Extended-A -->
-<!ENTITY OElig "Œ"> <!-- latin capital ligature OE,
- U+0152 ISOlat2 -->
-<!ENTITY oelig "œ"> <!-- latin small ligature oe, U+0153 ISOlat2 -->
-<!-- ligature is a misnomer, this is a separate character in some languages -->
-<!ENTITY Scaron "Š"> <!-- latin capital letter S with caron,
- U+0160 ISOlat2 -->
-<!ENTITY scaron "š"> <!-- latin small letter s with caron,
- U+0161 ISOlat2 -->
-<!ENTITY Yuml "Ÿ"> <!-- latin capital letter Y with diaeresis,
- U+0178 ISOlat2 -->
-
-<!-- Spacing Modifier Letters -->
-<!ENTITY circ "ˆ"> <!-- modifier letter circumflex accent,
- U+02C6 ISOpub -->
-<!ENTITY tilde "˜"> <!-- small tilde, U+02DC ISOdia -->
-
-<!-- General Punctuation -->
-<!ENTITY ensp " "> <!-- en space, U+2002 ISOpub -->
-<!ENTITY emsp " "> <!-- em space, U+2003 ISOpub -->
-<!ENTITY thinsp " "> <!-- thin space, U+2009 ISOpub -->
-<!ENTITY zwnj ""> <!-- zero width non-joiner,
- U+200C NEW RFC 2070 -->
-<!ENTITY zwj ""> <!-- zero width joiner, U+200D NEW RFC 2070 -->
-<!ENTITY lrm ""> <!-- left-to-right mark, U+200E NEW RFC 2070 -->
-<!ENTITY rlm ""> <!-- right-to-left mark, U+200F NEW RFC 2070 -->
-<!ENTITY ndash "–"> <!-- en dash, U+2013 ISOpub -->
-<!ENTITY mdash "—"> <!-- em dash, U+2014 ISOpub -->
-<!ENTITY lsquo "‘"> <!-- left single quotation mark,
- U+2018 ISOnum -->
-<!ENTITY rsquo "’"> <!-- right single quotation mark,
- U+2019 ISOnum -->
-<!ENTITY sbquo "‚"> <!-- single low-9 quotation mark, U+201A NEW -->
-<!ENTITY ldquo "“"> <!-- left double quotation mark,
- U+201C ISOnum -->
-<!ENTITY rdquo "”"> <!-- right double quotation mark,
- U+201D ISOnum -->
-<!ENTITY bdquo "„"> <!-- double low-9 quotation mark, U+201E NEW -->
-<!ENTITY dagger "†"> <!-- dagger, U+2020 ISOpub -->
-<!ENTITY Dagger "‡"> <!-- double dagger, U+2021 ISOpub -->
-<!ENTITY permil "‰"> <!-- per mille sign, U+2030 ISOtech -->
-<!ENTITY lsaquo "‹"> <!-- single left-pointing angle quotation mark,
- U+2039 ISO proposed -->
-<!-- lsaquo is proposed but not yet ISO standardized -->
-<!ENTITY rsaquo "›"> <!-- single right-pointing angle quotation mark,
- U+203A ISO proposed -->
-<!-- rsaquo is proposed but not yet ISO standardized -->
-
-<!-- Currency Symbols -->
-<!ENTITY euro "€"> <!-- euro sign, U+20AC NEW -->
=====================================
src/doc/WWW/xhtml-symbol.ent deleted
=====================================
@@ -1,237 +0,0 @@
-<!-- Mathematical, Greek and Symbolic characters for XHTML -->
-
-<!-- Character entity set. Typical invocation:
- <!ENTITY % HTMLsymbol PUBLIC
- "-//W3C//ENTITIES Symbols for XHTML//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml-symbol.ent">
- %HTMLsymbol;
--->
-
-<!-- Portions (C) International Organization for Standardization 1986:
- Permission to copy in any form is granted for use with
- conforming SGML systems and applications as defined in
- ISO 8879, provided this notice is included in all copies.
--->
-
-<!-- Relevant ISO entity set is given unless names are newly introduced.
- New names (i.e., not in ISO 8879 list) do not clash with any
- existing ISO 8879 entity names. ISO 10646 character numbers
- are given for each character, in hex. values are decimal
- conversions of the ISO 10646 values and refer to the document
- character set. Names are Unicode names.
--->
-
-<!-- Latin Extended-B -->
-<!ENTITY fnof "ƒ"> <!-- latin small letter f with hook = function
- = florin, U+0192 ISOtech -->
-
-<!-- Greek -->
-<!ENTITY Alpha "Α"> <!-- greek capital letter alpha, U+0391 -->
-<!ENTITY Beta "Β"> <!-- greek capital letter beta, U+0392 -->
-<!ENTITY Gamma "Γ"> <!-- greek capital letter gamma,
- U+0393 ISOgrk3 -->
-<!ENTITY Delta "Δ"> <!-- greek capital letter delta,
- U+0394 ISOgrk3 -->
-<!ENTITY Epsilon "Ε"> <!-- greek capital letter epsilon, U+0395 -->
-<!ENTITY Zeta "Ζ"> <!-- greek capital letter zeta, U+0396 -->
-<!ENTITY Eta "Η"> <!-- greek capital letter eta, U+0397 -->
-<!ENTITY Theta "Θ"> <!-- greek capital letter theta,
- U+0398 ISOgrk3 -->
-<!ENTITY Iota "Ι"> <!-- greek capital letter iota, U+0399 -->
-<!ENTITY Kappa "Κ"> <!-- greek capital letter kappa, U+039A -->
-<!ENTITY Lambda "Λ"> <!-- greek capital letter lamda,
- U+039B ISOgrk3 -->
-<!ENTITY Mu "Μ"> <!-- greek capital letter mu, U+039C -->
-<!ENTITY Nu "Ν"> <!-- greek capital letter nu, U+039D -->
-<!ENTITY Xi "Ξ"> <!-- greek capital letter xi, U+039E ISOgrk3 -->
-<!ENTITY Omicron "Ο"> <!-- greek capital letter omicron, U+039F -->
-<!ENTITY Pi "Π"> <!-- greek capital letter pi, U+03A0 ISOgrk3 -->
-<!ENTITY Rho "Ρ"> <!-- greek capital letter rho, U+03A1 -->
-<!-- there is no Sigmaf, and no U+03A2 character either -->
-<!ENTITY Sigma "Σ"> <!-- greek capital letter sigma,
- U+03A3 ISOgrk3 -->
-<!ENTITY Tau "Τ"> <!-- greek capital letter tau, U+03A4 -->
-<!ENTITY Upsilon "Υ"> <!-- greek capital letter upsilon,
- U+03A5 ISOgrk3 -->
-<!ENTITY Phi "Φ"> <!-- greek capital letter phi,
- U+03A6 ISOgrk3 -->
-<!ENTITY Chi "Χ"> <!-- greek capital letter chi, U+03A7 -->
-<!ENTITY Psi "Ψ"> <!-- greek capital letter psi,
- U+03A8 ISOgrk3 -->
-<!ENTITY Omega "Ω"> <!-- greek capital letter omega,
- U+03A9 ISOgrk3 -->
-
-<!ENTITY alpha "α"> <!-- greek small letter alpha,
- U+03B1 ISOgrk3 -->
-<!ENTITY beta "β"> <!-- greek small letter beta, U+03B2 ISOgrk3 -->
-<!ENTITY gamma "γ"> <!-- greek small letter gamma,
- U+03B3 ISOgrk3 -->
-<!ENTITY delta "δ"> <!-- greek small letter delta,
- U+03B4 ISOgrk3 -->
-<!ENTITY epsilon "ε"> <!-- greek small letter epsilon,
- U+03B5 ISOgrk3 -->
-<!ENTITY zeta "ζ"> <!-- greek small letter zeta, U+03B6 ISOgrk3 -->
-<!ENTITY eta "η"> <!-- greek small letter eta, U+03B7 ISOgrk3 -->
-<!ENTITY theta "θ"> <!-- greek small letter theta,
- U+03B8 ISOgrk3 -->
-<!ENTITY iota "ι"> <!-- greek small letter iota, U+03B9 ISOgrk3 -->
-<!ENTITY kappa "κ"> <!-- greek small letter kappa,
- U+03BA ISOgrk3 -->
-<!ENTITY lambda "λ"> <!-- greek small letter lamda,
- U+03BB ISOgrk3 -->
-<!ENTITY mu "μ"> <!-- greek small letter mu, U+03BC ISOgrk3 -->
-<!ENTITY nu "ν"> <!-- greek small letter nu, U+03BD ISOgrk3 -->
-<!ENTITY xi "ξ"> <!-- greek small letter xi, U+03BE ISOgrk3 -->
-<!ENTITY omicron "ο"> <!-- greek small letter omicron, U+03BF NEW -->
-<!ENTITY pi "π"> <!-- greek small letter pi, U+03C0 ISOgrk3 -->
-<!ENTITY rho "ρ"> <!-- greek small letter rho, U+03C1 ISOgrk3 -->
-<!ENTITY sigmaf "ς"> <!-- greek small letter final sigma,
- U+03C2 ISOgrk3 -->
-<!ENTITY sigma "σ"> <!-- greek small letter sigma,
- U+03C3 ISOgrk3 -->
-<!ENTITY tau "τ"> <!-- greek small letter tau, U+03C4 ISOgrk3 -->
-<!ENTITY upsilon "υ"> <!-- greek small letter upsilon,
- U+03C5 ISOgrk3 -->
-<!ENTITY phi "φ"> <!-- greek small letter phi, U+03C6 ISOgrk3 -->
-<!ENTITY chi "χ"> <!-- greek small letter chi, U+03C7 ISOgrk3 -->
-<!ENTITY psi "ψ"> <!-- greek small letter psi, U+03C8 ISOgrk3 -->
-<!ENTITY omega "ω"> <!-- greek small letter omega,
- U+03C9 ISOgrk3 -->
-<!ENTITY thetasym "ϑ"> <!-- greek theta symbol,
- U+03D1 NEW -->
-<!ENTITY upsih "ϒ"> <!-- greek upsilon with hook symbol,
- U+03D2 NEW -->
-<!ENTITY piv "ϖ"> <!-- greek pi symbol, U+03D6 ISOgrk3 -->
-
-<!-- General Punctuation -->
-<!ENTITY bull "•"> <!-- bullet = black small circle,
- U+2022 ISOpub -->
-<!-- bullet is NOT the same as bullet operator, U+2219 -->
-<!ENTITY hellip "…"> <!-- horizontal ellipsis = three dot leader,
- U+2026 ISOpub -->
-<!ENTITY prime "′"> <!-- prime = minutes = feet, U+2032 ISOtech -->
-<!ENTITY Prime "″"> <!-- double prime = seconds = inches,
- U+2033 ISOtech -->
-<!ENTITY oline "‾"> <!-- overline = spacing overscore,
- U+203E NEW -->
-<!ENTITY frasl "⁄"> <!-- fraction slash, U+2044 NEW -->
-
-<!-- Letterlike Symbols -->
-<!ENTITY weierp "℘"> <!-- script capital P = power set
- = Weierstrass p, U+2118 ISOamso -->
-<!ENTITY image "ℑ"> <!-- black-letter capital I = imaginary part,
- U+2111 ISOamso -->
-<!ENTITY real "ℜ"> <!-- black-letter capital R = real part symbol,
- U+211C ISOamso -->
-<!ENTITY trade "™"> <!-- trade mark sign, U+2122 ISOnum -->
-<!ENTITY alefsym "ℵ"> <!-- alef symbol = first transfinite cardinal,
- U+2135 NEW -->
-<!-- alef symbol is NOT the same as hebrew letter alef,
- U+05D0 although the same glyph could be used to depict both characters -->
-
-<!-- Arrows -->
-<!ENTITY larr "←"> <!-- leftwards arrow, U+2190 ISOnum -->
-<!ENTITY uarr "↑"> <!-- upwards arrow, U+2191 ISOnum-->
-<!ENTITY rarr "→"> <!-- rightwards arrow, U+2192 ISOnum -->
-<!ENTITY darr "↓"> <!-- downwards arrow, U+2193 ISOnum -->
-<!ENTITY harr "↔"> <!-- left right arrow, U+2194 ISOamsa -->
-<!ENTITY crarr "↵"> <!-- downwards arrow with corner leftwards
- = carriage return, U+21B5 NEW -->
-<!ENTITY lArr "⇐"> <!-- leftwards double arrow, U+21D0 ISOtech -->
-<!-- Unicode does not say that lArr is the same as the 'is implied by' arrow
- but also does not have any other character for that function. So lArr can
- be used for 'is implied by' as ISOtech suggests -->
-<!ENTITY uArr "⇑"> <!-- upwards double arrow, U+21D1 ISOamsa -->
-<!ENTITY rArr "⇒"> <!-- rightwards double arrow,
- U+21D2 ISOtech -->
-<!-- Unicode does not say this is the 'implies' character but does not have
- another character with this function so rArr can be used for 'implies'
- as ISOtech suggests -->
-<!ENTITY dArr "⇓"> <!-- downwards double arrow, U+21D3 ISOamsa -->
-<!ENTITY hArr "⇔"> <!-- left right double arrow,
- U+21D4 ISOamsa -->
-
-<!-- Mathematical Operators -->
-<!ENTITY forall "∀"> <!-- for all, U+2200 ISOtech -->
-<!ENTITY part "∂"> <!-- partial differential, U+2202 ISOtech -->
-<!ENTITY exist "∃"> <!-- there exists, U+2203 ISOtech -->
-<!ENTITY empty "∅"> <!-- empty set = null set, U+2205 ISOamso -->
-<!ENTITY nabla "∇"> <!-- nabla = backward difference,
- U+2207 ISOtech -->
-<!ENTITY isin "∈"> <!-- element of, U+2208 ISOtech -->
-<!ENTITY notin "∉"> <!-- not an element of, U+2209 ISOtech -->
-<!ENTITY ni "∋"> <!-- contains as member, U+220B ISOtech -->
-<!ENTITY prod "∏"> <!-- n-ary product = product sign,
- U+220F ISOamsb -->
-<!-- prod is NOT the same character as U+03A0 'greek capital letter pi' though
- the same glyph might be used for both -->
-<!ENTITY sum "∑"> <!-- n-ary summation, U+2211 ISOamsb -->
-<!-- sum is NOT the same character as U+03A3 'greek capital letter sigma'
- though the same glyph might be used for both -->
-<!ENTITY minus "−"> <!-- minus sign, U+2212 ISOtech -->
-<!ENTITY lowast "∗"> <!-- asterisk operator, U+2217 ISOtech -->
-<!ENTITY radic "√"> <!-- square root = radical sign,
- U+221A ISOtech -->
-<!ENTITY prop "∝"> <!-- proportional to, U+221D ISOtech -->
-<!ENTITY infin "∞"> <!-- infinity, U+221E ISOtech -->
-<!ENTITY ang "∠"> <!-- angle, U+2220 ISOamso -->
-<!ENTITY and "∧"> <!-- logical and = wedge, U+2227 ISOtech -->
-<!ENTITY or "∨"> <!-- logical or = vee, U+2228 ISOtech -->
-<!ENTITY cap "∩"> <!-- intersection = cap, U+2229 ISOtech -->
-<!ENTITY cup "∪"> <!-- union = cup, U+222A ISOtech -->
-<!ENTITY int "∫"> <!-- integral, U+222B ISOtech -->
-<!ENTITY there4 "∴"> <!-- therefore, U+2234 ISOtech -->
-<!ENTITY sim "∼"> <!-- tilde operator = varies with = similar to,
- U+223C ISOtech -->
-<!-- tilde operator is NOT the same character as the tilde, U+007E,
- although the same glyph might be used to represent both -->
-<!ENTITY cong "≅"> <!-- approximately equal to, U+2245 ISOtech -->
-<!ENTITY asymp "≈"> <!-- almost equal to = asymptotic to,
- U+2248 ISOamsr -->
-<!ENTITY ne "≠"> <!-- not equal to, U+2260 ISOtech -->
-<!ENTITY equiv "≡"> <!-- identical to, U+2261 ISOtech -->
-<!ENTITY le "≤"> <!-- less-than or equal to, U+2264 ISOtech -->
-<!ENTITY ge "≥"> <!-- greater-than or equal to,
- U+2265 ISOtech -->
-<!ENTITY sub "⊂"> <!-- subset of, U+2282 ISOtech -->
-<!ENTITY sup "⊃"> <!-- superset of, U+2283 ISOtech -->
-<!ENTITY nsub "⊄"> <!-- not a subset of, U+2284 ISOamsn -->
-<!ENTITY sube "⊆"> <!-- subset of or equal to, U+2286 ISOtech -->
-<!ENTITY supe "⊇"> <!-- superset of or equal to,
- U+2287 ISOtech -->
-<!ENTITY oplus "⊕"> <!-- circled plus = direct sum,
- U+2295 ISOamsb -->
-<!ENTITY otimes "⊗"> <!-- circled times = vector product,
- U+2297 ISOamsb -->
-<!ENTITY perp "⊥"> <!-- up tack = orthogonal to = perpendicular,
- U+22A5 ISOtech -->
-<!ENTITY sdot "⋅"> <!-- dot operator, U+22C5 ISOamsb -->
-<!-- dot operator is NOT the same character as U+00B7 middle dot -->
-
-<!-- Miscellaneous Technical -->
-<!ENTITY lceil "⌈"> <!-- left ceiling = APL upstile,
- U+2308 ISOamsc -->
-<!ENTITY rceil "⌉"> <!-- right ceiling, U+2309 ISOamsc -->
-<!ENTITY lfloor "⌊"> <!-- left floor = APL downstile,
- U+230A ISOamsc -->
-<!ENTITY rfloor "⌋"> <!-- right floor, U+230B ISOamsc -->
-<!ENTITY lang "〈"> <!-- left-pointing angle bracket = bra,
- U+2329 ISOtech -->
-<!-- lang is NOT the same character as U+003C 'less than sign'
- or U+2039 'single left-pointing angle quotation mark' -->
-<!ENTITY rang "〉"> <!-- right-pointing angle bracket = ket,
- U+232A ISOtech -->
-<!-- rang is NOT the same character as U+003E 'greater than sign'
- or U+203A 'single right-pointing angle quotation mark' -->
-
-<!-- Geometric Shapes -->
-<!ENTITY loz "◊"> <!-- lozenge, U+25CA ISOpub -->
-
-<!-- Miscellaneous Symbols -->
-<!ENTITY spades "♠"> <!-- black spade suit, U+2660 ISOpub -->
-<!-- black here seems to mean filled as opposed to hollow -->
-<!ENTITY clubs "♣"> <!-- black club suit = shamrock,
- U+2663 ISOpub -->
-<!ENTITY hearts "♥"> <!-- black heart suit = valentine,
- U+2665 ISOpub -->
-<!ENTITY diams "♦"> <!-- black diamond suit, U+2666 ISOpub -->
=====================================
src/doc/WWW/xhtml1-transitional.dtd deleted
=====================================
@@ -1,1201 +0,0 @@
-<!--
- Extensible HTML version 1.0 Transitional DTD
-
- This is the same as HTML 4 Transitional except for
- changes due to the differences between XML and SGML.
-
- Namespace = http://www.w3.org/1999/xhtml
-
- For further information, see: http://www.w3.org/TR/xhtml1
-
- Copyright (c) 1998-2002 W3C (MIT, INRIA, Keio),
- All Rights Reserved.
-
- This DTD module is identified by the PUBLIC and SYSTEM identifiers:
-
- PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
- SYSTEM "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"
-
- $Revision: 1.2 $
- $Date: 2002/08/01 18:37:55 $
-
--->
-
-<!--================ Character mnemonic entities =========================-->
-
-<!ENTITY % HTMLlat1 PUBLIC
- "-//W3C//ENTITIES Latin 1 for XHTML//EN"
- "xhtml-lat1.ent">
-%HTMLlat1;
-
-<!ENTITY % HTMLsymbol PUBLIC
- "-//W3C//ENTITIES Symbols for XHTML//EN"
- "xhtml-symbol.ent">
-%HTMLsymbol;
-
-<!ENTITY % HTMLspecial PUBLIC
- "-//W3C//ENTITIES Special for XHTML//EN"
- "xhtml-special.ent">
-%HTMLspecial;
-
-<!--================== Imported Names ====================================-->
-
-<!ENTITY % ContentType "CDATA">
- <!-- media type, as per [RFC2045] -->
-
-<!ENTITY % ContentTypes "CDATA">
- <!-- comma-separated list of media types, as per [RFC2045] -->
-
-<!ENTITY % Charset "CDATA">
- <!-- a character encoding, as per [RFC2045] -->
-
-<!ENTITY % Charsets "CDATA">
- <!-- a space separated list of character encodings, as per [RFC2045] -->
-
-<!ENTITY % LanguageCode "NMTOKEN">
- <!-- a language code, as per [RFC3066] -->
-
-<!ENTITY % Character "CDATA">
- <!-- a single character, as per section 2.2 of [XML] -->
-
-<!ENTITY % Number "CDATA">
- <!-- one or more digits -->
-
-<!ENTITY % LinkTypes "CDATA">
- <!-- space-separated list of link types -->
-
-<!ENTITY % MediaDesc "CDATA">
- <!-- single or comma-separated list of media descriptors -->
-
-<!ENTITY % URI "CDATA">
- <!-- a Uniform Resource Identifier, see [RFC2396] -->
-
-<!ENTITY % UriList "CDATA">
- <!-- a space separated list of Uniform Resource Identifiers -->
-
-<!ENTITY % Datetime "CDATA">
- <!-- date and time information. ISO date format -->
-
-<!ENTITY % Script "CDATA">
- <!-- script expression -->
-
-<!ENTITY % StyleSheet "CDATA">
- <!-- style sheet data -->
-
-<!ENTITY % Text "CDATA">
- <!-- used for titles etc. -->
-
-<!ENTITY % FrameTarget "NMTOKEN">
- <!-- render in this frame -->
-
-<!ENTITY % Length "CDATA">
- <!-- nn for pixels or nn% for percentage length -->
-
-<!ENTITY % MultiLength "CDATA">
- <!-- pixel, percentage, or relative -->
-
-<!ENTITY % Pixels "CDATA">
- <!-- integer representing length in pixels -->
-
-<!-- these are used for image maps -->
-
-<!ENTITY % Shape "(rect|circle|poly|default)">
-
-<!ENTITY % Coords "CDATA">
- <!-- comma separated list of lengths -->
-
-<!-- used for object, applet, img, input and iframe -->
-<!ENTITY % ImgAlign "(top|middle|bottom|left|right)">
-
-<!-- a color using sRGB: #RRGGBB as Hex values -->
-<!ENTITY % Color "CDATA">
-
-<!-- There are also 16 widely known color names with their sRGB values:
-
- Black = #000000 Green = #008000
- Silver = #C0C0C0 Lime = #00FF00
- Gray = #808080 Olive = #808000
- White = #FFFFFF Yellow = #FFFF00
- Maroon = #800000 Navy = #000080
- Red = #FF0000 Blue = #0000FF
- Purple = #800080 Teal = #008080
- Fuchsia= #FF00FF Aqua = #00FFFF
--->
-
-<!--=================== Generic Attributes ===============================-->
-
-<!-- core attributes common to most elements
- id document-wide unique id
- class space separated list of classes
- style associated style info
- title advisory title/amplification
--->
-<!ENTITY % coreattrs
- "id ID #IMPLIED
- class CDATA #IMPLIED
- style %StyleSheet; #IMPLIED
- title %Text; #IMPLIED"
- >
-
-<!-- internationalization attributes
- lang language code (backwards compatible)
- xml:lang language code (as per XML 1.0 spec)
- dir direction for weak/neutral text
--->
-<!ENTITY % i18n
- "lang %LanguageCode; #IMPLIED
- xml:lang %LanguageCode; #IMPLIED
- dir (ltr|rtl) #IMPLIED"
- >
-
-<!-- attributes for common UI events
- onclick a pointer button was clicked
- ondblclick a pointer button was double clicked
- onmousedown a pointer button was pressed down
- onmouseup a pointer button was released
- onmousemove a pointer was moved onto the element
- onmouseout a pointer was moved away from the element
- onkeypress a key was pressed and released
- onkeydown a key was pressed down
- onkeyup a key was released
--->
-<!ENTITY % events
- "onclick %Script; #IMPLIED
- ondblclick %Script; #IMPLIED
- onmousedown %Script; #IMPLIED
- onmouseup %Script; #IMPLIED
- onmouseover %Script; #IMPLIED
- onmousemove %Script; #IMPLIED
- onmouseout %Script; #IMPLIED
- onkeypress %Script; #IMPLIED
- onkeydown %Script; #IMPLIED
- onkeyup %Script; #IMPLIED"
- >
-
-<!-- attributes for elements that can get the focus
- accesskey accessibility key character
- tabindex position in tabbing order
- onfocus the element got the focus
- onblur the element lost the focus
--->
-<!ENTITY % focus
- "accesskey %Character; #IMPLIED
- tabindex %Number; #IMPLIED
- onfocus %Script; #IMPLIED
- onblur %Script; #IMPLIED"
- >
-
-<!ENTITY % attrs "%coreattrs; %i18n; %events;">
-
-<!-- text alignment for p, div, h1-h6. The default is
- align="left" for ltr headings, "right" for rtl -->
-
-<!ENTITY % TextAlign "align (left|center|right|justify) #IMPLIED">
-
-<!--=================== Text Elements ====================================-->
-
-<!ENTITY % special.extra
- "object | applet | img | map | iframe">
-
-<!ENTITY % special.basic
- "br | span | bdo">
-
-<!ENTITY % special
- "%special.basic; | %special.extra;">
-
-<!ENTITY % fontstyle.extra "big | small | font | basefont">
-
-<!ENTITY % fontstyle.basic "tt | i | b | u
- | s | strike ">
-
-<!ENTITY % fontstyle "%fontstyle.basic; | %fontstyle.extra;">
-
-<!ENTITY % phrase.extra "sub | sup">
-<!ENTITY % phrase.basic "em | strong | dfn | code | q |
- samp | kbd | var | cite | abbr | acronym">
-
-<!ENTITY % phrase "%phrase.basic; | %phrase.extra;">
-
-<!ENTITY % inline.forms "input | select | textarea | label | button">
-
-<!-- these can occur at block or inline level -->
-<!ENTITY % misc.inline "ins | del | script">
-
-<!-- these can only occur at block level -->
-<!ENTITY % misc "noscript | %misc.inline;">
-
-<!ENTITY % inline "a | %special; | %fontstyle; | %phrase; | %inline.forms;">
-
-<!-- %Inline; covers inline or "text-level" elements -->
-<!ENTITY % Inline "(#PCDATA | %inline; | %misc.inline;)*">
-
-<!--================== Block level elements ==============================-->
-
-<!ENTITY % heading "h1|h2|h3|h4|h5|h6">
-<!ENTITY % lists "ul | ol | dl | menu | dir">
-<!ENTITY % blocktext "pre | hr | blockquote | address | center | noframes">
-
-<!ENTITY % block
- "p | %heading; | div | %lists; | %blocktext; | isindex |fieldset | table">
-
-<!-- %Flow; mixes block and inline and is used for list items etc. -->
-<!ENTITY % Flow "(#PCDATA | %block; | form | %inline; | %misc;)*">
-
-<!--================== Content models for exclusions =====================-->
-
-<!-- a elements use %Inline; excluding a -->
-
-<!ENTITY % a.content
- "(#PCDATA | %special; | %fontstyle; | %phrase; | %inline.forms; | %misc.inline;)*">
-
-<!-- pre uses %Inline excluding img, object, applet, big, small,
- font, or basefont -->
-
-<!ENTITY % pre.content
- "(#PCDATA | a | %special.basic; | %fontstyle.basic; | %phrase.basic; |
- %inline.forms; | %misc.inline;)*">
-
-<!-- form uses %Flow; excluding form -->
-
-<!ENTITY % form.content "(#PCDATA | %block; | %inline; | %misc;)*">
-
-<!-- button uses %Flow; but excludes a, form, form controls, iframe -->
-
-<!ENTITY % button.content
- "(#PCDATA | p | %heading; | div | %lists; | %blocktext; |
- table | br | span | bdo | object | applet | img | map |
- %fontstyle; | %phrase; | %misc;)*">
-
-<!--================ Document Structure ==================================-->
-
-<!-- the namespace URI designates the document profile -->
-
-<!ELEMENT html (head, body)>
-<!ATTLIST html
- %i18n;
- id ID #IMPLIED
- xmlns %URI; #FIXED 'http://www.w3.org/1999/xhtml'
- >
-
-<!--================ Document Head =======================================-->
-
-<!ENTITY % head.misc "(script|style|meta|link|object|isindex)*">
-
-<!-- content model is %head.misc; combined with a single
- title and an optional base element in any order -->
-
-<!ELEMENT head (%head.misc;,
- ((title, %head.misc;, (base, %head.misc;)?) |
- (base, %head.misc;, (title, %head.misc;))))>
-
-<!ATTLIST head
- %i18n;
- id ID #IMPLIED
- profile %URI; #IMPLIED
- >
-
-<!-- The title element is not considered part of the flow of text.
- It should be displayed, for example as the page header or
- window title. Exactly one title is required per document.
- -->
-<!ELEMENT title (#PCDATA)>
-<!ATTLIST title
- %i18n;
- id ID #IMPLIED
- >
-
-<!-- document base URI -->
-
-<!ELEMENT base EMPTY>
-<!ATTLIST base
- id ID #IMPLIED
- href %URI; #IMPLIED
- target %FrameTarget; #IMPLIED
- >
-
-<!-- generic metainformation -->
-<!ELEMENT meta EMPTY>
-<!ATTLIST meta
- %i18n;
- id ID #IMPLIED
- http-equiv CDATA #IMPLIED
- name CDATA #IMPLIED
- content CDATA #REQUIRED
- scheme CDATA #IMPLIED
- >
-
-<!--
- Relationship values can be used in principle:
-
- a) for document specific toolbars/menus when used
- with the link element in document head e.g.
- start, contents, previous, next, index, end, help
- b) to link to a separate style sheet (rel="stylesheet")
- c) to make a link to a script (rel="script")
- d) by stylesheets to control how collections of
- html nodes are rendered into printed documents
- e) to make a link to a printable version of this document
- e.g. a PostScript or PDF version (rel="alternate" media="print")
--->
-
-<!ELEMENT link EMPTY>
-<!ATTLIST link
- %attrs;
- charset %Charset; #IMPLIED
- href %URI; #IMPLIED
- hreflang %LanguageCode; #IMPLIED
- type %ContentType; #IMPLIED
- rel %LinkTypes; #IMPLIED
- rev %LinkTypes; #IMPLIED
- media %MediaDesc; #IMPLIED
- target %FrameTarget; #IMPLIED
- >
-
-<!-- style info, which may include CDATA sections -->
-<!ELEMENT style (#PCDATA)>
-<!ATTLIST style
- %i18n;
- id ID #IMPLIED
- type %ContentType; #REQUIRED
- media %MediaDesc; #IMPLIED
- title %Text; #IMPLIED
- xml:space (preserve) #FIXED 'preserve'
- >
-
-<!-- script statements, which may include CDATA sections -->
-<!ELEMENT script (#PCDATA)>
-<!ATTLIST script
- id ID #IMPLIED
- charset %Charset; #IMPLIED
- type %ContentType; #REQUIRED
- language CDATA #IMPLIED
- src %URI; #IMPLIED
- defer (defer) #IMPLIED
- xml:space (preserve) #FIXED 'preserve'
- >
-
-<!-- alternate content container for non script-based rendering -->
-
-<!ELEMENT noscript %Flow;>
-<!ATTLIST noscript
- %attrs;
- >
-
-<!--======================= Frames =======================================-->
-
-<!-- inline subwindow -->
-
-<!ELEMENT iframe %Flow;>
-<!ATTLIST iframe
- %coreattrs;
- longdesc %URI; #IMPLIED
- name NMTOKEN #IMPLIED
- src %URI; #IMPLIED
- frameborder (1|0) "1"
- marginwidth %Pixels; #IMPLIED
- marginheight %Pixels; #IMPLIED
- scrolling (yes|no|auto) "auto"
- align %ImgAlign; #IMPLIED
- height %Length; #IMPLIED
- width %Length; #IMPLIED
- >
-
-<!-- alternate content container for non frame-based rendering -->
-
-<!ELEMENT noframes %Flow;>
-<!ATTLIST noframes
- %attrs;
- >
-
-<!--=================== Document Body ====================================-->
-
-<!ELEMENT body %Flow;>
-<!ATTLIST body
- %attrs;
- onload %Script; #IMPLIED
- onunload %Script; #IMPLIED
- background %URI; #IMPLIED
- bgcolor %Color; #IMPLIED
- text %Color; #IMPLIED
- link %Color; #IMPLIED
- vlink %Color; #IMPLIED
- alink %Color; #IMPLIED
- >
-
-<!ELEMENT div %Flow;> <!-- generic language/style container -->
-<!ATTLIST div
- %attrs;
- %TextAlign;
- >
-
-<!--=================== Paragraphs =======================================-->
-
-<!ELEMENT p %Inline;>
-<!ATTLIST p
- %attrs;
- %TextAlign;
- >
-
-<!--=================== Headings =========================================-->
-
-<!--
- There are six levels of headings from h1 (the most important)
- to h6 (the least important).
--->
-
-<!ELEMENT h1 %Inline;>
-<!ATTLIST h1
- %attrs;
- %TextAlign;
- >
-
-<!ELEMENT h2 %Inline;>
-<!ATTLIST h2
- %attrs;
- %TextAlign;
- >
-
-<!ELEMENT h3 %Inline;>
-<!ATTLIST h3
- %attrs;
- %TextAlign;
- >
-
-<!ELEMENT h4 %Inline;>
-<!ATTLIST h4
- %attrs;
- %TextAlign;
- >
-
-<!ELEMENT h5 %Inline;>
-<!ATTLIST h5
- %attrs;
- %TextAlign;
- >
-
-<!ELEMENT h6 %Inline;>
-<!ATTLIST h6
- %attrs;
- %TextAlign;
- >
-
-<!--=================== Lists ============================================-->
-
-<!-- Unordered list bullet styles -->
-
-<!ENTITY % ULStyle "(disc|square|circle)">
-
-<!-- Unordered list -->
-
-<!ELEMENT ul (li)+>
-<!ATTLIST ul
- %attrs;
- type %ULStyle; #IMPLIED
- compact (compact) #IMPLIED
- >
-
-<!-- Ordered list numbering style
-
- 1 arabic numbers 1, 2, 3, ...
- a lower alpha a, b, c, ...
- A upper alpha A, B, C, ...
- i lower roman i, ii, iii, ...
- I upper roman I, II, III, ...
-
- The style is applied to the sequence number which by default
- is reset to 1 for the first list item in an ordered list.
--->
-<!ENTITY % OLStyle "CDATA">
-
-<!-- Ordered (numbered) list -->
-
-<!ELEMENT ol (li)+>
-<!ATTLIST ol
- %attrs;
- type %OLStyle; #IMPLIED
- compact (compact) #IMPLIED
- start %Number; #IMPLIED
- >
-
-<!-- single column list (DEPRECATED) -->
-<!ELEMENT menu (li)+>
-<!ATTLIST menu
- %attrs;
- compact (compact) #IMPLIED
- >
-
-<!-- multiple column list (DEPRECATED) -->
-<!ELEMENT dir (li)+>
-<!ATTLIST dir
- %attrs;
- compact (compact) #IMPLIED
- >
-
-<!-- LIStyle is constrained to: "(%ULStyle;|%OLStyle;)" -->
-<!ENTITY % LIStyle "CDATA">
-
-<!-- list item -->
-
-<!ELEMENT li %Flow;>
-<!ATTLIST li
- %attrs;
- type %LIStyle; #IMPLIED
- value %Number; #IMPLIED
- >
-
-<!-- definition lists - dt for term, dd for its definition -->
-
-<!ELEMENT dl (dt|dd)+>
-<!ATTLIST dl
- %attrs;
- compact (compact) #IMPLIED
- >
-
-<!ELEMENT dt %Inline;>
-<!ATTLIST dt
- %attrs;
- >
-
-<!ELEMENT dd %Flow;>
-<!ATTLIST dd
- %attrs;
- >
-
-<!--=================== Address ==========================================-->
-
-<!-- information on author -->
-
-<!ELEMENT address (#PCDATA | %inline; | %misc.inline; | p)*>
-<!ATTLIST address
- %attrs;
- >
-
-<!--=================== Horizontal Rule ==================================-->
-
-<!ELEMENT hr EMPTY>
-<!ATTLIST hr
- %attrs;
- align (left|center|right) #IMPLIED
- noshade (noshade) #IMPLIED
- size %Pixels; #IMPLIED
- width %Length; #IMPLIED
- >
-
-<!--=================== Preformatted Text ================================-->
-
-<!-- content is %Inline; excluding
- "img|object|applet|big|small|sub|sup|font|basefont" -->
-
-<!ELEMENT pre %pre.content;>
-<!ATTLIST pre
- %attrs;
- width %Number; #IMPLIED
- xml:space (preserve) #FIXED 'preserve'
- >
-
-<!--=================== Block-like Quotes ================================-->
-
-<!ELEMENT blockquote %Flow;>
-<!ATTLIST blockquote
- %attrs;
- cite %URI; #IMPLIED
- >
-
-<!--=================== Text alignment ===================================-->
-
-<!-- center content -->
-<!ELEMENT center %Flow;>
-<!ATTLIST center
- %attrs;
- >
-
-<!--=================== Inserted/Deleted Text ============================-->
-
-<!--
- ins/del are allowed in block and inline content, but its
- inappropriate to include block content within an ins element
- occurring in inline content.
--->
-<!ELEMENT ins %Flow;>
-<!ATTLIST ins
- %attrs;
- cite %URI; #IMPLIED
- datetime %Datetime; #IMPLIED
- >
-
-<!ELEMENT del %Flow;>
-<!ATTLIST del
- %attrs;
- cite %URI; #IMPLIED
- datetime %Datetime; #IMPLIED
- >
-
-<!--================== The Anchor Element ================================-->
-
-<!-- content is %Inline; except that anchors shouldn't be nested -->
-
-<!ELEMENT a %a.content;>
-<!ATTLIST a
- %attrs;
- %focus;
- charset %Charset; #IMPLIED
- type %ContentType; #IMPLIED
- name NMTOKEN #IMPLIED
- href %URI; #IMPLIED
- hreflang %LanguageCode; #IMPLIED
- rel %LinkTypes; #IMPLIED
- rev %LinkTypes; #IMPLIED
- shape %Shape; "rect"
- coords %Coords; #IMPLIED
- target %FrameTarget; #IMPLIED
- >
-
-<!--===================== Inline Elements ================================-->
-
-<!ELEMENT span %Inline;> <!-- generic language/style container -->
-<!ATTLIST span
- %attrs;
- >
-
-<!ELEMENT bdo %Inline;> <!-- I18N BiDi over-ride -->
-<!ATTLIST bdo
- %coreattrs;
- %events;
- lang %LanguageCode; #IMPLIED
- xml:lang %LanguageCode; #IMPLIED
- dir (ltr|rtl) #REQUIRED
- >
-
-<!ELEMENT br EMPTY> <!-- forced line break -->
-<!ATTLIST br
- %coreattrs;
- clear (left|all|right|none) "none"
- >
-
-<!ELEMENT em %Inline;> <!-- emphasis -->
-<!ATTLIST em %attrs;>
-
-<!ELEMENT strong %Inline;> <!-- strong emphasis -->
-<!ATTLIST strong %attrs;>
-
-<!ELEMENT dfn %Inline;> <!-- definitional -->
-<!ATTLIST dfn %attrs;>
-
-<!ELEMENT code %Inline;> <!-- program code -->
-<!ATTLIST code %attrs;>
-
-<!ELEMENT samp %Inline;> <!-- sample -->
-<!ATTLIST samp %attrs;>
-
-<!ELEMENT kbd %Inline;> <!-- something user would type -->
-<!ATTLIST kbd %attrs;>
-
-<!ELEMENT var %Inline;> <!-- variable -->
-<!ATTLIST var %attrs;>
-
-<!ELEMENT cite %Inline;> <!-- citation -->
-<!ATTLIST cite %attrs;>
-
-<!ELEMENT abbr %Inline;> <!-- abbreviation -->
-<!ATTLIST abbr %attrs;>
-
-<!ELEMENT acronym %Inline;> <!-- acronym -->
-<!ATTLIST acronym %attrs;>
-
-<!ELEMENT q %Inline;> <!-- inlined quote -->
-<!ATTLIST q
- %attrs;
- cite %URI; #IMPLIED
- >
-
-<!ELEMENT sub %Inline;> <!-- subscript -->
-<!ATTLIST sub %attrs;>
-
-<!ELEMENT sup %Inline;> <!-- superscript -->
-<!ATTLIST sup %attrs;>
-
-<!ELEMENT tt %Inline;> <!-- fixed pitch font -->
-<!ATTLIST tt %attrs;>
-
-<!ELEMENT i %Inline;> <!-- italic font -->
-<!ATTLIST i %attrs;>
-
-<!ELEMENT b %Inline;> <!-- bold font -->
-<!ATTLIST b %attrs;>
-
-<!ELEMENT big %Inline;> <!-- bigger font -->
-<!ATTLIST big %attrs;>
-
-<!ELEMENT small %Inline;> <!-- smaller font -->
-<!ATTLIST small %attrs;>
-
-<!ELEMENT u %Inline;> <!-- underline -->
-<!ATTLIST u %attrs;>
-
-<!ELEMENT s %Inline;> <!-- strike-through -->
-<!ATTLIST s %attrs;>
-
-<!ELEMENT strike %Inline;> <!-- strike-through -->
-<!ATTLIST strike %attrs;>
-
-<!ELEMENT basefont EMPTY> <!-- base font size -->
-<!ATTLIST basefont
- id ID #IMPLIED
- size CDATA #REQUIRED
- color %Color; #IMPLIED
- face CDATA #IMPLIED
- >
-
-<!ELEMENT font %Inline;> <!-- local change to font -->
-<!ATTLIST font
- %coreattrs;
- %i18n;
- size CDATA #IMPLIED
- color %Color; #IMPLIED
- face CDATA #IMPLIED
- >
-
-<!--==================== Object ======================================-->
-<!--
- object is used to embed objects as part of HTML pages.
- param elements should precede other content. Parameters
- can also be expressed as attribute/value pairs on the
- object element itself when brevity is desired.
--->
-
-<!ELEMENT object (#PCDATA | param | %block; | form | %inline; | %misc;)*>
-<!ATTLIST object
- %attrs;
- declare (declare) #IMPLIED
- classid %URI; #IMPLIED
- codebase %URI; #IMPLIED
- data %URI; #IMPLIED
- type %ContentType; #IMPLIED
- codetype %ContentType; #IMPLIED
- archive %UriList; #IMPLIED
- standby %Text; #IMPLIED
- height %Length; #IMPLIED
- width %Length; #IMPLIED
- usemap %URI; #IMPLIED
- name NMTOKEN #IMPLIED
- tabindex %Number; #IMPLIED
- align %ImgAlign; #IMPLIED
- border %Pixels; #IMPLIED
- hspace %Pixels; #IMPLIED
- vspace %Pixels; #IMPLIED
- >
-
-<!--
- param is used to supply a named property value.
- In XML it would seem natural to follow RDF and support an
- abbreviated syntax where the param elements are replaced
- by attribute value pairs on the object start tag.
--->
-<!ELEMENT param EMPTY>
-<!ATTLIST param
- id ID #IMPLIED
- name CDATA #REQUIRED
- value CDATA #IMPLIED
- valuetype (data|ref|object) "data"
- type %ContentType; #IMPLIED
- >
-
-<!--=================== Java applet ==================================-->
-<!--
- One of code or object attributes must be present.
- Place param elements before other content.
--->
-<!ELEMENT applet (#PCDATA | param | %block; | form | %inline; | %misc;)*>
-<!ATTLIST applet
- %coreattrs;
- codebase %URI; #IMPLIED
- archive CDATA #IMPLIED
- code CDATA #IMPLIED
- object CDATA #IMPLIED
- alt %Text; #IMPLIED
- name NMTOKEN #IMPLIED
- width %Length; #REQUIRED
- height %Length; #REQUIRED
- align %ImgAlign; #IMPLIED
- hspace %Pixels; #IMPLIED
- vspace %Pixels; #IMPLIED
- >
-
-<!--=================== Images ===========================================-->
-
-<!--
- To avoid accessibility problems for people who aren't
- able to see the image, you should provide a text
- description using the alt and longdesc attributes.
- In addition, avoid the use of server-side image maps.
--->
-
-<!ELEMENT img EMPTY>
-<!ATTLIST img
- %attrs;
- src %URI; #REQUIRED
- alt %Text; #REQUIRED
- name NMTOKEN #IMPLIED
- longdesc %URI; #IMPLIED
- height %Length; #IMPLIED
- width %Length; #IMPLIED
- usemap %URI; #IMPLIED
- ismap (ismap) #IMPLIED
- align %ImgAlign; #IMPLIED
- border %Length; #IMPLIED
- hspace %Pixels; #IMPLIED
- vspace %Pixels; #IMPLIED
- >
-
-<!-- usemap points to a map element which may be in this document
- or an external document, although the latter is not widely supported -->
-
-<!--================== Client-side image maps ============================-->
-
-<!-- These can be placed in the same document or grouped in a
- separate document although this isn't yet widely supported -->
-
-<!ELEMENT map ((%block; | form | %misc;)+ | area+)>
-<!ATTLIST map
- %i18n;
- %events;
- id ID #REQUIRED
- class CDATA #IMPLIED
- style %StyleSheet; #IMPLIED
- title %Text; #IMPLIED
- name CDATA #IMPLIED
- >
-
-<!ELEMENT area EMPTY>
-<!ATTLIST area
- %attrs;
- %focus;
- shape %Shape; "rect"
- coords %Coords; #IMPLIED
- href %URI; #IMPLIED
- nohref (nohref) #IMPLIED
- alt %Text; #REQUIRED
- target %FrameTarget; #IMPLIED
- >
-
-<!--================ Forms ===============================================-->
-
-<!ELEMENT form %form.content;> <!-- forms shouldn't be nested -->
-
-<!ATTLIST form
- %attrs;
- action %URI; #REQUIRED
- method (get|post) "get"
- name NMTOKEN #IMPLIED
- enctype %ContentType; "application/x-www-form-urlencoded"
- onsubmit %Script; #IMPLIED
- onreset %Script; #IMPLIED
- accept %ContentTypes; #IMPLIED
- accept-charset %Charsets; #IMPLIED
- target %FrameTarget; #IMPLIED
- >
-
-<!--
- Each label must not contain more than ONE field
- Label elements shouldn't be nested.
--->
-<!ELEMENT label %Inline;>
-<!ATTLIST label
- %attrs;
- for IDREF #IMPLIED
- accesskey %Character; #IMPLIED
- onfocus %Script; #IMPLIED
- onblur %Script; #IMPLIED
- >
-
-<!ENTITY % InputType
- "(text | password | checkbox |
- radio | submit | reset |
- file | hidden | image | button)"
- >
-
-<!-- the name attribute is required for all but submit & reset -->
-
-<!ELEMENT input EMPTY> <!-- form control -->
-<!ATTLIST input
- %attrs;
- %focus;
- type %InputType; "text"
- name CDATA #IMPLIED
- value CDATA #IMPLIED
- checked (checked) #IMPLIED
- disabled (disabled) #IMPLIED
- readonly (readonly) #IMPLIED
- size CDATA #IMPLIED
- maxlength %Number; #IMPLIED
- src %URI; #IMPLIED
- alt CDATA #IMPLIED
- usemap %URI; #IMPLIED
- onselect %Script; #IMPLIED
- onchange %Script; #IMPLIED
- accept %ContentTypes; #IMPLIED
- align %ImgAlign; #IMPLIED
- >
-
-<!ELEMENT select (optgroup|option)+> <!-- option selector -->
-<!ATTLIST select
- %attrs;
- name CDATA #IMPLIED
- size %Number; #IMPLIED
- multiple (multiple) #IMPLIED
- disabled (disabled) #IMPLIED
- tabindex %Number; #IMPLIED
- onfocus %Script; #IMPLIED
- onblur %Script; #IMPLIED
- onchange %Script; #IMPLIED
- >
-
-<!ELEMENT optgroup (option)+> <!-- option group -->
-<!ATTLIST optgroup
- %attrs;
- disabled (disabled) #IMPLIED
- label %Text; #REQUIRED
- >
-
-<!ELEMENT option (#PCDATA)> <!-- selectable choice -->
-<!ATTLIST option
- %attrs;
- selected (selected) #IMPLIED
- disabled (disabled) #IMPLIED
- label %Text; #IMPLIED
- value CDATA #IMPLIED
- >
-
-<!ELEMENT textarea (#PCDATA)> <!-- multi-line text field -->
-<!ATTLIST textarea
- %attrs;
- %focus;
- name CDATA #IMPLIED
- rows %Number; #REQUIRED
- cols %Number; #REQUIRED
- disabled (disabled) #IMPLIED
- readonly (readonly) #IMPLIED
- onselect %Script; #IMPLIED
- onchange %Script; #IMPLIED
- >
-
-<!--
- The fieldset element is used to group form fields.
- Only one legend element should occur in the content
- and if present should only be preceded by whitespace.
--->
-<!ELEMENT fieldset (#PCDATA | legend | %block; | form | %inline; | %misc;)*>
-<!ATTLIST fieldset
- %attrs;
- >
-
-<!ENTITY % LAlign "(top|bottom|left|right)">
-
-<!ELEMENT legend %Inline;> <!-- fieldset label -->
-<!ATTLIST legend
- %attrs;
- accesskey %Character; #IMPLIED
- align %LAlign; #IMPLIED
- >
-
-<!--
- Content is %Flow; excluding a, form, form controls, iframe
--->
-<!ELEMENT button %button.content;> <!-- push button -->
-<!ATTLIST button
- %attrs;
- %focus;
- name CDATA #IMPLIED
- value CDATA #IMPLIED
- type (button|submit|reset) "submit"
- disabled (disabled) #IMPLIED
- >
-
-<!-- single-line text input control (DEPRECATED) -->
-<!ELEMENT isindex EMPTY>
-<!ATTLIST isindex
- %coreattrs;
- %i18n;
- prompt %Text; #IMPLIED
- >
-
-<!--======================= Tables =======================================-->
-
-<!-- Derived from IETF HTML table standard, see [RFC1942] -->
-
-<!--
- The border attribute sets the thickness of the frame around the
- table. The default units are screen pixels.
-
- The frame attribute specifies which parts of the frame around
- the table should be rendered. The values are not the same as
- CALS to avoid a name clash with the valign attribute.
--->
-<!ENTITY % TFrame "(void|above|below|hsides|lhs|rhs|vsides|box|border)">
-
-<!--
- The rules attribute defines which rules to draw between cells:
-
- If rules is absent then assume:
- "none" if border is absent or border="0" otherwise "all"
--->
-
-<!ENTITY % TRules "(none | groups | rows | cols | all)">
-
-<!-- horizontal placement of table relative to document -->
-<!ENTITY % TAlign "(left|center|right)">
-
-<!-- horizontal alignment attributes for cell contents
-
- char alignment char, e.g. char=':'
- charoff offset for alignment char
--->
-<!ENTITY % cellhalign
- "align (left|center|right|justify|char) #IMPLIED
- char %Character; #IMPLIED
- charoff %Length; #IMPLIED"
- >
-
-<!-- vertical alignment attributes for cell contents -->
-<!ENTITY % cellvalign
- "valign (top|middle|bottom|baseline) #IMPLIED"
- >
-
-<!ELEMENT table
- (caption?, (col*|colgroup*), thead?, tfoot?, (tbody+|tr+))>
-<!ELEMENT caption %Inline;>
-<!ELEMENT thead (tr)+>
-<!ELEMENT tfoot (tr)+>
-<!ELEMENT tbody (tr)+>
-<!ELEMENT colgroup (col)*>
-<!ELEMENT col EMPTY>
-<!ELEMENT tr (th|td)+>
-<!ELEMENT th %Flow;>
-<!ELEMENT td %Flow;>
-
-<!ATTLIST table
- %attrs;
- summary %Text; #IMPLIED
- width %Length; #IMPLIED
- border %Pixels; #IMPLIED
- frame %TFrame; #IMPLIED
- rules %TRules; #IMPLIED
- cellspacing %Length; #IMPLIED
- cellpadding %Length; #IMPLIED
- align %TAlign; #IMPLIED
- bgcolor %Color; #IMPLIED
- >
-
-<!ENTITY % CAlign "(top|bottom|left|right)">
-
-<!ATTLIST caption
- %attrs;
- align %CAlign; #IMPLIED
- >
-
-<!--
-colgroup groups a set of col elements. It allows you to group
-several semantically related columns together.
--->
-<!ATTLIST colgroup
- %attrs;
- span %Number; "1"
- width %MultiLength; #IMPLIED
- %cellhalign;
- %cellvalign;
- >
-
-<!--
- col elements define the alignment properties for cells in
- one or more columns.
-
- The width attribute specifies the width of the columns, e.g.
-
- width=64 width in screen pixels
- width=0.5* relative width of 0.5
-
- The span attribute causes the attributes of one
- col element to apply to more than one column.
--->
-<!ATTLIST col
- %attrs;
- span %Number; "1"
- width %MultiLength; #IMPLIED
- %cellhalign;
- %cellvalign;
- >
-
-<!--
- Use thead to duplicate headers when breaking table
- across page boundaries, or for static headers when
- tbody sections are rendered in scrolling panel.
-
- Use tfoot to duplicate footers when breaking table
- across page boundaries, or for static footers when
- tbody sections are rendered in scrolling panel.
-
- Use multiple tbody sections when rules are needed
- between groups of table rows.
--->
-<!ATTLIST thead
- %attrs;
- %cellhalign;
- %cellvalign;
- >
-
-<!ATTLIST tfoot
- %attrs;
- %cellhalign;
- %cellvalign;
- >
-
-<!ATTLIST tbody
- %attrs;
- %cellhalign;
- %cellvalign;
- >
-
-<!ATTLIST tr
- %attrs;
- %cellhalign;
- %cellvalign;
- bgcolor %Color; #IMPLIED
- >
-
-<!-- Scope is simpler than headers attribute for common tables -->
-<!ENTITY % Scope "(row|col|rowgroup|colgroup)">
-
-<!-- th is for headers, td for data and for cells acting as both -->
-
-<!ATTLIST th
- %attrs;
- abbr %Text; #IMPLIED
- axis CDATA #IMPLIED
- headers IDREFS #IMPLIED
- scope %Scope; #IMPLIED
- rowspan %Number; "1"
- colspan %Number; "1"
- %cellhalign;
- %cellvalign;
- nowrap (nowrap) #IMPLIED
- bgcolor %Color; #IMPLIED
- width %Length; #IMPLIED
- height %Length; #IMPLIED
- >
-
-<!ATTLIST td
- %attrs;
- abbr %Text; #IMPLIED
- axis CDATA #IMPLIED
- headers IDREFS #IMPLIED
- scope %Scope; #IMPLIED
- rowspan %Number; "1"
- colspan %Number; "1"
- %cellhalign;
- %cellvalign;
- nowrap (nowrap) #IMPLIED
- bgcolor %Color; #IMPLIED
- width %Length; #IMPLIED
- height %Length; #IMPLIED
- >
-
=====================================
src/testdata/swissSmall deleted
=====================================
@@ -1,176 +0,0 @@
-ID 100K_RAT STANDARD; PRT; 889 AA.
-AC Q62671;
-DT 01-NOV-1997 (Rel. 35, Created)
-DT 01-NOV-1997 (Rel. 35, Last sequence update)
-DT 15-JUL-1999 (Rel. 38, Last annotation update)
-DE 100 KD PROTEIN (EC 6.3.2.-).
-OS Rattus norvegicus (Rat).
-OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Mammalia;
-OC Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus.
-RN [1]
-RP SEQUENCE FROM N.A.
-RC STRAIN=WISTAR; TISSUE=TESTIS;
-RX MEDLINE; 92253337.
-RA MUELLER D., REHBEIN M., BAUMEISTER H., RICHTER D.;
-RT "Molecular characterization of a novel rat protein structurally
-RT related to poly(A) binding proteins and the 70K protein of the U1
-RT small nuclear ribonucleoprotein particle (snRNP).";
-RL Nucleic Acids Res. 20:1471-1475(1992).
-RN [2]
-RP ERRATUM.
-RA MUELLER D., REHBEIN M., BAUMEISTER H., RICHTER D.;
-RL Nucleic Acids Res. 20:2624-2624(1992).
-CC -!- FUNCTION: E3 UBIQUITIN-PROTEIN LIGASE WHICH ACCEPTS UBIQUITIN FROM
-CC AN E2 UBIQUITIN-CONJUGATING ENZYME IN THE FORM OF A THIOESTER AND
-CC THEN DIRECTLY TRANSFERS THE UBIQUITIN TO TARGETED SUBSTRATES (BY
-CC SIMILARITY). THIS PROTEIN MAY BE INVOLVED IN MATURATION AND/OR
-CC POST-TRANSCRIPTIONAL REGULATION OF MRNA.
-CC -!- TISSUE SPECIFICITY: HIGHEST LEVELS FOUND IN TESTIS. ALSO PRESENT
-CC IN LIVER, KIDNEY, LUNG AND BRAIN.
-CC -!- DEVELOPMENTAL STAGE: IN EARLY POST-NATAL LIFE, EXPRESSION IN
-CC THE TESTIS INCREASES TO REACH A MAXIMUM AROUND DAY 28.
-CC -!- MISCELLANEOUS: A CYSTEINE RESIDUE IS REQUIRED FOR
-CC UBIQUITIN-THIOLESTER FORMATION.
-CC -!- SIMILARITY: CONTAINS AN HECT-TYPE E3 UBIQUITIN-PROTEIN LIGASE
-CC DOMAIN.
-CC -!- SIMILARITY: A CENTRAL REGION (AA 485-514) IS SIMILAR TO THE
-CC C-TERMINAL DOMAINS OF MAMMALIAN AND YEAST POLY (A) RNA BINDING
-CC PROTEINS (PABP).
-CC -!- SIMILARITY: THE C-TERMINAL HALF SHOWS HIGH SIMILARITY TO
-CC DROSOPHILA HYPERPLASMIC DISC PROTEIN AND SOME, TO HUMAN E6-AP.
-CC -!- SIMILARITY: CONTAINS MIXED-CHARGE DOMAINS SIMILAR TO RNA-BINDING
-CC PROTEINS.
-CC --------------------------------------------------------------------------
-CC This SWISS-PROT entry is copyright. It is produced through a collaboration
-CC between the Swiss Institute of Bioinformatics and the EMBL outstation -
-CC the European Bioinformatics Institute. There are no restrictions on its
-CC use by non-profit institutions as long as its content is in no way
-CC modified and this statement is not removed. Usage by and for commercial
-CC entities requires a license agreement (See http://www.isb-sib.ch/announce/
-CC or send an email to license at isb-sib.ch).
-CC --------------------------------------------------------------------------
-DR EMBL; X64411; CAA45756.1; -.
-DR PFAM; PF00632; HECT; 1.
-DR PFAM; PF00658; PABP; 1.
-KW Ubiquitin conjugation; Ligase.
-FT DOMAIN 77 88 ASP/GLU-RICH (ACIDIC).
-FT DOMAIN 127 150 PRO-RICH.
-FT DOMAIN 420 439 ARG/GLU-RICH (MIXED CHARGE).
-FT DOMAIN 448 457 ARG/ASP-RICH (MIXED CHARGE).
-FT DOMAIN 485 514 PABP-LIKE.
-FT DOMAIN 579 590 ASP/GLU-RICH (ACIDIC).
-FT DOMAIN 786 889 HECT DOMAIN.
-FT DOMAIN 827 847 PRO-RICH.
-FT BINDING 858 858 UBIQUITIN (BY SIMILARITY).
-SQ SEQUENCE 889 AA; 100368 MW; DD7E6C7A CRC32;
- MMSARGDFLN YALSLMRSHN DEHSDVLPVL DVCSLKHVAY VFQALIYWIK AMNQQTTLDT
- PQLERKRTRE LLELGIDNED SEHENDDDTS QSATLNDKDD ESLPAETGQN HPFFRRSDSM
- TFLGCIPPNP FEVPLAEAIP LADQPHLLQP NARKEDLFGR PSQGLYSSSA GSGKCLVEVT
- MDRNCLEVLP TKMSYAANLK NVMNMQNRQK KAGEDQSMLA EEADSSKPGP SAHDVAAQLK
- SSLLAEIGLT ESEGPPLTSF RPQCSFMGMV ISHDMLLGRW RLSLELFGRV FMEDVGAEPG
- SILTELGGFE VKESKFRREM EKLRNQQSRD LSLEVDRDRD LLIQQTMRQL NNHFGRRCAT
- TPMAVHRVKV TFKDEPGEGS GVARSFYTAI AQAFLSNEKL PNLDCIQNAN KGTHTSLMQR
- LRNRGERDRE REREREMRRS SGLRAGSRRD RDRDFRRQLS IDTRPFRPAS EGNPSDDPDP
- LPAHRQALGE RLYPRVQAMQ PAFASKITGM LLELSPAQLL LLLASEDSLR ARVEEAMELI
- VAHGRENGAD SILDLGLLDS SEKVQENRKR HGSSRSVVDM DLDDTDDGDD NAPLFYQPGK
- RGFYTPRPGK NTEARLNCFR NIGRILGLCL LQNELCPITL NRHVIKVLLG RKVNWHDFAF
- FDPVMYESLR QLILASQSSD ADAVFSAMDL AFAVDLCKEE GGGQVELIPN GVNIPVTPQN
- VYEYVRKYAE HRMLVVAEQP LHAMRKGLLD VLPKNSLEDL TAEDFRLLVN GCGEVNVQML
- ISFTSFNDES GENAEKLLQF KRWFWSIVER MSMTERQDLV YFWTSSPSLP ASEEGFQPMP
- SITIRPPDDQ HLPTANTCIS RLYVPLYSSK QILKQKLLLA IKTKNFGFV
-//
-ID 104K_THEPA STANDARD; PRT; 924 AA.
-AC P15711;
-DT 01-APR-1990 (Rel. 14, Created)
-DT 01-APR-1990 (Rel. 14, Last sequence update)
-DT 01-AUG-1992 (Rel. 23, Last annotation update)
-DE 104 KD MICRONEME-RHOPTRY ANTIGEN.
-OS Theileria parva.
-OC Eukaryota; Alveolata; Apicomplexa; Piroplasmida; Theileriidae;
-OC Theileria.
-RN [1]
-RP SEQUENCE FROM N.A.
-RC STRAIN=MUGUGA;
-RX MEDLINE; 90158697.
-RA IAMS K.P., YOUNG J.R., NENE V., DESAI J., WEBSTER P.,
-RA OLE-MOIYOI O.K., MUSOKE A.J.;
-RT "Characterisation of the gene encoding a 104-kilodalton microneme-
-RT rhoptry protein of Theileria parva.";
-RL Mol. Biochem. Parasitol. 39:47-60(1990).
-CC -!- SUBCELLULAR LOCATION: IN MICRONEME/RHOPTRY COMPLEXES.
-CC -!- DEVELOPMENTAL STAGE: SPOROZOITE ANTIGEN.
-CC --------------------------------------------------------------------------
-CC This SWISS-PROT entry is copyright. It is produced through a collaboration
-CC between the Swiss Institute of Bioinformatics and the EMBL outstation -
-CC the European Bioinformatics Institute. There are no restrictions on its
-CC use by non-profit institutions as long as its content is in no way
-CC modified and this statement is not removed. Usage by and for commercial
-CC entities requires a license agreement (See http://www.isb-sib.ch/announce/
-CC or send an email to license at isb-sib.ch).
-CC --------------------------------------------------------------------------
-DR EMBL; M29954; AAA18217.1; -.
-DR PIR; A44945; A44945.
-KW Antigen; Sporozoite; Repeat.
-FT DOMAIN 1 19 HYDROPHOBIC.
-FT DOMAIN 905 924 HYDROPHOBIC.
-SQ SEQUENCE 924 AA; 103625 MW; 4563AAA0 CRC32;
- MKFLILLFNI LCLFPVLAAD NHGVGPQGAS GVDPITFDIN SNQTGPAFLT AVEMAGVKYL
- QVQHGSNVNI HRLVEGNVVI WENASTPLYT GAIVTNNDGP YMAYVEVLGD PNLQFFIKSG
- DAWVTLSEHE YLAKLQEIRQ AVHIESVFSL NMAFQLENNK YEVETHAKNG ANMVTFIPRN
- GHICKMVYHK NVRIYKATGN DTVTSVVGFF RGLRLLLINV FSIDDNGMMS NRYFQHVDDK
- YVPISQKNYE TGIVKLKDYK HAYHPVDLDI KDIDYTMFHL ADATYHEPCF KIIPNTGFCI
- TKLFDGDQVL YESFNPLIHC INEVHIYDRN NGSIICLHLN YSPPSYKAYL VLKDTGWEAT
- THPLLEEKIE ELQDQRACEL DVNFISDKDL YVAALTNADL NYTMVTPRPH RDVIRVSDGS
- EVLWYYEGLD NFLVCAWIYV SDGVASLVHL RIKDRIPANN DIYVLKGDLY WTRITKIQFT
- QEIKRLVKKS KKKLAPITEE DSDKHDEPPE GPGASGLPPK APGDKEGSEG HKGPSKGSDS
- SKEGKKPGSG KKPGPAREHK PSKIPTLSKK PSGPKDPKHP RDPKEPRKSK SPRTASPTRR
- PSPKLPQLSK LPKSTSPRSP PPPTRPSSPE RPEGTKIIKT SKPPSPKPPF DPSFKEKFYD
- DYSKAASRSK ETKTTVVLDE SFESILKETL PETPGTPFTT PRPVPPKRPR TPESPFEPPK
- DPDSPSTSPS EFFTPPESKR TRFHETPADT PLPDVTAELF KEPDVTAETK SPDEAMKRPR
- SPSEYEDTSP GDYPSLPMKR HRLERLRLTT TEMETDPGRM AKDASGKPVK LKRSKSFDDL
- TTVELAPEPK ASRIVVDDEG TEADDEETHP PEERQKTEVR RRRPPKKPSK SPRPSKPKKP
- KKPDSAYIPS ILAILVVSLI VGIL
-//
-ID 108_LYCES STANDARD; PRT; 102 AA.
-AC Q43495;
-DT 15-JUL-1999 (Rel. 38, Created)
-DT 15-JUL-1999 (Rel. 38, Last sequence update)
-DT 15-JUL-1999 (Rel. 38, Last annotation update)
-DE PROTEIN 108 PRECURSOR.
-OS Lycopersicon esculentum (Tomato).
-OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
-OC euphyllophytes; Spermatophyta; Magnoliophyta; eudicotyledons;
-OC core eudicots; Asteridae; euasterids I; Solanales; Solanaceae;
-OC Solanum.
-RN [1]
-RP SEQUENCE FROM N.A.
-RC STRAIN=CV. VF36; TISSUE=ANTHER;
-RX MEDLINE; 94143497.
-RA CHEN R., SMITH A.G.;
-RT "Nucleotide sequence of a stamen- and tapetum-specific gene from
-RT Lycopersicon esculentum.";
-RL Plant Physiol. 101:1413-1413(1993).
-CC -!- TISSUE SPECIFICITY: STAMEN- AND TAPETUM-SPECIFIC.
-CC -!- SIMILARITY: BELONGS TO THE A9 / FIL1 FAMILY.
-CC --------------------------------------------------------------------------
-CC This SWISS-PROT entry is copyright. It is produced through a collaboration
-CC between the Swiss Institute of Bioinformatics and the EMBL outstation -
-CC the European Bioinformatics Institute. There are no restrictions on its
-CC use by non-profit institutions as long as its content is in no way
-CC modified and this statement is not removed. Usage by and for commercial
-CC entities requires a license agreement (See http://www.isb-sib.ch/announce/
-CC or send an email to license at isb-sib.ch).
-CC --------------------------------------------------------------------------
-DR EMBL; Z14088; CAA78466.1; -.
-DR MENDEL; 8853; LYCes;1133;1.
-KW Signal.
-FT SIGNAL 1 30 POTENTIAL.
-FT CHAIN 31 102 PROTEIN 108.
-FT DISULFID 41 77 BY SIMILARITY.
-FT DISULFID 51 66 BY SIMILARITY.
-FT DISULFID 67 92 BY SIMILARITY.
-FT DISULFID 79 99 BY SIMILARITY.
-SQ SEQUENCE 102 AA; 10576 MW; AFA4875A CRC32;
- MASVKSSSSS SSSSFISLLL LILLVIVLQS QVIECQPQQS CTASLTGLNV CAPFLVPGSP
- TASTECCNAV QSINHDCMCN TMRIAAQIPA QCNLPPLSCS AN
-//
View it on GitLab: https://salsa.debian.org/med-team/vmatch/compare/d54735101a5a0a8a2fced27bef58e60540a1ed7b...fe11155363ed12267a97c1eeea5f3758e63ad13f
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View it on GitLab: https://salsa.debian.org/med-team/vmatch/compare/d54735101a5a0a8a2fced27bef58e60540a1ed7b...fe11155363ed12267a97c1eeea5f3758e63ad13f
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