diff --git a/manuscript/PLAIN.BST b/manuscript/PLAIN.BST deleted file mode 100644 index 3056ce2..0000000 --- a/manuscript/PLAIN.BST +++ /dev/null @@ -1,1109 +0,0 @@ -% BibTeX standard bibliography style `plain' - % version 0.99a for BibTeX versions 0.99a or later, LaTeX version 2.09. - % Copyright (C) 1985, all rights reserved. - % Copying of this file is authorized only if either - % (1) you make absolutely no changes to your copy, including name, or - % (2) if you do make changes, you name it something other than - % btxbst.doc, plain.bst, unsrt.bst, alpha.bst, and abbrv.bst. - % This restriction helps ensure that all standard styles are identical. - % The file btxbst.doc has the documentation for this style. - -ENTRY - { address - author - booktitle - chapter - edition - editor - howpublished - institution - journal - key - month - note - number - organization - pages - location - publisher - school - series - title - type - volume - year - doi - url - } - {} - { label } - -INTEGERS { output.state before.all mid.sentence after.sentence after.block } - -FUNCTION {init.state.consts} -{ #0 'before.all := - #1 'mid.sentence := - #2 'after.sentence := - #3 'after.block := -} - -STRINGS { s t } - -FUNCTION {output.nonnull} -{ 's := - output.state mid.sentence = - { ", " * write$ } - { output.state after.block = - { add.period$ write$ - newline$ - "\newblock " write$ - } - { output.state before.all = - 'write$ - { add.period$ " " * write$ } - if$ - } - if$ - mid.sentence 'output.state := - } - if$ - s -} - -FUNCTION {output} -{ duplicate$ empty$ - 'pop$ - 'output.nonnull - if$ -} - -FUNCTION {output.check} -{ 't := - duplicate$ empty$ - { pop$ "empty " t * " in " * cite$ * warning$ } - 'output.nonnull - if$ -} - -FUNCTION {output.bibitem} -{ newline$ - "\bibitem{" write$ - cite$ write$ - "}" write$ - newline$ - "" - before.all 'output.state := -} - -FUNCTION {fin.entry} -{ add.period$ - write$ - newline$ -} - -FUNCTION {new.block} -{ output.state before.all = - 'skip$ - { after.block 'output.state := } - if$ -} - -FUNCTION {new.sentence} -{ output.state after.block = - 'skip$ - { output.state before.all = - 'skip$ - { after.sentence 'output.state := } - if$ - } - if$ -} - -FUNCTION {not} -{ { #0 } - { #1 } - if$ -} - -FUNCTION {and} -{ 'skip$ - { pop$ #0 } - if$ -} - -FUNCTION {or} -{ { pop$ #1 } - 'skip$ - if$ -} - -FUNCTION {new.block.checka} -{ empty$ - 'skip$ - 'new.block - if$ -} - -FUNCTION {new.block.checkb} -{ empty$ - swap$ empty$ - and - 'skip$ - 'new.block - if$ -} - -FUNCTION {new.sentence.checka} -{ empty$ - 'skip$ - 'new.sentence - if$ -} - -FUNCTION {new.sentence.checkb} -{ empty$ - swap$ empty$ - and - 'skip$ - 'new.sentence - if$ -} - -FUNCTION {field.or.null} -{ duplicate$ empty$ - { pop$ "" } - 'skip$ - if$ -} - -FUNCTION {emphasize} -{ duplicate$ empty$ - { pop$ "" } - { "{\em " swap$ * "}" * } - if$ -} - -INTEGERS { nameptr namesleft numnames } - -FUNCTION {format.names} -{ 's := - #1 'nameptr := - s num.names$ 'numnames := - numnames 'namesleft := - { namesleft #0 > } - { s nameptr "{ff~}{vv~}{ll}{, jj}" format.name$ 't := - nameptr #1 > - { namesleft #1 > - { ", " * t * } - { numnames #2 > - { "," * } - 'skip$ - if$ - t "others" = - { " et~al." * } - { " and " * t * } - if$ - } - if$ - } - 't - if$ - nameptr #1 + 'nameptr := - namesleft #1 - 'namesleft := - } - while$ -} - -FUNCTION {format.authors} -{ author empty$ - { "" } - { author format.names } - if$ -} - -FUNCTION {format.editors} -{ editor empty$ - { "" } - { editor format.names - editor num.names$ #1 > - { ", editors" * } - { ", editor" * } - if$ - } - if$ -} - -FUNCTION {format.title} -{ title empty$ - { "" } - { title "t" change.case$ } - if$ -} - -FUNCTION {n.dashify} -{ 't := - "" - { t empty$ not } - { t #1 #1 substring$ "-" = - { t #1 #2 substring$ "--" = not - { "--" * - t #2 global.max$ substring$ 't := - } - { { t #1 #1 substring$ "-" = } - { "-" * - t #2 global.max$ substring$ 't := - } - while$ - } - if$ - } - { t #1 #1 substring$ * - t #2 global.max$ substring$ 't := - } - if$ - } - while$ -} - -FUNCTION {format.date} -{ year empty$ - { month empty$ - { "" } - { "there's a month but no year in " cite$ * warning$ - month - } - if$ - } - { month empty$ - 'year - { month " " * year * } - if$ - } - if$ -} - -FUNCTION {format.btitle} -{ title emphasize -} - -FUNCTION {tie.or.space.connect} -{ duplicate$ text.length$ #3 < - { "~" } - { " " } - if$ - swap$ * * -} - -FUNCTION {either.or.check} -{ empty$ - 'pop$ - { "can't use both " swap$ * " fields in " * cite$ * warning$ } - if$ -} - -FUNCTION {format.bvolume} -{ volume empty$ - { "" } - { "volume" volume tie.or.space.connect - series empty$ - 'skip$ - { " of " * series emphasize * } - if$ - "volume and number" number either.or.check - } - if$ -} - -FUNCTION {format.number.series} -{ volume empty$ - { number empty$ - { series field.or.null } - { output.state mid.sentence = - { "number" } - { "Number" } - if$ - number tie.or.space.connect - series empty$ - { "there's a number but no series in " cite$ * warning$ } - { " in " * series * } - if$ - } - if$ - } - { "" } - if$ -} - -FUNCTION {format.edition} -{ edition empty$ - { "" } - { output.state mid.sentence = - { edition "l" change.case$ " edition" * } - { edition "t" change.case$ " edition" * } - if$ - } - if$ -} - -INTEGERS { multiresult } - -FUNCTION {multi.page.check} -{ 't := - #0 'multiresult := - { multiresult not - t empty$ not - and - } - { t #1 #1 substring$ - duplicate$ "-" = - swap$ duplicate$ "," = - swap$ "+" = - or or - { #1 'multiresult := } - { t #2 global.max$ substring$ 't := } - if$ - } - while$ - multiresult -} - -FUNCTION {format.pages} -{ pages empty$ - { "" } - { pages multi.page.check - { "pp." pages n.dashify tie.or.space.connect } - { "p." pages tie.or.space.connect } - if$ - } - if$ -} - -FUNCTION {format.vol.num.pages} -{ volume field.or.null - number empty$ - 'skip$ - { "(" number * ")" * * - volume empty$ - { "there's a number but no volume in " cite$ * warning$ } - 'skip$ - if$ - } - if$ - pages empty$ - 'skip$ - { duplicate$ empty$ - { pop$ format.pages } - { ":" * pages n.dashify * } - if$ - } - if$ -} - -FUNCTION {format.chapter.pages} -{ chapter empty$ - 'format.pages - { type empty$ - { "chapter" } - { type "l" change.case$ } - if$ - chapter tie.or.space.connect - pages empty$ - 'skip$ - { ", " * format.pages * } - if$ - } - if$ -} - -FUNCTION {format.in.ed.booktitle} -{ booktitle empty$ - { "" } - { editor empty$ - { "In " booktitle emphasize * } - { "In " format.editors * ", " * booktitle emphasize * } - if$ - } - if$ -} - -FUNCTION {empty.misc.check} -{ author empty$ title empty$ howpublished empty$ - month empty$ year empty$ note empty$ - and and and and and - key empty$ not and - { "all relevant fields are empty in " cite$ * warning$ } - 'skip$ - if$ -} - -FUNCTION {format.thesis.type} -{ type empty$ - 'skip$ - { pop$ - type "t" change.case$ - } - if$ -} - -FUNCTION {format.tr.number} -{ type empty$ - { "Technical Report" } - 'type - if$ - number empty$ - { "t" change.case$ } - { number tie.or.space.connect } - if$ -} - -FUNCTION {format.article.crossref} -{ key empty$ - { journal empty$ - { "need key or journal for " cite$ * " to crossref " * crossref * - warning$ - "" - } - { "In {\em " journal * "\/}" * } - if$ - } - { "In " key * } - if$ - " \cite{" * crossref * "}" * -} - -FUNCTION {format.crossref.editor} -{ editor #1 "{vv~}{ll}" format.name$ - editor num.names$ duplicate$ - #2 > - { pop$ " et~al." * } - { #2 < - 'skip$ - { editor #2 "{ff }{vv }{ll}{ jj}" format.name$ "others" = - { " et~al." * } - { " and " * editor #2 "{vv~}{ll}" format.name$ * } - if$ - } - if$ - } - if$ -} - -FUNCTION {format.book.crossref} -{ volume empty$ - { "empty volume in " cite$ * "'s crossref of " * crossref * warning$ - "In " - } - { "Volume" volume tie.or.space.connect - " of " * - } - if$ - editor empty$ - editor field.or.null author field.or.null = - or - { key empty$ - { series empty$ - { "need editor, key, or series for " cite$ * " to crossref " * - crossref * warning$ - "" * - } - { "{\em " * series * "\/}" * } - if$ - } - { key * } - if$ - } - { format.crossref.editor * } - if$ - " \cite{" * crossref * "}" * -} - -FUNCTION {format.incoll.inproc.crossref} -{ editor empty$ - editor field.or.null author field.or.null = - or - { key empty$ - { booktitle empty$ - { "need editor, key, or booktitle for " cite$ * " to crossref " * - crossref * warning$ - "" - } - { "In {\em " booktitle * "\/}" * } - if$ - } - { "In " key * } - if$ - } - { "In " format.crossref.editor * } - if$ - " \cite{" * crossref * "}" * -} - -FUNCTION {article} -{ output.bibitem - format.authors "author" output.check - new.block - format.title "title" output.check - new.block - crossref missing$ - { journal emphasize "journal" output.check - format.vol.num.pages output - format.date "year" output.check - } - { format.article.crossref output.nonnull - format.pages output - format.doi output - format.url output - } - if$ - new.block - note output - fin.entry -} - -FUNCTION {book} -{ output.bibitem - author empty$ - { format.editors "author and editor" output.check } - { format.authors output.nonnull - crossref missing$ - { "author and editor" editor either.or.check } - 'skip$ - if$ - } - if$ - new.block - format.btitle "title" output.check - crossref missing$ - { format.bvolume output - new.block - format.number.series output - new.sentence - location "location" output.check - publisher "publisher" output.check - address output - } - { new.block - format.book.crossref output.nonnull - } - if$ - format.edition output - format.date "year" output.check - new.block - note output - fin.entry -} - -FUNCTION {booklet} -{ output.bibitem - format.authors output - new.block - format.title "title" output.check - howpublished address new.block.checkb - howpublished output - address output - format.date output - new.block - note output - fin.entry -} - -FUNCTION {inbook} -{ output.bibitem - author empty$ - { format.editors "author and editor" output.check } - { format.authors output.nonnull - crossref missing$ - { "author and editor" editor either.or.check } - 'skip$ - if$ - } - if$ - new.block - format.btitle "title" output.check - crossref missing$ - { format.bvolume output - format.chapter.pages "chapter and pages" output.check - new.block - format.number.series output - new.sentence - location "location" output.check - publisher "publisher" output.check - address output - } - { format.chapter.pages "chapter and pages" output.check - new.block - format.book.crossref output.nonnull - } - if$ - format.edition output - format.date "year" output.check - new.block - note output - fin.entry -} - -FUNCTION {incollection} -{ output.bibitem - format.authors "author" output.check - new.block - format.title "title" output.check - new.block - crossref missing$ - { format.in.ed.booktitle "booktitle" output.check - format.bvolume output - format.number.series output - format.chapter.pages output - new.sentence - location "location" output.check - publisher "publisher" output.check - address output - format.edition output - format.date "year" output.check - } - { format.incoll.inproc.crossref output.nonnull - format.chapter.pages output - } - if$ - new.block - note output - fin.entry -} - -FUNCTION {inproceedings} -{ output.bibitem - format.authors "author" output.check - new.block - format.title "title" output.check - new.block - crossref missing$ - { format.in.ed.booktitle "booktitle" output.check - format.bvolume output - format.number.series output - format.pages output - address empty$ - { organization publisher new.sentence.checkb - organization output - location output - publisher output - format.date "year" output.check - } - { address output.nonnull - format.date "year" output.check - new.sentence - organization output - location output - publisher output - } - if$ - } - { format.incoll.inproc.crossref output.nonnull - format.pages output - } - if$ - new.block - note output - fin.entry -} - -FUNCTION {conference} { inproceedings } - -FUNCTION {manual} -{ output.bibitem - author empty$ - { organization empty$ - 'skip$ - { organization output.nonnull - address output - } - if$ - } - { format.authors output.nonnull } - if$ - new.block - format.btitle "title" output.check - author empty$ - { organization empty$ - { address new.block.checka - address output - } - 'skip$ - if$ - } - { organization address new.block.checkb - organization output - address output - } - if$ - format.edition output - format.date output - new.block - note output - fin.entry -} - -FUNCTION {mastersthesis} -{ output.bibitem - format.authors "author" output.check - new.block - format.title "title" output.check - new.block - "Master's thesis" format.thesis.type output.nonnull - school "school" output.check - address output - format.date "year" output.check - new.block - note output - fin.entry -} - -FUNCTION {misc} -{ output.bibitem - format.authors output - title howpublished new.block.checkb - format.title output - howpublished new.block.checka - howpublished output - format.date output - new.block - note output - fin.entry - empty.misc.check -} - -FUNCTION {phdthesis} -{ output.bibitem - format.authors "author" output.check - new.block - format.btitle "title" output.check - new.block - "PhD thesis" format.thesis.type output.nonnull - school "school" output.check - address output - format.date "year" output.check - new.block - note output - fin.entry -} - -FUNCTION {proceedings} -{ output.bibitem - editor empty$ - { organization output } - { format.editors output.nonnull } - if$ - new.block - format.btitle "title" output.check - format.bvolume output - format.number.series output - address empty$ - { editor empty$ - { publisher new.sentence.checka } - { organization publisher new.sentence.checkb - organization output - } - if$ - location output - publisher output - format.date "year" output.check - } - { address output.nonnull - format.date "year" output.check - new.sentence - editor empty$ - 'skip$ - { organization output } - if$ - location output - publisher output - } - if$ - new.block - note output - fin.entry -} - -FUNCTION {techreport} -{ output.bibitem - format.authors "author" output.check - new.block - format.title "title" output.check - new.block - format.tr.number output.nonnull - institution "institution" output.check - address output - format.date "year" output.check - new.block - note output - fin.entry -} - -FUNCTION {unpublished} -{ output.bibitem - format.authors "author" output.check - new.block - format.title "title" output.check - new.block - note "note" output.check - format.date output - fin.entry -} - -FUNCTION {default.type} { misc } - -MACRO {jan} {"January"} - -MACRO {feb} {"February"} - -MACRO {mar} {"March"} - -MACRO {apr} {"April"} - -MACRO {may} {"May"} - -MACRO {jun} {"June"} - -MACRO {jul} {"July"} - -MACRO {aug} {"August"} - -MACRO {sep} {"September"} - -MACRO {oct} {"October"} - -MACRO {nov} {"November"} - -MACRO {dec} {"December"} - -MACRO {acmcs} {"ACM Computing Surveys"} - -MACRO {acta} {"Acta Informatica"} - -MACRO {cacm} {"Communications of the ACM"} - -MACRO {ibmjrd} {"IBM Journal of Research and Development"} - -MACRO {ibmsj} {"IBM Systems Journal"} - -MACRO {ieeese} {"IEEE Transactions on Software Engineering"} - -MACRO {ieeetc} {"IEEE Transactions on Computers"} - -MACRO {ieeetcad} - {"IEEE Transactions on Computer-Aided Design of Integrated Circuits"} - -MACRO {ipl} {"Information Processing Letters"} - -MACRO {jacm} {"Journal of the ACM"} - -MACRO {jcss} {"Journal of Computer and System Sciences"} - -MACRO {scp} {"Science of Computer Programming"} - -MACRO {sicomp} {"SIAM Journal on Computing"} - -MACRO {tocs} {"ACM Transactions on Computer Systems"} - -MACRO {tods} {"ACM Transactions on Database Systems"} - -MACRO {tog} {"ACM Transactions on Graphics"} - -MACRO {toms} {"ACM Transactions on Mathematical Software"} - -MACRO {toois} {"ACM Transactions on Office Information Systems"} - -MACRO {toplas} {"ACM Transactions on Programming Languages and Systems"} - -MACRO {tcs} {"Theoretical Computer Science"} - -READ - -FUNCTION {sortify} -{ purify$ - "l" change.case$ -} - -INTEGERS { len } - -FUNCTION {chop.word} -{ 's := - 'len := - s #1 len substring$ = - { s len #1 + global.max$ substring$ } - 's - if$ -} - -FUNCTION {sort.format.names} -{ 's := - #1 'nameptr := - "" - s num.names$ 'numnames := - numnames 'namesleft := - { namesleft #0 > } - { nameptr #1 > - { " " * } - 'skip$ - if$ - s nameptr "{vv{ } }{ll{ }}{ ff{ }}{ jj{ }}" format.name$ 't := - nameptr numnames = t "others" = and - { "et al" * } - { t sortify * } - if$ - nameptr #1 + 'nameptr := - namesleft #1 - 'namesleft := - } - while$ -} - -FUNCTION {sort.format.title} -{ 't := - "A " #2 - "An " #3 - "The " #4 t chop.word - chop.word - chop.word - sortify - #1 global.max$ substring$ -} - -FUNCTION {author.sort} -{ author empty$ - { key empty$ - { "to sort, need author or key in " cite$ * warning$ - "" - } - { key sortify } - if$ - } - { author sort.format.names } - if$ -} - -FUNCTION {author.editor.sort} -{ author empty$ - { editor empty$ - { key empty$ - { "to sort, need author, editor, or key in " cite$ * warning$ - "" - } - { key sortify } - if$ - } - { editor sort.format.names } - if$ - } - { author sort.format.names } - if$ -} - -FUNCTION {author.organization.sort} -{ author empty$ - { organization empty$ - { key empty$ - { "to sort, need author, organization, or key in " cite$ * warning$ - "" - } - { key sortify } - if$ - } - { "The " #4 organization chop.word sortify } - if$ - } - { author sort.format.names } - if$ -} - -FUNCTION {editor.organization.sort} -{ editor empty$ - { organization empty$ - { key empty$ - { "to sort, need editor, organization, or key in " cite$ * warning$ - "" - } - { key sortify } - if$ - } - { "The " #4 organization chop.word sortify } - if$ - } - { editor sort.format.names } - if$ -} - -FUNCTION {presort} -{ type$ "book" = - type$ "inbook" = - or - 'author.editor.sort - { type$ "proceedings" = - 'editor.organization.sort - { type$ "manual" = - 'author.organization.sort - 'author.sort - if$ - } - if$ - } - if$ - " " - * - year field.or.null sortify - * - " " - * - title field.or.null - sort.format.title - * - #1 entry.max$ substring$ - 'sort.key$ := -} - -ITERATE {presort} - -SORT - -STRINGS { longest.label } - -INTEGERS { number.label longest.label.width } - -FUNCTION {initialize.longest.label} -{ "" 'longest.label := - #1 'number.label := - #0 'longest.label.width := -} - -FUNCTION {longest.label.pass} -{ number.label int.to.str$ 'label := - number.label #1 + 'number.label := - label width$ longest.label.width > - { label 'longest.label := - label width$ 'longest.label.width := - } - 'skip$ - if$ -} - -EXECUTE {initialize.longest.label} - -ITERATE {longest.label.pass} - -FUNCTION {begin.bib} -{ preamble$ empty$ - 'skip$ - { preamble$ write$ newline$ } - if$ - "\begin{thebibliography}{" longest.label * "}" * write$ newline$ -} - -EXECUTE {begin.bib} - -EXECUTE {init.state.consts} - -ITERATE {call.type$} - -FUNCTION {end.bib} -{ newline$ - "\end{thebibliography}" write$ newline$ -} - -EXECUTE {end.bib} diff --git a/manuscript/alltt.sty b/manuscript/alltt.sty deleted file mode 100644 index 55d2832..0000000 --- a/manuscript/alltt.sty +++ /dev/null @@ -1,95 +0,0 @@ -%% -%% This is file `alltt.sty', -%% generated with the docstrip utility. -%% -%% The original source files were: -%% -%% alltt.dtx (with options: `package') -%% -%% This is a generated file. -%% -%% Copyright 1993 1994 1995 1996 1997 1998 1999 2000 -%% The LaTeX3 Project and any individual authors listed elsewhere -%% in this file. -%% -%% This file was generated from file(s) of the LaTeX base system. -%% -------------------------------------------------------------- -%% -%% It may be distributed and/or modified under the -%% conditions of the LaTeX Project Public License, either version 1.2 -%% of this license or (at your option) any later version. -%% The latest version of this license is in -%% http://www.latex-project.org/lppl.txt -%% and version 1.2 or later is part of all distributions of LaTeX -%% version 1999/12/01 or later. -%% -%% This file may only be distributed together with a copy of the LaTeX -%% base system. You may however distribute the LaTeX base system without -%% such generated files. -%% -%% The list of all files belonging to the LaTeX base distribution is -%% given in the file `manifest.txt'. See also `legal.txt' for additional -%% information. -%% -%% -%% File `alltt.dtx'. -%% Copyright (C) 1987 by Leslie Lamport -%% Copyright (C) 1994--1997 LaTeX3 project, Johannes Braams -%% all rights reserved. -%% -\NeedsTeXFormat{LaTeX2e} -\ProvidesPackage{alltt} - [1997/06/16 v2.0g defines alltt environment] -\begingroup -\lccode`\~=`\' -\lowercase{\endgroup -\newenvironment{alltt}{% - \trivlist - \item\relax - \if@minipage - \else - \vskip\parskip - \fi - \leftskip\@totalleftmargin - \rightskip\z@skip - \parindent\z@ - \parfillskip\@flushglue - \parskip\z@skip - \@@par - \@tempswafalse - \def\par{% - \if@tempswa - \leavevmode\null\@@par\penalty\interlinepenalty - \else - \@tempswatrue - \ifhmode\@@par\penalty\interlinepenalty\fi - \fi} - \obeylines - \verbatim@font - \let\org@prime~% - \@noligs - \everymath\expandafter{\the\everymath - \catcode`\'=12 \let~\org@prime} - \everydisplay\expandafter{\the\everydisplay - \catcode`\'=12 \let~\org@prime} - \let\org@dospecials\dospecials - \g@remfrom@specials{\\} - \g@remfrom@specials{\{} - \g@remfrom@specials{\}} - \let\do\@makeother - \dospecials - \let\dospecials\org@dospecials - \frenchspacing\@vobeyspaces - \everypar \expandafter{\the\everypar \unpenalty}} -{\endtrivlist}} -\def\g@remfrom@specials#1{% - \def\@new@specials{} - \def\@remove##1{% - \ifx##1#1\else - \g@addto@macro\@new@specials{\do ##1}\fi} - \let\do\@remove\dospecials - \let\dospecials\@new@specials - } -\endinput -%% -%% End of file `alltt.sty'. diff --git a/manuscript/array.sty b/manuscript/array.sty deleted file mode 100644 index bd03006..0000000 --- a/manuscript/array.sty +++ /dev/null @@ -1,368 +0,0 @@ -%% -%% This is file `array.sty', -%% generated with the docstrip utility. -%% -%% The original source files were: -%% -%% array.dtx (with options: `package,ncols') -%% -%% This is a generated file. -%% -%% Copyright 1993 1994 1995 1996 1997 1998 1999 2000 -%% The LaTeX3 Project and any individual authors listed elsewhere -%% in this file. -%% -%% This file was generated from file(s) of the Standard LaTeX `Tools Bundle'. -%% -------------------------------------------------------------------------- -%% -%% It may be distributed and/or modified under the -%% conditions of the LaTeX Project Public License, either version 1.2 -%% of this license or (at your option) any later version. -%% The latest version of this license is in -%% http://www.latex-project.org/lppl.txt -%% and version 1.2 or later is part of all distributions of LaTeX -%% version 1999/12/01 or later. -%% -%% This file may only be distributed together with a copy of the LaTeX -%% `Tools Bundle'. You may however distribute the LaTeX `Tools Bundle' -%% without such generated files. -%% -%% The list of all files belonging to the LaTeX `Tools Bundle' is -%% given in the file `manifest.txt'. -%% -%% Package `array' to use with LaTeX 2e -%% Copyright (C) 1989-1998 Frank Mittelbach, all rights reserved. -\NeedsTeXFormat{LaTeX2e}[1995/06/01] -\ProvidesPackage{array} - [1998/05/13 v2.3m Tabular extension package (FMi)] -%% \CharacterTable -%% {Upper-case \A\B\C\D\E\F\G\H\I\J\K\L\M\N\O\P\Q\R\S\T\U\V\W\X\Y\Z -%% Lower-case \a\b\c\d\e\f\g\h\i\j\k\l\m\n\o\p\q\r\s\t\u\v\w\x\y\z -%% Digits \0\1\2\3\4\5\6\7\8\9 -%% Exclamation \! Double quote \" Hash (number) \# -%% Dollar \$ Percent \% Ampersand \& -%% Acute accent \' Left paren \( Right paren \) -%% Asterisk \* Plus \+ Comma \, -%% Minus \- Point \. Solidus \/ -%% Colon \: Semicolon \; Less than \< -%% Equals \= Greater than \> Question mark \? -%% Commercial at \@ Left bracket \[ Backslash \\ -%% Right bracket \] Circumflex \^ Underscore \_ -%% Grave accent \` Left brace \{ Vertical bar \| -%% Right brace \} Tilde \~} -%% - -\def\@addtopreamble#1{\xdef\@preamble{\@preamble #1}} -\def\@testpach{\@chclass - \ifnum \@lastchclass=6 \@ne \@chnum \@ne \else - \ifnum \@lastchclass=7 5 \else - \ifnum \@lastchclass=8 \tw@ \else - \ifnum \@lastchclass=9 \thr@@ - \else \z@ - \ifnum \@lastchclass = 10 \else - \edef\@nextchar{\expandafter\string\@nextchar}% - \@chnum - \if \@nextchar c\z@ \else - \if \@nextchar l\@ne \else - \if \@nextchar r\tw@ \else - \z@ \@chclass - \if\@nextchar |\@ne \else - \if \@nextchar !6 \else - \if \@nextchar @7 \else - \if \@nextchar <8 \else - \if \@nextchar >9 \else - 10 - \@chnum - \if \@nextchar m\thr@@\else - \if \@nextchar p4 \else - \if \@nextchar b5 \else - \z@ \@chclass \z@ \@preamerr \z@ \fi \fi \fi \fi - \fi \fi \fi \fi \fi \fi \fi \fi \fi \fi \fi \fi} -\def\@xexpast#1*#2#3#4\@@{% - \@tempcnta #2 - \toks@={#1}\@temptokena={#3}% - \let\the@toksz\relax \let\the@toks\relax - \def\@tempa{\the@toksz}% - \ifnum\@tempcnta >0 \@whilenum\@tempcnta >0\do - {\edef\@tempa{\@tempa\the@toks}\advance \@tempcnta \m@ne}% - \let \@tempb \@xexpast \else - \let \@tempb \@xexnoop \fi - \def\the@toksz{\the\toks@}\def\the@toks{\the\@temptokena}% - \edef\@tempa{\@tempa}% - \expandafter \@tempb \@tempa #4\@@} -\def\prepnext@tok{\advance \count@ \@ne - \toks\count@{}} -\def\save@decl{\toks\count@ \expandafter{\@nextchar}} -\def\insert@column{% - \the@toks \the \@tempcnta - \ignorespaces \@sharp \unskip - \the@toks \the \count@ \relax} -\newdimen\col@sep -\def\@acol{\@addtopreamble{\hskip\col@sep}} -\def\@mkpream#1{\gdef\@preamble{}\@lastchclass 4 \@firstamptrue - \let\@sharp\relax \let\@startpbox\relax \let\@endpbox\relax - \@xexpast #1*0x\@@ - \count@\m@ne - \let\the@toks\relax - \prepnext@tok - \expandafter \@tfor \expandafter \@nextchar - \expandafter :\expandafter =\@tempa \do - {\@testpach - \ifcase \@chclass \@classz \or \@classi \or \@classii - \or \save@decl \or \or \@classv \or \@classvi - \or \@classvii \or \@classviii \or \@classix - \or \@classx \fi - \@lastchclass\@chclass}% - \ifcase\@lastchclass - \@acol \or - \or - \@acol \or - \@preamerr \thr@@ \or - \@preamerr \tw@ \@addtopreamble\@sharp \or - \or - \else \@preamerr \@ne \fi - \def\the@toks{\the\toks}} -\def\@classx{% - \ifcase \@lastchclass - \@acolampacol \or - \@addamp \@acol \or - \@acolampacol \or - \or - \@acol \@firstampfalse \or - \@addamp - \fi} -\def\@classz{\@classx - \@tempcnta \count@ - \prepnext@tok - \@addtopreamble{\ifcase \@chnum - \hfil - \d@llarbegin - \insert@column - \d@llarend \hfil \or - \hskip1sp\d@llarbegin \insert@column \d@llarend \hfil \or - \hfil\hskip1sp\d@llarbegin \insert@column \d@llarend \or - $\vcenter - \@startpbox{\@nextchar}\insert@column \@endpbox $\or - \vtop \@startpbox{\@nextchar}\insert@column \@endpbox \or - \vbox \@startpbox{\@nextchar}\insert@column \@endpbox - \fi}\prepnext@tok} -\def\@classix{\ifnum \@lastchclass = \thr@@ - \@preamerr \thr@@ \fi - \@classx} -\def\@classviii{\ifnum \@lastchclass >\z@ - \@preamerr 4\@chclass 6 \@classvi \fi} -\def\@arrayrule{\@addtopreamble \vline} -\def\@classvii{\ifnum \@lastchclass = \thr@@ - \@preamerr \thr@@ \fi} -\def\@classvi{\ifcase \@lastchclass - \@acol \or - \@addtopreamble{\hskip \doublerulesep}\or - \@acol \or - \@classvii - \fi} -\def\@classii{\advance \count@ \m@ne - \save@decl\prepnext@tok} -\def\@classv{\save@decl - \@addtopreamble{\d@llarbegin\the@toks\the\count@\relax\d@llarend}% - \prepnext@tok} -\def\@classi{\@classvi - \ifcase \@chnum \@arrayrule \or - \@classv \fi} -\def\@startpbox#1{\bgroup - \setlength\hsize{#1}\@arrayparboxrestore - \everypar{% - \vrule \@height \ht\@arstrutbox \@width \z@ - \everypar{}}% - } -\def\@endpbox{\@finalstrut\@arstrutbox \egroup\hfil} -\def\@array[#1]#2{% - \@tempdima \ht \strutbox - \advance \@tempdima by\extrarowheight - \setbox \@arstrutbox \hbox{\vrule - \@height \arraystretch \@tempdima - \@depth \arraystretch \dp \strutbox - \@width \z@}% - \begingroup - \@mkpream{#2}% - \xdef\@preamble{\noexpand \ialign \@halignto - \bgroup \@arstrut \@preamble - \tabskip \z@ \cr}% - \endgroup - \@arrayleft - \if #1t\vtop \else \if#1b\vbox \else \vcenter \fi \fi - \bgroup - \let \@sharp ##\let \protect \relax - \lineskip \z@ - \baselineskip \z@ - \m@th - \let\\\@arraycr \let\tabularnewline\\\let\par\@empty \@preamble} -\newdimen \extrarowheight -\extrarowheight=0pt -\def\@arstrut{\unhcopy\@arstrutbox} -\def\@arraycr{\relax\iffalse{\fi\ifnum 0=`}\fi - \@ifstar \@xarraycr \@xarraycr} -\def\@xarraycr{\@ifnextchar [% - \@argarraycr {\ifnum 0=`{}\fi\cr}} -\def\@argarraycr[#1]{\ifnum0=`{}\fi\ifdim #1>\z@ - \expandafter\@xargarraycr\else - \expandafter\@yargarraycr\fi{#1}} -\def\@xargarraycr#1{\unskip - \@tempdima #1\advance\@tempdima \dp\@arstrutbox - \vrule \@depth\@tempdima \@width\z@ \cr} -\def\@yargarraycr#1{\cr\noalign{\vskip #1}} -\long\def\multicolumn#1#2#3{% - \multispan{#1}\begingroup - \def\@addamp{\if@firstamp \@firstampfalse \else - \@preamerr 5\fi}% - \@mkpream{#2}\@addtopreamble\@empty - \endgroup - \def\@sharp{#3}% - \@arstrut \@preamble - \null - \ignorespaces} -\let\d@llarbegin\begingroup -\let\d@llarend\endgroup -\def\array{\col@sep\arraycolsep - \def\d@llarbegin{$}\let\d@llarend\d@llarbegin\gdef\@halignto{}% - \@tabarray} -\def\@tabarray{\@ifnextchar[{\@array}{\@array[c]}} -\def\tabular{\gdef\@halignto{}\@tabular} -\expandafter\def\csname tabular*\endcsname#1{% - \setlength\dimen@{#1}% - \xdef\@halignto{to\the\dimen@}\@tabular} -\def\@tabular{% - \leavevmode - \hbox \bgroup $\col@sep\tabcolsep \let\d@llarbegin\begingroup - \let\d@llarend\endgroup - \@tabarray} -\def\endarray{\crcr \egroup \egroup \gdef\@preamble{}} -\def\endtabular{\endarray $\egroup} -\expandafter\let\csname endtabular*\endcsname=\endtabular -\let\@ampacol=\relax \let\@expast=\relax -\let\@arrayclassiv=\relax \let\@arrayclassz=\relax -\let\@tabclassiv=\relax \let\@tabclassz=\relax -\let\@arrayacol=\relax \let\@tabacol=\relax -\let\@tabularcr=\relax \let\@@endpbox=\relax -\let\@argtabularcr=\relax \let\@xtabularcr=\relax -\def\@preamerr#1{\def\@tempd{{..} at wrong position: }% - \PackageError{array}{% - \ifcase #1 Illegal pream-token (\@nextchar): `c' used\or %0 - Missing arg: token ignored\or %1 - Empty preamble: `l' used\or %2 - >\@tempd token ignored\or %3 - <\@tempd changed to !{..}\or %4 - Only one column-spec. allowed.\fi}\@ehc} %5 -\def\newcolumntype#1{% - \edef\NC@char{\string#1}% - \@ifundefined{NC@find@\NC@char}% - {\@tfor\next:=<>clrmbp@!|\do{\if\noexpand\next\NC@char - \PackageWarning{array}% - {Redefining primitive column \NC@char}\fi}% - \NC@list\expandafter{\the\NC@list\NC@do#1}}% - {\PackageWarning{array}{Column \NC@char\space is already defined}}% - \@namedef{NC@find@\NC@char}##1#1{\NC@{##1}}% - \@ifnextchar[{\newcol@{\NC@char}}{\newcol@{\NC@char}[0]}} -\def\newcol@#1[#2]#3{\expandafter\@reargdef - \csname NC@rewrite@#1\endcsname[#2]{\NC@find#3}} -\def\NC@#1{% - \@temptokena\expandafter{\the\@temptokena#1}\futurelet\next\NC@ifend} -\def\NC@ifend{% - \ifx\next\relax - \else\@tempswatrue\expandafter\NC@rewrite\fi} -\def\NC@do#1{% - \expandafter\let\expandafter\NC@rewrite - \csname NC@rewrite@\string#1\endcsname - \expandafter\let\expandafter\NC@find - \csname NC@find@\string#1\endcsname - \expandafter\@temptokena\expandafter{\expandafter}% - \expandafter\NC@find\the\@temptokena#1\relax} -\def\showcols{{\def\NC@do##1{\let\NC@do\NC@show}\the\NC@list}} -\def\NC@show#1{% - \typeout{Column #1\expandafter\expandafter\expandafter\NC@strip - \expandafter\meaning\csname NC@rewrite@#1\endcsname\@@}} -\def\NC@strip#1:#2->#3 #4\@@{#2 -> #4} -\newtoks\NC@list -\newcolumntype{*}[2]{} -\long\@namedef{NC@rewrite@*}#1#2{% - \count@#1 - \loop - \ifnum\count@>\z@ - \advance\count@\m@ne - \@temptokena\expandafter{\the\@temptokena#2}% - \repeat - \NC@find} -\let\@xexpast\relax -\let\@xexnoop\relax -\def\save@decl{\toks \count@ = \expandafter\expandafter\expandafter - {\expandafter\@nextchar\the\toks\count@}} -\def\@mkpream#1{\gdef\@preamble{}\@lastchclass 4 \@firstamptrue - \let\@sharp\relax \let\@startpbox\relax \let\@endpbox\relax - \@temptokena{#1}\@tempswatrue - \@whilesw\if@tempswa\fi{\@tempswafalse\the\NC@list}% - \count@\m@ne - \let\the@toks\relax - \prepnext@tok - \expandafter \@tfor \expandafter \@nextchar - \expandafter :\expandafter =\the\@temptokena \do - {\@testpach - \ifcase \@chclass \@classz \or \@classi \or \@classii - \or \save@decl \or \or \@classv \or \@classvi - \or \@classvii \or \@classviii - \or \@classx - \or \@classx \fi - \@lastchclass\@chclass}% - \ifcase\@lastchclass - \@acol \or - \or - \@acol \or - \@preamerr \thr@@ \or - \@preamerr \tw@ \@addtopreamble\@sharp \or - \or - \else \@preamerr \@ne \fi - \def\the@toks{\the\toks}} -\let\@classix\relax -\def\@classviii{\ifnum \@lastchclass >\z@\ifnum\@lastchclass=\tw@\else - \@preamerr 4\@chclass 6 \@classvi \fi\fi} -\def\@classv{\save@decl - \expandafter\NC@ecs\@nextchar\extracolsep{}\extracolsep\@@@ - \@addtopreamble{\d@llarbegin\the@toks\the\count@\relax\d@llarend}% - \prepnext@tok} -\def\NC@ecs#1\extracolsep#2#3\extracolsep#4\@@@{\def\@tempa{#2}% - \ifx\@tempa\@empty\else\toks\count@={#1\tabskip#2\relax#3}\fi} -\def\@tabarray{\@ifnextchar[{\@@array}{\@@array[c]}} -\let\@@array\@array -\def\endarray{\crcr \egroup \egroup \@arrayright \gdef\@preamble{}} -\let\@arrayleft\@empty -\let\@arrayright\@empty -\newlength{\extratabsurround} -\setlength{\extratabsurround}{2pt} -\newlength{\backup@length} -\newcommand{\firsthline}{% - \multicolumn1c{% - \global\backup@length\ht\@arstrutbox - \global\advance\backup@length\dp\@arstrutbox - \global\advance\backup@length\arrayrulewidth - \raise\extratabsurround\copy\@arstrutbox - }\\[-\backup@length]\hline -} -\newcommand{\lasthline}{\hline\multicolumn1c{% - \global\backup@length2\ht\@arstrutbox - \global\advance\backup@length2\dp\@arstrutbox - \global\advance\backup@length\arrayrulewidth - }\\[-\backup@length]% - \multicolumn1c{% - \lower\extratabsurround\copy\@arstrutbox - }% -} -\CheckCommand*\@xhline{\ifx\reserved@a\hline - \vskip\doublerulesep - \vskip-\arrayrulewidth - \fi - \ifnum0=`{\fi}} -\renewcommand*\@xhline{\ifx\reserved@a\hline - \vskip\doublerulesep - \fi - \ifnum0=`{\fi}} -\endinput -%% -%% End of file `array.sty'. diff --git a/manuscript/bioinfo.cls b/manuscript/bioinfo.cls deleted file mode 100644 index bcb7a5c..0000000 --- a/manuscript/bioinfo.cls +++ /dev/null @@ -1,928 +0,0 @@ -\newcommand\classname{bioinfo} -\newcommand\lastmodifieddate{2003/02/08} -\newcommand\versionnumber{0.1} - -% Are we printing crop marks? -\newif\if@cropmarkson \@cropmarksontrue - -\NeedsTeXFormat{LaTeX2e}[2001/06/01] -\ProvidesClass{\classname}[\lastmodifieddate\space\versionnumber] - -\setlength{\paperheight}{11truein} -\setlength{\paperwidth}{8.5truein} - -\newif\if@final - -\DeclareOption{draft}{\PassOptionsToPackage{draft}{graphicx}} -\DeclareOption{a4paper}{\PassOptionsToPackage{a4}{crop}} -\DeclareOption{centre}{\PassOptionsToPackage{center}{crop}} -\DeclareOption{crop}{\PassOptionsToPackage{cam}{crop}\global\@cropmarksontrue} -\DeclareOption{nocrop}{\PassOptionsToPackage{off}{crop}\global\@cropmarksonfalse} -\DeclareOption{info}{\PassOptionsToPackage{info}{crop}} -\DeclareOption{noinfo}{\PassOptionsToPackage{noinfo}{crop}} -\DeclareOption{final}{\global\@finaltrue} - -\ExecuteOptions{a4paper,nocrop,centre,info} - -\ProcessOptions - -% Load all necessary packages -\RequirePackage{inputenc,crop,graphicx,amsmath,array,color,amssymb,flushend,stfloats,amsthm,chngpage,times} -%\RequirePackage[LY1]{fontenc} -%\RequirePackage[LY1,mtbold]{mathtime} -\def\helvetica{\fontfamily{phv}\selectfont} -\def\helveticaitalic{\fontfamily{phv}\itshape\selectfont} -\def\helveticabold{\fontfamily{phv}\bfseries\selectfont} -\def\helveticabolditalic{\fontfamily{phv}\bfseries\itshape\selectfont} - -% Not sure if needed. -\newcommand\@ptsize{0} - -% Set twoside printing -\@twosidetrue - -% Marginal notes are on the outside edge -\@mparswitchfalse - -\reversemarginpar - -\renewcommand\normalsize{% - \@setfontsize\normalsize{9}{11}% - \abovedisplayskip 10\p@ \@plus2\p@ \@minus5\p@ - \abovedisplayshortskip \z@ \@plus3\p@ - \belowdisplayshortskip 6\p@ \@plus3\p@ \@minus3\p@ - \belowdisplayskip \abovedisplayskip - \let\@listi\@listI} -\normalsize -\let\@bls\baselineskip - -\newcommand\small{% - \@setfontsize\small{9}{11}% - \abovedisplayskip 11\p@ minus 3\p@ - \belowdisplayskip \abovedisplayskip - \abovedisplayshortskip \z@ plus 2\p@ - \belowdisplayshortskip 4\p@ plus 2\p@ minus2\p@ - \def\@listi{\topsep 4.5\p@ plus 2\p@ minus 1\p@ - \itemsep \parsep - \topsep 4\p@ plus 2\p@ minus 2\p@}} - -\newcommand\footnotesize{% - \@setfontsize\footnotesize{8}{10}% - \abovedisplayskip 6\p@ minus 3\p@ - \belowdisplayskip\abovedisplayskip - \abovedisplayshortskip \z@ plus 3\p@ - \belowdisplayshortskip 6\p@ plus 3\p@ minus 3\p@ - \def\@listi{\topsep 3\p@ plus 1\p@ minus 1\p@ - \parsep 2\p@ plus 1\p@ minus 1\p@\itemsep \parsep}} - -\def\scriptsize{\@setfontsize\scriptsize{7pt}{9pt}} -\def\tiny{\@setfontsize\tiny{5pt}{7pt}} -\def\large{\@setfontsize\large{11.5pt}{12pt}} -\def\Large{\@setfontsize\Large{14pt}{16}} -\def\LARGE{\@setfontsize\LARGE{15pt}{17pt}} -\def\huge{\@setfontsize\huge{22pt}{22pt}} -\def\Huge{\@setfontsize\Huge{30pt}{30pt}} - -\DeclareOldFontCommand{\rm}{\normalfont\rmfamily}{\mathrm} -\DeclareOldFontCommand{\sf}{\normalfont\sffamily}{\mathsf} -\DeclareOldFontCommand{\tt}{\normalfont\ttfamily}{\mathtt} -\DeclareOldFontCommand{\bf}{\normalfont\bfseries}{\mathbf} -\DeclareOldFontCommand{\it}{\normalfont\itshape}{\mathit} -\DeclareOldFontCommand{\sl}{\normalfont\slshape}{\@nomath\sl} -\DeclareOldFontCommand{\sc}{\normalfont\scshape}{\@nomath\sc} - -% Line spacing -\setlength\lineskip{1\p@} -\setlength\normallineskip{1\p@} -\renewcommand\baselinestretch{} - -% Paragraph dimensions and inter-para spacing -\setlength\parskip{0\p@} -\setlength\parindent{3mm} - -% Set inter-para skips -\setlength\smallskipamount{3\p@ \@plus 1\p@ \@minus 1\p@} -\setlength\medskipamount{6\p@ \@plus 2\p@} -\setlength\bigskipamount{12\p@ \@plus 4\p@ \@minus 4\p@} - -% Page break penalties -\@lowpenalty 51 -\@medpenalty 151 -\@highpenalty 301 - -% Disallow widows and orphans -\clubpenalty 10000 -\widowpenalty 10000 - -% Disable page breaks before equations, allow pagebreaks after -% equations and discourage widow lines before equations. -\displaywidowpenalty 100 -\predisplaypenalty 10000 -\postdisplaypenalty 2500 - -% Allow breaking the page in the middle of a paragraph -\interlinepenalty 0 - -% Disallow breaking the page after a hyphenated line -\brokenpenalty 10000 - -% Hyphenation; don't split words into less than three characters -\lefthyphenmin=3 -\righthyphenmin=3 - -% -% Set page layout dimensions -% -\setlength\headheight{16\p@} % height of running head -\setlength\topmargin{2.9pc} % head margin -\addtolength\topmargin{-1in} % subtract out the 1 inch driver margin - 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\hbox to \textwidth{% - {\helvetica\itshape\bfseries\fontsize{19}{12}\selectfont {\color{gray}BIOINFORMATICS} - \hfil - \if@appnotes APPLICATIONS NOTE\hfil\fi - }% -\enskip \parbox[b]{11.3pc}{% - \helvetica - \flushright\fontsize{8}{10}\fontshape{it}\selectfont - Vol. 00\ no. 00 \@pubyear\\ - \hfill Pages \thepagerange - }} - \rule{\textwidth}{1\p@}\par% - \helvetica - \hbox to \textwidth{% - \parbox[t]{36.5pc}{% - \vspace*{1sp} - {\helveticabold\fontsize{16}{21}\selectfont\raggedright \@title \par}% - \vspace{4.5\p@} - {\helvetica\fontsize{13}{15}\selectfont\raggedright \@author \par}% - \vspace{4\p@} - {\helvetica\fontsize{10}{12}\selectfont\raggedright \@address \par}% - \vspace{4\p@} - {\helvetica\fontsize{8}{10}\selectfont\raggedright \@history \par} - \vspace{24\p@} - {\helvetica\fontsize{10}{12}\selectfont\raggedright \@editor \par} - %\vspace{20\p@} - }% - } - \vspace{14.5\p@}% - \rule{\textwidth}{1\p@}% - \vspace{12\p@ plus 6\p@ minus 6\p@}% - \vspace{\extraspace} - } -%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% - -%%%%%%%%%%%%%%%%%%%%%%%%%%%% Abstract %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -\newcommand{\absection}[1]{% - \par\noindent{\bfseries #1}\space\ignorespaces} - -\newenvironment{abstract}{% - \begingroup - \let\section\absection - \fontfamily{\sfdefault}\fontsize{8}{11}\sffamily\selectfont - {\fontseries{b}\selectfont ABSTRACT}\par} -{\endgroup\bigskip\@afterheading\@afterindentfalse\vskip 12pt plus 3pt minus 1pt} - -% Section macros - -% Lowest level heading that takes a number by default -\setcounter{secnumdepth}{3} - -\renewcommand{\@seccntformat}[1]{\csname the#1\endcsname\quad} - -\def\section{% - \@startsection{section}{1}{\z@} - {-22\p@ plus -3\p@}{3\p@} - {\reset@font\raggedright\helveticabold\fontsize{10}{12}\selectfont\MakeUppercase}} - -\def\subsection{% - \@startsection{subsection}{2}{\z@} - {-11\p@ plus -2\p@}{3\p@} - {\reset@font\raggedright\mathversion{bold}\fontseries{b}\fontsize{10}{12}\selectfont}} - -\def\subsubsection{% - \@startsection{subsubsection}{3}{\z@} - {-11\p@ plus -1\p@}{-1em} - {\reset@font\normalfont\normalsize\itshape}} - -\def\textcolon{\text{\rm :}} - - \def\paragraph{% - \@startsection{paragraph}{4}{\z@} - {-6\p@} - {-.4em} - {\reset@font\itshape}} - -% ******************** -% Figures and tables * -% ******************** - -% Table and array parameters -\setlength\arraycolsep{.5em} -\setlength\tabcolsep{.5em} -\setlength\arrayrulewidth{.5pt} -\setlength\doublerulesep{2.5pt} -\setlength\extrarowheight{\z@} -\renewcommand\arraystretch{1} - -\newlength{\abovecaptionskip} -\newlength{\belowcaptionskip} -\setlength{\abovecaptionskip}{13pt} -\setlength{\belowcaptionskip}{10.5pt} - -\long\def\@makecaption#1#2{\vspace{\abovecaptionskip}% - \begingroup - \footnotesize - \textbf{#1.}\enskip{#2}\par - \endgroup} - -\long\def\@tablecaption#1#2{% - \begingroup - \footnotesize - \textbf{#1.}\enskip{#2\strut\par} - \endgroup\vspace{\belowcaptionskip}} - -% Table rules -\def\toprule{\noalign{\ifnum0=`}\fi\hrule \@height 0.5pt \hrule \@height 6pt \@width 0pt \futurelet - \@tempa\@xhline} -\def\midrule{\noalign{\ifnum0=`}\fi \hrule \@height 6.75pt \@width 0pt \hrule \@height 0.5pt - \hrule \@height 6pt \@width 0pt \futurelet \@tempa\@xhline} -\def\botrule{\noalign{\ifnum0=`}\fi \hrule \@height 5.75pt \@width 0pt \hrule \@height 0.5pt \futurelet - \@tempa\@xhline} -\def\hrulefill{\leavevmode\leaders\hrule height .5pt\hfill\kern\z@} - -\def\thefigure{\@arabic\c@figure} -\def\fps@figure{tbp} -\def\ftype@figure{1} -\def\ext@figure{lof} -\def\fnum@figure{\figurename~\thefigure} -\def\figure{\@float{figure}} -\let\endfigure\end@float -\@namedef{figure*}{\@dblfloat{figure}} -\@namedef{endfigure*}{\end@dblfloat} -\def\thetable{\@arabic\c@table} -\def\fps@table{tbp} -\def\ftype@table{2} -\def\ext@table{lot} -\def\fnum@table{Table~\thetable} -\def\table{\let\@makecaption\@tablecaption\let\source\tablesource\@float{table}} -\def\endtable{\end@float} -\@namedef{table*}{\let\@makecaption\@tablecaption\@dblfloat{table}} -\@namedef{endtable*}{\end@dblfloat} - -\newif\if@rotate \@rotatefalse -\newif\if@rotatecenter \@rotatecenterfalse -\def\rotatecenter{\global\@rotatecentertrue} -\def\rotateendcenter{\global\@rotatecenterfalse} -\def\rotate{\global\@rotatetrue} -\def\endrotate{\global\@rotatefalse} -\newdimen\rotdimen -\def\rotstart#1{\special{ps: gsave currentpoint currentpoint translate - #1 neg exch neg exch translate}} -\def\rotfinish{\special{ps: currentpoint grestore moveto}} -\def\rotl#1{\rotdimen=\ht#1\advance\rotdimen by \dp#1 - \hbox to \rotdimen{\vbox to\wd#1{\vskip \wd#1 - \rotstart{270 rotate}\box #1\vss}\hss}\rotfinish} -\def\rotr#1{\rotdimen=\ht #1\advance\rotdimen by \dp#1 - \hbox to \rotdimen{\vbox to \wd#1{\vskip \wd#1 - \rotstart{90 rotate}\box #1\vss}\hss}\rotfinish} - -\newdimen\tempdime -\newbox\temptbox - -% From ifmtarg.sty -% Copyright Peter Wilson and Donald Arseneau, 2000 -\begingroup -\catcode`\Q=3 -\long\gdef\@ifmtarg#1{\@xifmtarg#1QQ\@secondoftwo\@firstoftwo\@nil} -\long\gdef\@xifmtarg#1#2Q#3#4#5\@nil{#4} -\long\gdef\@ifnotmtarg#1{\@xifmtarg#1QQ\@firstofone\@gobble\@nil} -\endgroup - -\def\tablesize{\@setfontsize\tablesize{8\p@}{10\p@}} - -\newenvironment{processtable}[3]{\setbox\temptbox=\hbox{{\tablesize #2}}% -\tempdime\wd\temptbox\@processtable{#1}{#2}{#3}{\tempdime}} -{\relax} - -\newcommand{\@processtable}[4]{% -\if@rotate -\setbox4=\vbox to \hsize{\vss\hbox to \textheight{% -\begin{minipage}{#4}% -\@ifmtarg{#1}{}{\caption{#1}}{\tablesize #2}% -\vskip7\p@\noindent -\parbox{#4}{\fontsize{7}{9}\selectfont #3\par}% -\end{minipage}}\vss}% -\rotr{4} -\else -\hbox to \hsize{\hss\begin{minipage}[t]{#4}% -\vskip2.9pt -\@ifmtarg{#1}{}{\caption{#1}}{\tablesize #2}% -\vskip6\p@\noindent -\parbox{#4}{\fontsize{7}{9}\selectfont #3\par}% -\end{minipage}\hss}\fi}% - -\newcolumntype{P}[1]{>{\raggedright\let\\\@arraycr\hangindent1em}p{#1}} - -% ****************************** -% List numbering and lettering * -% ****************************** -\def\labelenumi{{\rm\arabic{enumi}.}} -\def\theenumi{\arabic{enumi}} -\def\labelenumii{{\rm\alph{enumii}.}} -\def\theenumii{\alph{enumii}} -\def\p@enumii{\theenumi} -\def\labelenumiii{{\rm(\arabic{enumiii})}} -\def\theenumiii{\roman{enumiii}} -\def\p@enumiii{\theenumi(\theenumii)} -\def\labelenumiv{{\rm(\arabic{enumiv})}} -\def\theenumiv{\Alph{enumiv}} -\def\p@enumiv{\p@enumiii\theenumiii} -\def\labelitemi{{\small$\bullet$}} -\def\labelitemii{{\small$\bullet$}} -\def\labelitemiii{{\small$\bullet$}} -\def\labelitemiv{{\small$\bullet$}} - -\def\@listI{\leftmargin\leftmargini \topsep\medskipamount} -\let\@listi\@listI -\@listi -\def\@listii{\topsep\z@\leftmargin\leftmarginii} -\def\@listiii{\leftmargin\leftmarginiii \topsep\z@} -\def\@listiv{\leftmargin\leftmarginiv \topsep\z@} -\def\@listv{\leftmargin\leftmarginv \topsep\z@} -\def\@listvi{\leftmargin\leftmarginvi \topsep\z@} - -\setlength{\leftmargini}{3mm} -\setlength{\leftmarginii}{\z@} -\setlength{\leftmarginiii}{\z@} -\setlength{\leftmarginiv}{\z@} - -% Changes to the list parameters for enumerate -\def\enumargs{% - \partopsep \z@ - \itemsep 3\p@ - \parsep \z@ - \labelsep 0.5em - \listparindent \parindent - \itemindent \z@ - \topsep 11\p@ -} - -\def\enumerate{% - \@ifnextchar[{\@numerate}{\@numerate[0]}} - -\def\@numerate[#1]{% - \ifnum \@enumdepth >3 \@toodeep\else - \advance\@enumdepth \@ne - \edef\@enumctr{enum\romannumeral\the\@enumdepth} - \list{\csname label\@enumctr\endcsname}{% - \enumargs - \setlength{\leftmargin}{\csname leftmargin\romannumeral\the\@enumdepth\endcsname} - \usecounter{\@enumctr} - \settowidth\labelwidth{#1} - \addtolength{\leftmargin}{\labelwidth} - \addtolength{\leftmargin}{\labelsep} - \def\makelabel##1{\hss \llap{##1}}}% - \fi - } -\let\endenumerate\endlist - -% Changes to the list parameters for itemize -\def\itemargs{% - \partopsep \z@ - \itemsep 3\p@ - \parsep \z@ - \labelsep 0.5em - \rightmargin \z@ - \listparindent \parindent - \itemindent \z@ - \topsep11\p@ -} - -\def\itemize{% - \@ifnextchar[{\@itemize}{\@itemize[$\bullet$]}} - -\def\@itemize[#1]{% - \ifnum \@itemdepth >3 \@toodeep\else - \advance\@itemdepth \@ne - \edef\@itemctr{item\romannumeral\the\@itemdepth} - \list{\csname label\@itemctr\endcsname}{% - \itemargs - \setlength{\leftmargin}{\csname leftmargin\romannumeral\the\@itemdepth\endcsname} - \settowidth\labelwidth{#1} - \addtolength{\leftmargin}{\labelwidth} - \addtolength{\leftmargin}{\labelsep} - \def\makelabel##1{\hss \llap{##1}}}% - \fi - } -\let\enditemize\endlist - -\newenvironment{unlist}{% - \begin{list}{}% - {\setlength{\labelwidth}{\z@}% - \setlength{\labelsep}{\z@}% - \setlength{\topsep}{\medskipamount}% - \setlength{\itemsep}{3\p@}% - \setlength{\leftmargin}{2em}% - \setlength{\itemindent}{-2em}}} -{\end{list}} - - -% *********************** -% Quotes and Quotations * -% *********************** -\def\quotation{\par\begin{list}{}{ - \setlength{\topsep}{\medskipamount} - \setlength{\leftmargin}{2em}% - \setlength{\rightmargin}{\z@}% - \setlength\labelwidth{0pt}% - \setlength\labelsep{0pt}% - \listparindent\parindent}% - \item[]} -\def\endquotation{\end{list}} -\let\quote\quotation -\let\endquote\endquotation - -\skip\@mpfootins = \skip\footins -\fboxsep=6\p@ -\fboxrule=1\p@ - -% ******************* -% Table of contents * -% ******************* -\newcommand\@pnumwidth{4em} -\newcommand\@tocrmarg{2.55em plus 1fil} -\newcommand\@dotsep{1000} -\setcounter{tocdepth}{4} - -\def\numberline#1{\hbox to \@tempdima{{#1}}} - -\def\@authortocline#1#2#3#4#5{% - \vskip 1.5\p@ - \ifnum #1>\c@tocdepth \else - {\leftskip #2\relax \rightskip \@tocrmarg \parfillskip -\rightskip - \parindent #2\relax\@afterindenttrue - \interlinepenalty\@M - \leavevmode - \@tempdima #3\relax - \advance\leftskip \@tempdima \null\nobreak\hskip -\leftskip - {\itshape #4}\nobreak - \leaders\hbox{$\m@th - \mkern \@dotsep mu\hbox{.}\mkern \@dotsep - mu$}\hfill - \nobreak - \hb@xt@\@pnumwidth{\hfil}% - \par}% - \fi} - -\newcommand*\l@author{\@authortocline{2}{0pt}{30pt}} -\newcommand*\l@section{\@dottedtocline{3}{11pt}{20pt}} -\newcommand*\l@subsection{\@dottedtocline{4}{31pt}{29pt}} -\newcommand*\l@subsubsection[2]{} - - - -% *********** -% Footnotes * -% *********** - -\def\footnoterule{\noindent\rule{\columnwidth}{0.5pt}} -\def\@makefnmark{\@textsuperscript{\normalfont\@thefnmark}}% -\newcommand\@makefntext[1]{\noindent{\@makefnmark}\enskip#1} - -% *********** -% References * -% *********** - -\providecommand{\newblock}{} -\newenvironment{thebibliography}{% - \section{\bibname}% - \begingroup - \small - \begin{list}{}{% - \setlength{\topsep}{\z@}% - \setlength{\labelsep}{\z@}% - \settowidth{\labelwidth}{\z@}% - \setlength{\leftmargin}{4mm}% - \setlength{\itemindent}{-4mm}}\small} -{\end{list}\endgroup} - -\RequirePackage{natbib} - -% ********** -% Appendix * -% ********** -\newif\ifappend % Are we in the Appendix? -\def\appendix{\par - \setcounter{section}{0} - \setcounter{subsection}{0} - \appendtrue -} - -%Math parameters - -\setlength{\jot}{5\p@} -\mathchardef\@m=1500 % adapted value - -\def\frenchspacing{\sfcode`\.\@m \sfcode`\?\@m \sfcode`\!\@m - \sfcode`\:\@m \sfcode`\;\@m \sfcode`\,\@m} - -% Theorems -\def\th@plain{% -%% \let\thm@indent\noindent % no indent -\thm@headfont{\quad\scshape}% heading font is bold -\thm@notefont{\upshape\mdseries}% same as heading font -\thm@headpunct{.}% no period after heading -\thm@headsep 5\p@ plus\p@ minus\p@\relax -%% \let\thm@swap\@gobble -%% \thm@preskip\topsep -%% \thm@postskip\theorempreskipamount -\itshape % body font -} - -\vbadness=9999 -\tolerance=9999 -\doublehyphendemerits=10000 -\doublehyphendemerits 640000 % corresponds to badness 800 -\finalhyphendemerits 1000000 % corresponds to badness 1000 - -\flushbottom -\frenchspacing -\ps@headings -\twocolumn - -% Screen PDF compatability -\newcommand{\medline}[1]{% - \unskip\unskip\ignorespaces} - - -%%%%for smaller size text -\newenvironment{methods}{% - \begingroup -\def\section{% - \@startsection{section}{1}{\z@} - {-24\p@ plus -3\p@}{4\p@} - {\reset@font\raggedright\helveticabold\fontsize{10}{12}\selectfont\MakeUppercase}} - \def\subsection{% - \@startsection{subsection}{2}{\z@} - {-5\p@ plus -2\p@}{4\p@} - {\reset@font\raggedright\mathversion{bold}\fontseries{b}\fontsize{10}{12}\selectfont}} - \def\subsubsection{% - \@startsection{subsubsection}{3}{\z@} - {-6\p@ plus -1\p@}{-1em} - {\reset@font\normalfont\normalsize\itshape}} -\footnotesize - \par} -{\par\endgroup\bigskip\@afterheading\@afterindentfalse} - - - -\graphicspath{{g:/artwork/oup/bioinfo/}} - -\language=2 - -\hyphenation{Figure Table Figures Tables} - -\newcommand{\href}[2]{#2} - -\renewenvironment{proof}[1][\proofname]{\par - \normalfont \topsep6\p@\@plus6\p@\relax - \labelsep 0.5em - \trivlist - \item[\hskip\labelsep\hskip1em\textsc{#1}.]\ignorespaces -}{\endtrivlist\@endpefalse} - -%%Different Bonds - -\def\sbond{\ensuremath{\raise.25ex\hbox{${-}\!\!\!\!{-}$}}\kern -.9pt} -\def\dbond{\ensuremath{\raise.25ex\hbox{=$\!$=}}} -\def\tbond{\ensuremath{\raise.20ex\hbox{${\equiv}\!\!\!{\equiv}$}}} - -% Author queries -%\fboxsep=4\p@ -%\fboxrule=0.5\p@ -\newcommand{\query}[2][0pt]{}% -% \marginpar{\vspace*{#1}% -% {\parbox{\marginparwidth}{% -% \raggedright\fontsize{6}{8}\selectfont -% #2}}}} - -\renewcommand{\dag}{{\mathversion{normal}$^{\dagger}$}} - -\endinput diff --git a/manuscript/chngpage.sty b/manuscript/chngpage.sty deleted file mode 100644 index fd7e4e4..0000000 --- a/manuscript/chngpage.sty +++ /dev/null @@ -1,295 +0,0 @@ -% chngpage.sty -% -% Provides commands to change the page layout in the middle of a document, -% and to robustly check for typesetting on odd or even pages. -% Instructions for use are at the end of this file. -% -% author: Peter Wilson (CUA) -% (now at peter.r.wilson@boeing.com) -% Copyright 2000 -% Released under the Latex Project Public License -% -% -\NeedsTeXFormat{LaTeX2e} -\ProvidesPackage{chngpage}[2001/01/31 v1.1b change page layout] - -%% Note: internal package commands all include the string `cp@' -%% new \if for the strict option -\newif\ifcpstrict - \cpstrictfalse - -%% Declare and process options -\DeclareOption{strict}{\cpstricttrue} -\ProcessOptions\relax - -%% new commands for getting a page number from a label (see ltxref.dtx) -\newif\ifcpoddpage -\newcounter{cp@cnt} -\newcounter{cp@tempcnt} -\newcommand{\cplabelprefix}{^_} - -\newcommand{\cp@setref}[3]{% - \ifx#1\relax - 0% in case no label in the *.aux file (page number made = 0) - \else - \expandafter#2#1% - \fi} - -\newcommand{\cp@pageref}[1]{% - \expandafter\cp@setref\csname r@#1\endcsname\@secondoftwo{#1}} - -%% User level command to check for odd/even page -\DeclareRobustCommand{\checkoddpage}{% - \stepcounter{cp@cnt}\label{\cplabelprefix\thecp@cnt}% - \cpoddpagefalse% - \setcounter{cp@tempcnt}{\cp@pageref{\cplabelprefix\thecp@cnt}}% - \ifodd\c@cp@tempcnt\cpoddpagetrue\fi} - - -%% copy of some of the code from the ifmtarg package to save requiring ifmtarg -\begingroup -\catcode`\Q=3 -\long\gdef\@ifmtarg#1{\@xifmtarg#1QQ\@secondoftwo\@firstoftwo\@nil} -\long\gdef\@xifmtarg#1#2Q#3#4#5\@nil{#4} -\endgroup - -%% set the page output parameters -%\newcommand{\ch@ngetext}{% -\DeclareRobustCommand{\ch@ngetext}{% - \setlength{\@colht}{\textheight}\setlength{\@colroom}{\textheight}% - \setlength{\vsize}{\textheight}\setlength{\columnwidth}{\textwidth}% - \if@twocolumn% - \advance\columnwidth-\columnsep \divide\columnwidth\tw@% - \@firstcolumntrue% - \fi% - \setlength{\hsize}{\columnwidth}% - \setlength{\linewidth}{\hsize}% -} - -%\newcommand{\changetext}[5]{% -\DeclareRobustCommand{\changetext}[5]{% - \@ifmtarg{#1}{}{\addtolength{\textheight}{#1}}% - \@ifmtarg{#2}{}{\addtolength{\textwidth}{#2}}% - \@ifmtarg{#3}{}{\addtolength{\evensidemargin}{#3}}% - \@ifmtarg{#4}{}{\addtolength{\oddsidemargin}{#4}}% - \@ifmtarg{#5}{}{\addtolength{\columnsep}{#5}}% - \ch@ngetext% -} - -%\newcommand{\changepage}[9]{% -\DeclareRobustCommand{\changepage}[9]{% - \@ifmtarg{#1}{}{\addtolength{\textheight}{#1}}% - \@ifmtarg{#2}{}{\addtolength{\textwidth}{#2}}% - \@ifmtarg{#3}{}{\addtolength{\evensidemargin}{#3}}% - \@ifmtarg{#4}{}{\addtolength{\oddsidemargin}{#4}}% - \@ifmtarg{#5}{}{\addtolength{\columnsep}{#5}}% - \ch@ngetext% - \@ifmtarg{#6}{}{\addtolength{\topmargin}{#6}}% - \@ifmtarg{#7}{}{\addtolength{\headheight}{#7}}% - \@ifmtarg{#8}{}{\addtolength{\headsep}{#8}}% - \@ifmtarg{#9}{}{\addtolength{\footskip}{#9}}% -} - - -\newenvironment{adjustwidth}[3][\@empty]{% - \begin{list}{}{% - \topsep\z@% - \listparindent\parindent% - \parsep\parskip% - \@ifmtarg{#2}{\setlength{\leftmargin}{\z@}}{\setlength{\leftmargin}{#2}}% - \@ifmtarg{#3}{\setlength{\rightmargin}{\z@}}{\setlength{\rightmargin}{#3}}% - \ifx\@empty #1\relax \else - \cpoddpagefalse - \ifcpstrict\checkoddpage\else - \ifodd\c@page\cpoddpagetrue\fi - \fi - \ifcpoddpage\else % even numbered page - \@ifmtarg{#3}{\setlength{\leftmargin}{\z@}}{\setlength{\leftmargin}{#3}}% - \@ifmtarg{#2}{\setlength{\rightmargin}{\z@}}{\setlength{\rightmargin}{#2}}% - \fi - \fi} - \item[]}{\end{list}} - - - -\endinput - -% Usage: -% ------ -% -%%%%%%%%%%%%% -% \changetext -%%%%%%%%%%%%% -% The \changetext command is for changing the size and horizontal position -% of the text block on a page. The command takes 5 arguments, each of which -% is a length or is empty. i.e., -% -% \changetext{textheight}{textwidth}{evensidemargin}{oddsidemargin}{columnsep} -% -% The given lengths are added to the corresponding current lengths and -% the remainder of the current page is typeset using the changed text block -% layout. The new layout remains in effect until another \change... command -% is issued. -% -%%%%%%%%%%%%% -% \changepage -%%%%%%%%%%%%% -% The \changepage command is for changing the general layout of -% a page. The command takes 9 arguments, each of which is a length or is empty. -% The first 5 arguments are the same as for \changetext and have the same effect. -% The last four arguments are: -% -% \changepage{5 args}{topmargin}{headheight}{headsep}{footskip} -% -% These lengths are added to the corresponding current lengths and -% thus modify the vertical positions of the elements of the page. The -% remainder of the current page is typeset using the changed text block -% and page layout. The new layout remains in effect until another -% \change... command is issued. -% -% NOTE 1: Not supplying a value for a length argument is equivalent -% to giving it a zero length value. -% -% NOTE 2: For any given page, everything is constant except for the textwidth -% and columnsep (for example, what is the meaning of two -% topmargins on a single column page?). -% It is therefore best to change anything else at the -% start of a new page. Further, any changes only apply to whole -% paragraphs. If you want an odd shaped paragraph use either -% the hanging package or the TeX \parshape command. -% -% For example, to change from single column pages to double column -% pages where the text block is both shorter and wider, then to revert -% back to the initial layout: -% ... single column normal page -% \newpage % or \clearpage -% \changetext{-5\baselineskip}{10em}{-5em}{-5em}{} -% \twocolumn -% ... two column pages -% \clearpage -% \changetext{5\baselineskip}{-10em}{5em}{5em}{} -% \onecolumn -% ... normal pages -% -% Note the adjustments to the margins which will keep the vertical centerline -% of the textblock at the same position on the page. -% -% As another example, to increase the width of a single paragraph: -% -% \changetext{0pt}{5em}{}{}{}% -% Start of wider paragraph text ... -% ... end of paragraph. -% -% \changetext{0pt}{-5em}{}{}{} -% Start of a normal paragraph ... -% -% Under some circumstances you can include a \change... command as part of -% the argument to \afterpage (from the afterpage package) and it may work. -% Similarly it may work in a heading style used for \thispagestyle to change -% a single page. -% -%%%%%%%%%%%%% -% adjustwidth -%%%%%%%%%%%%% -% Within an adjustwidth environment the left and right margins can be -% adjusted. The environment takes one optional argument and two required -% length arguments: -% -% \begin{adjustwidth}[]{leftmargin}{rightmargin} -% -% A positive length value will increase the relevant margin (shortening -% the text lines) while a negative length value will decrease the margin -% (lengthening text lines). An empty length argument means no change -% to the margin. At the end of the environment the margins revert to -% their original values. -% -% For example, to extend the text into the right margin: -% \begin{adjustwidth}{}{-8em} -% -% Any appearance of the optional argument (even just []) will cause -% the values of the margins to switch between odd and even pages. -% -% If the document is being set twosided it might be advantageous -% to have any wider text extending into the outside margin. This -% could be done via the optional argument, as: -% \begin{adjustwidth}[]{}{-8em} -% -% To have the adjusted text horizontally centered with respect to -% any surrounding text, the margins should be adjusted equally: -% \begin{adjustwidth}{-4em}{-4em} -% -% For interest, \begin{quotation} is pretty much equivalent -% to \begin{adjustwidth}{2.5em}{2.5em} -% -% The environment may also be used inside a float if the contents are -% a bit too wide for the text block, but can still fit within the physical -% page: -% \begin{figure} -% \begin{adjustwidth}{-2em}{-2em} -% \includegraphics{wide} -% \caption{Wide figure} -% \end{adjustwidth} -% \end{figure} -% -% Sometimes, because of the asynchronous nature of the TeX output -% routine, the margin switching may be incorrect (like \marginpar sometimes) -% near the top of a page. This can be corrected by using the package -% option `strict' (i.e., \usepackage[strict]{chngpage}), which causes -% adjustwidth to use the \checkoddpage command (see below). -% -% A disadvantage of the strict option is that the package generates -% a new label for each adjustwidth environment, and TeX may run out -% of space if there are an excessive number of labels in the document. -% -% Whether or not the strict option is used, `strict adjustwidths' -% can be turned on by putting the command \cpstricttrue before -% the environment, and turned of by using \cpstrictfalse. -% -% NOTE: In a twocolumn document, the adjustwidth environment -% treats both columns equally. For example, if the width is meant -% to be wider at the outer margin, then on odd pages the extra width -% will be at the right of any column, and on even pages the extra -% will be at the left of any column. You can get interesting effects -% by careful hand tuning on two column pages. -% -%%%%%%%%%%%%%%% -% \checkoddpage -%%%%%%%%%%%%%%% -% The \checkoddpage command can be used anywhere in the body of -% a document to determine if TeX is typesetting on an odd or -% even numbered page. If on an odd page then \ifcpoddpage is -% set TRUE, otherwise (on an even page) \ifcpoddpage is set -% FALSE. -% -% This works by the \checkoddpage command generating a label and -% then checking the \pageref for the label (actually, a special version -% of \pageref is required and is used internally by \checkoddpage). -% This mechanism requires at least two LaTeX passes to ensure that -% the labels have settled (on the initial pass there will be no labels -% in the *.aux file to be checked). -% -% The label identifier is composed of the command \cplabelprefix -% and an automatically generated number. \cplabelprefix, initially -% defined as `^_', can be changed in the preamble if it will cause -% a clash with any author-defined labels. The default labels will -% be of the form `^_N' where N is a positive integer. -% -% -% Changes in version 1.1b (2001/01/31) -% ---------------------- -% o Added strict option for robust adjustwidth; checks odd/even -% pages via labels instead of by the page counter. -% -% Changes in version 1.1a (2001/01/18) -% ---------------------- -% o Added missing {} in last 4 arguments of \changepage -% -% Changes in version 1.1 (2000/07/22) -% ---------------------- -% o Empty arguments made available -% o Added adjustwidth environment -% -% -% Peter W. -% -% diff --git a/manuscript/color.sty b/manuscript/color.sty deleted file mode 100644 index 6f68af6..0000000 --- a/manuscript/color.sty +++ /dev/null @@ -1,176 +0,0 @@ -%% -%% This is file `color.sty', -%% generated with the docstrip utility. -%% -%% The original source files were: -%% -%% color.dtx (with options: `package') -%% -%% color.dtx Copyright (C) 1994--1999 David Carlisle -%% -%% This file is part of the Standard LaTeX `Graphics Bundle'. -%% It may be distributed under the terms of the LaTeX Project Public -%% License, as described in lppl.txt in the base LaTeX distribution. -%% Either version 1.0 or, at your option, any later version. -%% -\NeedsTeXFormat{LaTeX2e}[1995/12/01] -\ProvidesPackage{color} - [1999/02/16 v1.0i Standard LaTeX Color (DPC)] -\edef\Gin@codes{% - \catcode`\noexpand\^^A\the\catcode`\^^A\relax - \catcode`\noexpand\"\the\catcode`\"\relax - \catcode`\noexpand\*\the\catcode`\*\relax - \catcode`\noexpand\!\the\catcode`\!\relax - \catcode`\noexpand\:\the\catcode`\:\relax} -\catcode`\^^A=\catcode`\% -\catcode`\"=12 -\catcode`\*=11 -\catcode`\!=12 -\catcode`\:=12 -\providecommand\Gin@driver{} -\def\c@lor@error#1{% - \@latex@error{Undefined color #1}\@ehd} -\DeclareOption{monochrome}{% - \def\c@lor@error#1{\PackageInfo{color}{Undefined color #1}}% - \AtEndOfPackage{% - \colors@false - \def\set@color{% - \c@lor@special\m@ne - {color push \current@color}\aftergroup\reset@color}% - \def\reset@color{\c@lor@special\m@ne{color pop}}% - \def\set@page@color{% - \c@lor@special\m@ne{background \current@color}}% - \def\define@color#1#2{% - \c@lor@special\m@ne{define #1 #2}}}} -\DeclareOption{debugshow}{\catcode`\^^A=9 \let\GDebug\typeout} -\DeclareOption{dvips}{\def\Gin@driver{dvips.def}% - \def\c@lor@namefile{dvipsnam.def}} -\DeclareOption{xdvi}{\ExecuteOptions{dvips,monochrome}} -\DeclareOption{dvipdf}{\def\Gin@driver{dvipdf.def}} -\DeclareOption{dvipdfm}{\def\Gin@driver{dvipdfm.def}} -\DeclareOption{pdftex}{\def\Gin@driver{pdftex.def}} -\DeclareOption{dvipsone}{\def\Gin@driver{dvipsone.def}} -\DeclareOption{dviwindo}{\ExecuteOptions{dvipsone}} -\DeclareOption{emtex}{\def\Gin@driver{emtex.def}} -\DeclareOption{dviwin}{\def\Gin@driver{dviwin.def}} -\DeclareOption{oztex}{\ExecuteOptions{dvips}} -\DeclareOption{textures}{\def\Gin@driver{textures.def}} -\DeclareOption{pctexps}{\def\Gin@driver{pctexps.def}} -\DeclareOption{pctexwin}{\def\Gin@driver{pctexwin.def}} -\DeclareOption{pctexhp}{\def\Gin@driver{pctexhp.def}} -\DeclareOption{pctex32}{\def\Gin@driver{pctex32.def}} -\DeclareOption{truetex}{\def\Gin@driver{truetex.def}} -\DeclareOption{tcidvi}{\def\Gin@driver{tcidvi.def}} -\DeclareOption{vtex}{\def\Gin@driver{vtex.def}} -\DeclareOption{dvipsnames}{\def\c@lor@namefile{dvipsnam.def}} -\DeclareOption{nodvipsnames}{\let\c@lor@namefile\relax} -\let\c@lor@usename\@gobble -\DeclareOption{usenames}{% - \def\c@lor@usename#1{% - \expandafter\color@named\csname\string\color @#1\endcsname{#1}}} -\DeclareRobustCommand\color{% - \@ifnextchar[\@undeclaredcolor\@declaredcolor} -\def\@undeclaredcolor[#1]#2{% - \@ifundefined{color@#1}% - {\c@lor@error{model `#1'}}% - {\csname color@#1\endcsname\current@color{#2}% - \set@color}% - \ignorespaces} -\def\@declaredcolor#1{% - \@ifundefined{\string\color @#1}% - {\c@lor@error{`#1'}}% - {\expandafter\let\expandafter\current@color - \csname\string\color @#1\endcsname - \set@color}% - \ignorespaces} -\def\textcolor#1#{\@textcolor{#1}} -\def\@textcolor#1#2#3{\protect\leavevmode{\color#1{#2}#3}} -\def\pagecolor{% - \begingroup - \let\ignorespaces\endgroup - \let\set@color\set@page@color - \color} -\def\definecolor#1#2#3{% - \@ifundefined{color@#2}% - {\c@lor@error{model `#2'}}% - {\@ifundefined{\string\color @#1}{}% - {\PackageInfo{color}{Redefining color #1}}% - \csname color@#2\expandafter\endcsname - \csname\string\color @#1\endcsname{#3}}} -\def\DefineNamedColor#1#2#3#4{% - \@ifundefined{define@color@#1}% - {\c@lor@error{model `#1'}}% - {\@ifundefined{color@#3}% - {\c@lor@error{model `#3'}}% - {\@ifundefined{c@lor@#1@#2}{}% - {\PackageInfo{color}{Redefining color #2 in named color model}}% - \csname color@#3\endcsname\@tempa{#4}% - \csname define@color@#1\endcsname{#2}\@tempa - \c@lor@usename{#2}}}} -\@onlypreamble\DefineNamedColor -\newif\ifcolors@ -\colors@true -\def\c@lor@special#1#2{% - \edef\@tempa{\write#1{#2}}\@tempa} -\InputIfFileExists{color.cfg}{}{} -\ProcessOptions -\if!\Gin@driver! - \PackageError{color} - {No driver specified} - {You should make a default driver option in a file \MessageBreak - color.cfg\MessageBreak - eg: \protect\ExecuteOptions{dvips}% - } -\else - \PackageInfo{color}{Driver file: \Gin@driver} - \@ifundefined{ver@\Gin@driver}{\input{\Gin@driver}}{} -\fi -\@ifundefined{c@lor@namefile}{}{\input{\c@lor@namefile}} -\def\normalcolor{\let\current@color\default@color\set@color} -\AtBeginDocument{\let\default@color\current@color} -\def\color@block#1#2#3{% - {\set@color\rlap{\ifcolors@\vrule\@width#1\@height#2\@depth#3\fi}}} -\def\colorbox#1#{\color@box{#1}} -\def\color@box#1#2{\color@b@x\relax{\color#1{#2}}} -\def\fcolorbox#1#{\color@fbox{#1}} -\def\color@fbox#1#2#3{% - \color@b@x{\fboxsep\z@\color#1{#2}\fbox}{\color#1{#3}}} - -\long\def\color@b@x#1#2#3{% - \leavevmode - \setbox\z@\hbox{\kern\fboxsep{\set@color#3}\kern\fboxsep}% - \dimen@\ht\z@\advance\dimen@\fboxsep\ht\z@\dimen@ - \dimen@\dp\z@\advance\dimen@\fboxsep\dp\z@\dimen@ - {#1{#2\color@block{\wd\z@}{\ht\z@}{\dp\z@}% - \box\z@}}} -\def\color@setgroup{\begingroup\set@color} -\let\color@begingroup\begingroup -\def\color@endgroup{\endgraf\endgroup} -\def\color@hbox{\hbox\bgroup\color@begingroup} -\def\color@vbox{\vbox\bgroup\color@begingroup} -\def\color@endbox{\color@endgroup\egroup} -\ifx\color@gray\@undefined - \ifx\color@rgb\@undefined - \else - \definecolor{black}{rgb}{0,0,0} - \definecolor{white}{rgb}{1,1,1} - \fi -\else - \definecolor{black}{gray}{0} - \definecolor{white}{gray}{1} -\fi -\ifx\color@rgb\@undefined\else - \definecolor{red}{rgb}{1,0,0} - \definecolor{green}{rgb}{0,1,0} - \definecolor{blue}{rgb}{0,0,1} -\fi -\ifx\color@cmyk\@undefined\else - \definecolor{cyan}{cmyk}{1,0,0,0} - \definecolor{magenta}{cmyk}{0,1,0,0} - \definecolor{yellow}{cmyk}{0,0,1,0} -\fi -\Gin@codes -\let\Gin@codes\relax -\endinput -%% -%% End of file `color.sty'. diff --git a/manuscript/crop.cfg b/manuscript/crop.cfg deleted file mode 100644 index 9ce819d..0000000 --- a/manuscript/crop.cfg +++ /dev/null @@ -1,47 +0,0 @@ -\renewcommand*\CROP@font{\normalcolor\normalsize\sf} -\renewcommand*\CROP@@ulc{% - \begin{picture}(0,0)\unitlength\p@\thinlines - \put(-35,0){\line(1,0){30}} - \put(0,35){\line(0,-1){30}} - \end{picture}} -\renewcommand*\CROP@@urc{% - \begin{picture}(0,0)\unitlength\p@\thinlines - \put(35,0){\line(-1,0){30}} - \put(0,35){\line(0,-1){30}} - \end{picture}} -\renewcommand*\CROP@@llc{% - \begin{picture}(0,0)\unitlength\p@\thinlines - \put(-35,0){\line(1,0){30}} - \put(0,-35){\line(0,1){30}} - \end{picture}} -\renewcommand*\CROP@@lrc{% - \begin{picture}(0,0)\unitlength\p@\thinlines - \put(35,0){\line(-1,0){30}} - \put(0,-35){\line(0,1){30}} - \end{picture}} -\renewcommand*\CROP@@info{{\global\advance\CROP@index\@ne - \def\x{\discretionary{}{}{\hbox{\kern.5em---\kern.5em}}}% - \hskip10\p@\advance\paperwidth-20\p@ - \raise8\p@\vbox to\z@{\centering\hsize\paperwidth\vss - \reset@font\let\protect\relax\CROP@font{% - ``\MakeLowercase\jobname''\x\the\year/\the\month/\the\day\x - page\kern.5em\thepage\x\#\the\CROP@index\strut}}}} -\cropdef\CROP@@ulc\CROP@@urc\CROP@@llc\CROP@@lrc{cam} - -\renewcommand*\CROP@kernel{\color@setgroup - \vbox to\z@{\vskip\CROP@vorigin - \hb@xt@\z@{\hskip\CROP@horigin - \CROP@every - \vbox to\paperheight{% - \hb@xt@\paperwidth{% - \CROP@ulc\CROP@uedge\CROP@urc}% - \CROP@ledge - \vskip3pc - \hb@xt@\paperwidth{% - \setbox\z@\hbox{\CROP@@@info}% - \ht\z@\z@ \dp\z@\z@ \hss\box\z@\hss}% - \vskip-3pc - \hb@xt@\paperwidth{% - \CROP@llc\hfil\CROP@lrc}}% - \hss}% - \vss}\color@endgroup} \ No newline at end of file diff --git a/manuscript/crop.sty b/manuscript/crop.sty deleted file mode 100644 index d83d485..0000000 --- a/manuscript/crop.sty +++ /dev/null @@ -1,349 +0,0 @@ -%% -%% This is file `crop.sty', -%% generated with the docstrip utility. -%% -%% The original source files were: -%% -%% crop.dtx (with options: `package') -%% -%% IMPORTANT NOTICE: -%% -%% For the copyright see the source file. -%% -%% Any modified versions of this file must be renamed -%% with new filenames distinct from crop.sty. -%% -%% For distribution of the original source see the terms -%% for copying and modification in the file crop.dtx. -%% -%% This generated file may be distributed as long as the -%% original source files, as listed above, are part of the -%% same distribution. (The sources need not necessarily be -%% in the same archive or directory.) -%% File: crop.dtx Copyright (C) 1998, 1999, 2000, 2001 Melchior FRANZ -%% $Id: crop.dtx,v 1.21 2001/11/16 21:12:14 m Exp $ -\NeedsTeXFormat{LaTeX2e} -\ProvidesPackage{crop}[2001/11/16 v1.6 cropmarks (mf)] -\newdimen\CROP@width \CROP@width\z@ -\newdimen\CROP@height \CROP@height\z@ -\newcount\CROP@index \CROP@index\z@ -\newcommand*\CROP@includegraphics{% - \PackageError{crop}% - {Package file `graphics.sty' not found.}{The options - `nographics' and `graphics' require the graphics package.}} -\newcommand*\CROP@driver{} -\IfFileExists{graphics.sty}{% - \RequirePackage{graphics}% - \let\CROP@includegraphics\includegraphics - \ifx\Gin@driver\@empty\else - \filename@parse{\Gin@driver}% - \edef\CROP@driver{\filename@base}% - \fi -}{} -\newcommand*\CROP@font{} -\newcommand*\CROP@size[2]{\CROP@width#1 \CROP@height#2 } -\DeclareOption{landscape}{% - \def\CROP@size#1#2{\CROP@height#1 \CROP@width#2 }} -\DeclareOption{a0}{\CROP@size{841truemm}{1189truemm}} -\DeclareOption{a1}{\CROP@size{595truemm}{841truemm}} -\DeclareOption{a2}{\CROP@size{420truemm}{595truemm}} -\DeclareOption{a3}{\CROP@size{297truemm}{420truemm}} -\DeclareOption{a4}{\CROP@size{210truemm}{297truemm}} -\DeclareOption{a5}{\CROP@size{149truemm}{210truemm}} -\DeclareOption{a6}{\CROP@size{105truemm}{149truemm}} -\DeclareOption{b0}{\CROP@size{1000truemm}{1414truemm}} -\DeclareOption{b1}{\CROP@size{707truemm}{1000truemm}} -\DeclareOption{b2}{\CROP@size{500truemm}{707truemm}} -\DeclareOption{b3}{\CROP@size{353truemm}{500truemm}} -\DeclareOption{b4}{\CROP@size{250truemm}{353truemm}} -\DeclareOption{b5}{\CROP@size{176truemm}{250truemm}} -\DeclareOption{b6}{\CROP@size{125truemm}{176truemm}} -\DeclareOption{letter}{\CROP@size{8.5truein}{11truein}} -\DeclareOption{legal}{\CROP@size{8.5truein}{14truein}} -\DeclareOption{executive}{\CROP@size{7.25truein}{10.5truein}} -\DeclareOption{center}{\AtEndOfPackage{\CROP@center}} -\newcommand*\CROP@center{% - \ifdim\CROP@width=\z@ - \PackageError{crop}{no printing paper size selected}{% - you have to select a paper size before you can use % - the `center' option - }% - \else - \voffset\CROP@height - \advance\voffset-\paperheight\voffset.5\voffset - \hoffset\CROP@width - \advance\hoffset-\paperwidth\hoffset.5\hoffset - \fi -} -\DeclareOption*{\CROP@execopt\CurrentOption} -\newcommand*\crop[1][cam,noaxes]{% - \@for\CROP@@:=#1\do{\CROP@execopt\CROP@@}} -\newcommand*\CROP@execopt[1]{% - \def\CROP@##1=##2=##3\@nil{\def\CROP@{##1}\def\CROP@@{##2}}% - \expandafter\CROP@#1==\@nil% - \@ifundefined{CROP@opt@\CROP@}% - {\PackageError{crop}{Requested option `#1' not provided}% - {Note that the `*center' options are obsolete. You have to - request\MessageBreak e.g. [a4,center] instead of [a4center].}}% - {\@nameuse{CROP@opt@\CROP@}}} -\newcommand*\cropdef[6][\CROP@@info]{% - \@namedef{CROP@opt@#6}{% - \CROP@on - \def\CROP@info{#1}% - \let\CROP@ulc#2 - \let\CROP@urc#3 - \let\CROP@llc#4 - \let\CROP@lrc#5}} -\newcommand*\CROP@@vaxis{% - \hfil - \setbox\z@\hbox{\vtop{\hrule\@height12\p@\@depth-2\p@\@width.4\p@ - \vskip\paperheight\vskip4\p@ - \hrule\@height\z@\@depth10\p@\@width.4\p@}}% - \ht\z@\z@ \dp\z@\z@ \box\z@ - \hfil} -\newcommand*\CROP@@haxis{% - \vfil - \hb@xt@\paperwidth{% - \llap{\vrule\@height.2\p@\@depth.2\p@\@width10\p@\hskip2\p@}% - \hfil - \rlap{\hskip2\p@\vrule\@height.2\p@\@depth.2\p@\@width10\p@}}% - \vfil} -\newcommand*\CROP@time{} -{\count@\time \divide\time60 \count\@ne\time -\multiply\time60 \advance\count@-\time -\xdef\CROP@time{\the\count\@ne:\two@digits{\count@}}} -\newcommand*\CROP@@info{{\global\advance\CROP@index\@ne - \def\x{\discretionary{}{}{\hbox{\kern.5em---\kern.5em}}}% - \hskip10\p@\advance\paperwidth-20\p@ - \raise8\p@\vbox to\z@{\centering\hsize\paperwidth\vss - \normalfont\let\protect\relax\CROP@font{% - ``\jobname''\x\the\year/\the\month/\the\day\x\CROP@time\x - page\kern.5em\thepage\x\#\the\CROP@index\strut}}}} -\newcommand*\CROP@opt@font{\let\CROP@font\CROP@@} -\newcommand*\CROP@@ulc{% - \begin{picture}(0,0)\unitlength\p@\thinlines - \put(-30,0){\circle{10}} - \put(-30,-5){\line(0,1){10}} - \put(-35,0){\line(1,0){30}} - \put(0,30){\circle{10}} - \put(-5,30){\line(1,0){10}} - \put(0,35){\line(0,-1){30}} - \end{picture}} -\newcommand*\CROP@@urc{% - \begin{picture}(0,0)\unitlength\p@\thinlines - \put(30,0){\circle{10}} - \put(30,-5){\line(0,1){10}} - \put(35,0){\line(-1,0){30}} - \put(0,30){\circle{10}} - \put(-5,30){\line(1,0){10}} - \put(0,35){\line(0,-1){30}} - \end{picture}} -\newcommand*\CROP@@llc{% - \begin{picture}(0,0)\unitlength\p@\thinlines - \put(-30,0){\circle{10}} - \put(-30,-5){\line(0,1){10}} - \put(-35,0){\line(1,0){30}} - \put(0,-30){\circle{10}} - \put(-5,-30){\line(1,0){10}} - \put(0,-35){\line(0,1){30}} - \end{picture}} -\newcommand*\CROP@@lrc{% - \begin{picture}(0,0)\unitlength\p@\thinlines - \put(30,0){\circle{10}} - \put(30,-5){\line(0,1){10}} - \put(35,0){\line(-1,0){30}} - \put(0,-30){\circle{10}} - \put(-5,-30){\line(1,0){10}} - \put(0,-35){\line(0,1){30}} - \end{picture}} -\cropdef\CROP@@ulc\CROP@@urc\CROP@@llc\CROP@@lrc{cam} -\newcommand*\CROP@@cross{% - \begin{picture}(0,0)\unitlength1in\thinlines - \put(-1,0){\line(1,0){2}} - \put(0,-1){\line(0,1){2}} - \end{picture}} -\cropdef\CROP@@cross\CROP@@cross\CROP@@cross\CROP@@cross{cross} -\newcommand*\CROP@@frame{% - \begin{picture}(0,0)\unitlength\p@\thinlines - \put(0,0){\line(1,0){\strip@pt\paperwidth}} - \put(0,0){\line(0,-1){\strip@pt\paperheight}} - \put(\strip@pt\paperwidth,0){\line(0,-1){\strip@pt\paperheight}} - \put(0,-\strip@pt\paperheight){\line(1,0){\strip@pt\paperwidth}} - \end{picture}} -\cropdef\CROP@@frame\relax\relax\relax{frame} -\let\CROP@shipout\shipout -\renewcommand*\shipout{\afterassignment\CROP@ship\setbox\@cclv=} -\newcommand*\CROP@ship{% - \ifvoid\@cclv\expandafter\aftergroup\fi\CROP@@ship} -\newcommand*\CROP@shiplist{\CROP@@@ship\box\@cclv} -\newcommand*\CROP@@ship{\CROP@shipout\vbox{\CROP@shiplist}} -\newcommand*\CROP@shipadd[1]{\begingroup - \toks@\expandafter{\expandafter#1\expandafter{\CROP@shiplist}}% - \xdef\CROP@shiplist{\the\toks@}% - \endgroup} -\newcommand*\CROP@kernel{\color@setgroup - \vbox to\z@{\vskip\CROP@vorigin - \hb@xt@\z@{\hskip\CROP@horigin - \CROP@every - \vbox to\paperheight{% - \hb@xt@\paperwidth{% - \setbox\z@\hbox{\normalfont\CROP@@@info}% - \ht\z@\z@ \dp\z@\z@ \wd\z@\z@ \box\z@ - \CROP@ulc\CROP@uedge\CROP@urc}% - \CROP@ledge - \hb@xt@\paperwidth{% - \CROP@llc\hfil\CROP@lrc}}% - \hss}% - \vss}\color@endgroup} -\newcommand*\CROP@opt@horigin{\let\CROP@horigin\CROP@@} -\newcommand*\CROP@opt@vorigin{\let\CROP@vorigin\CROP@@} -\newcommand*\CROP@@@ship{} -\newcommand*\CROP@on{\let\CROP@@@ship\CROP@kernel} -\newcommand*\CROP@opt@off{\let\CROP@@@ship\relax} -\newcommand*\CROP@@@info{} -\newcommand*\CROP@opt@info{\def\CROP@@@info{\CROP@info}} -\newcommand*\CROP@opt@noinfo{\let\CROP@@@info\relax} -\newcommand*\CROP@opt@axes{% - \let\CROP@uedge\CROP@@vaxis - \let\CROP@ledge\CROP@@haxis} -\newcommand*\CROP@opt@noaxes{% - \let\CROP@uedge\hfil - \let\CROP@ledge\vfil} -\expandafter\newcommand\expandafter*\csname CROP@opt@mount1\endcsname - {\let\CROP@every\relax} -\newcount\CROP@offset -\expandafter\newcommand\expandafter*\csname CROP@opt@mount2\endcsname - {\CROP@offset=\ifx\CROP@@\empty\z@\else\CROP@@\fi - \def\CROP@every{\count@\c@page - \advance\count@\CROP@offset - \ifodd\count@ - \let\CROP@ulc\relax\let\CROP@llc\relax - \else - \let\CROP@urc\relax\let\CROP@lrc\relax\let\CROP@info\relax - \fi}} -\DeclareOption{mirror}{% - \AtBeginDocument{\CROP@shipadd\CROP@reflect\CROP@setps}} -\newcommand*\CROP@reflect[1]{% - \vbox to\z@{\vskip\CROP@vorigin\hb@xt@\z@{\hskip\CROP@horigin - \CROP@ps{gsave currentpoint}\kern\paperwidth - \CROP@ps{currentpoint}\hss}\vss}% - \CROP@ps{translate -1 1 scale neg exch neg exch translate}% - \vbox{#1}% - \CROP@ps{grestore}} -\DeclareOption{rotate}{% - \AtBeginDocument{\CROP@shipadd\CROP@rotate\CROP@setps}} -\newcommand*\CROP@rotate[1]{% - \hb@xt@\z@{\hskip\CROP@horigin\vbox to\z@{\vskip\CROP@vorigin - \CROP@ps{gsave currentpoint}\kern\paperheight - \hb@xt@\z@{\kern\paperwidth\CROP@ps{currentpoint}\hss}\vss}\hss}% - \CROP@ps{translate 180 rotate neg exch neg exch translate}% - \vbox{#1}% - \CROP@ps{grestore}} -\newcommand*\CROP@setps{% - \ifx\Gin@PS@raw\@undefined - \PackageWarning{crop}{internal PostScript interface used}% - \newcommand*\CROP@ps[1]{\special{ps: ##1}}% - \else - \PackageInfo{crop}{graphics/color PostScript interface used}{}% - \let\CROP@ps\Gin@PS@raw - \fi - \let\CROP@setps\relax} -\DeclareOption{invert}{% - \AtEndOfPackage{\RequirePackage{color}}% - \AtBeginDocument{\CROP@invert{black}}} -\newcommand*\CROP@invert[1]{% - \ifx\color\@undefined - \PackageWarning{crop}% - {The `color' package could not be loaded, so I'm\MessageBreak - ignoring the `invert' and `notext' option}% - \else - \pagecolor{#1}\color{white}% - \newcommand\CROP@color[2][]{}% - \DeclareRobustCommand\color{\CROP@color}% - \DeclareRobustCommand\pagecolor{\CROP@color}% - \DeclareRobustCommand\textcolor{\CROP@color}% - \let\normalcolor\relax - \fi - \let\CROP@invert\relax} -\DeclareOption{notext}{% - \AtEndOfPackage{\RequirePackage{color}}% - \AtBeginDocument{\CROP@invert{white}}} -\newcommand*\CROP@incgrph{} -\newcommand*\CROP@opt@nographics{% - \def\includegraphics##1##{\bgroup - \let\special\@gobble -\CROP@incgrph{##1} -}% -\def\CROP@incgrph##1##2{% -\CROP@includegraphics##1{##2}\egroup -}% -} -\newcommand*\CROP@opt@graphics{% - \let\includegraphics\CROP@includegraphics} -\newcommand*\CROP@compat{\PackageWarning{crop}{center options like - `a4center' are obsolete and only\MessageBreak provided for - compatibility reasons. They will be removed\MessageBreak in future - releases. 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The spatial conformation - of RNA sequences largely determines their function, and therefore - RNA alignment algorithms have to take structural information into - account. RESULTS: We present a graph-based representation for sequence-structure - alignments, which we model as an integer linear program (ILP). We - sketch how we compute an optimal or near-optimal solution to the - ILP using methods from combinatorial optimization, and present results - on a recently published benchmark set for RNA alignments. CONCLUSION: - The implementation of our algorithm yields better alignments in terms - of two published scores than the other programs that we tested: This - is especially the case with an increasing number of input sequences. - Our program LARA is freely available for academic purposes from http://www.planet-lisa.net.}, - doi = {10.1186/1471-2105-8-271}, - institution = {Department of Mathematics and Computer Science, Free University Berlin, - Berlin, Germany. mbauer@inf.fu-berlin.de}, - keywords = {Algorithms; Computer Simulation; Linear Models; Models, Chemical; - Models, Genetic; RNA; Sensitivity and Specificity; Sequence Alignment; - Sequence Analysis, RNA; Sequence Homology, Nucleic Acid}, - owner = {binf007}, - pii = {1471-2105-8-271}, - pmid = {17662141}, - timestamp = {2008.01.21}, - url = {http://dx.doi.org/10.1186/1471-2105-8-271} -} - -@ARTICLE{Bag01, - author = {Joachim Friedrich and Thomas Dandekar and Matthias Wolf and Tobias - Müller}, - title = {{ProfDist: a tool for the construction of large phylogenetic trees - based on profile distances.}}, - journal = {Bionformatics}, - year = {2005}, - volume = {21}, - pages = {2108--2109}, - number = {9}, - month = {May}, - abstract = {SUMMARY: ProfDist is a user-friendly software package using the profile-neighbor-joining - method (PNJ) in inferring phylogenies based on profile distances - on DNA or RNA sequences. It is a tool for reconstructing and visualizing - large phylogenetic trees providing new and standard features with - a special focus on time efficency, robustness and accuracy. AVAILABILITY: - A Windows version of ProfDist comes with a graphical user interface - and is freely available at http://profdist.bioapps.biozentrum.uni-wuerzburg.de}, - doi = {10.1093/bioinformatics/bti289}, - institution = {Department of Bioinformatics, Biocenter, University of Würzburg, - Germany.}, - keywords = {Algorithms; Chromosome Mapping; DNA Mutational Analysis; Gene Expression - Profiling; Linkage Disequilibrium; Phylogeny; Sequence Alignment; - Sequence Analysis, DNA; Software; User-Computer Interface}, - owner = {binf007}, - pii = {bti289}, - pmid = {15677706}, - timestamp = {2008.01.21}, - url = {http://dx.doi.org/10.1093/bioinformatics/bti289} -} - -@ARTICLE{Gascuel1997, - author = {O. Gascuel}, - title = {{BIONJ: an improved version of the NJ algorithm based on a simple - model of sequence data.}}, - journal = {Mol Biol Evol}, - year = {1997}, - volume = {14}, - pages = {685--695}, - number = {7}, - month = {Jul}, - abstract = {We propose an improved version of the neighbor-joining (NJ) algorithm - of Saitou and Nei. This new algorithm, BIONJ, follows the same agglomerative - scheme as NJ, which consists of iteratively picking a pair of taxa, - creating a new mode which represents the cluster of these taxa, and - reducing the distance matrix by replacing both taxa by this node. - Moreover, BIONJ uses a simple first-order model of the variances - and covariances of evolutionary distance estimates. This model is - well adapted when these estimates are obtained from aligned sequences. - At each step it permits the selection, from the class of admissible - reductions, of the reduction which minimizes the variance of the - new distance matrix. In this way, we obtain better estimates to choose - the pair of taxa to be agglomerated during the next steps. Moreover, - in comparison with NJ's estimates, these estimates become better - and better as the algorithm proceeds. BIONJ retains the good properties - of NJ--especially its low run time. Computer simulations have been - performed with 12-taxon model trees to determine BIONJ's efficiency. - When the substitution rates are low (maximum pairwise divergence - approximately 0.1 substitutions per site) or when they are constant - among lineages, BIONJ is only slightly better than NJ. When the substitution - rates are higher and vary among lineages,BIONJ clearly has better - topological accuracy. In the latter case, for the model trees and - the conditions of evolution tested, the topological error reduction - is on the average around 20\%. With highly-varying-rate trees and - with high substitution rates (maximum pairwise divergence approximately - 1.0 substitutions per site), the error reduction may even rise above - 50\%, while the probability of finding the correct tree may be augmented - by as much as 15\%.}, - institution = {GERAD, Ecole des HEC, Montreal, Quebec, Canada. gascuel@lirmm.fr}, - keywords = {Algorithms; Evolution; Models, Biological; Phylogeny; Sequence Analysis; - Software}, - owner = {binf007}, - pmid = {9254330}, - timestamp = {2008.01.21} -} - -@ARTICLE{Gerlach2007, - author = {Daniel Gerlach and Matthias Wolf and Thomas Dandekar and Tobias Müller - and Andreas Pokorny and Sven Rahmann}, - title = {{Deep metazoan phylogeny.}}, - journal = {In Silico Biol}, - year = {2007}, - volume = {7}, - pages = {151--154}, - number = {2}, - abstract = {We reconstructed a robust phylogenetic tree of the Metazoa, consisting - of almost 1,500 taxa, by profile neighbor joining (PNJ), an automated - computational method that inherits the efficiency of the neighbor - joining algorithm. This tree supports the one proposed in the latest - review on metazoan phylogeny. Our main goal is not to discuss aspects - of the phylogeny itself, but rather to point out that PNJ can be - a valuable tool when the basal branching pattern of a large phylogenetic - tree must be estimated, whereas traditional methods would be computationally - impractical.}, - institution = {Department of Bioinformatics, Biocenter, University of Würzburg, - Am Hubland, D-97074 Würzburg, Germany.}, - keywords = {Algorithms; Animals; Computational Biology; Models, Genetic; Phylogeny; - RNA, Ribosomal, 18S}, - owner = {binf007}, - pii = {2007070015}, - pmid = {17688440}, - timestamp = {2008.01.21} -} - -@ARTICLE{Grajales2007, - author = {Alejandro Grajales and Catalina Aguilar and Juan A Sánchez}, - title = {Phylogenetic reconstruction using secondary structures of Internal - Transcribed Spacer 2 (ITS2, rDNA): finding the molecular and morphological - gap in Caribbean gorgonian corals.}, - journal = {BMC Evol Biol}, - year = {2007}, - volume = {7}, - pages = {90}, - abstract = {BACKGROUND: Most phylogenetic studies using current methods have focused - on primary DNA sequence information. However, RNA secondary structures - are particularly useful in systematics because they include characteristics, - not found in the primary sequence, that give "morphological" information. - Despite the number of recent molecular studies on octocorals, there - is no consensus opinion about a region that carries enough phylogenetic - resolution to solve intrageneric or close species relationships. - Moreover, intrageneric morphological information by itself does not - always produce accurate phylogenies; intra-species comparisons can - reveal greater differences than intra-generic ones. The search for - new phylogenetic approaches, such as by RNA secondary structure analysis, - is therefore a priority in octocoral research. RESULTS: Initially, - twelve predicted RNA secondary structures were reconstructed to provide - the basic information for phylogenetic analyses; they accorded with - the 6 helicoidal ring model, also present in other groups of corals - and eukaryotes. We obtained three similar topologies for nine species - of the Caribbean gorgonian genus Eunicea (candelabrum corals) with - two sister taxa as outgroups (genera Plexaura and Pseudoplexaura) - on the basis of molecular morphometrics of ITS2 RNA secondary structures - only, traditional primary sequence analyses and maximum likelihood, - and a Bayesian analysis of the combined data. The latter approach - allowed us to include both primary sequence and RNA molecular morphometrics; - each data partition was allowed to have a different evolution rate. - In addition, each helix was partitioned as if it had evolved at a - distinct rate. Plexaura flexuosa was found to group within Eunicea; - this was best supported by both the molecular morphometrics and combined - analyses. We suggest Eunicea flexuosa (Lamouroux, 1821) comb. nov., - and we present a new species description including Scanning Electron - Microscopy (SEM) images of morphological characteristics (sclerites). - Eunicea flexuosa, E. pallida, E. laxispica and E. mammosa formed - a separate clade in the molecular phylogenies, and were reciprocally - monophyletic with respect to other Eunicea (Euniceopsis subgenus, - e.g. E. tourneforti and E. laciniata) in the molecular morphometrics - tree, with the exception of E. fusca. Moreover, we suggest a new - diagnostic character for Eunicea, also present in E. flexuosa: middle - layer sclerites > 1 mm in length. CONCLUSION: ITS2 was a reliable - sequence for intrageneric studies in gorgonian octocorals because - of the amount of phylogenetic signal, and was corroborated against - morphological characters separating Eunicea from Plexaura. The ITS2 - RNA secondary structure approach to phylogeny presented here did - not rely on alignment methods such as INDELS, but provided clearly - homologous characters for partition analysis and RNA molecular morphometrics. - These approaches support the divergence of Eunicea flexuosa comb. - nov. from the outgroup Plexaura, although it has been considered - part of this outgroup for nearly two centuries because of morphological - resemblance.}, - doi = {10.1186/1471-2148-7-90}, - institution = {>}, - keywords = {Animals; Anthozoa; DNA, Ribosomal Spacer; Evolution, Molecular; Genetic - Speciation; Nucleic Acid Conformation; Phylogeny; RNA, Ribosomal; - Variation (Genetics)}, - owner = {binf007}, - pii = {1471-2148-7-90}, - pmid = {17562014}, - timestamp = {2008.07.30}, - url = {http://dx.doi.org/10.1186/1471-2148-7-90} -} - -@ARTICLE{Hochsmann2004, - author = {Hochsmann, M. and Hochsmann, M. and Voss, B. and Giegerich, R.}, - title = {{Pure multiple RNA secondary structure alignments: a progressive - profile approach}}, - journal = {IEEE/ACM Transactions on Computational Biology and Bioinformatics}, - year = {2004}, - volume = {1}, - pages = {53--62}, - number = {1}, - abstract = {In functional, noncoding RNA, structure is often essential to function. - While the full 3D structure is very difficult to determine, the 2D - structure of an RNA molecule gives good clues to its 3D structure, - and for molecules of moderate length, it can be predicted with good - reliability. Structure comparison is, in analogy to sequence comparison, - the essential technique to infer related function. We provide a method - for computing multiple alignments of RNA secondary structures under - the tree alignment model, which is suitable to cluster RNA molecules - purely on the structural level, i.e., sequence similarity is not - required. We give a systematic generalization of the profile alignment - method from strings to trees and forests. We introduce a tree profile - representation of RNA secondary structure alignments which allows - reasonable scoring in structure comparison. Besides the technical - aspects, an RNA profile is a useful data structure to represent multiple - structures of RNA sequences. Moreover, we propose a visualization - of RNA consensus structures that is enriched by the full sequence - information.}, - booktitle = {IEEE/ACM Transactions on Computational Biology and Bioinformatics}, - doi = {10.1109/TCBB.2004.11}, - editor = {Voss, B.}, - issn = {1545-5963}, - keywords = {biology computing, macromolecules, molecular biophysics, trees (mathematics), - forest alignment, functional noncoding RNA structure, progressive - profile approach, pure multiple RNA secondary structure alignments, - strings, structure comparison, tree alignment model, tree profile - representation, 65, Index Terms- Alignment of trees, RNA secondary - structures, noncoding RNAs.}, - owner = {binf007}, - timestamp = {2008.01.23} -} - -@ARTICLE{Hudelot2003, - author = {Cendrine Hudelot and Vivek Gowri-Shankar and Howsun Jow and Magnus - Rattray and Paul G Higgs}, - title = {{RNA-based phylogenetic methods: application to mammalian mitochondrial - RNA sequences.}}, - journal = {Mol Phylogenet Evol}, - year = {2003}, - volume = {28}, - pages = {241--252}, - number = {2}, - month = {Aug}, - abstract = {The PHASE software package allows phylogenetic tree construction with - a number of evolutionary models designed specifically for use with - RNA sequences that have conserved secondary structure. Evolution - in the paired regions of RNAs occurs via compensatory substitutions, - hence changes on either side of a pair are correlated. Accounting - for this correlation is important for phylogenetic inference because - it affects the likelihood calculation. In the present study we use - the complete set of tRNA and rRNA sequences from 69 complete mammalian - mitochondrial genomes. The likelihood calculation uses two evolutionary - models simultaneously for different parts of the sequence: a paired-site - model for the paired sites and a single-site model for the unpaired - sites. We use Bayesian phylogenetic methods and a Markov chain Monte - Carlo algorithm is used to obtain the most probable trees and posterior - probabilities of clades. The results are well resolved for almost - all the important branches on the mammalian tree. They support the - arrangement of mammalian orders within the four supra-ordinal clades - that have been identified by studies of much larger data sets mainly - comprising nuclear genes. Groups such as the hedgehogs and the murid - rodents, which have been problematic in previous studies with mitochondrial - proteins, appear in their expected position with the other members - of their order. Our choice of genes and evolutionary model appears - to be more reliable and less subject to biases caused by variation - in base composition than previous studies with mitochondrial genomes.}, - institution = {School of Biological Sciences, University of Manchester, UK.}, - keywords = {Animals; Bayes Theorem; Mammals; Models, Genetic; Phylogeny; RNA}, - owner = {binf007}, - pii = {S1055790303000617}, - pmid = {12878461}, - timestamp = {2008.01.21} -} - -@ARTICLE{Jow2002, - author = {H. Jow and C. Hudelot and M. Rattray and P. G. Higgs}, - title = {Bayesian phylogenetics using an RNA substitution model applied to - early mammalian evolution.}, - journal = {Mol Biol Evol}, - year = {2002}, - volume = {19}, - pages = {1591--1601}, - number = {9}, - month = {Sep}, - abstract = {We study the phylogeny of the placental mammals using molecular data - from all mitochondrial tRNAs and rRNAs of 54 species. We use probabilistic - substitution models specific to evolution in base paired regions - of RNA. A number of these models have been implemented in a new phylogenetic - inference software package for carrying out maximum likelihood and - Bayesian phylogenetic inferences. We describe our Bayesian phylogenetic - method which uses a Markov chain Monte Carlo algorithm to provide - samples from the posterior distribution of tree topologies. Our results - show support for four primary mammalian clades, in agreement with - recent studies of much larger data sets mainly comprising nuclear - DNA. We discuss some issues arising when using Bayesian techniques - on RNA sequence data.}, - institution = {Department of Computer Science, University of Manchester, UK.}, - keywords = {Animals; Base Sequence; Bayes Theorem; Databases, Genetic; Evolution, - Molecular; Humans; Mammals; Models, Genetic; Phylogeny; RNA; Species - Specificity}, - owner = {binf007}, - pmid = {12200486}, - timestamp = {2008.06.06} -} - -@INCOLLECTION{Jukes69, - author = {Jukes, T. and Cantor, C.R.}, - title = {Evolution of protein molecules}, - booktitle = {Mammalian Protein Metabolism}, - publisher = {Academic Press}, - year = {1969}, - editor = {Munro, H}, - pages = {21-132}, - address = {New York, USA} -} - -@ARTICLE{Mueller2004, - author = {Tobias Müller and Sven Rahmann and Thomas Dandekar and Matthias Wolf}, - title = {{Accurate and robust phylogeny estimation based on profile distances: - a study of the Chlorophyceae (Chlorophyta).}}, - journal = {BMC Evol Biol}, - year = {2004}, - volume = {4}, - pages = {20}, - month = {Jun}, - abstract = {BACKGROUND: In phylogenetic analysis we face the problem that several - subclade topologies are known or easily inferred and well supported - by bootstrap analysis, but basal branching patterns cannot be unambiguously - estimated by the usual methods (maximum parsimony (MP), neighbor-joining - (NJ), or maximum likelihood (ML)), nor are they well supported. We - represent each subclade by a sequence profile and estimate evolutionary - distances between profiles to obtain a matrix of distances between - subclades. RESULTS: Our estimator of profile distances generalizes - the maximum likelihood estimator of sequence distances. The basal - branching pattern can be estimated by any distance-based method, - such as neighbor-joining. Our method (profile neighbor-joining, PNJ) - then inherits the accuracy and robustness of profiles and the time - efficiency of neighbor-joining. CONCLUSIONS: Phylogenetic analysis - of Chlorophyceae with traditional methods (MP, NJ, ML and MrBayes) - reveals seven well supported subclades, but the methods disagree - on the basal branching pattern. The tree reconstructed by our method - is better supported and can be confirmed by known morphological characters. - Moreover the accuracy is significantly improved as shown by parametric - bootstrap.}, - doi = {10.1186/1471-2148-4-20}, - institution = {Department of Bioinformatics, Biocenter, University of Würzburg, - Am Hubland, D-97074 Würzburg, Germany. tobias.mueller@biozentrum.uni-wuerzburg.de}, - keywords = {Algae, Green; Animals; Computational Biology; Evolution, Molecular; - Models, Genetic; Phylogeny; RNA, Plant; RNA, Ribosomal; RNA, Ribosomal, - 18S}, - owner = {binf007}, - pii = {1471-2148-4-20}, - pmid = {15222898}, - timestamp = {2008.01.21}, - url = {http://dx.doi.org/10.1186/1471-2148-4-20} -} - -@ARTICLE{Mueller2002, - author = {Tobias Müller and Rainer Spang and Martin Vingron}, - title = {{Estimating amino acid substitution models: a comparison of Dayhoff's - estimator, the resolvent approach and a maximum likelihood method.}}, - journal = {Mol Biol Evol}, - year = {2002}, - volume = {19}, - pages = {8--13}, - number = {1}, - month = {Jan}, - abstract = {Evolution of proteins is generally modeled as a Markov process acting - on each site of the sequence. Replacement frequencies need to be - estimated based on sequence alignments. Here we compare three approaches: - First, the original method by Dayhoff, Schwartz, and Orcutt (1978) - Atlas Protein Seq. Struc. 5:345-352, secondly, the resolvent method - (RV) by Müller and Vingron (2000) J. Comput. Biol. 7(6):761-776, - and finally a maximum likelihood approach (ML) developed in this - paper. We evaluate the methods using a highly divergent and inhomogeneous - set of sequence alignments as an input to the estimation procedure. - ML is the method of choice for small sets of input data. Although - the RV method is computationally much less demanding it performs - only slightly worse than ML. Therefore, it is perfectly appropriate - for large-scale applications.}, - institution = {Deutsches Krebsforschungszentrum, Theoretische Bioinformatik, Im - Neuenheimer Feld 280, 69120 Heidelberg, Germany. t.mueller@dkfz.de}, - keywords = {Algorithms; Amino Acid Sequence; Amino Acid Substitution; Computer - Simulation; Evolution, Molecular; Likelihood Functions; Markov Chains; - Models, Genetic; Proteins; Sequence Alignment}, - owner = {binf007}, - pmid = {11752185}, - timestamp = {2008.01.25} -} - -@ARTICLE{Mueller2000, - author = {T. Müller and M. Vingron}, - title = {{Modeling amino acid replacement.}}, - journal = {J Comput Biol}, - year = {2000}, - volume = {7}, - pages = {761--776}, - number = {6}, - abstract = {The estimation of amino acid replacement frequencies during molecular - evolution is crucial for many applications in sequence analysis. - Score matrices for database search programs or phylogenetic analysis - rely on such models of protein evolution. Pioneering work was done - by Dayhoff et al. (1978) who formulated a Markov model of evolution - and derived the famous PAM score matrices. Her estimation procedure - for amino acid exchange frequencies is restricted to pairs of proteins - that have a constant and small degree of divergence. Here we present - an improved estimator, called the resolvent method, that is not subject - to these limitations. This extension of Dayhoff's approach enables - us to estimate an amino acid substitution model from alignments of - varying degree of divergence. Extensive simulations show the capability - of the new estimator to recover accurately the exchange frequencies - among amino acids. Based on the SYSTERS database of aligned protein - families (Krause and Vingron, 1998) we recompute a series of score - matrices.}, - doi = {10.1089/10665270050514918}, - institution = {Deutsches Krebsforschungszentrum, Theoretische Bioinformatik, 69120 - Heidelberg, Germany. t.mueller/m.vingron}, - keywords = {Amino Acid Substitution; Computer Simulation; Evolution, Molecular; - Likelihood Functions; Markov Chains; Models, Biological; Proteins; - Stochastic Processes; Time Factors}, - owner = {binf007}, - pmid = {11382360}, - timestamp = {2008.01.25}, - url = {http://dx.doi.org/10.1089/10665270050514918} -} - -@INCOLLECTION{Buch2006, - author = {Sven Rahmann and Tobias Muller and Thomas Dandekar and Matthias Wolf}, - title = {{Efficient and robust analysis of large phylogenetic datasets}}, - booktitle = {Advanced Data Mining Technologies in Bioinformatics}, - publisher = {Idea Group, Inc.}, - year = {2006}, - editor = {Hui-Huang Hsu}, - pages = {104-117}, - address = {Hershey, PA, USA}, - abstract = {The goal of phylogenetics is to reconstruct ancestral relationships - between different taxa, e.g., different species in the tree of life, - by means of certain characters, such as genomic sequences. We consider - the prominent problem of reconstructing the basal phylogenetic tree - topology when several subclades have already been identified or are - well known by other means, such as morphological characteristics. - Whereas most available tools attempt to estimate a fully resolved - tree from scratch, the profile neighbor-joining (PNJ) method focuses - directly on the mentioned problem and has proven a robust and efficient - method for large-scale data sets, especially when used in an iterative - way. We describe an implementation of this idea, the ProfDist software - package, which is freely available, and apply the method to estimate - the phylogeny of the eukaryotes. Overall, the PNJ approach provides - a novel effective way to mine large sequence datasets for relevant - phylogenetic information.} -} - -@ARTICLE{Saitou1987, - author = {N. Saitou and M. Nei}, - title = {{The neighbor-joining method: a new method for reconstructing phylogenetic - trees.}}, - journal = {Mol Biol Evol}, - year = {1987}, - volume = {4}, - pages = {406--425}, - number = {4}, - month = {Jul}, - abstract = {A new method called the neighbor-joining method is proposed for reconstructing - phylogenetic trees from evolutionary distance data. The principle - of this method is to find pairs of operational taxonomic units (OTUs - [= neighbors]) that minimize the total branch length at each stage - of clustering of OTUs starting with a starlike tree. The branch lengths - as well as the topology of a parsimonious tree can quickly be obtained - by using this method. Using computer simulation, we studied the efficiency - of this method in obtaining the correct unrooted tree in comparison - with that of five other tree-making methods: the unweighted pair - group method of analysis, Farris's method, Sattath and Tversky's - method, Li's method, and Tateno et al.'s modified Farris method. - The new, neighbor-joining method and Sattath and Tversky's method - are shown to be generally better than the other methods.}, - institution = {Center for Demographic and Population Genetics, University of Texas - Health Science Center, Houston 77225.}, - keywords = {Animals; Biometry; Evolution; Models, Genetic; Phylogeny; Ranidae}, - owner = {binf007}, - pmid = {3447015}, - timestamp = {2008.01.21} -} - -@ARTICLE{Schultz2005, - author = {Jörg Schultz and Stefanie Maisel and Daniel Gerlach and Tobias Müller - and Matthias Wolf}, - title = {{A common core of secondary structure of the internal transcribed - spacer 2 (ITS2) throughout the Eukaryota.}}, - journal = {RNA}, - year = {2005}, - volume = {11}, - pages = {361--364}, - number = {4}, - month = {Apr}, - abstract = {The ongoing characterization of novel species creates the need for - a molecular marker which can be used for species- and, simultaneously, - for mega-systematics. Recently, the use of the internal transcribed - spacer 2 (ITS2) sequence was suggested, as it shows a high divergence - in sequence with an assumed conservation in structure. This hypothesis - was mainly based on small-scale analyses, comparing a limited number - of sequences. Here, we report a large-scale analysis of more than - 54,000 currently known ITS2 sequences with the goal to evaluate the - hypothesis of a conserved structural core and to assess its use for - automated large-scale phylogenetics. Structure prediction revealed - that the previously described core structure can be found for more - than 5000 sequences in a wide variety of taxa within the eukaryotes, - indicating that the core secondary structure is indeed conserved. - This conserved structure allowed an automated alignment of extremely - divergent sequences as exemplified for the ITS2 sequences of a ctenophorean - eumetazoon and a volvocalean green alga. All classified sequences, - together with their structures can be accessed at http://www.biozentrum.uni-wuerzburg.de/bioinformatik/projects/ITS2.html. - Furthermore, we found that, although sample sequences are known for - most major taxa, there exists a profound divergence in coverage, - which might become a hindrance for general usage. In summary, our - analysis strengthens the potential of ITS2 as a general phylogenetic - marker and provides a data source for further ITS2-based analyses.}, - doi = {10.1261/rna.7204505}, - institution = {entrum.uni-wuerzburg.de}, - keywords = {Algae; Animals; Base Sequence; Conserved Sequence; DNA, Ribosomal - Spacer; Fungi; Genetic Markers; Invertebrates; Molecular Sequence - Data; Nucleic Acid Conformation; Phylogeny; Plants; Sequence Alignment; - Transcription, Genetic}, - owner = {binf007}, - pii = {11/4/361}, - pmid = {15769870}, - timestamp = {2008.01.21}, - url = {http://dx.doi.org/10.1261/rna.7204505} -} - -@ARTICLE{Schultz2006, - author = {Jörg Schultz and Tobias Müller and Marco Achtziger and Philipp N - Seibel and Thomas Dandekar and Matthias Wolf}, - title = {{The internal transcribed spacer 2 database--a web server for (not - only) low level phylogenetic analyses.}}, - journal = {Nucleic Acids Res}, - year = {2006}, - volume = {34}, - pages = {W704--W707}, - number = {Web Server issue}, - month = {Jul}, - abstract = {The internal transcribed spacer 2 (ITS2) is a phylogenetic marker - which has been of broad use in generic and infrageneric level classifications, - as its sequence evolves comparably fast. Only recently, it became - clear, that the ITS2 might be useful even for higher level systematic - analyses. As the secondary structure is highly conserved within all - eukaryotes it serves as a valuable template for the construction - of highly reliable sequence-structure alignments, which build a fundament - for subsequent analyses. Thus, any phylogenetic study using ITS2 - has to consider both sequence and structure. We have integrated a - homology based RNA structure prediction algorithm into a web server, - which allows the detection and secondary structure prediction for - ITS2 in any given sequence. Furthermore, the resource contains more - than 25,000 pre-calculated secondary structures for the currently - known ITS2 sequences. These can be taxonomically searched and browsed. - Thus, our resource could become a starting point for ITS2-based phylogenetic - analyses and is therefore complementary to databases of other phylogenetic - markers, which focus on higher level analyses. The current version - of the ITS2 database can be accessed via http://its2.bioapps.biozentrum.uni-wuerzburg.de.}, - doi = {10.1093/nar/gkl129}, - institution = {Department of Bioinformatics, Biocenter, University of Würzburg Am - Hubland, 97074 Würzburg, Germany. Joerg.Schultz@biozentrum.uni-wuerzburg.de}, - keywords = {DNA, Ribosomal Spacer; Databases, Nucleic Acid; Internet; Nucleic - Acid Conformation; Phylogeny; Sequence Analysis, RNA; Software; User-Computer - Interface}, - owner = {binf007}, - pii = {34/suppl_2/W704}, - pmid = {16845103}, - timestamp = {2008.01.21}, - url = {http://dx.doi.org/10.1093/nar/gkl129} -} - -@ARTICLE{Schoeniger1994, - author = {M. Schöniger and A. von Haeseler}, - title = {{A stochastic model for the evolution of autocorrelated DNA sequences.}}, - journal = {Mol Phylogenet Evol}, - year = {1994}, - volume = {3}, - pages = {240--247}, - number = {3}, - month = {Sep}, - abstract = {Currently used stochastic models of DNA sequence evolution assume - independent and identically distributed nucleotide sites. They are - too simple to account for dependence structures obviously present - in molecular data. Up to now more realistic stochastic models for - nucleotide substitutions have been considered intractable. In this - paper a procedure that accounts for non-overlapping correlations - among pairs of sites of a DNA sequence is developed. We show that - currently used models that ignore correlated sites underestimate - distances inferred from observed sequence dissimilarities. For the - analyzed mitochondrial sequence data this underestimation is not - drastic in contrast to paired regions (stems) of bacterial 23S rRNA - sequences.}, - doi = {10.1006/mpev.1994.1026}, - institution = {Technical University Munich, Germany.}, - keywords = {Animals; DNA; DNA, Mitochondrial; Evolution; Mammals; Markov Chains; - Mutation; RNA, Bacterial; RNA, Ribosomal, 23S; Species Specificity; - Stochastic Processes}, - owner = {binf007}, - pii = {S1055-7903(84)71026-8}, - pmid = {7529616}, - timestamp = {2008.01.25}, - url = {http://dx.doi.org/10.1006/mpev.1994.1026} -} - -@ARTICLE{Seibel2006, - author = {Philipp N Seibel and Tobias Müller and Thomas Dandekar and Jörg Schultz - and Matthias Wolf}, - title = {{4SALE--a tool for synchronous RNA sequence and secondary structure - alignment and editing.}}, - journal = {BMC Bioinformatics}, - year = {2006}, - volume = {7}, - pages = {498}, - abstract = {BACKGROUND: In sequence analysis the multiple alignment builds the - fundament of all proceeding analyses. Errors in an alignment could - strongly influence all succeeding analyses and therefore could lead - to wrong predictions. Hand-crafted and hand-improved alignments are - necessary and meanwhile good common practice. For RNA sequences often - the primary sequence as well as a secondary structure consensus is - well known, e.g., the cloverleaf structure of the t-RNA. Recently, - some alignment editors are proposed that are able to include and - model both kinds of information. However, with the advent of a large - amount of reliable RNA sequences together with their solved secondary - structures (available from e.g. the ITS2 Database), we are faced - with the problem to handle sequences and their associated secondary - structures synchronously. RESULTS: 4SALE fills this gap. The application - allows a fast sequence and synchronous secondary structure alignment - for large data sets and for the first time synchronous manual editing - of aligned sequences and their secondary structures. This study describes - an algorithm for the synchronous alignment of sequences and their - associated secondary structures as well as the main features of 4SALE - used for further analyses and editing. 4SALE builds an optimal and - unique starting point for every RNA sequence and structure analysis. - CONCLUSION: 4SALE, which provides an user-friendly and intuitive - interface, is a comprehensive toolbox for RNA analysis based on sequence - and secondary structure information. The program connects sequence - and structure databases like the ITS2 Database to phylogeny programs - as for example the CBCAnalyzer. 4SALE is written in JAVA and therefore - platform independent. The software is freely available and distributed - from the website at http://4sale.bioapps.biozentrum.uni-wuerzburg.de.}, - doi = {10.1186/1471-2105-7-498}, - institution = {>}, - keywords = {Algorithms; Base Pairing; Computational Biology; Databases, Genetic; - Nucleic Acid Conformation; RNA; Sequence Alignment; Sequence Analysis, - RNA; Software Validation; Time Factors; User-Computer Interface}, - owner = {binf007}, - pii = {1471-2105-7-498}, - pmid = {17101042}, - timestamp = {2008.01.21}, - url = {http://dx.doi.org/10.1186/1471-2105-7-498} -} - -@ARTICLE{Selig2008, - author = {Christian Selig and Matthias Wolf and Tobias Müller and Thomas Dandekar - and Jörg Schultz}, - title = {{The ITS2 Database II: homology modelling RNA structure for molecular - systematics.}}, - journal = {Nucleic Acids Res}, - year = {2008}, - volume = {36}, - pages = {D377--D380}, - number = {Database issue}, - month = {Jan}, - abstract = {An increasing number of phylogenetic analyses are based on the internal - transcribed spacer 2 (ITS2). They mainly use the fast evolving sequence - for low-level analyses. When considering the highly conserved structure, - the same marker could also be used for higher level phylogenies. - Furthermore, structural features of the ITS2 allow distinguishing - different species from each other. Despite its importance, the correct - structure is only rarely found by standard RNA folding algorithms. - To overcome this hindrance for a wider application of the ITS2, we - have developed a homology modelling approach to predict the structure - of RNA and present the results of modelling the ITS2 in the ITS2 - Database. Here, we describe the database and the underlying algorithms - which allowed us to predict the structure for 86 784 sequences, which - is more than 55\% of all GenBank entries concerning the ITS2. These - are not equally distributed over all genera. There is a substantial - amount of genera where the structure of nearly all sequences is predicted - whereas for others no structure at all was found despite high sequence - coverage. These genera might have evolved an ITS2 structure diverging - from the standard one. The current version of the ITS2 Database can - be accessed via http://its2.bioapps.biozentrum.uni-wuerzburg.de.}, - doi = {10.1093/nar/gkm827}, - institution = {Department of Bioinformatics, Biocenter, University of Würzburg, - Am Hubland 97074 Würzburg, Germany.}, - owner = {binf007}, - pii = {gkm827}, - pmid = {17933769}, - timestamp = {2008.01.21}, - url = {http://dx.doi.org/10.1093/nar/gkm827} -} - -@ARTICLE{Siebert2005, - author = {Sven Siebert and Rolf Backofen}, - title = {{MARNA: multiple alignment and consensus structure prediction of - RNAs based on sequence structure comparisons.}}, - journal = {Bioinformatics}, - year = {2005}, - volume = {21}, - pages = {3352--3359}, - number = {16}, - month = {Aug}, - abstract = {MOTIVATION: Due to the importance of considering secondary structures - in aligning functional RNAs, several pairwise sequence-structure - alignment methods have been developed. They use extended alignment - scores that evaluate secondary structure information in addition - to sequence information. However, two problems for the multiple alignment - step remain. First, how to combine pairwise sequence-structure alignments - into a multiple alignment and second, how to generate secondary structure - information for sequences whose explicit structural information is - missing. RESULTS: We describe a novel approach for multiple alignment - of RNAs (MARNA) taking into consideration both the primary and the - secondary structures. It is based on pairwise sequence-structure - comparisons of RNAs. From these sequence-structure alignments, libraries - of weighted alignment edges are generated. The weights reflect the - sequential and structural conservation. For sequences whose secondary - structures are missing, the libraries are generated by sampling low - energy conformations. The libraries are then processed by the T-Coffee - system, which is a consistency based multiple alignment method. Furthermore, - we are able to extract a consensus-sequence and -structure from a - multiple alignment. We have successfully tested MARNA on several - datasets taken from the Rfam database.}, - doi = {10.1093/bioinformatics/bti550}, - institution = {Department of Bioinformatics, Institute of Computer Science, Friedrich-Schiller-University - Jena, Ernst-Abbe Platz 2, 07743 Jena, Germany.}, - keywords = {Algorithms; Computer Simulation; Consensus Sequence; RNA; Sensitivity - and Specificity; Sequence Alignment; Sequence Analysis, RNA; Sequence - Homology, Nucleic Acid; Software; Structure-Activity Relationship}, - owner = {binf007}, - pii = {bti550}, - pmid = {15972285}, - timestamp = {2008.01.21}, - url = {http://dx.doi.org/10.1093/bioinformatics/bti550} -} - -@ARTICLE{Smith2004, - author = {Andrew D Smith and Thomas W H Lui and Elisabeth R M Tillier}, - title = {{Empirical models for substitution in ribosomal RNA.}}, - journal = {Mol Biol Evol}, - year = {2004}, - volume = {21}, - pages = {419--427}, - number = {3}, - month = {Mar}, - abstract = {Empirical models of substitution are often used in protein sequence - analysis because the large alphabet of amino acids requires that - many parameters be estimated in all but the simplest parametric models. - When information about structure is used in the analysis of substitutions - in structured RNA, a similar situation occurs. The number of parameters - necessary to adequately describe the substitution process increases - in order to model the substitution of paired bases. We have developed - a method to obtain substitution rate matrices empirically from RNA - alignments that include structural information in the form of base - pairs. Our data consisted of alignments from the European Ribosomal - RNA Database of Bacterial and Eukaryotic Small Subunit and Large - Subunit Ribosomal RNA ( Wuyts et al. 2001. Nucleic Acids Res. 29:175-177; - Wuyts et al. 2002. Nucleic Acids Res. 30:183-185). Using secondary - structural information, we converted each sequence in the alignments - into a sequence over a 20-symbol code: one symbol for each of the - four individual bases, and one symbol for each of the 16 ordered - pairs. Substitutions in the coded sequences are defined in the natural - way, as observed changes between two sequences at any particular - site. For given ranges (windows) of sequence divergence, we obtained - substitution frequency matrices for the coded sequences. Using a - technique originally developed for modeling amino acid substitutions - ( Veerassamy, Smith, and Tillier. 2003. J. Comput. Biol. 10:997-1010), - we were able to estimate the actual evolutionary distance for each - window. The actual evolutionary distances were used to derive instantaneous - rate matrices, and from these we selected a universal rate matrix. - The universal rate matrices were incorporated into the Phylip Software - package ( Felsenstein 2002. http://evolution.genetics.washington.edu/phylip.html), - and we analyzed the ribosomal RNA alignments using both distance - and maximum likelihood methods. The empirical substitution models - performed well on simulated data, and produced reasonable evolutionary - trees for 16S ribosomal RNA sequences from sequenced Bacterial genomes. - Empirical models have the advantage of being easily implemented, - and the fact that the code consists of 20 symbols makes the models - easily incorporated into existing programs for protein sequence analysis. - In addition, the models are useful for simulating the evolution of - RNA sequence and structure simultaneously.}, - doi = {10.1093/molbev/msh029}, - institution = {Department of Medical Biophysics, University of Toronto, and Ontario - Cancer Institute, University Health Network, Toronto, Ontario, Canada.}, - keywords = {Amino Acid Substitution; Animals; Computer Simulation; Databases, - Nucleic Acid; Evolution, Molecular; Likelihood Functions; Models, - Genetic; Phylogeny; RNA, Ribosomal; Sequence Alignment}, - owner = {binf007}, - pii = {msh029}, - pmid = {14660689}, - timestamp = {2008.01.21}, - url = {http://dx.doi.org/10.1093/molbev/msh029} -} - -@MISC{QT, - author = {Trolltech}, - title = {http://trolltech.com/products/qt/}, - year = {2008}, - owner = {binf007}, - timestamp = {2008.07.19}, - url = {http://trolltech.com/products/qt/} -} - -@ARTICLE{Vanormelingen2007, - author = {P Vanormelingen and E Hegewald and A Braband and M Kitschke and T - Friedl and K Sabbe and W Vyverman}, - title = {{The systematics of a small spineless Desmodesmus species, D-costato-granulatus - (Sphaeropleales, Chlorophyceae), based on ITS2 rDNA sequence analyses - and cell wall morphology}}, - journal = {Journal of Phyclology}, - year = {2007}, - volume = {43}, - pages = {378-396}, - number = {2}, - month = {APR} -} - -@ARTICLE{Wheeler2000, - author = {D. L. Wheeler and C. Chappey and A. E. Lash and D. D. Leipe and T. - L. Madden and G. D. Schuler and T. A. Tatusova and B. A. Rapp}, - title = {{Database resources of the National Center for Biotechnology Information.}}, - journal = {Nucleic Acids Res}, - year = {2000}, - volume = {28}, - pages = {10--14}, - number = {1}, - month = {Jan}, - abstract = {In addition to maintaining the GenBank(R) nucleic acid sequence database, - the National Center for Biotechnology Information (NCBI) provides - data analysis and retrieval and resources that operate on the data - in GenBank and a variety of other biological data made available - through NCBI's Web site. NCBI data retrieval resources include Entrez, - PubMed, LocusLink and the Taxonomy Browser. Data analysis resources - include BLAST, Electronic PCR, OrfFinder, RefSeq, UniGene, Database - of Single Nucleotide Polymorphisms (dbSNP), Human Genome Sequencing - pages, GeneMap'99, Davis Human-Mouse Homology Map, Cancer Chromosome - Aberration Project (CCAP) pages, Entrez Genomes, Clusters of Orthologous - Groups (COGs) database, Retroviral Genotyping Tools, Cancer Genome - Anatomy Project (CGAP) pages, SAGEmap, Online Mendelian Inheritance - in Man (OMIM) and the Molecular Modeling Database (MMDB). Augmenting - many of the Web applications are custom implementations of the BLAST - program optimized to search specialized data sets. All of the resources - can be accessed through the NCBI home page at: http://www.ncbi.nlm.nih. - gov}, - institution = {National Center for Biotechnology Information, National Library of - Medicine, National Institutes of Health, Building 38A, 8600 Rockville - Pike, Bethesda, MD 20894, USA.}, - keywords = {Animals; Biology; Databases, Factual; Gene Expression; Genome, Human; - Humans; Information Storage and Retrieval; Mice; Models, Molecular; - National Library of Medicine (U.S.); Neoplasms; Phenotype; United - States}, - owner = {binf007}, - pii = {gkd055}, - pmid = {10592169}, - timestamp = {2008.01.21} -} - -@ARTICLE{Wolf2005, - author = {Matthias Wolf and Marco Achtziger and Jörg Schultz and Thomas Dandekar - and Tobias Müller}, - title = {{Homology modeling revealed more than 20,000 rRNA internal transcribed - spacer 2 (ITS2) secondary structures.}}, - journal = {RNA}, - year = {2005}, - volume = {11}, - pages = {1616--1623}, - number = {11}, - month = {Nov}, - abstract = {Structural genomics meets phylogenetics and vice versa: Knowing rRNA - secondary structures is a prerequisite for constructing rRNA alignments - for inferring phylogenies, and inferring phylogenies is a precondition - to understand the evolution of such rRNA secondary structures. Here, - both scientific worlds go together. The rRNA internal transcribed - spacer 2 (ITS2) region is a widely used phylogenetic marker. Because - of its high variability at the sequence level, correct alignments - have to take into account structural information. In this study, - we examine the extent of the conservation in structure. We present - (1) the homology modeled secondary structure of more than 20,000 - ITS2 covering about 14,000 species; (2) a computational approach - for homology modeling of rRNA structures, which additionally can - be applied to other RNA families; and (3) a database providing about - 25,000 ITS2 sequences with their associated secondary structures, - a refined ITS2 specific general time reversible (GTR) substitution - model, and a scoring matrix, available at http://its2.bioapps.biozentrum.uni-wuerzburg.de.}, - doi = {10.1261/rna.2144205}, - institution = {Department of Bioinformatics, University of Würzburg, Biocenter, - Am Hubland, Germany. matthias.wolf@biozentrum.uni-wuerzburg.de}, - keywords = {Algae; Animals; Base Sequence; DNA, Ribosomal Spacer; Evolution, Molecular; - Fungi; Models, Molecular; Molecular Sequence Data; Nucleic Acid Conformation; - RNA, Ribosomal; Sequence Alignment}, - owner = {binf007}, - pii = {11/11/1616}, - pmid = {16244129}, - timestamp = {2008.01.21}, - url = {http://dx.doi.org/10.1261/rna.2144205} -} - -@comment{jabref-meta: selector_publisher:} - -@comment{jabref-meta: selector_author:} - -@comment{jabref-meta: selector_journal:} - -@comment{jabref-meta: selector_keywords:} diff --git a/manuscript/document.dvi b/manuscript/document.dvi deleted file mode 100644 index 6f71f8f..0000000 Binary files a/manuscript/document.dvi and /dev/null differ diff --git a/manuscript/document.pdf b/manuscript/document.pdf deleted file mode 100644 index 4ef81fb..0000000 Binary files a/manuscript/document.pdf and /dev/null differ diff --git a/manuscript/document.tex b/manuscript/document.tex deleted file mode 100644 index d897927..0000000 --- a/manuscript/document.tex +++ /dev/null @@ -1,227 +0,0 @@ -\documentclass{bioinfo} -\copyrightyear{2005} -\pubyear{2005} - -\begin{document} -\firstpage{1} - -\title[short Title]{This is a title} -\author[Sample \textit{et~al}]{Corresponding Author\,$^{1,*}$, Co-Author\,$^{2}$ and Co-Author\,$^2$\footnote{to whom correspondence should be addressed}} -\address{$^{1}$Department of XXXXXXX, Address XXXX etc.\\ -$^{2}$Department of XXXXXXXX, Address XXXX etc.} - -\history{Received on XXXXX; revised on XXXXX; accepted on XXXXX} - -\editor{Associate Editor: XXXXXXX} - -\maketitle - -\begin{abstract} - -\section{Motivation:} -Text Text Text Text Text Text Text Text Text Text Text -Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text. - -\section{Results:} -Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text - -\section{Availability:} -Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text - -\section{Contact:} \href{name@bio.com}{name@bio.com} -\end{abstract} - -\section{Introduction} - -Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text. Figure~\ref{fig:01} shows that the above method Text Text Text Text Text Text Text Text Text Text Text Text. \citep{Bag01} wants to know about …… text follows. - -\begin{equation} -\sum x+ y =Z\label{eq:01} -\end{equation} - - - - - - -\section{Approach} - -Equation~(\ref{eq:01}) Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text. Figure \ref{fig:02} shows that the above method Text Text Text Text Text Text Text Text Text Text Text Text. \citealp{Boffelli03} might want to know about text text text text …… - - -\begin{methods} -\section{Methods} - -Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text. Figure \ref{fig:02} shows that the above method Text Text Text Text Text Text Text Text Text Text Text Text. \citealp{Boffelli03} might want to know about text text text text -Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text. 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Figure \ref{fig:02} shows that the above method Text Text Text Text Text Text Text Text Text Text Text Text. \citealp{Boffelli03} might want to know about text text text text -Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text. Figure \ref{fig:02} shows that the above method Text Text Text Text Text Text Text Text Text Text Text Text. - - - -Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text. Figure \ref{fig:02} shows that the above method Text Text Text Text Text Text Text Text Text Text Text Text. \citealp{Boffelli03} might want to know about text text text text - - - - - -\begin{enumerate} -\item this is item, use enumerate -\item this is item, use enumerate -\item this is item, use enumerate -\end{enumerate} - -Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text. Figure \ref{fig:02} shows that the above method Text Text Text Text Text Text Text Text Text Text Text Text. \citealp{Boffelli03} might want to know about text text text text -Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text. Figure \ref{fig:02} shows that the above method Text Text Text Text Text Text Text Text Text Text Text Text. \citealp{Boffelli03} might want to know about text text text text -Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text. - - - - - - -Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text. Figure \ref{fig:02} shows that the above method Text Text Text Text - - -\section*{Acknowledgement} -Text Text Text Text Text Text Text Text. \citealp{Boffelli03} might want to know about text text text text - -\paragraph{Funding\textcolon} Text Text Text Text Text Text Text Text. - -%\bibliographystyle{natbib} -%\bibliographystyle{achemnat} -%\bibliographystyle{plainnat} -%\bibliographystyle{abbrv} -%\bibliographystyle{bioinformatics} -% -%\bibliographystyle{plain} -% -%\bibliography{Document} - - -\begin{thebibliography}{} -\bibitem[Bofelli {\it et~al}., 2000]{Boffelli03} Bofelli,F., Name2, Name3 (2003) Article title, {\it Journal Name}, {\bf 199}, 133-154. - -\bibitem[Bag {\it et~al}., 2001]{Bag01} Bag,M., Name2, Name3 (2001) Article title, {\it Journal Name}, {\bf 99}, 33-54. - -\bibitem[Yoo \textit{et~al}., 2003]{Yoo03} -Yoo,M.S. \textit{et~al}. (2003) Oxidative stress regulated genes -in nigral dopaminergic neurnol cell: correlation with the known -pathology in Parkinson's disease. \textit{Brain Res. Mol. Brain -Res.}, \textbf{110}(Suppl. 1), 76--84. - -\bibitem[Lehmann, 1986]{Leh86} -Lehmann,E.L. (1986) Chapter title. \textit{Book Title}. Vol.~1, 2nd edn. Springer-Verlag, New York. - -\bibitem[Crenshaw and Jones, 2003]{Cre03} -Crenshaw, B.,III, and Jones, W.B.,Jr (2003) The future of clinical -cancer management: one tumor, one chip. \textit{Bioinformatics}, -doi:10.1093/bioinformatics/btn000. - -\bibitem[Auhtor \textit{et~al}. (2000)]{Aut00} -Auhtor,A.B. \textit{et~al}. (2000) Chapter title. In Smith, A.C. -(ed.), \textit{Book Title}, 2nd edn. Publisher, Location, Vol. 1, pp. -???--???. - -\bibitem[Bardet, 1920]{Bar20} -Bardet, G. (1920) Sur un syndrome d'obesite infantile avec -polydactylie et retinite pigmentaire (contribution a l'etude des -formes cliniques de l'obesite hypophysaire). PhD Thesis, name of -institution, Paris, France. - -\end{thebibliography} -\end{document} diff --git a/manuscript/documentation.doc b/manuscript/documentation.doc deleted file mode 100644 index 7485542..0000000 Binary files a/manuscript/documentation.doc and /dev/null differ diff --git a/manuscript/float.sty b/manuscript/float.sty deleted file mode 100644 index 1e7d234..0000000 --- a/manuscript/float.sty +++ /dev/null @@ -1,167 +0,0 @@ -%% -%% This is file `float.sty', -%% generated with the docstrip utility. -%% -%% The original source files were: -%% -%% float.dtx (with options: `package') -%% -%% IMPORTANT NOTICE: -%% This file is a stripped version of `float.dtx', -%% copyright (c) 1991-2000 Anselm Lingnau -%% (lingnau@tm.informatik.uni-frankfurt.de) -%% -%% This file may only be distributed together with the corresponding -%% `float.dtx' file. 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To stretch right column by #1 add command \vskip-#1 just before -% command \end{document}. -% TO shrink right column by #1 add command \vskip#1 just before -% command \end{document}. -% Example: \vskip-10pt -% \end{document} -% -% \changes{1997/05/16}{first version} -% \changes{1997/09/09}{support for compatibility with cuted.sty} -% \changes{1997/10/01}{\vipersep changed to \stripsep for compatibility with cuted.sty} -% -\NeedsTeXFormat{LaTeX2e} -\ProvidesPackage{flushend}[1997/10/01] -% -\newbox\@aaa -\newbox\@ccc -\@ifundefined{@viper}{\newbox\@viper}{} -\@ifundefined{hold@viper}{\newbox\hold@viper}{} -\newtoks\atColsBreak \atColsBreak={} -\newdimen\@extra@skip \@extra@skip\z@ -\newdimen\@nd@page@rule \@nd@page@rule\z@ -\def\last@outputdblcol{% - \if@firstcolumn - \global \@firstcolumnfalse - \global \setbox\@leftcolumn \box\@outputbox - \else - \global \@firstcolumntrue - \if@lastpage - \@tempdima\ht\@leftcolumn - \splittopskip\topskip\splitmaxdepth\maxdepth - \setbox\@tempboxa\vbox{% - \unvbox\@leftcolumn\setbox0\lastbox\unskip% - \the\atColsBreak% - \unvbox\@outputbox\setbox0\lastbox\unskip}% - \@tempdimb .5\ht\@tempboxa% - \loop - \setbox\@aaa\copy\@tempboxa% - \setbox\@ccc\vbox to\@tempdimb{% - \vsplit\@aaa to\@tempdimb\vss\vsplit\@aaa to\@tempdimb}% - \wlog{Extra height:\the\ht\@aaa\space when \the\@tempdimb}% - \ifvoid\@aaa \else \advance\@tempdimb 1pt \repeat% - \loop - \setbox\@aaa\copy\@tempboxa% - \setbox\@ccc\vbox to\@tempdimb{% - \vsplit\@aaa to\@tempdimb\vss}% - \wlog{(2)Left:\the\ht\@ccc\space Right:\the\ht\@aaa\space Output:\the\@tempdimb}% - \ifdim \ht\@ccc<\ht\@aaa \@tempdimb \the\ht\@aaa \repeat% - \wlog{- LAST -^^JExtra skip:\the\@extra@skip^^JLeft:\the\ht\@ccc^^JRight:\the\ht\@aaa^^JOutput:\the\@tempdimb}% - \setbox\@ccc\vbox to\@tempdimb{% - \vsplit\@tempboxa to\@tempdimb\vss}% - \setbox\@leftcolumn\vbox to\@tempdima{% - \vbox to\@tempdimb{\unvbox\@ccc}% - \hrule\@height\@nd@page@rule% - \vss}% - \setbox\@outputbox\vbox to\@tempdima{% - \vbox to\@tempdimb{\unvbox\@tempboxa\vfilneg\vskip\@extra@skip}% - \hrule\@height\@nd@page@rule% - \vss}% - \setbox\@outputbox \vbox {% - \hb@xt@\textwidth {% - \hb@xt@\columnwidth {% - \box\@leftcolumn \hss}% - \hfil - \vrule \@width\columnseprule - \hfil - \hb@xt@\columnwidth {% - \box\@outputbox \hss}% - }% - }% - \else - \setbox\@outputbox \vbox {% - \hb@xt@\textwidth {% - \hb@xt@\columnwidth {% - \box\@leftcolumn \hss}% - \hfil - \vrule \@width\columnseprule - \hfil - \hb@xt@\columnwidth {% - \box\@outputbox \hss}% - }% - }% - \fi - \ifvoid\hold@viper - \else - \setbox\@outputbox \vbox{\box\hold@viper\box\@outputbox}% - \fi - \@combinedblfloats - \@outputpage - \begingroup - \@dblfloatplacement - \@startdblcolumn - \@whilesw\if@fcolmade \fi - {\@outputpage - \@startdblcolumn}% - \ifvoid\@viper - \else - \global\setbox\@viper\vbox{% - \vskip-\stripsep\unvbox\@viper}\@viperoutput - \fi - \endgroup - \fi -} -\let\prev@enddocument\enddocument -\newif\if@lastpage \@lastpagefalse -\def\enddocument{\global\@lastpagetrue\let\@outputdblcol\last@outputdblcol\prev@enddocument} -\def\raggedend{\global\let\enddocument\prev@enddocument} -\def\flushend{\gdef\enddocument{\global\@lastpagetrue\let\@outputdblcol\last@outputdblcol\prev@enddocument}} -\def\showcolsendrule{\global\@nd@page@rule=.4pt} -\endinput diff --git a/manuscript/graphicx.sty b/manuscript/graphicx.sty deleted file mode 100644 index 1ff76dd..0000000 --- a/manuscript/graphicx.sty +++ /dev/null @@ -1,238 +0,0 @@ -%% -%% This is file `graphicx.sty', -%% generated with the docstrip utility. -%% -%% The original source files were: -%% -%% graphicx.dtx (with options: `package') -%% -%% graphicx.dtx Copyright (C) 1994 David Carlisle Sebastian Rahtz -%% Copyright (C) 1995 1996 1997 1999 David Carlisle -%% -%% This file is part of the Standard LaTeX `Graphics Bundle'. -%% It may be distributed under the terms of the LaTeX Project Public -%% License, as described in lppl.txt in the base LaTeX distribution. -%% Either version 1.0 or, at your option, any later version. -%% -\NeedsTeXFormat{LaTeX2e}[1995/12/01] -\ProvidesPackage{graphicx} - 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{\Gin@esetsize - \@tempswatrue - \edef\@tempa{\toks@{\noexpand\Gin@erotate{#1}{\the\toks@}}}% - \@tempa} -\define@key{Gin}{origin}[c]{% - \def\Gin@erotate{\Grot@box@kv[origin=#1]}} -\define@key{Gin}{width}{\def\Gin@ewidth{#1}} -\define@key{Gin}{height}{\def\Gin@eheight{#1}} -\define@key{Gin}{totalheight}{% - \def\Gin@eresize{\totalheight}\def\Gin@eheight{#1}} -\define@key{Gin}{keepaspectratio}[true]{% - \lowercase{\Gin@boolkey{#1}}{iso}} -\define@key{Gin}{scale}{% - \if@tempswa - \edef\@tempa{\toks@{\noexpand\Gscale@box{#1}[#1]{\the\toks@}}}% - \@tempa - \else - \def\Gin@req@sizes{% - \def\Gin@scalex{#1}\let\Gin@scaley\Gin@exclamation - \Gin@req@height\Gin@scalex\Gin@nat@height - \Gin@req@width\Gin@scalex\Gin@nat@width}% - \fi - \@tempswatrue} -\define@key{Gin}{draft}[true]{% - \lowercase{\Gin@boolkey{#1}}{draft}} -\define@key{Gin}{clip}[true]{% - \lowercase{\Gin@boolkey{#1}}{clip}} -\define@key{Gin}{type}{% - \def\Ginclude@graphics##1{% - \begingroup - \def\Gin@base{##1}% - \edef\@tempa{{#1}{\Gin@eread}{\Gin@ecom{##1\Gin@eext}}}% - \expandafter\Gin@setfile\@tempa - \endgroup}} -\define@key{Gin}{ext}{\def\Gin@eext{#1}} -\let\Gin@eext\@empty -\define@key{Gin}{read}{% - \def\Gin@eread{#1}% - \def\@tempa{*}\ifx\@tempa\Gin@eread\def\Gin@eread{\Gin@eext}\fi} -\let\Gin@eread\@empty -\define@key{Gin}{command}{\def\Gin@ecom##1{#1}} -\let\Gin@ecom\@firstofone -\def\Gin@boolkey#1#2{% - \csname Gin@#2\ifx\relax#1\relax true\else#1\fi\endcsname} -\def\Gin@eresize{\height} -\def\Gin@esetsize{% - \let\@tempa\Gin@exclamation - \if@tempswa - \edef\@tempa{\toks@{\noexpand - \Gscale@@box\noexpand\Gin@eresize - {\Gin@ewidth}{\Gin@eheight}{\the\toks@}}}% - \@tempa - \else - \ifx\Gin@ewidth\@tempa - \ifx\Gin@eheight\@tempa - \else - \let\Gin@@eheight\Gin@eheight - \def\Gin@req@sizes{% - \Gscale@div\Gin@scaley\Gin@@eheight\Gin@nat@height - \let\Gin@scalex\Gin@exclamation - \setlength\Gin@req@height\Gin@@eheight - \Gin@req@width\Gin@scaley\Gin@nat@width}% - \fi - \else - \ifx\Gin@eheight\@tempa - \let\Gin@@ewidth\Gin@ewidth - \def\Gin@req@sizes{% - \Gscale@div\Gin@scalex\Gin@@ewidth\Gin@nat@width - \let\Gin@scaley\Gin@exclamation - \setlength\Gin@req@width\Gin@@ewidth - \Gin@req@height\Gin@scalex\Gin@nat@height}% - \else - \let\Gin@@ewidth\Gin@ewidth - \let\Gin@@eheight\Gin@eheight - \def\Gin@nosize##1{% - \KV@Gin@natwidth\Gin@@ewidth - \KV@Gin@natheight\Gin@@eheight}% - \def\Gin@req@sizes{% - \Gscale@div\Gin@scalex\Gin@@ewidth\Gin@nat@width - \Gscale@div\Gin@scaley\Gin@@eheight\Gin@nat@height - \ifGin@iso - \ifdim\Gin@scaley\p@>\Gin@scalex\p@ - \let\Gin@scaley\Gin@scalex - \else - \let\Gin@scalex\Gin@scaley - \fi - \fi - \Gin@req@width\Gin@scalex\Gin@nat@width - \Gin@req@height\Gin@scaley\Gin@nat@height}% - \fi - \fi - \fi - \let\Gin@ewidth\Gin@exclamation - \let\Gin@eheight\Gin@ewidth} -\newdimen\Gin@req@height -\newdimen\Gin@req@width -\let\Gin@outer@scalex\relax -\let\Gin@outer@scaley\relax -\let\Gin@angle\relax -\let\Gin@ewidth\Gin@exclamation -\let\Gin@eheight\Gin@ewidth -\def\Gin@scalex{1} -\let\Gin@scaley\Gin@exclamation -\def\Gin@i{% - \def\Gin@req@sizes{% - \Gin@req@height\Gin@nat@height - \Gin@req@width\Gin@nat@width}% - \@ifnextchar[\Gin@ii{\Gin@ii[]}} -\def\Gin@ii[#1]#2{% - \def\@tempa{[}\def\@tempb{#2}% - \ifx\@tempa\@tempb - \def\@tempa{\Gin@iii[#1][}% - \expandafter\@tempa - \else - \begingroup - \@tempswafalse - \toks@{\Ginclude@graphics{#2}}% - \setkeys{Gin}{#1}% - \Gin@esetsize - \the\toks@ - \endgroup - \fi} -\def\rotatebox{% - \@ifnextchar[\Grot@box@kv\Grot@box@std} -\def\Grot@box@std#1#2{% - \Grot@setangle{#1}% - \setbox\z@\hbox{{#2}}% - \Grot@x\z@ - \Grot@y\z@ - \Grot@box} -\def\Grot@box@kv[#1]#2#3{% - \@begin@tempboxa\hbox{#3}% - \Grot@x\width \divide\Grot@x\tw@ - \Grot@y\height \advance\Grot@y-\depth \divide\Grot@y\tw@ - \setkeys{Grot}{#1}% - \setbox\z@\box\@tempboxa - \Grot@setangle{#2}% - \Grot@box - \@end@tempboxa} -\define@key{Grot}{origin}[c]{% - \@tfor\@tempa:=#1\do{% - \if l\@tempa \Grot@x\z@\else - \if r\@tempa \Grot@x\width\else - \if t\@tempa \Grot@y\height\else - \if b\@tempa \Grot@y-\depth\else - \if B\@tempa \Grot@y\z@\fi\fi\fi\fi\fi}} -\define@key{Grot}{x}{\setlength\Grot@x{#1}} -\define@key{Grot}{y}{\setlength\Grot@y{#1}} -\define@key{Grot}{units}{% - \def\Grot@setangle##1{% - \dimen@##1\p@ - \dimen@ii#1\p@ - \divide\dimen@ii360\relax - \divide\dimen@\dimen@ii - \edef\Grot@angle{\number\dimen@}}} -\let\Gin@erotate\Grot@box@std -\endinput -%% -%% End of file `graphicx.sty'. diff --git a/manuscript/landscap.sty b/manuscript/landscap.sty deleted file mode 100644 index b6f7850..0000000 --- a/manuscript/landscap.sty +++ /dev/null @@ -1,12 +0,0 @@ -% Landscape style file -% Don Hosek 2/5/88 -\marginparwidth 0pt -\oddsidemargin 0pt -\evensidemargin 0pt -\marginparsep 0pt - -\topmargin 0pt - -\textwidth 9in -\textheight 6in - diff --git a/manuscript/natbib.bst b/manuscript/natbib.bst deleted file mode 100644 index a679e1d..0000000 --- a/manuscript/natbib.bst +++ /dev/null @@ -1,1288 +0,0 @@ -%% -%% This is file `natbib.bst', generated -%% on <1994/9/16> with the docstrip utility (2.2h). -%% -%% The original source files were: -%% -%% genbst.mbs (with options: `ay,nat,seq-lab,nm-rev,dt-beg,yr-par,vol-bf, -%% volp-com,etal-it') -%% ---------------------------------------- -%% *** Personal bib style, PWD *** -%% -%% (Here are the specifications of the source file) -%% \ProvidesFile{genbst.mbs}[1994/09/16 1.5 (PWD)] -%% For use with BibTeX version 0.99a or later -%% and with LaTeX 2.09 or 2e -%%------------------------------------------------------------------- -%% NOTICE: -%% This file may be used for non-profit purposes. -%% It may not be distributed in exchange for money, -%% other than distribution costs. -%% -%% The author provides it `as is' and does not guarantee it in any way. -%% -%% Copyright (C) 1994 Patrick W. Daly -%% Max-Planck-Institut f\"ur Aeronomie -%% Postfach 20 -%% D-37189 Katlenburg-Lindau -%% Germany -%% -%% E-mail: -%% SPAN-- nsp::linmpi::daly (note nsp also known as ecd1) -%% Internet-- daly@linmpi.dnet.gwdg.de -%%----------------------------------------------------------- -%% \CharacterTable -%% {Upper-case \A\B\C\D\E\F\G\H\I\J\K\L\M\N\O\P\Q\R\S\T\U\V\W\X\Y\Z -%% Lower-case \a\b\c\d\e\f\g\h\i\j\k\l\m\n\o\p\q\r\s\t\u\v\w\x\y\z -%% Digits \0\1\2\3\4\5\6\7\8\9 -%% Exclamation \! Double quote \" Hash (number) \# -%% Dollar \$ Percent \% Ampersand \& -%% Acute accent \' Left paren \( Right paren \) -%% Asterisk \* Plus \+ Comma \, -%% Minus \- Point \. Solidus \/ -%% Colon \: Semicolon \; Less than \< -%% Equals \= Greater than \> Question mark \? -%% Commercial at \@ Left bracket \[ Backslash \\ -%% Right bracket \] Circumflex \^ Underscore \_ -%% Grave accent \` Left brace \{ Vertical bar \| -%% Right brace \} Tilde \~} -%%--------------------------------------------------------------------- - % This is an author-year citation style bibliography. As such, it is - % non-standard LaTeX, and requires a special package file to function properly. - % Such a package is natbib.sty by Patrick W. Daly - % The form of the \bibitem entries is - % \bibitem[Jones et al.(1990)]{key}... - % \bibitem[Jones et al.(1990)Jones, Baker, and Smith]{key}... - % The essential feature is that the label (the part in brackets) consists - % of the author names, as they should appear in the citation, with the year - % in parentheses following. There must be no space before the opening - % parenthesis! - % With natbib v5.3, a full list of authors may also follow the year. - % In natbib.sty, it is possible to define the type of enclosures that is - % really wanted (brackets or parentheses), but in either case, there must - % be parentheses in the label. - % The \cite command functions as follows: - % \cite{key} ==>> Jones et al. (1990) - % \cite[]{key} ==>> (Jones et al., 1990) - % \cite[chap. 2]{key} ==>> (Jones et al., 1990, chap. 2) - % \cite[e.g.][]{key} ==>> (e.g. Jones et al., 1990) - % \cite[e.g.][p. 32]{key} ==>> (e.g. Jones et al., p. 32) - % \citeauthor{key} Jones et al. - % \citefullauthor{key} Jones, Baker, and Smith - % \citeyear{key} 1990 -%%--------------------------------------------------------------------- - -ENTRY - { address - author - booktitle - chapter - edition - editor - howpublished - institution - journal - key - month - note - number - organization - pages - publisher - school - series - title - type - volume - year - } - {} - { label extra.label sort.label } - -INTEGERS { output.state before.all mid.sentence after.sentence after.block } - -FUNCTION {init.state.consts} -{ #0 'before.all := - #1 'mid.sentence := - #2 'after.sentence := - #3 'after.block := -} - -STRINGS { s t } - -FUNCTION {output.nonnull} -{ 's := - output.state mid.sentence = - { ", " * write$ } - { output.state after.block = - { add.period$ write$ - newline$ - "\newblock " write$ - } - { output.state before.all = - 'write$ - { add.period$ " " * write$ } - if$ - } - if$ - mid.sentence 'output.state := - } - if$ - s -} - -FUNCTION {output} -{ duplicate$ empty$ - 'pop$ - 'output.nonnull - if$ -} - -FUNCTION {output.check} -{ 't := - duplicate$ empty$ - { pop$ "empty " t * " in " * cite$ * warning$ } - 'output.nonnull - if$ -} - -FUNCTION {fin.entry} -{ add.period$ - write$ - newline$ -} - -FUNCTION {new.block} -{ output.state before.all = - 'skip$ - { after.block 'output.state := } - if$ -} - -FUNCTION {new.sentence} -{ output.state after.block = - 'skip$ - { output.state before.all = - 'skip$ - { after.sentence 'output.state := } - if$ - } - if$ -} - -FUNCTION {not} -{ { #0 } - { #1 } - if$ -} - -FUNCTION {and} -{ 'skip$ - { pop$ #0 } - if$ -} - -FUNCTION {or} -{ { pop$ #1 } - 'skip$ - if$ -} - -FUNCTION {non.stop} -{ duplicate$ - "}" * add.period$ - #-1 #1 substring$ "." = -} - -FUNCTION {new.block.checkb} -{ empty$ - swap$ empty$ - and - 'skip$ - 'new.block - if$ -} - -FUNCTION {field.or.null} -{ duplicate$ empty$ - { pop$ "" } - 'skip$ - if$ -} - -FUNCTION {emphasize} -{ duplicate$ empty$ - { pop$ "" } - { "{\em " swap$ * non.stop - { "\/}" * } - { "}" * } - if$ - } - if$ -} - -FUNCTION {bolden} -{ duplicate$ empty$ - { pop$ "" } - { "{\bf " swap$ * "}" * } - if$ -} - -INTEGERS { nameptr namesleft numnames } - -FUNCTION {format.names} -{ 's := - #1 'nameptr := - s num.names$ 'numnames := - numnames 'namesleft := - { namesleft #0 > } - { s nameptr - "{vv~}{ll}{, jj}{, f.}" format.name$ 't := - nameptr #1 > - { - namesleft #1 > - { ", " * t * } - { - numnames #2 > - { "," * } - 'skip$ - if$ - t "others" = - { " " * "et~al." emphasize * } - { " and " * t * } - if$ - } - if$ - } - 't - if$ - nameptr #1 + 'nameptr := - namesleft #1 - 'namesleft := - } - while$ -} - -FUNCTION {format.names.ed} -{ 's := - #1 'nameptr := - s num.names$ 'numnames := - numnames 'namesleft := - { namesleft #0 > } - { s nameptr - "{f.~}{vv~}{ll}{, jj}" - format.name$ 't := - nameptr #1 > - { - namesleft #1 > - { ", " * t * } - { - numnames #2 > - { "," * } - 'skip$ - if$ - t "others" = - { " " * "et~al." emphasize * } - { " and " * t * } - if$ - } - if$ - } - 't - if$ - nameptr #1 + 'nameptr := - namesleft #1 - 'namesleft := - } - while$ -} - -FUNCTION {format.key} -{ empty$ - { key field.or.null } - { "" } - if$ -} - -FUNCTION {format.authors} -{ author empty$ - { "" } - { author format.names } - if$ -} - -FUNCTION {format.editors} -{ editor empty$ - { "" } - { editor format.names - editor num.names$ #1 > - { ", editors" * } - { ", editor" * } - if$ - } - if$ -} - -FUNCTION {format.in.editors} -{ editor empty$ - { "" } - { editor format.names.ed - editor num.names$ #1 > - { ", editors" * } - { ", editor" * } - if$ - } - if$ -} - -FUNCTION {format.title} -{ title empty$ - { "" } - { title "t" change.case$ - } - if$ -} - -FUNCTION {format.full.names} -{'s := - #1 'nameptr := - s num.names$ 'numnames := - numnames 'namesleft := - { namesleft #0 > } - { s nameptr - "{vv~}{ll}" format.name$ 't := - nameptr #1 > - { - namesleft #1 > - { ", " * t * } - { - numnames #2 > - { "," * } - 'skip$ - if$ - t "others" = - { " " * "et~al." emphasize * } - { " and " * t * } - if$ - } - if$ - } - 't - if$ - nameptr #1 + 'nameptr := - namesleft #1 - 'namesleft := - } - while$ -} - -FUNCTION {author.editor.key.full} -{ author empty$ - { editor empty$ - { key empty$ - { cite$ #1 #3 substring$ } - 'key - if$ - } - { editor format.full.names } - if$ - } - { author format.full.names } - if$ -} - -FUNCTION {author.key.full} -{ author empty$ - { key empty$ - { cite$ #1 #3 substring$ } - 'key - if$ - } - { author format.full.names } - if$ -} - -FUNCTION {editor.key.full} -{ editor empty$ - { key empty$ - { cite$ #1 #3 substring$ } - 'key - if$ - } - { editor format.full.names } - if$ -} - -FUNCTION {make.full.names} -{ type$ "book" = - type$ "inbook" = - or - 'author.editor.key.full - { type$ "proceedings" = - 'editor.key.full - 'author.key.full - if$ - } - if$ -} - -FUNCTION {output.bibitem} -{ newline$ - "\bibitem[" write$ - label write$ - ")" make.full.names * "]{" * write$ - cite$ write$ - "}" write$ - newline$ - "" - before.all 'output.state := -} - -FUNCTION {n.dashify} -{ 't := - "" - { t empty$ not } - { t #1 #1 substring$ "-" = - { t #1 #2 substring$ "--" = not - { "--" * - t #2 global.max$ substring$ 't := - } - { { t #1 #1 substring$ "-" = } - { "-" * - t #2 global.max$ substring$ 't := - } - while$ - } - if$ - } - { t #1 #1 substring$ * - t #2 global.max$ substring$ 't := - } - if$ - } - while$ -} - -FUNCTION {word.in} -{ "In " } - -FUNCTION {format.date} -{ year duplicate$ empty$ - { "empty year in " cite$ * "; set to ????" * warning$ - pop$ "????" } - 'skip$ - if$ - before.all 'output.state := - " (" swap$ * extra.label * ")" * -} - -FUNCTION {format.btitle} -{ title emphasize -} - -FUNCTION {tie.or.space.connect} -{ duplicate$ text.length$ #3 < - { "~" } - { " " } - if$ - swap$ * * -} - -FUNCTION {either.or.check} -{ empty$ - 'pop$ - { "can't use both " swap$ * " fields in " * cite$ * warning$ } - if$ -} - -FUNCTION {format.bvolume} -{ volume empty$ - { "" } - { "volume" volume tie.or.space.connect - series empty$ - 'skip$ - { " of " * series emphasize * } - if$ - "volume and number" number either.or.check - } - if$ -} - -FUNCTION {format.number.series} -{ volume empty$ - { number empty$ - { series field.or.null } - { output.state mid.sentence = - { "number" } - { "Number" } - if$ - number tie.or.space.connect - series empty$ - { "there's a number but no series in " cite$ * warning$ } - { " in " * series * } - if$ - } - if$ - } - { "" } - if$ -} - -FUNCTION {format.edition} -{ edition empty$ - { "" } - { output.state mid.sentence = - { edition "l" change.case$ " edition" * } - { edition "t" change.case$ " edition" * } - if$ - } - if$ -} - -INTEGERS { multiresult } - -FUNCTION {multi.page.check} -{ 't := - #0 'multiresult := - { multiresult not - t empty$ not - and - } - { t #1 #1 substring$ - duplicate$ "-" = - swap$ duplicate$ "," = - swap$ "+" = - or or - { #1 'multiresult := } - { t #2 global.max$ substring$ 't := } - if$ - } - while$ - multiresult -} - -FUNCTION {format.pages} -{ pages empty$ - { "" } - { pages multi.page.check - { "pages" pages n.dashify tie.or.space.connect } - { "page" pages tie.or.space.connect } - if$ - } - if$ -} - -FUNCTION {format.vol.num.pages} -{ volume field.or.null - bolden - number empty$ - 'skip$ - { "(" number * ")" * * - volume empty$ - { "there's a number but no volume in " cite$ * warning$ } - 'skip$ - if$ - } - if$ - pages empty$ - 'skip$ - { duplicate$ empty$ - { pop$ format.pages } - { ", " * pages n.dashify * } - if$ - } - if$ -} - -FUNCTION {format.chapter.pages} -{ chapter empty$ - 'format.pages - { type empty$ - { "chapter" } - { type "l" change.case$ } - if$ - chapter tie.or.space.connect - pages empty$ - 'skip$ - { ", " * format.pages * } - if$ - } - if$ -} - -FUNCTION {format.in.ed.booktitle} -{ booktitle empty$ - { "" } - { editor empty$ - { word.in booktitle emphasize * } - { word.in format.in.editors * ", " * booktitle emphasize * } - if$ - } - if$ -} - -FUNCTION {format.thesis.type} -{ type empty$ - 'skip$ - { pop$ - type "t" change.case$ - } - if$ -} - -FUNCTION {format.tr.number} -{ type empty$ - { "Technical Report" } - 'type - if$ - number empty$ - { "t" change.case$ } - { number tie.or.space.connect } - if$ -} - -FUNCTION {format.article.crossref} -{ - word.in - "\cite{" * crossref * "}" * -} - -FUNCTION {format.book.crossref} -{ volume empty$ - { "empty volume in " cite$ * "'s crossref of " * crossref * warning$ - word.in - } - { "Volume" volume tie.or.space.connect - " of " * - } - if$ - "\cite{" * crossref * "}" * -} - -FUNCTION {format.incoll.inproc.crossref} -{ - word.in - "\cite{" * crossref * "}" * -} - -FUNCTION {article} -{ output.bibitem - format.authors "author" output.check - author format.key output - format.date "year" output.check - new.block - format.title "title" output.check - new.block - crossref missing$ - { journal emphasize "journal" output.check - format.vol.num.pages output - } - { format.article.crossref output.nonnull - format.pages output - } - if$ - new.block - note output - fin.entry -} - -FUNCTION {book} -{ output.bibitem - author empty$ - { format.editors "author and editor" output.check - editor format.key output - } - { format.authors output.nonnull - crossref missing$ - { "author and editor" editor either.or.check } - 'skip$ - if$ - } - if$ - format.date "year" output.check - new.block - format.btitle "title" output.check - crossref missing$ - { format.bvolume output - new.block - format.number.series output - new.sentence - publisher "publisher" output.check - address output - } - { - new.block - format.book.crossref output.nonnull - } - if$ - format.edition output - new.block - note output - fin.entry -} - -FUNCTION {booklet} -{ output.bibitem - format.authors output - author format.key output - format.date "year" output.check - new.block - format.title "title" output.check - new.block - howpublished output - address output - new.block - note output - fin.entry -} - -FUNCTION {inbook} -{ output.bibitem - author empty$ - { format.editors "author and editor" output.check - editor format.key output - } - { format.authors output.nonnull - crossref missing$ - { "author and editor" editor either.or.check } - 'skip$ - if$ - } - if$ - format.date "year" output.check - new.block - format.btitle "title" output.check - crossref missing$ - { format.bvolume output - format.chapter.pages "chapter and pages" output.check - new.block - format.number.series output - new.sentence - publisher "publisher" output.check - address output - } - { format.chapter.pages "chapter and pages" output.check - new.block - format.book.crossref output.nonnull - } - if$ - format.edition output - new.block - note output - fin.entry -} - -FUNCTION {incollection} -{ output.bibitem - format.authors "author" output.check - author format.key output - format.date "year" output.check - new.block - format.title "title" output.check - new.block - crossref missing$ - { format.in.ed.booktitle "booktitle" output.check - format.bvolume output - format.number.series output - format.chapter.pages output - new.sentence - publisher "publisher" output.check - address output - format.edition output - } - { format.incoll.inproc.crossref output.nonnull - format.chapter.pages output - } - if$ - new.block - note output - fin.entry -} - -FUNCTION {inproceedings} -{ output.bibitem - format.authors "author" output.check - author format.key output - format.date "year" output.check - new.block - format.title "title" output.check - new.block - crossref missing$ - { format.in.ed.booktitle "booktitle" output.check - format.bvolume output - format.number.series output - format.pages output - address output - new.sentence - organization output - publisher output - } - { format.incoll.inproc.crossref output.nonnull - format.pages output - } - if$ - new.block - note output - fin.entry -} - -FUNCTION {conference} { inproceedings } - -FUNCTION {manual} -{ output.bibitem - format.authors output - author format.key output - format.date "year" output.check - new.block - format.btitle "title" output.check - organization address new.block.checkb - organization output - address output - format.edition output - new.block - note output - fin.entry -} - -FUNCTION {mastersthesis} -{ output.bibitem - format.authors "author" output.check - author format.key output - format.date "year" output.check - new.block - format.btitle "title" output.check - new.block - "Master's thesis" format.thesis.type output.nonnull - school "school" output.check - address output - new.block - note output - fin.entry -} - -FUNCTION {misc} -{ output.bibitem - format.authors output - author format.key output - format.date "year" output.check - new.block - format.title output - new.block - howpublished output - new.block - note output - fin.entry -} - -FUNCTION {phdthesis} -{ output.bibitem - format.authors "author" output.check - author format.key output - format.date "year" output.check - new.block - format.btitle "title" output.check - new.block - "Ph.D. thesis" format.thesis.type output.nonnull - school "school" output.check - address output - new.block - note output - fin.entry -} - -FUNCTION {proceedings} -{ output.bibitem - format.editors output - editor format.key output - format.date "year" output.check - new.block - format.btitle "title" output.check - format.bvolume output - format.number.series output - address output - new.sentence - organization output - publisher output - new.block - note output - fin.entry -} - -FUNCTION {techreport} -{ output.bibitem - format.authors "author" output.check - author format.key output - format.date "year" output.check - new.block - format.title "title" output.check - new.block - format.tr.number output.nonnull - institution "institution" output.check - address output - new.block - note output - fin.entry -} - -FUNCTION {unpublished} -{ output.bibitem - format.authors "author" output.check - author format.key output - format.date "year" output.check - new.block - format.title "title" output.check - new.block - note "note" output.check - fin.entry -} - -FUNCTION {default.type} { misc } - -MACRO {jan} {"January"} - -MACRO {feb} {"February"} - -MACRO {mar} {"March"} - -MACRO {apr} {"April"} - -MACRO {may} {"May"} - -MACRO {jun} {"June"} - -MACRO {jul} {"July"} - -MACRO {aug} {"August"} - -MACRO {sep} {"September"} - -MACRO {oct} {"October"} - -MACRO {nov} {"November"} - -MACRO {dec} {"December"} - -MACRO {acmcs} {"ACM Computing Surveys"} - -MACRO {acta} {"Acta Informatica"} - -MACRO {cacm} {"Communications of the ACM"} - -MACRO {ibmjrd} {"IBM Journal of Research and Development"} - -MACRO {ibmsj} {"IBM Systems Journal"} - -MACRO {ieeese} {"IEEE Transactions on Software Engineering"} - -MACRO {ieeetc} {"IEEE Transactions on Computers"} - -MACRO {ieeetcad} - {"IEEE Transactions on Computer-Aided Design of Integrated Circuits"} - -MACRO {ipl} {"Information Processing Letters"} - -MACRO {jacm} {"Journal of the ACM"} - -MACRO {jcss} {"Journal of Computer and System Sciences"} - -MACRO {scp} {"Science of Computer Programming"} - -MACRO {sicomp} {"SIAM Journal on Computing"} - -MACRO {tocs} {"ACM Transactions on Computer Systems"} - -MACRO {tods} {"ACM Transactions on Database Systems"} - -MACRO {tog} {"ACM Transactions on Graphics"} - -MACRO {toms} {"ACM Transactions on Mathematical Software"} - -MACRO {toois} {"ACM Transactions on Office Information Systems"} - -MACRO {toplas} {"ACM Transactions on Programming Languages and Systems"} - -MACRO {tcs} {"Theoretical Computer Science"} - -READ - -FUNCTION {sortify} -{ purify$ - "l" change.case$ -} - -INTEGERS { len } - -FUNCTION {chop.word} -{ 's := - 'len := - s #1 len substring$ = - { s len #1 + global.max$ substring$ } - 's - if$ -} - -FUNCTION {format.lab.names} -{ 's := - s #1 "{vv~}{ll}" format.name$ - s num.names$ duplicate$ - #2 > - { pop$ " " * "et~al." emphasize * } - { #2 < - 'skip$ - { s #2 "{ff }{vv }{ll}{ jj}" format.name$ "others" = - { " " * "et~al." emphasize * } - { " and " * s #2 "{vv~}{ll}" format.name$ * } - if$ - } - if$ - } - if$ -} - -FUNCTION {author.key.label} -{ author empty$ - { key empty$ - { cite$ #1 #3 substring$ } - 'key - if$ - } - { author format.lab.names } - if$ -} - -FUNCTION {author.editor.key.label} -{ author empty$ - { editor empty$ - { key empty$ - { cite$ #1 #3 substring$ } - 'key - if$ - } - { editor format.lab.names } - if$ - } - { author format.lab.names } - if$ -} - -FUNCTION {editor.key.label} -{ editor empty$ - { key empty$ - { cite$ #1 #3 substring$ } - 'key - if$ - } - { editor format.lab.names } - if$ -} - -FUNCTION {calc.label} -{ type$ "book" = - type$ "inbook" = - or - 'author.editor.key.label - { type$ "proceedings" = - 'editor.key.label - 'author.key.label - if$ - } - if$ - "(" - * - year duplicate$ empty$ - { pop$ "????" } - { purify$ #-1 #4 substring$ } - if$ - * - 'label := -} - -FUNCTION {sort.format.names} -{ 's := - #1 'nameptr := - "" - s num.names$ 'numnames := - numnames 'namesleft := - { namesleft #0 > } - { nameptr #1 > - { " " * } - 'skip$ - if$ - s nameptr - "{vv{ } }{ll{ }}{ f{ }}{ jj{ }}" - format.name$ 't := - nameptr numnames = t "others" = and - { "et al" * } - { numnames #2 > nameptr #2 = and - { "zzzzzz" * #1 'namesleft := } - { t sortify * } - if$ - } - if$ - nameptr #1 + 'nameptr := - namesleft #1 - 'namesleft := - } - while$ -} - -FUNCTION {sort.format.title} -{ 't := - "A " #2 - "An " #3 - "The " #4 t chop.word - chop.word - chop.word - sortify - #1 global.max$ substring$ -} - -FUNCTION {author.sort} -{ author empty$ - { key empty$ - { "to sort, need author or key in " cite$ * warning$ - "" - } - { key sortify } - if$ - } - { author sort.format.names } - if$ -} - -FUNCTION {author.editor.sort} -{ author empty$ - { editor empty$ - { key empty$ - { "to sort, need author, editor, or key in " cite$ * warning$ - "" - } - { key sortify } - if$ - } - { editor sort.format.names } - if$ - } - { author sort.format.names } - if$ -} - -FUNCTION {editor.sort} -{ editor empty$ - { key empty$ - { "to sort, need editor or key in " cite$ * warning$ - "" - } - { key sortify } - if$ - } - { editor sort.format.names } - if$ -} - -FUNCTION {presort} -{ calc.label - label sortify - " " - * - type$ "book" = - type$ "inbook" = - or - 'author.editor.sort - { type$ "proceedings" = - 'editor.sort - 'author.sort - if$ - } - if$ - #1 entry.max$ substring$ - 'sort.label := - sort.label - * - " " - * - title field.or.null - sort.format.title - * - #1 entry.max$ substring$ - 'sort.key$ := -} - -ITERATE {presort} - -SORT - -STRINGS { last.label next.extra } - -INTEGERS { last.extra.num } - -FUNCTION {initialize.extra.label.stuff} -{ #0 int.to.chr$ 'last.label := - "" 'next.extra := - #0 'last.extra.num := -} - -FUNCTION {forward.pass} -{ last.label label = - { last.extra.num #1 + 'last.extra.num := - last.extra.num int.to.chr$ 'extra.label := - } - { "a" chr.to.int$ 'last.extra.num := - "" 'extra.label := - label 'last.label := - } - if$ -} - -FUNCTION {reverse.pass} -{ next.extra "b" = - { "a" 'extra.label := } - 'skip$ - if$ - extra.label 'next.extra := - label extra.label * 'label := -} - -EXECUTE {initialize.extra.label.stuff} - -ITERATE {forward.pass} - -REVERSE {reverse.pass} - -FUNCTION {bib.sort.order} -{ sort.label - " " - * - year field.or.null sortify - * - " " - * - title field.or.null - sort.format.title - * - #1 entry.max$ substring$ - 'sort.key$ := -} - -ITERATE {bib.sort.order} - -SORT - -FUNCTION {begin.bib} -{ preamble$ empty$ - 'skip$ - { preamble$ write$ newline$ } - if$ - "\begin{thebibliography}{}" write$ newline$ -} - -EXECUTE {begin.bib} - -EXECUTE {init.state.consts} - -ITERATE {call.type$} - -FUNCTION {end.bib} -{ newline$ - "\end{thebibliography}" write$ newline$ -} - -EXECUTE {end.bib} -%% End of customized bst file - diff --git a/manuscript/natbib.sty b/manuscript/natbib.sty deleted file mode 100644 index 4c8c948..0000000 --- a/manuscript/natbib.sty +++ /dev/null @@ -1,803 +0,0 @@ -%% -%% This is file `natbib.sty', -%% generated with the docstrip utility. -%% -%% The original source files were: -%% -%% natbib.dtx (with options: `package,all') -%% ============================================= -%% IMPORTANT NOTICE: -%% -%% This program can be redistributed and/or modified under the terms -%% of the LaTeX Project Public License Distributed from CTAN -%% archives in directory macros/latex/base/lppl.txt; either -%% version 1 of the License, or any later version. -%% -%% This is a generated file. -%% It may not be distributed without the original source file natbib.dtx. -%% -%% Full documentation can be obtained by LaTeXing that original file. -%% Only a few abbreviated comments remain here to describe the usage. -%% ============================================= -%% Copyright 1993-2000 Patrick W Daly -%% Max-Planck-Institut f\"ur Aeronomie -%% Max-Planck-Str. 2 -%% D-37191 Katlenburg-Lindau -%% Germany -%% E-mail: daly@linmpi.mpg.de -\NeedsTeXFormat{LaTeX2e}[1995/06/01] -\ProvidesPackage{natbib} - [2000/07/24 7.0a (PWD)] - % This package reimplements the LaTeX \cite command to be used for various - % citation styles, both author-year and numerical. It accepts BibTeX - % output intended for many other packages, and therefore acts as a - % general, all-purpose citation-style interface. - % - % With standard numerical .bst files, only numerical citations are - % possible. With an author-year .bst file, both numerical and - % author-year citations are possible. - % - % If author-year citations are selected, \bibitem must have one of the - % following forms: - % \bibitem[Jones et al.(1990)]{key}... - % \bibitem[Jones et al.(1990)Jones, Baker, and Williams]{key}... - % \bibitem[Jones et al., 1990]{key}... - % \bibitem[\protect\citeauthoryear{Jones, Baker, and Williams}{Jones - % et al.}{1990}]{key}... - % \bibitem[\protect\citeauthoryear{Jones et al.}{1990}]{key}... - % \bibitem[\protect\astroncite{Jones et al.}{1990}]{key}... - % \bibitem[\protect\citename{Jones et al., }1990]{key}... - % \harvarditem[Jones et al.]{Jones, Baker, and Williams}{1990}{key}... - % - % This is either to be made up manually, or to be generated by an - % appropriate .bst file with BibTeX. - % Author-year mode || Numerical mode - % Then, \citet{key} ==>> Jones et al. (1990) || Jones et al. [21] - % \citep{key} ==>> (Jones et al., 1990) || [21] - % Multiple citations as normal: - % \citep{key1,key2} ==>> (Jones et al., 1990; Smith, 1989) || [21,24] - % or (Jones et al., 1990, 1991) || [21,24] - % or (Jones et al., 1990a,b) || [21,24] - % \cite{key} is the equivalent of \citet{key} in author-year mode - % and of \citep{key} in numerical mode - % Full author lists may be forced with \citet* or \citep*, e.g. - % \citep*{key} ==>> (Jones, Baker, and Williams, 1990) - % Optional notes as: - % \citep[chap. 2]{key} ==>> (Jones et al., 1990, chap. 2) - % \citep[e.g.,][]{key} ==>> (e.g., Jones et al., 1990) - % \citep[see][pg. 34]{key}==>> (see Jones et al., 1990, pg. 34) - % (Note: in standard LaTeX, only one note is allowed, after the ref. - % Here, one note is like the standard, two make pre- and post-notes.) - % \citealt{key} ==>> Jones et al. 1990 - % \citealt*{key} ==>> Jones, Baker, and Williams 1990 - % \citealp{key} ==>> Jones et al., 1990 - % \citealp*{key} ==>> Jones, Baker, and Williams, 1990 - % Additional citation possibilities (both author-year and numerical modes) - % \citeauthor{key} ==>> Jones et al. - % \citeauthor*{key} ==>> Jones, Baker, and Williams - % \citeyear{key} ==>> 1990 - % \citeyearpar{key} ==>> (1990) - % \citetext{priv. comm.} ==>> (priv. comm.) - % Note: full author lists depends on whether the bib style supports them; - % if not, the abbreviated list is printed even when full requested. - % - % For names like della Robbia at the start of a sentence, use - % \Citet{dRob98} ==>> Della Robbia (1998) - % \Citep{dRob98} ==>> (Della Robbia, 1998) - % \Citeauthor{dRob98} ==>> Della Robbia - % - % - % Citation aliasing is achieved with - % \defcitealias{key}{text} - % \citetalias{key} ==>> text - % \citepalias{key} ==>> (text) - % - % Defining the citation style of a given bib style: - % Use \bibpunct (in the preamble only) with 6 mandatory arguments: - % 1. opening bracket for citation - % 2. closing bracket - % 3. citation separator (for multiple citations in one \cite) - % 4. the letter n for numerical styles, s for superscripts - % else anything for author-year - % 5. punctuation between authors and date - % 6. punctuation between years (or numbers) when common authors missing - % One optional argument is the character coming before post-notes. It - % appears in square braces before all other arguments. May be left off. - % Example (and default) \bibpunct[, ]{(}{)}{;}{a}{,}{,} - % - % To make this automatic for a given bib style, named newbib, say, make - % a local configuration file, natbib.cfg, with the definition - % \newcommand{\bibstyle@newbib}{\bibpunct...} - % Then the \bibliographystyle{newbib} will cause \bibstyle@newbib to - % be called on THE NEXT LATEX RUN (via the aux file). - % - % Such preprogrammed definitions may be invoked in the text (preamble only) - % by calling \citestyle{newbib}. This is only useful if the style specified - % differs from that in \bibliographystyle. - % - % With \citeindextrue and \citeindexfalse, one can control whether the - % \cite commands make an automatic entry of the citation in the .idx - % indexing file. For this, \makeindex must also be given in the preamble. - % - % LaTeX2e Options: (for selecting punctuation) - % round - round parentheses are used (default) - % square - square brackets are used [option] - % curly - curly braces are used {option} - % angle - angle brackets are used