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added Bioinformatics Journal style

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commit 2bb72f9d7098e46707a642f1e0026a7f5779a29b 1 parent 8361197
@vsbuffalo authored
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1,109 paper/PLAIN.BST
@@ -0,0 +1,1109 @@
+% 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}
View
95 paper/alltt.sty
@@ -0,0 +1,95 @@
+%%
+%% 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'.
View
368 paper/array.sty
@@ -0,0 +1,368 @@
+%%
+%% 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'.
View
928 paper/bioinfo.cls
@@ -0,0 +1,928 @@
+\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
+
+\setlength\topskip{10\p@} % height of first line of text
+\setlength\headsep{19\p@} % space below running head --
+
+\setlength\footskip{34\p@} % space above footer line
+\setlength\maxdepth{.5\topskip} % pages can be short or deep by half a line?
+
+\setlength\textwidth{42pc} % text measure excluding margins
+
+\setlength\textheight{58\baselineskip} % 54 lines on a full page,
+\addtolength\textheight{\topskip} % including the first
+ % line on the page
+
+% Set the margins
+\setlength\marginparsep{3\p@}
+\setlength\marginparpush{3\p@}
+\setlength\marginparwidth{35\p@}
+
+\setlength\oddsidemargin{4.5pc}
+\addtolength\oddsidemargin{-1in} % subtract out the 1 inch driver margin
+\setlength\@tempdima{\paperwidth}
+\addtolength\@tempdima{-\textwidth}
+\addtolength\@tempdima{-4.5pc}
+\setlength\evensidemargin{\@tempdima}
+\addtolength\evensidemargin{-1in}
+
+\setlength\columnsep{1.5pc} % space between columns for double-column text
+\setlength\columnseprule{0\p@} % width of rule between two columns
+
+% Footnotes
+\setlength\footnotesep{9\p@} % space between footnotes
+% space between text and footnote
+\setlength{\skip\footins}{12\p@ \@plus 6\p@ \@minus 1\p@}
+
+% Float placement parameters
+
+% The total number of floats that can be allowed on a page.
+\setcounter{totalnumber}{10}
+% The maximum number of floats at the top and bottom of a page.
+\setcounter{topnumber}{5}
+\setcounter{bottomnumber}{5}
+% The maximum part of the top or bottom of a text page that can be
+% occupied by floats. This is set so that at least four lines of text
+% fit on the page.
+\renewcommand\topfraction{.9}
+\renewcommand\bottomfraction{.9}
+% The minimum amount of a text page that must be occupied by text.
+% This should accomodate four lines of text.
+\renewcommand\textfraction{.06}
+% The minimum amount of a float page that must be occupied by floats.
+\renewcommand\floatpagefraction{.94}
+
+% The same parameters repeated for double column output
+\renewcommand\dbltopfraction{.9}
+\renewcommand\dblfloatpagefraction{.9}
+
+% Space between floats
+\setlength\floatsep {12\p@ \@plus 2\p@ \@minus 2\p@}
+% Space between floats and text
+\setlength\textfloatsep{20\p@ \@plus 2\p@ \@minus 4\p@}
+% Space above and below an inline figure
+\setlength\intextsep {18\p@ \@plus 2\p@ \@minus 2\p@}
+
+% For double column floats
+\setlength\dblfloatsep {12\p@ \@plus 2\p@ \@minus 2\p@}
+\setlength\dbltextfloatsep{20\p@ \@plus 2\p@ \@minus 4\p@}
+
+% Space left at top, bottom and inbetween floats on a float page.
+\setlength\@fptop{0\p@} % no space above float page figures
+\setlength\@fpsep{12\p@ \@plus 1fil}
+\setlength\@fpbot{0\p@}
+
+% The same for double column
+\setlength\@dblfptop{0\p@}
+\setlength\@dblfpsep{12\p@ \@plus 1fil}
+\setlength\@dblfpbot{0\p@}
+
+% Override settings in mathtime back to TeX defaults
+\DeclareMathSizes{5} {5} {5} {5}
+\DeclareMathSizes{6} {6} {5} {5}
+\DeclareMathSizes{7} {7} {5} {5}
+\DeclareMathSizes{8} {8} {6} {5}
+\DeclareMathSizes{9} {9} {6.5} {5}
+\DeclareMathSizes{10} {10} {7.5} {5}
+\DeclareMathSizes{12} {12} {9} {7}
+
+% Page styles
+\def\ps@headings
+ {%
+ \def\@oddfoot{\vbox to 12.5\p@{\hbox{\rule{\textwidth}{0.5\p@}}\vss
+ \hbox to \textwidth{\hfill\helveticabold\small\thepage}%
+ }}%
+ \def\@evenfoot{\vbox to 12.5\p@{\rule{\textwidth}{0.5\p@}\vss
+ \hbox to \textwidth{\helveticabold\small\thepage\hfill}%
+ }}%
+ \def\@evenhead{\vbox{\hbox to \textwidth{\fontsize{8}{10}\selectfont
+ \helveticabold{\fontshape{it}\selectfont
+ \strut\leftmark}\hfill}\vspace{6.5\p@}\rule{\textwidth}{0.5\p@}}}%
+ \def\@oddhead{\vbox{\hbox to \textwidth{\hfill\fontsize{8}{10}\selectfont
+ \helveticabold{\fontshape{it}\selectfont\strut\rightmark}}%
+ \vspace{6.5\p@}\rule{\textwidth}{0.5\p@}}}%
+ \def\titlemark##1{\markboth{##1}{##1}}%
+ \def\authormark##1{\gdef\leftmark{##1}}%
+ }
+
+\def\ps@opening
+ {%
+ \def\@oddfoot{\vbox to 13\p@{\hbox{\rule{\textwidth}{1\p@}}\vss
+ \hbox to \textwidth{\helvetica
+ \fontsize{7}{9}\fontshape{n}\selectfont \copyright\space Oxford University Press \@copyrightyear.%
+ \hfill\small\helveticabold\thepage}%
+ }}%
+ \def\@evenfoot{\vbox to 13\p@{\rule{\textwidth}{1\p@}\vss
+ \hbox to \textwidth{\helvetica\thepage\hfill
+ \fontsize{7}{9}\fontshape{n}\selectfont \copyright\space Oxford University Press \@copyrightyear.}%
+ }}%
+ \let\@evenhead\relax
+ \let\@oddhead\relax}
+
+% Page range
+\newif\iflastpagegiven \lastpagegivenfalse
+\newcommand\firstpage[1]{%
+ \gdef\@firstpage{#1}%
+ \ifnum\@firstpage>\c@page
+ \setcounter{page}{#1}%
+ \ClassWarning{BIO}{Increasing pagenumber to \@firstpage}%
+ \else \ifnum\@firstpage<\c@page
+ \ClassWarning{BIO}{Firstpage lower than pagenumber}\fi\fi
+ \xdef\@firstpage{\the\c@page}%
+ }
+\def\@firstpage{1}
+\def\pagenumbering#1{%
+ \global\c@page \@ne
+ \gdef\thepage{\csname @#1\endcsname \c@page}%
+ \gdef\thefirstpage{%
+ \csname @#1\endcsname \@firstpage}%
+ \gdef\thelastpage{%
+ \csname @#1\endcsname \@lastpage}%
+ }
+
+\newcommand\lastpage[1]{\xdef\@lastpage{#1}%
+ \global\lastpagegiventrue}
+\def\@lastpage{0}
+\def\setlastpage{\iflastpagegiven\else
+ \edef\@tempa{@lastpage@}%
+ \expandafter
+ \ifx \csname \@tempa \endcsname \relax
+ \gdef\@lastpage{0}%
+ \else
+ \xdef\@lastpage{\@nameuse{@lastpage@}}%
+ \fi
+ \fi }
+\def\writelastpage{%
+ \iflastpagegiven \else
+ \immediate\write\@auxout%
+ {\string\global\string\@namedef{@lastpage@}{\the\c@page}}%
+ \fi
+ }
+\def\thepagerange{%
+ \ifnum\@lastpage =0 {\ \bf ???} \else
+ \ifnum\@lastpage = \@firstpage \ \thefirstpage\else
+ \thefirstpage--\thelastpage \fi\fi}
+
+\AtBeginDocument{\setlastpage
+ \pagenumbering{arabic}%
+ }
+\AtEndDocument{%
+ \writelastpage
+ \if@final
+ \clearemptydoublepage
+ \else
+ \clearpage
+ \fi}
+
+%
+% Sectional units
+%
+
+% Counters
+\newcounter{section}
+\newcounter{subsection}[section]
+\newcounter{subsubsection}[subsection]
+\newcounter{paragraph}[subsubsection]
+\newcounter{subparagraph}[paragraph]
+\newcounter{figure}
+\newcounter{table}
+
+% Form of the numbers
+\newcommand\thepage{\arabic{page}}
+\renewcommand\thesection{\arabic{section}}
+\renewcommand\thesubsection{{\thesection.\arabic{subsection}}}
+\renewcommand\thesubsubsection{{\thesubsection.\arabic{subsubsection}}}
+\renewcommand\theparagraph{\thesubsubsection.\arabic{paragraph}}
+\renewcommand\thesubparagraph{\theparagraph.\arabic{subparagraph}}
+\renewcommand\theequation{\arabic{equation}}
+
+% Form of the words
+\newcommand\contentsname{Contents}
+\newcommand\listfigurename{List of Figures}
+\newcommand\listtablename{List of Tables}
+\newcommand\partname{Part}
+\newcommand\appendixname{Appendix}
+\newcommand\abstractname{Abstract}
+\newcommand\refname{References}
+\newcommand\bibname{References}
+\newcommand\indexname{Index}
+\newcommand\figurename{Fig.}
+\newcommand\tablename{Table}
+
+% Clearemptydoublepage should really clear the running heads too
+\newcommand{\clearemptydoublepage}{\newpage{\pagestyle{empty}\cleardoublepage}}
+
+% Frontmatter, mainmatter and backmatter
+
+\newif\if@mainmatter \@mainmattertrue
+
+\newcommand\frontmatter{%
+ \clearpage
+ \@mainmatterfalse
+ \pagenumbering{roman}}
+
+\newcommand\mainmatter{%
+ \clearpage
+ \@mainmattertrue
+ \pagenumbering{arabic}}
+
+\newcommand\backmatter{%
+ \clearpage
+ \@mainmatterfalse}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% TITLE %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\newlength{\dropfromtop}
+\setlength{\dropfromtop}{\z@}
+
+% Application Notes
+\newif\if@appnotes
+\newcommand{\application}{%
+% \setlength{\dropfromtop}{-2.25pc}%
+ \global\@appnotestrue}
+
+\long\def\title{\@ifnextchar[{\short@title}{\@@title}}
+\def\short@title[#1]{\titlemark{#1}\@@@title}
+\def\@@title#1{\authormark{#1}\@@@title{#1}}
+\long\def\@@@title#1{\gdef\@title{#1}}
+
+\long\def\author{\@ifnextchar[{\short@uthor}{\@uthor}}
+\def\short@uthor[#1]{\authormark{#1}\@@author}
+\def\@uthor#1{\authormark{#1}\@@author{#1}}
+\long\def\@@author#1{\gdef\@author{#1}}
+
+\def\vol#1{\global\def\@vol{#1}}
+\def\issue#1{\global\def\@issue{#1}}
+\def\address#1{\global\def\@issue{#1}}
+\def\history#1{\global\def\@history{#1}}
+\def\editor#1{\global\def\@editor{#1}}
+\def\pubyear#1{\global\def\@pubyear{#1}}
+\def\copyrightyear#1{\global\def\@copyrightyear{#1}}
+\def\address#1{\global\def\@address{#1}}
+\def\DOI#1{\global\def\@DOI{#1}}
+
+\definecolor{gray}{cmyk}{0, 0, 0, 0.15}
+\newlength{\extraspace}
+\setlength{\extraspace}{\z@}
+
+\newcommand\maketitle{\par
+ \begingroup
+ \renewcommand\thefootnote{\@fnsymbol\c@footnote}%
+ \def\@makefnmark{\rlap{\@textsuperscript{\normalfont\@thefnmark}}}%
+ \long\def\@makefntext##1{\parindent 3mm\noindent
+% \@textsuperscript{\normalfont\@thefnmark}\raggedright##1}%
+ \@textsuperscript{\normalfont\@thefnmark}##1}%
+ \if@twocolumn
+ \ifnum \col@number=\@ne
+ \@maketitle
+ \else
+ \twocolumn[\@maketitle]%
+ \fi
+ \else
+ \newpage
+ \global\@topnum\z@ % Prevents figures from going at top of page.
+ \@maketitle
+ \fi
+ \thispagestyle{opening}\@thanks
+ \endgroup
+ \setcounter{footnote}{0}%
+ \global\let\thanks\relax
+ \global\let\maketitle\relax
+ \global\let\@maketitle\relax
+ \global\let\@address\@empty
+ \global\let\@history\@empty
+ \global\let\@editor\@empty
+ \global\let\@thanks\@empty
+ \global\let\@author\@empty
+ \global\let\@date\@empty
+ \global\let\@title\@empty
+ \global\let\@pubyear\@empty
+ \global\let\address\relax
+ \global\let\history\relax
+ \global\let\editor\relax
+ \global\let\title\relax
+ \global\let\author\relax
+ \global\let\date\relax
+ \global\let\pubyear\relax
+ \global\let\@copyrightline\@empty
+ \global\let\and\relax
+ \@afterindentfalse\@afterheading
+}
+
+\newlength{\aboveskipchk}%for checking oddpage or evenpage top skip
+\setlength{\aboveskipchk}{\z@}%
+
+\def\@maketitle{%
+ \let\footnote\thanks
+ \clearemptydoublepage
+ \checkoddpage\ifcpoddpage\setlength{\aboveskipchk}{-3pc}\else\setlength{\aboveskipchk}{-5pc}\fi%for checking oddpage or evenpage top skip%%
+ \vspace*{\aboveskipchk}%
+ \vspace{\dropfromtop}%
+ \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
View
295 paper/chngpage.sty
@@ -0,0 +1,295 @@
+% 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}}%
+