added tech notes
This commit is contained in:
Heng Li
parent
46de0fbdad
commit
d6181de844
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\newcommand\classname{bioinfo}
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\newcommand\lastmodifieddate{2003/02/08}
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\newcommand\versionnumber{0.1}
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% Are we printing crop marks?
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\newif\if@cropmarkson \@cropmarksontrue
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\NeedsTeXFormat{LaTeX2e}[2001/06/01]
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\ProvidesClass{\classname}[\lastmodifieddate\space\versionnumber]
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\setlength{\paperheight}{11truein}
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\setlength{\paperwidth}{8.5truein}
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\newif\if@final
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\DeclareOption{draft}{\PassOptionsToPackage{draft}{graphicx}}
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\DeclareOption{a4paper}{\PassOptionsToPackage{a4}{crop}}
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\DeclareOption{centre}{\PassOptionsToPackage{center}{crop}}
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\DeclareOption{crop}{\PassOptionsToPackage{cam}{crop}\global\@cropmarksontrue}
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\DeclareOption{nocrop}{\PassOptionsToPackage{off}{crop}\global\@cropmarksonfalse}
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\DeclareOption{info}{\PassOptionsToPackage{info}{crop}}
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\DeclareOption{noinfo}{\PassOptionsToPackage{noinfo}{crop}}
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\DeclareOption{final}{\global\@finaltrue}
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\ExecuteOptions{a4paper,nocrop,centre,info}
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\ProcessOptions
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% Load all necessary packages
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\RequirePackage{inputenc,crop,graphicx,amsmath,array,color,amssymb,flushend,stfloats,amsthm,chngpage,times}
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%\RequirePackage[LY1]{fontenc}
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%\RequirePackage[LY1,mtbold]{mathtime}
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\def\authoraffliate{\fontfamily{phv}\selectfont}
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\def\helvetica{\fontfamily{phv}\selectfont}
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\def\helveticaitalic{\fontfamily{phv}\itshape\selectfont}
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\def\helveticabold{\fontfamily{phv}\bfseries\selectfont}
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\def\helveticabolditalic{\fontfamily{phv}\bfseries\itshape\selectfont}
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% Not sure if needed.
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\newcommand\@ptsize{0}
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% Set twoside printing
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\@twosidetrue
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% Marginal notes are on the outside edge
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\@mparswitchfalse
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\reversemarginpar
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\renewcommand\normalsize{%
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\@setfontsize\normalsize{9}{11}%
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\abovedisplayskip 10\p@ \@plus2\p@ \@minus5\p@
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\abovedisplayshortskip \z@ \@plus3\p@
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\belowdisplayshortskip 6\p@ \@plus3\p@ \@minus3\p@
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\belowdisplayskip \abovedisplayskip
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\let\@listi\@listI}
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\normalsize
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\let\@bls\baselineskip
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\newcommand\small{%
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\@setfontsize\small{9}{11}%
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\abovedisplayskip 11\p@ minus 3\p@
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\belowdisplayskip \abovedisplayskip
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\abovedisplayshortskip \z@ plus 2\p@
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\belowdisplayshortskip 4\p@ plus 2\p@ minus2\p@
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\def\@listi{\topsep 4.5\p@ plus 2\p@ minus 1\p@
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\itemsep \parsep
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\topsep 4\p@ plus 2\p@ minus 2\p@}}
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\newcommand\footnotesize{%
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\@setfontsize\footnotesize{8}{10}%
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\abovedisplayskip 6\p@ minus 3\p@
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\belowdisplayskip\abovedisplayskip
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\abovedisplayshortskip \z@ plus 3\p@
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\belowdisplayshortskip 6\p@ plus 3\p@ minus 3\p@
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\def\@listi{\topsep 3\p@ plus 1\p@ minus 1\p@
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\parsep 2\p@ plus 1\p@ minus 1\p@\itemsep \parsep}}
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\def\scriptsize{\@setfontsize\scriptsize{7pt}{9pt}}
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\def\tiny{\@setfontsize\tiny{5pt}{7pt}}
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\def\large{\@setfontsize\large{11.5pt}{12pt}}
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\def\Large{\@setfontsize\Large{14pt}{16}}
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\def\LARGE{\@setfontsize\LARGE{15pt}{17pt}}
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\def\huge{\@setfontsize\huge{22pt}{22pt}}
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\def\Huge{\@setfontsize\Huge{30pt}{30pt}}
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\DeclareOldFontCommand{\rm}{\normalfont\rmfamily}{\mathrm}
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\DeclareOldFontCommand{\sf}{\normalfont\sffamily}{\mathsf}
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\DeclareOldFontCommand{\tt}{\normalfont\ttfamily}{\mathtt}
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\DeclareOldFontCommand{\bf}{\normalfont\bfseries}{\mathbf}
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\DeclareOldFontCommand{\it}{\normalfont\itshape}{\mathit}
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\DeclareOldFontCommand{\sl}{\normalfont\slshape}{\@nomath\sl}
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\DeclareOldFontCommand{\sc}{\normalfont\scshape}{\@nomath\sc}
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% Line spacing
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\setlength\lineskip{1\p@}
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\setlength\normallineskip{1\p@}
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\renewcommand\baselinestretch{}
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% Paragraph dimensions and inter-para spacing
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\setlength\parskip{0\p@}
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\setlength\parindent{3mm}
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% Set inter-para skips
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\setlength\smallskipamount{3\p@ \@plus 1\p@ \@minus 1\p@}
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\setlength\medskipamount{6\p@ \@plus 2\p@}
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\setlength\bigskipamount{12\p@ \@plus 4\p@ \@minus 4\p@}
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% Page break penalties
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\@lowpenalty 51
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\@medpenalty 151
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\@highpenalty 301
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% Disallow widows and orphans
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\clubpenalty 10000
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\widowpenalty 10000
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% Disable page breaks before equations, allow pagebreaks after
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% equations and discourage widow lines before equations.
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\displaywidowpenalty 100
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\predisplaypenalty 10000
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\postdisplaypenalty 2500
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% Allow breaking the page in the middle of a paragraph
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\interlinepenalty 0
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% Disallow breaking the page after a hyphenated line
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\brokenpenalty 10000
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% Hyphenation; don't split words into less than three characters
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\lefthyphenmin=3
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\righthyphenmin=3
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%
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% Set page layout dimensions
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%
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\setlength\headheight{16\p@} % height of running head
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\setlength\topmargin{2.9pc} % head margin
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\addtolength\topmargin{-1in} % subtract out the 1 inch driver margin
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\setlength\topskip{10\p@} % height of first line of text
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\setlength\headsep{19\p@} % space below running head --
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\setlength\footskip{34\p@} % space above footer line
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\setlength\maxdepth{.5\topskip} % pages can be short or deep by half a line?
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\setlength\textwidth{42pc} % text measure excluding margins
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\setlength\textheight{58\baselineskip} % 54 lines on a full page,
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\addtolength\textheight{\topskip} % including the first
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% line on the page
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% Set the margins
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\setlength\marginparsep{3\p@}
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\setlength\marginparpush{3\p@}
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\setlength\marginparwidth{35\p@}
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\setlength\oddsidemargin{4.5pc}
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\addtolength\oddsidemargin{-1in} % subtract out the 1 inch driver margin
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\setlength\@tempdima{\paperwidth}
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\addtolength\@tempdima{-\textwidth}
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\addtolength\@tempdima{-4.5pc}
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\setlength\evensidemargin{\@tempdima}
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\addtolength\evensidemargin{-1in}
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\setlength\columnsep{1.5pc} % space between columns for double-column text
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\setlength\columnseprule{0\p@} % width of rule between two columns
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% Footnotes
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\setlength\footnotesep{9\p@} % space between footnotes
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% space between text and footnote
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\setlength{\skip\footins}{12\p@ \@plus 6\p@ \@minus 1\p@}
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% Float placement parameters
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% The total number of floats that can be allowed on a page.
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\setcounter{totalnumber}{10}
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% The maximum number of floats at the top and bottom of a page.
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\setcounter{topnumber}{5}
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\setcounter{bottomnumber}{5}
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% The maximum part of the top or bottom of a text page that can be
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% occupied by floats. This is set so that at least four lines of text
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% fit on the page.
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\renewcommand\topfraction{.9}
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\renewcommand\bottomfraction{.9}
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% The minimum amount of a text page that must be occupied by text.
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% This should accomodate four lines of text.
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\renewcommand\textfraction{.06}
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% The minimum amount of a float page that must be occupied by floats.
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\renewcommand\floatpagefraction{.94}
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% The same parameters repeated for double column output
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\renewcommand\dbltopfraction{.9}
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\renewcommand\dblfloatpagefraction{.9}
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% Space between floats
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\setlength\floatsep {12\p@ \@plus 2\p@ \@minus 2\p@}
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% Space between floats and text
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\setlength\textfloatsep{20\p@ \@plus 2\p@ \@minus 4\p@}
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% Space above and below an inline figure
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\setlength\intextsep {18\p@ \@plus 2\p@ \@minus 2\p@}
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% For double column floats
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\setlength\dblfloatsep {12\p@ \@plus 2\p@ \@minus 2\p@}
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\setlength\dbltextfloatsep{20\p@ \@plus 2\p@ \@minus 4\p@}
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% Space left at top, bottom and inbetween floats on a float page.
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\setlength\@fptop{0\p@} % no space above float page figures
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\setlength\@fpsep{12\p@ \@plus 1fil}
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\setlength\@fpbot{0\p@}
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% The same for double column
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\setlength\@dblfptop{0\p@}
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\setlength\@dblfpsep{12\p@ \@plus 1fil}
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\setlength\@dblfpbot{0\p@}
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% Override settings in mathtime back to TeX defaults
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\DeclareMathSizes{5} {5} {5} {5}
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\DeclareMathSizes{6} {6} {5} {5}
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\DeclareMathSizes{7} {7} {5} {5}
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\DeclareMathSizes{8} {8} {6} {5}
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\DeclareMathSizes{9} {9} {6.5} {5}
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\DeclareMathSizes{10} {10} {7.5} {5}
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\DeclareMathSizes{12} {12} {9} {7}
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% Page styles
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\def\ps@headings
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{%
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\def\@oddfoot{\vbox to 12.5\p@{\hbox{\rule{\textwidth}{0.5\p@}}\vss
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\hbox to \textwidth{\hfill\helveticabold\small\thepage}%
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}}%
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\def\@evenfoot{\vbox to 12.5\p@{\rule{\textwidth}{0.5\p@}\vss
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\hbox to \textwidth{\helveticabold\small\thepage\hfill}%
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}}%
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\def\@evenhead{\vbox{\hbox to \textwidth{\fontsize{8}{10}\selectfont
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\helveticabold{\fontshape{it}\selectfont
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\strut\leftmark}\hfill}\vspace{6.5\p@}\rule{\textwidth}{0.5\p@}}}%
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\def\@oddhead{\vbox{\hbox to \textwidth{\hfill\fontsize{8}{10}\selectfont
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\helveticabold{\fontshape{it}\selectfont\strut\rightmark}}%
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\vspace{6.5\p@}\rule{\textwidth}{0.5\p@}}}%
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\def\titlemark##1{\markboth{##1}{##1}}%
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\def\authormark##1{\gdef\leftmark{##1}}%
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}
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\def\ps@opening
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{%
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\def\@oddfoot{\vbox to 13\p@{\hbox{\rule{\textwidth}{1\p@}}\vss
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\hbox to \textwidth{\helvetica
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\fontsize{7}{9}\fontshape{n}\selectfont%
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\hfill\small\helveticabold\thepage}%
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}}%
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\def\@evenfoot{\vbox to 13\p@{\rule{\textwidth}\vss
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\hbox to \textwidth{\helvetica\thepage\hfill
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\fontsize{7}{9}\fontshape{n}\selectfont}%
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}}%
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\let\@evenhead\relax
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\let\@oddhead\relax}
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% Page range
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\newif\iflastpagegiven \lastpagegivenfalse
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\newcommand\firstpage[1]{%
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\gdef\@firstpage{#1}%
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\ifnum\@firstpage>\c@page
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\setcounter{page}{#1}%
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\ClassWarning{BIO}{Increasing pagenumber to \@firstpage}%
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\else \ifnum\@firstpage<\c@page
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\ClassWarning{BIO}{Firstpage lower than pagenumber}\fi\fi
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\xdef\@firstpage{\the\c@page}%
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}
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\def\@firstpage{1}
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\def\pagenumbering#1{%
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\global\c@page \@ne
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\gdef\thepage{\csname @#1\endcsname \c@page}%
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\gdef\thefirstpage{%
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\csname @#1\endcsname \@firstpage}%
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\gdef\thelastpage{%
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\csname @#1\endcsname \@lastpage}%
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}
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\newcommand\lastpage[1]{\xdef\@lastpage{#1}%
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\global\lastpagegiventrue}
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\def\@lastpage{0}
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\def\setlastpage{\iflastpagegiven\else
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\edef\@tempa{@lastpage@}%
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\expandafter
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\ifx \csname \@tempa \endcsname \relax
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\gdef\@lastpage{0}%
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\else
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\xdef\@lastpage{\@nameuse{@lastpage@}}%
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\fi
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\fi }
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\def\writelastpage{%
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\iflastpagegiven \else
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\immediate\write\@auxout%
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{\string\global\string\@namedef{@lastpage@}{\the\c@page}}%
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\fi
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}
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\def\thepagerange{%
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\ifnum\@lastpage =0 {\ \bf ???} \else
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\ifnum\@lastpage = \@firstpage \ \thefirstpage\else
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\thefirstpage--\thelastpage \fi\fi}
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\AtBeginDocument{\setlastpage
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\pagenumbering{arabic}%
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}
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\AtEndDocument{%
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\writelastpage
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\if@final
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\clearemptydoublepage
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\else
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\clearpage
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\fi}
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%
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% Sectional units
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%
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% Counters
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\newcounter{section}
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\newcounter{subsection}[section]
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\newcounter{subsubsection}[subsection]
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\newcounter{paragraph}[subsubsection]
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\newcounter{subparagraph}[paragraph]
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\newcounter{figure}
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\newcounter{table}
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% Form of the numbers
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\newcommand\thepage{\arabic{page}}
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\renewcommand\thesection{\arabic{section}}
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\renewcommand\thesubsection{{\thesection.\arabic{subsection}}}
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\renewcommand\thesubsubsection{{\thesubsection.\arabic{subsubsection}}}
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\renewcommand\theparagraph{\thesubsubsection.\arabic{paragraph}}
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\renewcommand\thesubparagraph{\theparagraph.\arabic{subparagraph}}
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\renewcommand\theequation{\arabic{equation}}
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% Form of the words
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\newcommand\contentsname{Contents}
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\newcommand\listfigurename{List of Figures}
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\newcommand\listtablename{List of Tables}
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\newcommand\partname{Part}
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\newcommand\appendixname{Appendix}
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\newcommand\abstractname{Abstract}
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\newcommand\refname{References}
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\newcommand\bibname{References}
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\newcommand\indexname{Index}
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\newcommand\figurename{Fig.}
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\newcommand\tablename{Table}
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% Clearemptydoublepage should really clear the running heads too
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||||||
|
\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}TECHNICAL NOTES}
|
||||||
|
\hfil
|
||||||
|
\if@appnotes APPLICATIONS NOTE\hfil\fi
|
||||||
|
}%
|
||||||
|
\enskip \parbox[b]{11.3pc}{%
|
||||||
|
\helvetica
|
||||||
|
\flushright\fontsize{8}{10}\fontshape{it}\selectfont
|
||||||
|
\hfill
|
||||||
|
}}
|
||||||
|
\rule{\textwidth}{1\p@}\par%
|
||||||
|
\helvetica
|
||||||
|
\hbox to \textwidth{%
|
||||||
|
\parbox[t]{41pc}{%
|
||||||
|
\vspace*{1sp}
|
||||||
|
{\helveticabold\fontsize{16}{21}\selectfont\raggedright \@title \par}%
|
||||||
|
\vspace{4.5\p@}
|
||||||
|
{\authoraffliate\fontsize{11}{13}\selectfont\raggedright \@author \par}%
|
||||||
|
\vspace{4\p@}
|
||||||
|
{\authoraffliate\fontsize{9}{11}\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{4.5\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
|
||||||
|
|
@ -0,0 +1,103 @@
|
||||||
|
@article{Chaisson:2012aa,
|
||||||
|
Author = {Chaisson, Mark J and Tesler, Glenn},
|
||||||
|
Journal = {BMC Bioinformatics},
|
||||||
|
Pages = {238},
|
||||||
|
Title = {{Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory}},
|
||||||
|
Volume = {13},
|
||||||
|
Year = {2012}}
|
||||||
|
|
||||||
|
@article{Liu:2016ab,
|
||||||
|
Author = {Liu, Bo and Guan, Dengfeng and Teng, Mingxiang and Wang, Yadong},
|
||||||
|
Journal = {Bioinformatics},
|
||||||
|
Pages = {1625-31},
|
||||||
|
Title = {{rHAT}: fast alignment of noisy long reads with regional hashing},
|
||||||
|
Volume = {32},
|
||||||
|
Year = {2016}}
|
||||||
|
|
||||||
|
@article{Liu:2017aa,
|
||||||
|
Author = {Liu, Bo and Gao, Yan and Wang, Yadong},
|
||||||
|
Journal = {Bioinformatics},
|
||||||
|
Pages = {192-201},
|
||||||
|
Title = {{LAMSA}: fast split read alignment with long approximate matches},
|
||||||
|
Volume = {33},
|
||||||
|
Year = {2017}}
|
||||||
|
|
||||||
|
@article{Lin:2017aa,
|
||||||
|
Author = {Lin, Hsin-Nan and Hsu, Wen-Lian},
|
||||||
|
Journal = {Bioinformatics},
|
||||||
|
Title = {Kart: a divide-and-conquer algorithm for {NGS} read alignment},
|
||||||
|
Year = {2017}}
|
||||||
|
|
||||||
|
@article{Li:2013aa,
|
||||||
|
Author = {Li, Heng},
|
||||||
|
Journal = {arXiv:1303.3997},
|
||||||
|
Title = {Aligning sequence reads, clone sequences and assembly contigs with {BWA-MEM}},
|
||||||
|
archivePrefix = "arXiv",
|
||||||
|
eprint = {0902.0885},
|
||||||
|
primaryClass = "q-bio",
|
||||||
|
Year = {2013}}
|
||||||
|
|
||||||
|
@article{Sovic:2016aa,
|
||||||
|
Author = {Sovi{\'c}, Ivan and {\v S}iki{\'c}, Mile and Wilm, Andreas and Fenlon, Shannon Nicole and Chen, Swaine and others},
|
||||||
|
Journal = {Nat Commun},
|
||||||
|
Pages = {11307},
|
||||||
|
Title = {Fast and sensitive mapping of nanopore sequencing reads with {GraphMap}},
|
||||||
|
Volume = {7},
|
||||||
|
Year = {2016}}
|
||||||
|
|
||||||
|
@article{Langmead:2012fk,
|
||||||
|
Author = {Langmead, Ben and Salzberg, Steven L},
|
||||||
|
Journal = {Nat Methods},
|
||||||
|
Pages = {357-9},
|
||||||
|
Title = {Fast gapped-read alignment with {Bowtie} 2},
|
||||||
|
Volume = {9},
|
||||||
|
Year = {2012}}
|
||||||
|
|
||||||
|
@article{Li:2016aa,
|
||||||
|
Author = {Li, Heng},
|
||||||
|
Journal = {Bioinformatics},
|
||||||
|
Pages = {2103-10},
|
||||||
|
Title = {Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences},
|
||||||
|
Volume = {32},
|
||||||
|
Year = {2016}}
|
||||||
|
|
||||||
|
@misc{Suzuki:2016,
|
||||||
|
title = {Fast and accurate alignment tool for PacBio and Nanopore long reads},
|
||||||
|
author = {Hajime Suzuki},
|
||||||
|
journal = {Unpublished},
|
||||||
|
howpublished = {\href{https://github.com/ocxtal/minialign}{https://github.com/ocxtal/minialign}},
|
||||||
|
year = {2016}}
|
||||||
|
|
||||||
|
@article{Miller:1988aa,
|
||||||
|
Author = {Miller, W and Myers, E W},
|
||||||
|
Journal = {Bull Math Biol},
|
||||||
|
Number = {2},
|
||||||
|
Pages = {97-120},
|
||||||
|
Title = {Sequence comparison with concave weighting functions},
|
||||||
|
Volume = {50},
|
||||||
|
Year = {1988}}
|
||||||
|
|
||||||
|
@article{Gotoh:1990aa,
|
||||||
|
Author = {Gotoh, O},
|
||||||
|
Journal = {Bull Math Biol},
|
||||||
|
Pages = {359-73},
|
||||||
|
Title = {Optimal sequence alignment allowing for long gaps},
|
||||||
|
Volume = {52},
|
||||||
|
Year = {1990}}
|
||||||
|
|
||||||
|
@article{Wu:1996aa,
|
||||||
|
Author = {Wu, Sun and Manber, U and Myers, Gene},
|
||||||
|
Journal = {Algorithmica},
|
||||||
|
Pages = {50-67},
|
||||||
|
Title = {A subquadratic algorithm for approximate limited expression matching},
|
||||||
|
Volume = {15},
|
||||||
|
Year = {1996}}
|
||||||
|
|
||||||
|
@article{Daily:2016aa,
|
||||||
|
Author = {Daily, Jeff},
|
||||||
|
Journal = {BMC Bioinformatics},
|
||||||
|
Month = {Feb},
|
||||||
|
Pages = {81},
|
||||||
|
Title = {Parasail: SIMD C library for global, semi-global, and local pairwise sequence alignments},
|
||||||
|
Volume = {17},
|
||||||
|
Year = {2016}}
|
||||||
|
|
@ -0,0 +1,180 @@
|
||||||
|
\documentclass{bioinfo}
|
||||||
|
\copyrightyear{2017}
|
||||||
|
\pubyear{2017}
|
||||||
|
|
||||||
|
\usepackage{hyperref}
|
||||||
|
\usepackage{url}
|
||||||
|
\usepackage{amsmath}
|
||||||
|
\usepackage[ruled,vlined]{algorithm2e}
|
||||||
|
\newcommand\mycommfont[1]{\footnotesize\rmfamily{\it #1}}
|
||||||
|
\SetCommentSty{mycommfont}
|
||||||
|
\SetKwComment{Comment}{$\triangleright$\ }{}
|
||||||
|
|
||||||
|
\usepackage{natbib}
|
||||||
|
\bibliographystyle{apalike}
|
||||||
|
\usepackage{hyperref}
|
||||||
|
|
||||||
|
\DeclareMathOperator*{\argmax}{argmax}
|
||||||
|
|
||||||
|
\begin{document}
|
||||||
|
\firstpage{1}
|
||||||
|
|
||||||
|
\title[Long-read and assembly alignment with minimap2]{Minimap2: fast sequence alignment for long noisy reads and assembly contigs}
|
||||||
|
\author[Li]{Heng Li}
|
||||||
|
\address{Broad Institute, 415 Main Street, Cambridge, MA 02142, USA}
|
||||||
|
|
||||||
|
\maketitle
|
||||||
|
|
||||||
|
\begin{abstract}
|
||||||
|
\section{Summary:} Minimap2 is a program to align long noisy sequences against
|
||||||
|
a large reference database. It targets query sequences of 1kb--100Mb in length
|
||||||
|
with sequence divergence typically below 25\%. Minimap2 is $\sim$30 times
|
||||||
|
faster than most existing long-read aligners and achieves higher accuracy on
|
||||||
|
simulated data. It also employs concave gap cost and rescues inversions for
|
||||||
|
improved alignment around potential structural variations.
|
||||||
|
|
||||||
|
\section{Availability and implementation:}
|
||||||
|
\href{https://github.com/lh3/minimap2}{https://github.com/lh3/minimap2}
|
||||||
|
|
||||||
|
\section{Contact:} hengli@broadinstitute.org
|
||||||
|
\end{abstract}
|
||||||
|
|
||||||
|
\section{Introduction}
|
||||||
|
|
||||||
|
Single Molecule Real-Time (SMRT) sequencing technology and Oxford Nanopore
|
||||||
|
technologies (ONT) produce reads over 10kbp in length at an error rate
|
||||||
|
$\sim$15\%. Several aligners have been developed for such
|
||||||
|
data~\citep{Chaisson:2012aa,Li:2013aa,Liu:2016ab,Sovic:2016aa,Liu:2017aa,Lin:2017aa}.
|
||||||
|
They are usually five times as slow as mainstream short-read
|
||||||
|
aligners~\citep{Langmead:2012fk,Li:2013aa}. We speculated there could be
|
||||||
|
substantial room for speedup on the thought that 10kb long sequences should be
|
||||||
|
easier to map than 100bp reads because we can more effectively skip repetitive
|
||||||
|
regions and dramatically reduce computation. We confirmed our speculation by
|
||||||
|
achieving approximate mapping 50 times faster than BWA-MEM~\citep{Li:2016aa}.
|
||||||
|
\citet{Suzuki:2016} extended our work with with a fast and novel algorithm on
|
||||||
|
generating detailed alignment, which in turn inspired us to develop minimap2
|
||||||
|
towards higher accuracy.
|
||||||
|
|
||||||
|
\begin{methods}
|
||||||
|
\section{Methods}
|
||||||
|
|
||||||
|
Minimap2 is the successor of minimap~\citep{Li:2016aa}. It uses similar
|
||||||
|
indexing and seeding algorithms except that minimap2 optionally uses
|
||||||
|
homopolymer-compressed (HPC; cite) $k$-mers in addition to normal $k$-mers.
|
||||||
|
Indexing with HPC $k$-mers leads to higher mapping sensitivity for SMRT reads.
|
||||||
|
Minimap2 further implements a more accurate chaining algorithm and adds
|
||||||
|
the ability to produce detailed alignment.
|
||||||
|
|
||||||
|
\subsection{Chaining}
|
||||||
|
|
||||||
|
\subsubsection{Chaining}
|
||||||
|
An \emph{anchor} is a 3-tuple $(x,y,w)$, indicating interval $[x-w+1,x]$ on the
|
||||||
|
reference matching interval $[y-w+1,y]$ on the query. Given a list of anchors
|
||||||
|
sorted by the ending reference position $x$, let $f(i)$ be the maximal chaining
|
||||||
|
score up to the $i$-th anchor in the list. $f(i)$ can be calculated with
|
||||||
|
dynamic programming (DP):
|
||||||
|
\begin{equation}\label{eq:chain}
|
||||||
|
f(i)=\max\big\{\max_{i>j\ge 1} \{ f(j)+d(j,i)-\gamma(j,i) \},w_i\big\}
|
||||||
|
\end{equation}
|
||||||
|
where $d(j,i)=\min\big\{\min\{y_i-y_j,x_i-x_j\},w_i\big\}$ is the number of
|
||||||
|
matching bases between the two anchors. $\gamma(j,i)>0$ is the gap cost. It
|
||||||
|
equals $\infty$ if $y_j\ge y_i$ or $\max\{y_i-y_j,x_i-x_j\}>G$ (i.e. the
|
||||||
|
distance between two anchors is too large); otherwise
|
||||||
|
\[
|
||||||
|
\gamma(j,i)=\gamma'(\max\{y_i-y_j,x_i-x_j\}-\min\{y_i-y_j,x_i-x_j\})
|
||||||
|
\]
|
||||||
|
In implementation, a gap of length $l$ costs $\gamma'(l)=\alpha\cdot
|
||||||
|
l+\beta\log_2(l)$, which is concave. For $m$ anchors, computing all $f(\cdot)$
|
||||||
|
with Eq.~(\ref{eq:chain}) takes $O(m^2)$ time. We note that if anchor $i$ is
|
||||||
|
appended to $j$, appending $i$ to a predecessor of $j$ is likely to yield a
|
||||||
|
lower score. When evaluating Eq.~(\ref{eq:chain}), we start from anchor $i-1$
|
||||||
|
and stop the evaluation if we cannot find a better $\max$ after up to $h$
|
||||||
|
iterations. This heuristic reduces the average time to $O(h\cdot m)$. In
|
||||||
|
practical, we can almost always find the optimal chain with $h=50$; even if the
|
||||||
|
heuristic fails, the optimal chain often looks dubious.
|
||||||
|
|
||||||
|
\subsubsection{Backtracking}
|
||||||
|
Let $P(i)$ be the index of the best predecessor of anchor $i$. It equals 0 if
|
||||||
|
$f(i)=w_i$ or $\argmax_j\{f(j)+\eta(j,i)-\gamma(j,i)\}$ otherwise. For each
|
||||||
|
anchor $i$ in the descending order of $f(i)$, we mark $i$ as `used' and apply
|
||||||
|
$P(\cdot)$ repeatedly to find its predecessor. This process stops at $P(j)=0$
|
||||||
|
or at a `used' $j$. This way we find all chains with no anchors used in
|
||||||
|
more than one chains.
|
||||||
|
|
||||||
|
\subsection{Alignment}
|
||||||
|
Minimap2 performs DP to align sequences between adjacent anchors in a chain. It
|
||||||
|
adopted difference-based formulation to derive
|
||||||
|
alignment~\citep{Wu:1996aa,Suzuki:2016}. When combined with SSE vectorization,
|
||||||
|
this formulation has two advantages. First, because each score in the DP matrix
|
||||||
|
is bounded by the gap cost and the maximum matching score, we can usually
|
||||||
|
achieve 16-way SSE vectorization regardless of the peak score of the
|
||||||
|
alignment. Second, filling the DP matrix along the diagonal, we can simplify
|
||||||
|
banded alignment, which is critical to performance. In practice, our
|
||||||
|
implementation is three times as fast as Parasail's 4-way
|
||||||
|
vectorization~\citep{Daily:2016aa} for global alignment.
|
||||||
|
|
||||||
|
|
||||||
|
Minimap2 uses a 2-piece affine gap cost~\citep{Gotoh:1990aa}:
|
||||||
|
\[
|
||||||
|
\gamma(l)=\min\{q+l\cdot e,\tilde{q}+l\cdot\tilde{e}\}
|
||||||
|
\]
|
||||||
|
On the condition that $q+e<\tilde{q}+\tilde{e}$ and $e>\tilde{e}$, this
|
||||||
|
cost function is concave. It applies cost $q+l\cdot e$ to gaps shorter than
|
||||||
|
$\lceil(\tilde{q}-q)/(e-\tilde{e})\rceil$ and applies
|
||||||
|
$\tilde{q}+l\cdot\tilde{e}$ to longer gaps. This scheme helps to recover
|
||||||
|
longer insertions and deletions.
|
||||||
|
|
||||||
|
%\begin{equation}\label{eq:ae86}
|
||||||
|
%\left\{\begin{array}{l}
|
||||||
|
%H_{ij} = \max\{H_{i-1,j-1}+s(i,j),E_{ij},F_{ij},\tilde{E}_{ij},\tilde{F}_{ij}\}\\
|
||||||
|
%E_{i+1,j}= \max\{H_{ij}-q,E_{ij}\}-e\\
|
||||||
|
%F_{i,j+1}= \max\{H_{ij}-q,F_{ij}\}-e\\
|
||||||
|
%\tilde{E}_{i+1,j}= \max\{H_{ij}-\tilde{q},\tilde{E}_{ij}\}-\tilde{e}\\
|
||||||
|
%\tilde{F}_{i,j+1}= \max\{H_{ij}-\tilde{q},\tilde{F}_{ij}\}-\tilde{e}
|
||||||
|
%\end{array}\right.
|
||||||
|
%\end{equation}
|
||||||
|
%where $s(i,j)$ is the score between the $i$-th reference base and $j$-th query
|
||||||
|
%base. If we define~\citep{Wu:1996aa,Suzuki:2016}
|
||||||
|
%\[
|
||||||
|
%\left\{\begin{array}{ll}
|
||||||
|
%u_{ij}\triangleq H_{ij}-H_{i-1,j} & v_{ij}\triangleq H_{ij}-H_{i,j-1} \\
|
||||||
|
%x_{ij}\triangleq E_{i+1,j}-H_{ij} & \tilde{x}_{ij}\triangleq \tilde{E}_{i+1,j}-\tilde{H}_{ij} \\
|
||||||
|
%y_{ij}\triangleq F_{i,j+1}-H_{ij} & \tilde{y}_{ij}\triangleq \tilde{F}_{i,j+1}-\tilde{H}_{ij}
|
||||||
|
%\end{array}\right.
|
||||||
|
%\]
|
||||||
|
%we can transform Eq.~(\ref{eq:ae86}) to
|
||||||
|
%\[
|
||||||
|
%\left\{\begin{array}{lll}
|
||||||
|
%z_{ij}&=&\max\{s(i,j),x_{i-1,j}+v_{i-1,j},y_{i,j-1}+u_{i,j-1},\\
|
||||||
|
%&&\tilde{x}_{i-1,j}+v_{i-1,j},\tilde{y}_{i,j-1}+u_{i,j-1}\}\\
|
||||||
|
%u_{ij}&=&z_{ij}-v_{i-1,j}\\
|
||||||
|
%v_{ij}&=&z_{ij}-u_{i,j-1}\\
|
||||||
|
%x_{ij}&=&\max\{0,x_{i-1,j}+v_{i-1,j}-z_{ij}+q\}-q-e\\
|
||||||
|
%y_{ij}&=&\max\{0,y_{i,j-1}+u_{i,j-1}-z_{ij}+q\}-q-e\\
|
||||||
|
%\tilde{x}_{ij}&=&\max\{0,\tilde{x}_{i-1,j}+v_{i-1,j}-z_{ij}+\tilde{q}\}-\tilde{q}-\tilde{e}\\
|
||||||
|
%\tilde{y}_{ij}&=&\max\{0,\tilde{y}_{i,j-1}+u_{i,j-1}-z_{ij}+\tilde{q}\}-\tilde{q}-\tilde{e}
|
||||||
|
%\end{array}\right.
|
||||||
|
%\]
|
||||||
|
%with boundary conditions
|
||||||
|
%\[
|
||||||
|
%\left\{\begin{array}{l}
|
||||||
|
%x_{-1,\cdot}=y_{\cdot,-1}=-q-e\\
|
||||||
|
%\tilde{x}_{-1,\cdot}=\tilde{y}_{\cdot,-1}=-\tilde{q}-\tilde{e}\\
|
||||||
|
%u_{i,-1}=\eta(i)\\
|
||||||
|
%v_{-1,j}=\eta(j)
|
||||||
|
%\end{array}\right.
|
||||||
|
%\]
|
||||||
|
%where
|
||||||
|
%\[
|
||||||
|
%\eta(k)=\left\{\begin{array}{ll}
|
||||||
|
%-q-e & (k=0) \\
|
||||||
|
%-e & (k<\lceil\frac{\tilde{q}-q}{e-\tilde{e}}-1\rceil) \\
|
||||||
|
%i\cdot(e-\tilde{e})-(\tilde{q}-q)-\tilde{e} & (k=\lceil\frac{\tilde{q}-q}{e-\tilde{e}}-1\rceil) \\
|
||||||
|
%-\tilde{e} & (k>\lceil\frac{\tilde{q}-q}{e-\tilde{e}}-1\rceil)
|
||||||
|
%\end{array}\right.
|
||||||
|
%\]
|
||||||
|
|
||||||
|
\end{methods}
|
||||||
|
|
||||||
|
\bibliography{minimap2}
|
||||||
|
\end{document}
|
||||||
File diff suppressed because it is too large
Load Diff
|
|
@ -0,0 +1,803 @@
|
||||||
|
%%
|
||||||
|
%% 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 <option>
|
||||||
|
% colon - multiple citations separated by colon (default)
|
||||||
|
% comma - separated by comma
|
||||||
|
% authoryear - selects author-year citations (default)
|
||||||
|
% numbers- selects numerical citations
|
||||||
|
% super - numerical citations as superscripts
|
||||||
|
% sort - sorts multiple citations according to order in ref. list
|
||||||
|
% sort&compress - like sort, but also compresses numerical citations
|
||||||
|
% longnamesfirst - makes first citation full author list
|
||||||
|
% sectionbib - puts bibliography in a \section* instead of \chapter*
|
||||||
|
% Punctuation so selected dominates over any predefined ones.
|
||||||
|
% LaTeX2e options are called as, e.g.
|
||||||
|
% \usepackage[square,comma]{natbib}
|
||||||
|
% LaTeX the source file natbib.dtx to obtain more details
|
||||||
|
% or the file natnotes.tex for a brief reference sheet.
|
||||||
|
%-----------------------------------------------------------
|
||||||
|
\@ifclassloaded{aguplus}{\PackageError{natbib}
|
||||||
|
{The aguplus class already includes natbib coding,\MessageBreak
|
||||||
|
so you should not add it explicitly}
|
||||||
|
{Type <Return> for now, but then later remove\MessageBreak
|
||||||
|
the command \protect\usepackage{natbib} from the document}
|
||||||
|
\endinput}{}
|
||||||
|
\@ifclassloaded{nlinproc}{\PackageError{natbib}
|
||||||
|
{The nlinproc class already includes natbib coding,\MessageBreak
|
||||||
|
so you should not add it explicitly}
|
||||||
|
{Type <Return> for now, but then later remove\MessageBreak
|
||||||
|
the command \protect\usepackage{natbib} from the document}
|
||||||
|
\endinput}{}
|
||||||
|
\@ifclassloaded{egs}{\PackageError{natbib}
|
||||||
|
{The egs class already includes natbib coding,\MessageBreak
|
||||||
|
so you should not add it explicitly}
|
||||||
|
{Type <Return> for now, but then later remove\MessageBreak
|
||||||
|
the command \protect\usepackage{natbib} from the document}
|
||||||
|
\endinput}{}
|
||||||
|
% Define citation punctuation for some author-year styles
|
||||||
|
% One may add and delete at this point
|
||||||
|
% Or put additions into local configuration file natbib.cfg
|
||||||
|
\newcommand\bibstyle@chicago{\bibpunct{(}{)}{;}{a}{,}{,}}
|
||||||
|
\newcommand\bibstyle@named{\bibpunct{[}{]}{;}{a}{,}{,}}
|
||||||
|
\newcommand\bibstyle@agu{\bibpunct{[}{]}{;}{a}{,}{,~}}%Amer. Geophys. Union
|
||||||
|
\newcommand\bibstyle@egs{\bibpunct{(}{)}{;}{a}{,}{,}}%Eur. Geophys. Soc.
|
||||||
|
\newcommand\bibstyle@agsm{\bibpunct{(}{)}{,}{a}{}{,}\gdef\harvardand{\&}}
|
||||||
|
\newcommand\bibstyle@kluwer{\bibpunct{(}{)}{,}{a}{}{,}\gdef\harvardand{\&}}
|
||||||
|
\newcommand\bibstyle@dcu{\bibpunct{(}{)}{;}{a}{;}{,}\gdef\harvardand{and}}
|
||||||
|
\newcommand\bibstyle@aa{\bibpunct{(}{)}{;}{a}{}{,}} %Astronomy & Astrophysics
|
||||||
|
\newcommand\bibstyle@pass{\bibpunct{(}{)}{;}{a}{,}{,}}%Planet. & Space Sci
|
||||||
|
\newcommand\bibstyle@anngeo{\bibpunct{(}{)}{;}{a}{,}{,}}%Annales Geophysicae
|
||||||
|
\newcommand\bibstyle@nlinproc{\bibpunct{(}{)}{;}{a}{,}{,}}%Nonlin.Proc.Geophys.
|
||||||
|
% Define citation punctuation for some numerical styles
|
||||||
|
\newcommand\bibstyle@cospar{\bibpunct{/}{/}{,}{n}{}{}%
|
||||||
|
\gdef\NAT@biblabelnum##1{##1.}}
|
||||||
|
\newcommand\bibstyle@esa{\bibpunct{(Ref.~}{)}{,}{n}{}{}%
|
||||||
|
\gdef\NAT@biblabelnum##1{##1.\hspace{1em}}}
|
||||||
|
\newcommand\bibstyle@nature{\bibpunct{}{}{,}{s}{}{\textsuperscript{,}}%
|
||||||
|
\gdef\NAT@biblabelnum##1{##1.}}
|
||||||
|
% The standard LaTeX styles
|
||||||
|
\newcommand\bibstyle@plain{\bibpunct{[}{]}{,}{n}{}{,}}
|
||||||
|
\let\bibstyle@alpha=\bibstyle@plain
|
||||||
|
\let\bibstyle@abbrv=\bibstyle@plain
|
||||||
|
\let\bibstyle@unsrt=\bibstyle@plain
|
||||||
|
% The author-year modifications of the standard styles
|
||||||
|
\newcommand\bibstyle@plainnat{\bibpunct{[}{]}{,}{a}{,}{,}}
|
||||||
|
\let\bibstyle@abbrvnat=\bibstyle@plainnat
|
||||||
|
\let\bibstyle@unsrtnat=\bibstyle@plainnat
|
||||||
|
\newif\ifNAT@numbers \NAT@numbersfalse
|
||||||
|
\newif\ifNAT@super \NAT@superfalse
|
||||||
|
\DeclareOption{numbers}{\NAT@numberstrue
|
||||||
|
\ExecuteOptions{square,comma,nobibstyle}}
|
||||||
|
\DeclareOption{super}{\NAT@supertrue\NAT@numberstrue
|
||||||
|
\renewcommand\NAT@open{}\renewcommand\NAT@close{}
|
||||||
|
\ExecuteOptions{nobibstyle}}
|
||||||
|
\DeclareOption{authoryear}{\NAT@numbersfalse
|
||||||
|
\ExecuteOptions{round,colon,bibstyle}}
|
||||||
|
\DeclareOption{round}{%
|
||||||
|
\renewcommand\NAT@open{(} \renewcommand\NAT@close{)}
|
||||||
|
\ExecuteOptions{nobibstyle}}
|
||||||
|
\DeclareOption{square}{%
|
||||||
|
\renewcommand\NAT@open{[} \renewcommand\NAT@close{]}
|
||||||
|
\ExecuteOptions{nobibstyle}}
|
||||||
|
\DeclareOption{angle}{%
|
||||||
|
\renewcommand\NAT@open{$<$} \renewcommand\NAT@close{$>$}
|
||||||
|
\ExecuteOptions{nobibstyle}}
|
||||||
|
\DeclareOption{curly}{%
|
||||||
|
\renewcommand\NAT@open{\{} \renewcommand\NAT@close{\}}
|
||||||
|
\ExecuteOptions{nobibstyle}}
|
||||||
|
\DeclareOption{comma}{\renewcommand\NAT@sep{,}
|
||||||
|
\ExecuteOptions{nobibstyle}}
|
||||||
|
\DeclareOption{colon}{\renewcommand\NAT@sep{;}
|
||||||
|
\ExecuteOptions{nobibstyle}}
|
||||||
|
\DeclareOption{nobibstyle}{\let\bibstyle=\@gobble}
|
||||||
|
\DeclareOption{bibstyle}{\let\bibstyle=\@citestyle}
|
||||||
|
\newif\ifNAT@openbib \NAT@openbibfalse
|
||||||
|
\DeclareOption{openbib}{\NAT@openbibtrue}
|
||||||
|
\DeclareOption{sectionbib}{\def\NAT@sectionbib{on}}
|
||||||
|
\def\NAT@sort{0}
|
||||||
|
\DeclareOption{sort}{\def\NAT@sort{1}}
|
||||||
|
\DeclareOption{sort&compress}{\def\NAT@sort{2}}
|
||||||
|
\@ifpackageloaded{cite}{\PackageWarningNoLine{natbib}
|
||||||
|
{The `cite' package should not be used\MessageBreak
|
||||||
|
with natbib. Use option `sort' instead}\ExecuteOptions{sort}}{}
|
||||||
|
\newif\ifNAT@longnames\NAT@longnamesfalse
|
||||||
|
\DeclareOption{longnamesfirst}{\NAT@longnamestrue}
|
||||||
|
\DeclareOption{nonamebreak}{\def\NAT@nmfmt#1{\mbox{\NAT@up#1}}}
|
||||||
|
\def\NAT@nmfmt#1{{\NAT@up#1}}
|
||||||
|
\renewcommand\bibstyle[1]{\@ifundefined{bibstyle@#1}{\relax}
|
||||||
|
{\csname bibstyle@#1\endcsname}}
|
||||||
|
\AtBeginDocument{\global\let\bibstyle=\@gobble}
|
||||||
|
\let\@citestyle\bibstyle
|
||||||
|
\newcommand\citestyle[1]{\@citestyle{#1}\let\bibstyle\@gobble}
|
||||||
|
\@onlypreamble{\citestyle}\@onlypreamble{\@citestyle}
|
||||||
|
\newcommand\bibpunct[7][, ]%
|
||||||
|
{\gdef\NAT@open{#2}\gdef\NAT@close{#3}\gdef
|
||||||
|
\NAT@sep{#4}\global\NAT@numbersfalse\ifx #5n\global\NAT@numberstrue
|
||||||
|
\else
|
||||||
|
\ifx #5s\global\NAT@numberstrue\global\NAT@supertrue
|
||||||
|
\fi\fi
|
||||||
|
\gdef\NAT@aysep{#6}\gdef\NAT@yrsep{#7}%
|
||||||
|
\gdef\NAT@cmt{#1}%
|
||||||
|
\global\let\bibstyle\@gobble
|
||||||
|
}
|
||||||
|
\@onlypreamble{\bibpunct}
|
||||||
|
\newcommand\NAT@open{(} \newcommand\NAT@close{)}
|
||||||
|
\newcommand\NAT@sep{;}
|
||||||
|
\ProcessOptions
|
||||||
|
\newcommand\NAT@aysep{,} \newcommand\NAT@yrsep{,}
|
||||||
|
\newcommand\NAT@cmt{, }
|
||||||
|
\newcommand\NAT@cite%
|
||||||
|
[3]{\ifNAT@swa\NAT@@open\if*#2*\else#2\ \fi
|
||||||
|
#1\if*#3*\else\NAT@cmt#3\fi\NAT@@close\else#1\fi\endgroup}
|
||||||
|
\newcommand\NAT@citenum%
|
||||||
|
[3]{\ifNAT@swa\NAT@@open\if*#2*\else#2\ \fi
|
||||||
|
#1\if*#3*\else\NAT@cmt#3\fi\NAT@@close\else#1\fi\endgroup}
|
||||||
|
\newcommand\NAT@citesuper[3]{\ifNAT@swa
|
||||||
|
\unskip\hspace{1\p@}\textsuperscript{#1}%
|
||||||
|
\if*#3*\else\ (#3)\fi\else #1\fi\endgroup}
|
||||||
|
\providecommand
|
||||||
|
\textsuperscript[1]{\mbox{$^{\mbox{\scriptsize#1}}$}}
|
||||||
|
\providecommand\@firstofone[1]{#1}
|
||||||
|
\newcommand\NAT@citexnum{}
|
||||||
|
\def\NAT@citexnum[#1][#2]#3{%
|
||||||
|
\NAT@sort@cites{#3}%
|
||||||
|
\let\@citea\@empty
|
||||||
|
\@cite{\def\NAT@num{-1}\let\NAT@last@yr\relax\let\NAT@nm\@empty
|
||||||
|
\@for\@citeb:=\NAT@cite@list\do
|
||||||
|
{\edef\@citeb{\expandafter\@firstofone\@citeb}%
|
||||||
|
\if@filesw\immediate\write\@auxout{\string\citation{\@citeb}}\fi
|
||||||
|
\@ifundefined{b@\@citeb\@extra@b@citeb}{%
|
||||||
|
{\reset@font\bfseries?}
|
||||||
|
\NAT@citeundefined\PackageWarning{natbib}%
|
||||||
|
{Citation `\@citeb' on page \thepage \space undefined}}%
|
||||||
|
{\let\NAT@last@num\NAT@num\let\NAT@last@nm\NAT@nm
|
||||||
|
\NAT@parse{\@citeb}%
|
||||||
|
\ifNAT@longnames\@ifundefined{bv@\@citeb\@extra@b@citeb}{%
|
||||||
|
\let\NAT@name=\NAT@all@names
|
||||||
|
\global\@namedef{bv@\@citeb\@extra@b@citeb}{}}{}%
|
||||||
|
\fi
|
||||||
|
\ifNAT@full\let\NAT@nm\NAT@all@names\else
|
||||||
|
\let\NAT@nm\NAT@name\fi
|
||||||
|
\ifNAT@swa
|
||||||
|
\ifnum\NAT@ctype>1\relax\@citea
|
||||||
|
\hyper@natlinkstart{\@citeb\@extra@b@citeb}%
|
||||||
|
\ifnum\NAT@ctype=2\relax\NAT@test{\NAT@ctype}%
|
||||||
|
\else\NAT@alias
|
||||||
|
\fi\hyper@natlinkend\else
|
||||||
|
\ifnum\NAT@sort>1
|
||||||
|
\begingroup\catcode`\_=8
|
||||||
|
\ifcat _\ifnum\z@<0\NAT@num _\else A\fi
|
||||||
|
\global\let\NAT@nm=\NAT@num \else \gdef\NAT@nm{-2}\fi
|
||||||
|
\ifcat _\ifnum\z@<0\NAT@last@num _\else A\fi
|
||||||
|
\global\@tempcnta=\NAT@last@num \global\advance\@tempcnta by\@ne
|
||||||
|
\else \global\@tempcnta\m@ne\fi
|
||||||
|
\endgroup
|
||||||
|
\ifnum\NAT@nm=\@tempcnta
|
||||||
|
\ifx\NAT@last@yr\relax
|
||||||
|
\edef\NAT@last@yr{\@citea \mbox{\noexpand\citenumfont{\NAT@num}}}%
|
||||||
|
\else
|
||||||
|
\edef\NAT@last@yr{--\penalty\@m\mbox{\noexpand\citenumfont{\NAT@num}}}%
|
||||||
|
\fi
|
||||||
|
\else
|
||||||
|
\NAT@last@yr \@citea \mbox{\citenumfont{\NAT@num}}%
|
||||||
|
\let\NAT@last@yr\relax
|
||||||
|
\fi
|
||||||
|
\else
|
||||||
|
\@citea \mbox{\hyper@natlinkstart{\@citeb\@extra@b@citeb}%
|
||||||
|
{\citenumfont{\NAT@num}}\hyper@natlinkend}%
|
||||||
|
\fi
|
||||||
|
\fi
|
||||||
|
\def\@citea{\NAT@sep\penalty\@m\NAT@space}%
|
||||||
|
\else
|
||||||
|
\ifcase\NAT@ctype\relax
|
||||||
|
\ifx\NAT@last@nm\NAT@nm \NAT@yrsep\penalty\@m\NAT@space\else
|
||||||
|
\@citea \NAT@test{1}\ \NAT@@open
|
||||||
|
\if*#1*\else#1\ \fi\fi \NAT@mbox{%
|
||||||
|
\hyper@natlinkstart{\@citeb\@extra@b@citeb}%
|
||||||
|
{\citenumfont{\NAT@num}}\hyper@natlinkend}%
|
||||||
|
\def\@citea{\NAT@@close\NAT@sep\penalty\@m\ }%
|
||||||
|
\or\@citea
|
||||||
|
\hyper@natlinkstart{\@citeb\@extra@b@citeb}%
|
||||||
|
\NAT@test{\NAT@ctype}\hyper@natlinkend
|
||||||
|
\def\@citea{\NAT@sep\penalty\@m\ }%
|
||||||
|
\or\@citea
|
||||||
|
\hyper@natlinkstart{\@citeb\@extra@b@citeb}%
|
||||||
|
\NAT@test{\NAT@ctype}\hyper@natlinkend
|
||||||
|
\def\@citea{\NAT@sep\penalty\@m\ }%
|
||||||
|
\or\@citea
|
||||||
|
\hyper@natlinkstart{\@citeb\@extra@b@citeb}%
|
||||||
|
\NAT@alias\hyper@natlinkend
|
||||||
|
\def\@citea{\NAT@sep\penalty\@m\ }%
|
||||||
|
\fi
|
||||||
|
\fi
|
||||||
|
}}%
|
||||||
|
\ifnum\NAT@sort>1\relax\NAT@last@yr\fi
|
||||||
|
\ifNAT@swa\else\ifnum\NAT@ctype=0\if*#2*\else
|
||||||
|
\NAT@cmt#2\fi \NAT@@close\fi\fi}{#1}{#2}}
|
||||||
|
\newcommand\NAT@test[1]{\ifnum#1=1 \ifx\NAT@nm\NAT@noname
|
||||||
|
{\reset@font\bfseries(author?)}\PackageWarning{natbib}
|
||||||
|
{Author undefined for citation`\@citeb'
|
||||||
|
\MessageBreak
|
||||||
|
on page \thepage}\else \NAT@nm \fi
|
||||||
|
\else \if\relax\NAT@date\relax
|
||||||
|
{\reset@font\bfseries(year?)}\PackageWarning{natbib}
|
||||||
|
{Year undefined for citation`\@citeb'
|
||||||
|
\MessageBreak
|
||||||
|
on page \thepage}\else \NAT@date \fi \fi}
|
||||||
|
\let\citenumfont=\relax
|
||||||
|
\newcommand\NAT@citex{}
|
||||||
|
\def\NAT@citex%
|
||||||
|
[#1][#2]#3{%
|
||||||
|
\NAT@sort@cites{#3}%
|
||||||
|
\let\@citea\@empty
|
||||||
|
\@cite{\let\NAT@nm\@empty\let\NAT@year\@empty
|
||||||
|
\@for\@citeb:=\NAT@cite@list\do
|
||||||
|
{\edef\@citeb{\expandafter\@firstofone\@citeb}%
|
||||||
|
\if@filesw\immediate\write\@auxout{\string\citation{\@citeb}}\fi
|
||||||
|
\@ifundefined{b@\@citeb\@extra@b@citeb}{\@citea%
|
||||||
|
{\reset@font\bfseries ?}\NAT@citeundefined
|
||||||
|
\PackageWarning{natbib}%
|
||||||
|
{Citation `\@citeb' on page \thepage \space undefined}\def\NAT@date{}}%
|
||||||
|
{\let\NAT@last@nm=\NAT@nm\let\NAT@last@yr=\NAT@year
|
||||||
|
\NAT@parse{\@citeb}%
|
||||||
|
\ifNAT@longnames\@ifundefined{bv@\@citeb\@extra@b@citeb}{%
|
||||||
|
\let\NAT@name=\NAT@all@names
|
||||||
|
\global\@namedef{bv@\@citeb\@extra@b@citeb}{}}{}%
|
||||||
|
\fi
|
||||||
|
\ifNAT@full\let\NAT@nm\NAT@all@names\else
|
||||||
|
\let\NAT@nm\NAT@name\fi
|
||||||
|
\ifNAT@swa\ifcase\NAT@ctype
|
||||||
|
\if\relax\NAT@date\relax
|
||||||
|
\@citea\hyper@natlinkstart{\@citeb\@extra@b@citeb}%
|
||||||
|
\NAT@nmfmt{\NAT@nm}\NAT@date\hyper@natlinkend
|
||||||
|
\else
|
||||||
|
\ifx\NAT@last@nm\NAT@nm\NAT@yrsep
|
||||||
|
\ifx\NAT@last@yr\NAT@year
|
||||||
|
\hyper@natlinkstart{\@citeb\@extra@b@citeb}\NAT@exlab
|
||||||
|
\hyper@natlinkend
|
||||||
|
\else\unskip\
|
||||||
|
\hyper@natlinkstart{\@citeb\@extra@b@citeb}\NAT@date
|
||||||
|
\hyper@natlinkend
|
||||||
|
\fi
|
||||||
|
\else\@citea\hyper@natlinkstart{\@citeb\@extra@b@citeb}%
|
||||||
|
\NAT@nmfmt{\NAT@nm}%
|
||||||
|
\hyper@natlinkbreak{\NAT@aysep\ }{\@citeb\@extra@b@citeb}%
|
||||||
|
\NAT@date\hyper@natlinkend
|
||||||
|
\fi
|
||||||
|
\fi
|
||||||
|
\or\@citea\hyper@natlinkstart{\@citeb\@extra@b@citeb}%
|
||||||
|
\NAT@nmfmt{\NAT@nm}\hyper@natlinkend
|
||||||
|
\or\@citea\hyper@natlinkstart{\@citeb\@extra@b@citeb}%
|
||||||
|
\NAT@date\hyper@natlinkend
|
||||||
|
\or\@citea\hyper@natlinkstart{\@citeb\@extra@b@citeb}%
|
||||||
|
\NAT@alias\hyper@natlinkend
|
||||||
|
\fi \def\@citea{\NAT@sep\ }%
|
||||||
|
\else\ifcase\NAT@ctype
|
||||||
|
\if\relax\NAT@date\relax
|
||||||
|
\@citea\hyper@natlinkstart{\@citeb\@extra@b@citeb}%
|
||||||
|
\NAT@nmfmt{\NAT@nm}\hyper@natlinkend
|
||||||
|
\else
|
||||||
|
\ifx\NAT@last@nm\NAT@nm\NAT@yrsep
|
||||||
|
\ifx\NAT@last@yr\NAT@year
|
||||||
|
\hyper@natlinkstart{\@citeb\@extra@b@citeb}\NAT@exlab
|
||||||
|
\hyper@natlinkend
|
||||||
|
\else\unskip\
|
||||||
|
\hyper@natlinkstart{\@citeb\@extra@b@citeb}\NAT@date
|
||||||
|
\hyper@natlinkend
|
||||||
|
\fi
|
||||||
|
\else\@citea\hyper@natlinkstart{\@citeb\@extra@b@citeb}%
|
||||||
|
\NAT@nmfmt{\NAT@nm}%
|
||||||
|
\hyper@natlinkbreak{\ \NAT@@open\if*#1*\else#1\ \fi}%
|
||||||
|
{\@citeb\@extra@b@citeb}%
|
||||||
|
\NAT@date\hyper@natlinkend\fi
|
||||||
|
\fi
|
||||||
|
\or\@citea\hyper@natlinkstart{\@citeb\@extra@b@citeb}%
|
||||||
|
\NAT@nmfmt{\NAT@nm}\hyper@natlinkend
|
||||||
|
\or\@citea\hyper@natlinkstart{\@citeb\@extra@b@citeb}%
|
||||||
|
\NAT@date\hyper@natlinkend
|
||||||
|
\or\@citea\hyper@natlinkstart{\@citeb\@extra@b@citeb}%
|
||||||
|
\NAT@alias\hyper@natlinkend
|
||||||
|
\fi \if\relax\NAT@date\relax\def\@citea{\NAT@sep\ }%
|
||||||
|
\else\def\@citea{\NAT@@close\NAT@sep\ }\fi
|
||||||
|
\fi
|
||||||
|
}}\ifNAT@swa\else\if*#2*\else\NAT@cmt#2\fi
|
||||||
|
\if\relax\NAT@date\relax\else\NAT@@close\fi\fi}{#1}{#2}}
|
||||||
|
\newif\ifNAT@par \NAT@partrue
|
||||||
|
\newcommand\NAT@@open{\ifNAT@par\NAT@open\fi}
|
||||||
|
\newcommand\NAT@@close{\ifNAT@par\NAT@close\fi}
|
||||||
|
\newcommand\NAT@alias{\@ifundefined{al@\@citeb\@extra@b@citeb}{%
|
||||||
|
{\reset@font\bfseries(alias?)}\PackageWarning{natbib}
|
||||||
|
{Alias undefined for citation `\@citeb'
|
||||||
|
\MessageBreak on page \thepage}}{\@nameuse{al@\@citeb\@extra@b@citeb}}}
|
||||||
|
\let\NAT@up\relax
|
||||||
|
\newcommand\NAT@Up[1]{{\let\protect\@unexpandable@protect\let~\relax
|
||||||
|
\expandafter\NAT@deftemp#1}\expandafter\NAT@UP\NAT@temp}
|
||||||
|
\newcommand\NAT@deftemp[1]{\xdef\NAT@temp{#1}}
|
||||||
|
\newcommand\NAT@UP[1]{\let\@tempa\NAT@UP\ifcat a#1\MakeUppercase{#1}%
|
||||||
|
\let\@tempa\relax\else#1\fi\@tempa}
|
||||||
|
\newcommand\shortcites[1]{%
|
||||||
|
\@bsphack\@for\@citeb:=#1\do
|
||||||
|
{\edef\@citeb{\expandafter\@firstofone\@citeb}%
|
||||||
|
\global\@namedef{bv@\@citeb\@extra@b@citeb}{}}\@esphack}
|
||||||
|
\newcommand\NAT@biblabel[1]{\hfill}
|
||||||
|
\newcommand\NAT@biblabelnum[1]{\bibnumfmt{#1}}
|
||||||
|
\newcommand\bibnumfmt[1]{[#1]}
|
||||||
|
\def\@tempa#1{[#1]}
|
||||||
|
\ifx\@tempa\@biblabel\let\@biblabel\@empty\fi
|
||||||
|
\newcommand\NAT@bibsetnum[1]{\settowidth\labelwidth{\@biblabel{#1}}%
|
||||||
|
\setlength{\leftmargin}{\labelwidth}\addtolength{\leftmargin}{\labelsep}%
|
||||||
|
\setlength{\itemsep}{\bibsep}\setlength{\parsep}{\z@}%
|
||||||
|
\ifNAT@openbib
|
||||||
|
\addtolength{\leftmargin}{4mm}%
|
||||||
|
\setlength{\itemindent}{-4mm}%
|
||||||
|
\setlength{\listparindent}{\itemindent}%
|
||||||
|
\setlength{\parsep}{0pt}%
|
||||||
|
\fi
|
||||||
|
}
|
||||||
|
\newlength{\bibhang}
|
||||||
|
\setlength{\bibhang}{1em}
|
||||||
|
\newlength{\bibsep}
|
||||||
|
{\@listi \global\bibsep\itemsep \global\advance\bibsep by\parsep}
|
||||||
|
|
||||||
|
\newcommand\NAT@bibsetup%
|
||||||
|
[1]{\setlength{\leftmargin}{\bibhang}\setlength{\itemindent}{-\leftmargin}%
|
||||||
|
\setlength{\itemsep}{\bibsep}\setlength{\parsep}{\z@}}
|
||||||
|
\newcommand\NAT@set@cites{\ifNAT@numbers
|
||||||
|
\ifNAT@super \let\@cite\NAT@citesuper
|
||||||
|
\def\NAT@mbox##1{\unskip\nobreak\hspace{1\p@}\textsuperscript{##1}}%
|
||||||
|
\let\citeyearpar=\citeyear
|
||||||
|
\let\NAT@space\relax\else
|
||||||
|
\let\NAT@mbox=\mbox
|
||||||
|
\let\@cite\NAT@citenum \def\NAT@space{ }\fi
|
||||||
|
\let\@citex\NAT@citexnum
|
||||||
|
\ifx\@biblabel\@empty\let\@biblabel\NAT@biblabelnum\fi
|
||||||
|
\let\@bibsetup\NAT@bibsetnum
|
||||||
|
\def\natexlab##1{}%
|
||||||
|
\else
|
||||||
|
\let\@cite\NAT@cite
|
||||||
|
\let\@citex\NAT@citex
|
||||||
|
\let\@biblabel\NAT@biblabel
|
||||||
|
\let\@bibsetup\NAT@bibsetup
|
||||||
|
\def\natexlab##1{##1}%
|
||||||
|
\fi}
|
||||||
|
\AtBeginDocument{\NAT@set@cites}
|
||||||
|
\AtBeginDocument{\ifx\SK@def\@undefined\else
|
||||||
|
\ifx\SK@cite\@empty\else
|
||||||
|
\SK@def\@citex[#1][#2]#3{\SK@\SK@@ref{#3}\SK@@citex[#1][#2]{#3}}\fi
|
||||||
|
\ifx\SK@citeauthor\@undefined\def\HAR@checkdef{}\else
|
||||||
|
\let\citeauthor\SK@citeauthor
|
||||||
|
\let\citefullauthor\SK@citefullauthor
|
||||||
|
\let\citeyear\SK@citeyear\fi
|
||||||
|
\fi}
|
||||||
|
\AtBeginDocument{\@ifpackageloaded{hyperref}{%
|
||||||
|
\ifnum\NAT@sort=2\def\NAT@sort{1}\fi}{}}
|
||||||
|
\newif\ifNAT@full\NAT@fullfalse
|
||||||
|
\newif\ifNAT@swa
|
||||||
|
\DeclareRobustCommand\citet
|
||||||
|
{\begingroup\NAT@swafalse\def\NAT@ctype{0}\NAT@partrue
|
||||||
|
\@ifstar{\NAT@fulltrue\NAT@citetp}{\NAT@fullfalse\NAT@citetp}}
|
||||||
|
\newcommand\NAT@citetp{\@ifnextchar[{\NAT@@citetp}{\NAT@@citetp[]}}
|
||||||
|
\newcommand\NAT@@citetp{}
|
||||||
|
\def\NAT@@citetp[#1]{\@ifnextchar[{\@citex[#1]}{\@citex[][#1]}}
|
||||||
|
\DeclareRobustCommand\citep
|
||||||
|
{\begingroup\NAT@swatrue\def\NAT@ctype{0}\NAT@partrue
|
||||||
|
\@ifstar{\NAT@fulltrue\NAT@citetp}{\NAT@fullfalse\NAT@citetp}}
|
||||||
|
\DeclareRobustCommand\cite
|
||||||
|
{\begingroup\def\NAT@ctype{0}\NAT@partrue\NAT@swatrue
|
||||||
|
\@ifstar{\NAT@fulltrue\NAT@cites}{\NAT@fullfalse\NAT@cites}}
|
||||||
|
\newcommand\NAT@cites{\@ifnextchar [{\NAT@@citetp}{%
|
||||||
|
\ifNAT@numbers\else
|
||||||
|
\NAT@swafalse
|
||||||
|
\fi
|
||||||
|
\NAT@@citetp[]}}
|
||||||
|
\DeclareRobustCommand\citealt
|
||||||
|
{\begingroup\NAT@swafalse\def\NAT@ctype{0}\NAT@parfalse
|
||||||
|
\@ifstar{\NAT@fulltrue\NAT@citetp}{\NAT@fullfalse\NAT@citetp}}
|
||||||
|
\DeclareRobustCommand\citealp
|
||||||
|
{\begingroup\NAT@swatrue\def\NAT@ctype{0}\NAT@parfalse
|
||||||
|
\@ifstar{\NAT@fulltrue\NAT@citetp}{\NAT@fullfalse\NAT@citetp}}
|
||||||
|
\DeclareRobustCommand\citeauthor
|
||||||
|
{\begingroup\NAT@swafalse\def\NAT@ctype{1}\NAT@parfalse
|
||||||
|
\@ifstar{\NAT@fulltrue\NAT@citetp}{\NAT@fullfalse\NAT@citetp}}
|
||||||
|
\DeclareRobustCommand\Citet
|
||||||
|
{\begingroup\NAT@swafalse\def\NAT@ctype{0}\NAT@partrue
|
||||||
|
\let\NAT@up\NAT@Up
|
||||||
|
\@ifstar{\NAT@fulltrue\NAT@citetp}{\NAT@fullfalse\NAT@citetp}}
|
||||||
|
\DeclareRobustCommand\Citep
|
||||||
|
{\begingroup\NAT@swatrue\def\NAT@ctype{0}\NAT@partrue
|
||||||
|
\let\NAT@up\NAT@Up
|
||||||
|
\@ifstar{\NAT@fulltrue\NAT@citetp}{\NAT@fullfalse\NAT@citetp}}
|
||||||
|
\DeclareRobustCommand\Citealt
|
||||||
|
{\begingroup\NAT@swafalse\def\NAT@ctype{0}\NAT@parfalse
|
||||||
|
\let\NAT@up\NAT@Up
|
||||||
|
\@ifstar{\NAT@fulltrue\NAT@citetp}{\NAT@fullfalse\NAT@citetp}}
|
||||||
|
\DeclareRobustCommand\Citealp
|
||||||
|
{\begingroup\NAT@swatrue\def\NAT@ctype{0}\NAT@parfalse
|
||||||
|
\let\NAT@up\NAT@Up
|
||||||
|
\@ifstar{\NAT@fulltrue\NAT@citetp}{\NAT@fullfalse\NAT@citetp}}
|
||||||
|
\DeclareRobustCommand\Citeauthor
|
||||||
|
{\begingroup\NAT@swafalse\def\NAT@ctype{1}\NAT@parfalse
|
||||||
|
\let\NAT@up\NAT@Up
|
||||||
|
\@ifstar{\NAT@fulltrue\NAT@citetp}{\NAT@fullfalse\NAT@citetp}}
|
||||||
|
\DeclareRobustCommand\citeyear
|
||||||
|
{\begingroup\NAT@swafalse\def\NAT@ctype{2}\NAT@parfalse\NAT@citetp}
|
||||||
|
\DeclareRobustCommand\citeyearpar
|
||||||
|
{\begingroup\NAT@swatrue\def\NAT@ctype{2}\NAT@partrue\NAT@citetp}
|
||||||
|
\newcommand\citetext[1]{\NAT@open#1\NAT@close}
|
||||||
|
\DeclareRobustCommand\citefullauthor
|
||||||
|
{\citeauthor*}
|
||||||
|
\newcommand\defcitealias[2]{%
|
||||||
|
\@ifundefined{al@#1\@extra@b@citeb}{}
|
||||||
|
{\PackageWarning{natbib}{Overwriting existing alias for citation #1}}
|
||||||
|
\@namedef{al@#1\@extra@b@citeb}{#2}}
|
||||||
|
\DeclareRobustCommand\citetalias{\begingroup
|
||||||
|
\NAT@swafalse\def\NAT@ctype{3}\NAT@parfalse\NAT@citetp}
|
||||||
|
\DeclareRobustCommand\citepalias{\begingroup
|
||||||
|
\NAT@swatrue\def\NAT@ctype{3}\NAT@partrue\NAT@citetp}
|
||||||
|
\renewcommand\nocite[1]{\@bsphack
|
||||||
|
\@for\@citeb:=#1\do{%
|
||||||
|
\edef\@citeb{\expandafter\@firstofone\@citeb}%
|
||||||
|
\if@filesw\immediate\write\@auxout{\string\citation{\@citeb}}\fi
|
||||||
|
\if*\@citeb\else
|
||||||
|
\@ifundefined{b@\@citeb\@extra@b@citeb}{%
|
||||||
|
\NAT@citeundefined \PackageWarning{natbib}%
|
||||||
|
{Citation `\@citeb' undefined}}{}\fi}%
|
||||||
|
\@esphack}
|
||||||
|
\newcommand\NAT@parse[1]{{%
|
||||||
|
\let\protect=\@unexpandable@protect\let~\relax
|
||||||
|
\let\active@prefix=\@gobble
|
||||||
|
\xdef\NAT@temp{\csname b@#1\@extra@b@citeb\endcsname}}%
|
||||||
|
\expandafter\NAT@split\NAT@temp
|
||||||
|
\expandafter\NAT@parse@date\NAT@date??????@@%
|
||||||
|
\ifciteindex\NAT@index\fi
|
||||||
|
}
|
||||||
|
\newcommand\NAT@split[4]{%
|
||||||
|
\gdef\NAT@num{#1}\gdef\NAT@name{#3}\gdef\NAT@date{#2}%
|
||||||
|
\gdef\NAT@all@names{#4}%
|
||||||
|
\ifx\NAT@noname\NAT@all@names \gdef\NAT@all@names{#3}\fi}
|
||||||
|
\newcommand\NAT@parse@date{}
|
||||||
|
\def\NAT@parse@date#1#2#3#4#5#6@@{%
|
||||||
|
\ifnum\the\catcode`#1=11\def\NAT@year{}\def\NAT@exlab{#1}\else
|
||||||
|
\ifnum\the\catcode`#2=11\def\NAT@year{#1}\def\NAT@exlab{#2}\else
|
||||||
|
\ifnum\the\catcode`#3=11\def\NAT@year{#1#2}\def\NAT@exlab{#3}\else
|
||||||
|
\ifnum\the\catcode`#4=11\def\NAT@year{#1#2#3}\def\NAT@exlab{#4}\else
|
||||||
|
\def\NAT@year{#1#2#3#4}\def\NAT@exlab{{#5}}\fi\fi\fi\fi}
|
||||||
|
\newcommand\NAT@index{}
|
||||||
|
\let\NAT@makeindex=\makeindex
|
||||||
|
\renewcommand\makeindex{\NAT@makeindex
|
||||||
|
\renewcommand\NAT@index{\@bsphack\begingroup
|
||||||
|
\def~{\string~}\@wrindex{\NAT@idxtxt}}}
|
||||||
|
\newcommand\NAT@idxtxt{\NAT@name\ \NAT@open\NAT@date\NAT@close}
|
||||||
|
\@ifundefined{@indexfile}{}{\let\NAT@makeindex\relax\makeindex}
|
||||||
|
\newif\ifciteindex \citeindexfalse
|
||||||
|
\newcommand\citeindextype{default}
|
||||||
|
\newcommand\NAT@index@alt{{\let\protect=\noexpand\let~\relax
|
||||||
|
\xdef\NAT@temp{\NAT@idxtxt}}\expandafter\NAT@exp\NAT@temp\@nil}
|
||||||
|
\newcommand\NAT@exp{}
|
||||||
|
\def\NAT@exp#1\@nil{\mbox{}\index[\citeindextype]{#1}}
|
||||||
|
|
||||||
|
\AtBeginDocument{%
|
||||||
|
\@ifpackageloaded{index}{\let\NAT@index=\NAT@index@alt}{}}
|
||||||
|
\newcommand\NAT@ifcmd{\futurelet\NAT@temp\NAT@ifxcmd}
|
||||||
|
\newcommand\NAT@ifxcmd{\ifx\NAT@temp\relax\else\expandafter\NAT@bare\fi}
|
||||||
|
\def\NAT@bare#1(#2)#3(@)#4\@nil#5{%
|
||||||
|
\if @#2
|
||||||
|
\expandafter\NAT@apalk#1, , \@nil{#5}\else
|
||||||
|
\stepcounter{NAT@ctr}%
|
||||||
|
\NAT@wrout{\arabic {NAT@ctr}}{#2}{#1}{#3}{#5}
|
||||||
|
\fi
|
||||||
|
}
|
||||||
|
\newcommand\NAT@wrout[5]{%
|
||||||
|
\if@filesw
|
||||||
|
{\let\protect\noexpand\let~\relax
|
||||||
|
\immediate
|
||||||
|
\write\@auxout{\string\bibcite{#5}{{#1}{#2}{{#3}}{{#4}}}}}\fi
|
||||||
|
\ignorespaces}
|
||||||
|
\def\NAT@noname{{}}
|
||||||
|
\renewcommand\bibitem{%
|
||||||
|
\@ifnextchar[{\@lbibitem}{%
|
||||||
|
\global\NAT@stdbsttrue
|
||||||
|
\stepcounter{NAT@ctr}\@lbibitem[\arabic{NAT@ctr}]}}
|
||||||
|
\def\@lbibitem[#1]#2{%
|
||||||
|
\if\relax\@extra@b@citeb\relax\else
|
||||||
|
\@ifundefined{br@#2\@extra@b@citeb}{}{%
|
||||||
|
\@namedef{br@#2}{\@nameuse{br@#2\@extra@b@citeb}}}\fi
|
||||||
|
\@ifundefined{b@#2\@extra@b@citeb}{\def\NAT@num{}}{\NAT@parse{#2}}%
|
||||||
|
\item[\hfil\hyper@natanchorstart{#2\@extra@b@citeb}\@biblabel{\NAT@num}%
|
||||||
|
\hyper@natanchorend]%
|
||||||
|
\NAT@ifcmd#1(@)(@)\@nil{#2}}
|
||||||
|
\ifx\SK@lbibitem\@undefined\else
|
||||||
|
\let\SK@lbibitem\@lbibitem
|
||||||
|
\def\@lbibitem[#1]#2{%
|
||||||
|
\SK@lbibitem[#1]{#2}\SK@\SK@@label{#2}\ignorespaces}\fi
|
||||||
|
\newif\ifNAT@stdbst \NAT@stdbstfalse
|
||||||
|
|
||||||
|
\AtEndDocument
|
||||||
|
{\ifNAT@stdbst\if@filesw\immediate\write\@auxout{\string
|
||||||
|
\global\string\NAT@numberstrue}\fi\fi
|
||||||
|
}
|
||||||
|
\providecommand\bibcite{}
|
||||||
|
\renewcommand\bibcite[2]{\@ifundefined{b@#1\@extra@binfo}\relax
|
||||||
|
{\NAT@citemultiple
|
||||||
|
\PackageWarningNoLine{natbib}{Citation `#1' multiply defined}}%
|
||||||
|
\global\@namedef{b@#1\@extra@binfo}{#2}}
|
||||||
|
\AtEndDocument{\NAT@swatrue\let\bibcite\NAT@testdef}
|
||||||
|
\newcommand\NAT@testdef[2]{%
|
||||||
|
\def\NAT@temp{#2}\expandafter \ifx \csname b@#1\@extra@binfo\endcsname
|
||||||
|
\NAT@temp \else \ifNAT@swa \NAT@swafalse
|
||||||
|
\PackageWarningNoLine{natbib}{Citation(s) may have
|
||||||
|
changed.\MessageBreak
|
||||||
|
Rerun to get citations correct}\fi\fi}
|
||||||
|
\newcommand\NAT@apalk{}
|
||||||
|
\def\NAT@apalk#1, #2, #3\@nil#4{\if\relax#2\relax
|
||||||
|
\global\NAT@stdbsttrue
|
||||||
|
\NAT@wrout{#1}{}{}{}{#4}\else
|
||||||
|
\stepcounter{NAT@ctr}%
|
||||||
|
\NAT@wrout{\arabic {NAT@ctr}}{#2}{#1}{}{#4}\fi}
|
||||||
|
\newcommand\citeauthoryear{}
|
||||||
|
\def\citeauthoryear#1#2#3(@)(@)\@nil#4{\stepcounter{NAT@ctr}\if\relax#3\relax
|
||||||
|
\NAT@wrout{\arabic {NAT@ctr}}{#2}{#1}{}{#4}\else
|
||||||
|
\NAT@wrout{\arabic {NAT@ctr}}{#3}{#2}{#1}{#4}\fi}
|
||||||
|
\newcommand\citestarts{\NAT@open}
|
||||||
|
\newcommand\citeends{\NAT@close}
|
||||||
|
\newcommand\betweenauthors{and}
|
||||||
|
\newcommand\astroncite{}
|
||||||
|
\def\astroncite#1#2(@)(@)\@nil#3{\stepcounter{NAT@ctr}\NAT@wrout{\arabic
|
||||||
|
{NAT@ctr}}{#2}{#1}{}{#3}}
|
||||||
|
\newcommand\citename{}
|
||||||
|
\def\citename#1#2(@)(@)\@nil#3{\expandafter\NAT@apalk#1#2, \@nil{#3}}
|
||||||
|
\newcommand\harvarditem[4][]%
|
||||||
|
{\if\relax#1\relax\bibitem[#2(#3)]{#4}\else
|
||||||
|
\bibitem[#1(#3)#2]{#4}\fi }
|
||||||
|
\newcommand\harvardleft{\NAT@open}
|
||||||
|
\newcommand\harvardright{\NAT@close}
|
||||||
|
\newcommand\harvardyearleft{\NAT@open}
|
||||||
|
\newcommand\harvardyearright{\NAT@close}
|
||||||
|
\AtBeginDocument{\providecommand{\harvardand}{and}}
|
||||||
|
\newcommand\harvardurl[1]{\textbf{URL:} \textit{#1}}
|
||||||
|
\providecommand\bibsection{}
|
||||||
|
\@ifundefined{chapter}%
|
||||||
|
{\renewcommand\bibsection{\section*{\refname
|
||||||
|
\@mkboth{\MakeUppercase{\refname}}{\MakeUppercase{\refname}}}}}
|
||||||
|
{\@ifundefined{NAT@sectionbib}%
|
||||||
|
{\renewcommand\bibsection{\chapter*{\bibname
|
||||||
|
\@mkboth{\MakeUppercase{\bibname}}{\MakeUppercase{\bibname}}}}}
|
||||||
|
{\renewcommand\bibsection{\section*{\bibname
|
||||||
|
\ifx\@mkboth\@gobbletwo\else\markright{\MakeUppercase{\bibname}}\fi}}}}
|
||||||
|
\@ifclassloaded{amsart}%
|
||||||
|
{\renewcommand\bibsection{\section*{\refname}}}{}
|
||||||
|
\@ifclassloaded{amsbook}%
|
||||||
|
{\renewcommand\bibsection{\chapter*{\bibname}}}{}
|
||||||
|
\@ifundefined{bib@heading}{}{\let\bibsection\bib@heading}
|
||||||
|
\newcounter{NAT@ctr}
|
||||||
|
\renewenvironment{thebibliography}[1]{%
|
||||||
|
\bibsection
|
||||||
|
\vspace{1\p@}\parindent \z@\bibpreamble\bibfont\list
|
||||||
|
{\@biblabel{\arabic{NAT@ctr}}}{\@bibsetup{#1}%
|
||||||
|
\setcounter{NAT@ctr}{0}}%
|
||||||
|
\ifNAT@openbib
|
||||||
|
\renewcommand\newblock{\par}
|
||||||
|
\else
|
||||||
|
\renewcommand\newblock{\hskip .11em \@plus.33em \@minus.07em}%
|
||||||
|
\fi
|
||||||
|
\sloppy\clubpenalty4000\widowpenalty4000
|
||||||
|
\sfcode`\.=1000\relax
|
||||||
|
\let\citeN\cite \let\shortcite\cite
|
||||||
|
\let\citeasnoun\cite\fontsize{7}{9}\selectfont
|
||||||
|
}{\def\@noitemerr{%
|
||||||
|
\PackageWarning{natbib}
|
||||||
|
{Empty `thebibliography' environment}}%
|
||||||
|
\endlist\vskip-\lastskip}
|
||||||
|
\let\bibfont\relax
|
||||||
|
\let\bibpreamble\relax
|
||||||
|
\providecommand\reset@font{\relax}
|
||||||
|
\providecommand\bibname{Bibliography}
|
||||||
|
\providecommand\refname{References}
|
||||||
|
\newcommand\NAT@citeundefined{\gdef \NAT@undefined {%
|
||||||
|
\PackageWarningNoLine{natbib}{There were undefined citations}}}
|
||||||
|
\let \NAT@undefined \relax
|
||||||
|
\newcommand\NAT@citemultiple{\gdef \NAT@multiple {%
|
||||||
|
\PackageWarningNoLine{natbib}{There were multiply defined citations}}}
|
||||||
|
\let \NAT@multiple \relax
|
||||||
|
\AtEndDocument{\NAT@undefined\NAT@multiple}
|
||||||
|
\providecommand\@mkboth[2]{}
|
||||||
|
\providecommand\MakeUppercase{\uppercase}
|
||||||
|
\providecommand{\@extra@b@citeb}{}
|
||||||
|
\gdef\@extra@binfo{}
|
||||||
|
\providecommand\hyper@natanchorstart[1]{}
|
||||||
|
\providecommand\hyper@natanchorend{}
|
||||||
|
\providecommand\hyper@natlinkstart[1]{}
|
||||||
|
\providecommand\hyper@natlinkend{}
|
||||||
|
\providecommand\hyper@natlinkbreak[2]{#1}
|
||||||
|
\@ifundefined{bbl@redefine}{}{%
|
||||||
|
\bbl@redefine\nocite#1{%
|
||||||
|
\@safe@activestrue\org@nocite{#1}\@safe@activesfalse}%
|
||||||
|
\bbl@redefine\@lbibitem[#1]#2{%
|
||||||
|
\@safe@activestrue\org@@lbibitem[#1]{#2}\@safe@activesfalse}%
|
||||||
|
}
|
||||||
|
\AtBeginDocument{\@ifundefined{bbl@redefine}{}{%
|
||||||
|
\bbl@redefine\@citex[#1][#2]#3{%
|
||||||
|
\@safe@activestrue\org@@citex[#1][#2]{#3}\@safe@activesfalse}%
|
||||||
|
\bbl@redefine\NAT@testdef#1#2{%
|
||||||
|
\@safe@activestrue\org@NAT@testdef{#1}{#2}\@safe@activesfalse}%
|
||||||
|
\@ifundefined{org@@lbibitem}{%
|
||||||
|
\bbl@redefine\@lbibitem[#1]#2{%
|
||||||
|
\@safe@activestrue\org@@lbibitem[#1]{#2}\@safe@activesfalse}}{}%
|
||||||
|
}}
|
||||||
|
\ifnum\NAT@sort>0
|
||||||
|
\newcommand\NAT@sort@cites[1]{%
|
||||||
|
\@tempcntb\m@ne
|
||||||
|
\let\@celt\delimiter
|
||||||
|
\def\NAT@num@list{}%
|
||||||
|
\def\NAT@cite@list{}%
|
||||||
|
\def\NAT@nonsort@list{}%
|
||||||
|
\@for \@citeb:=#1\do{\NAT@make@cite@list}%
|
||||||
|
\edef\NAT@cite@list{\NAT@cite@list\NAT@nonsort@list}%
|
||||||
|
\edef\NAT@cite@list{\expandafter\NAT@xcom\NAT@cite@list @@}}
|
||||||
|
\begingroup \catcode`\_=8
|
||||||
|
\gdef\NAT@make@cite@list{%
|
||||||
|
\edef\@citeb{\expandafter\@firstofone\@citeb}%
|
||||||
|
\@ifundefined{b@\@citeb\@extra@b@citeb}{\def\NAT@num{A}}%
|
||||||
|
{\NAT@parse{\@citeb}}%
|
||||||
|
\ifcat _\ifnum\z@<0\NAT@num _\else A\fi
|
||||||
|
\@tempcnta\NAT@num \relax
|
||||||
|
\ifnum \@tempcnta>\@tempcntb
|
||||||
|
\edef\NAT@num@list{\NAT@num@list \@celt{\NAT@num}}%
|
||||||
|
\edef\NAT@cite@list{\NAT@cite@list\@citeb,}%
|
||||||
|
\@tempcntb\@tempcnta
|
||||||
|
\else
|
||||||
|
\let\NAT@@cite@list=\NAT@cite@list \def\NAT@cite@list{}%
|
||||||
|
\edef\NAT@num@list{\expandafter\NAT@num@celt \NAT@num@list \@gobble @}%
|
||||||
|
{\let\@celt=\NAT@celt\NAT@num@list}%
|
||||||
|
\fi
|
||||||
|
\else
|
||||||
|
\edef\NAT@nonsort@list{\NAT@nonsort@list\@citeb,}%
|
||||||
|
\fi}
|
||||||
|
\endgroup
|
||||||
|
\def\NAT@celt#1{\ifnum #1<\@tempcnta
|
||||||
|
\xdef\NAT@cite@list{\NAT@cite@list\expandafter\NAT@nextc\NAT@@cite@list @@}%
|
||||||
|
\xdef\NAT@@cite@list{\expandafter\NAT@restc\NAT@@cite@list}%
|
||||||
|
\else
|
||||||
|
\xdef\NAT@cite@list{\NAT@cite@list\@citeb,\NAT@@cite@list}\let\@celt\@gobble%
|
||||||
|
\fi}
|
||||||
|
\def\NAT@num@celt#1#2{\ifx \@celt #1%
|
||||||
|
\ifnum #2<\@tempcnta
|
||||||
|
\@celt{#2}%
|
||||||
|
\expandafter\expandafter\expandafter\NAT@num@celt
|
||||||
|
\else
|
||||||
|
\@celt{\number\@tempcnta}\@celt{#2}%
|
||||||
|
\fi\fi}
|
||||||
|
\def\NAT@nextc#1,#2@@{#1,}
|
||||||
|
\def\NAT@restc#1,#2{#2}
|
||||||
|
\def\NAT@xcom#1,@@{#1}
|
||||||
|
\else
|
||||||
|
\newcommand\NAT@sort@cites[1]{\edef\NAT@cite@list{#1}}\fi
|
||||||
|
\InputIfFileExists{natbib.cfg}
|
||||||
|
{\typeout{Local config file natbib.cfg used}}{}
|
||||||
|
%%
|
||||||
|
%% <<<<< End of generated file <<<<<<
|
||||||
|
%%
|
||||||
|
%% End of file `natbib.sty'.
|
||||||
Loading…
Reference in New Issue