forked from SynBioDex/SBOL-specification
-
Notifications
You must be signed in to change notification settings - Fork 0
/
sbmlpkgspec.cls
1150 lines (968 loc) · 38.7 KB
/
sbmlpkgspec.cls
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
%% Filename: sbmlpkgspec.cls -*- mode: latex -*-
%% Description: LaTeX style file for SBML Level 3 package specifications
%% Author(s): Michael Hucka <mhucka@caltech.edu>
%% Organization: California Institute of Technology
%% Date created: 2011-08-11
%%
%% Copyright 2007-2013 California Institute of Technology, Pasadena, CA, USA.
%%
%% This file is free software; you can redistribute it and/or modify it
%% under the terms of the GNU Lesser General Public License as published
%% by the Free Software Foundation; either version 2.1 of the License, or
%% any later version.
%%
%% This library is distributed in the hope that it will be useful, but
%% WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
%% MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
%% documentation provided hereunder is on an "as is" basis, and the
%% California Institute of Technology has no obligations to provide
%% maintenance, support, updates, enhancements or modifications. In no
%% event shall the California Institute of Technology be liable to any
%% party for direct, indirect, special, incidental or consequential
%% damages, including lost profits, arising out of the use of this software
%% and its documentation, even if the California Institute of Technology
%% has been advised of the possibility of such damage. See the
%% GNU Lesser General Public License for more details.
%%
%% You should have received a copy of the GNU Lesser General Public License
%% along with this library; if not, write to the Free Software Foundation,
%% Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
\def\filedate{2013/07/24}
\NeedsTeXFormat{LaTeX2e}
\ProvidesClass{sbmlpkgspec}[\filedate\space SBML Level 3
Package Specification Style]
%% ----------------------------------------------------------------------------
%% Package references and options.
%% ----------------------------------------------------------------------------
%% Keep in mind that hyperref needs to be almost the last package loaded.
\newif\if@draftspec
\DeclareOption{draftspec}{\global\let\if@draftspec\iftrue}
\DeclareOption{finalspec}{\global\let\if@draftspec\iffalse}
\newif\if@notoc
\DeclareOption{toc}{\global\let\if@notoc\iffalse}
\DeclareOption{notoc}{\global\let\if@notoc\iftrue}
\newif\if@twocolumntoc
\DeclareOption{twocolumntoc}{\global\let\if@twocolumntoc\iftrue}
\DeclareOption{singlecolumntoc}{\global\let\if@twocolumntoc\iffalse}
\DeclareOption*{\PassOptionsToClass{\CurrentOption}{article}}
\ExecuteOptions{toc,twoside}
\ExecuteOptions{singlecolumntoc}
\ProcessOptions
\LoadClass{article}
%% ----------------------------------------------------------------------------
%% Dependencies on other packages.
%% ----------------------------------------------------------------------------
\RequirePackage{lastpage}
\RequirePackage{ifpdf}
\RequirePackage{booktabs}
\RequirePackage{multicol}
\RequirePackage{array}
\RequirePackage[round,sort]{natbib}
\RequirePackage{xspace}
\RequirePackage{scalefnt}
\RequirePackage{pifont}
\RequirePackage[pagewise,mathlines,edtable,right]{lineno}
\RequirePackage{calc}
\RequirePackage{fancyhdr}
\RequirePackage{fancybox}
\RequirePackage{amsmath}
\RequirePackage{amssymb}
\RequirePackage{bbding}
\RequirePackage{wasysym}
\RequirePackage{enumitem}
\RequirePackage{accsupp}
\RequirePackage[T1]{fontenc}
\RequirePackage{suffix}
\RequirePackage{varwidth}
\RequirePackage{txfonts}
% We use the "optional" package to indicate whether to generate a grayscale
% vs a color version of the document without having to alter the .tex file
% itself. Unfortunately, the "optional" package doesn't offer an "or" type
% switch or a way to set a default, so we have to go through some
% contortions here. Also, it needs *something* in the optional argument
% to RequirePackage or UsePackage, hence the "dummyoption" thing below.
%
% To produce grayscale output without modifying the source file, invoke
% latex with a command of the following form:
%
% pdflatex "\newcommand\UseOption{grayscale}\input{sbml-level-2-version-2}"
\newif\ifgrayscalespec
\global\let\ifgrayscalespec\iffalse
\RequirePackage[dummyoption]{optional}
\opt{grayscale}{\global\let\ifgrayscalespec\iftrue}
% Load varioref only if not generating HTML, because on HTML
% pages it doesn't make sense to use varioref.
% \RequirePackage{html}
% \latexhtml{
%begin{latexonly}
\RequirePackage[american]{varioref}
%end{latexonly}
% }{
% \newcommand{\vref}[1]{\ref{#1}}
% }
% Hyperref, xcolor, graphicx and possibly others have a flag "pdftex"
% that needs to be used if pdflatex is being used. The following puts
% these inside a conditional for that situation.
\ifpdf
% Case: using pdflatex
\RequirePackage[pdftex]{graphicx}
% Options get even more complicated. If we're producing grayscale output,
% we don't want to bother with coloring links, but we still want to load
% hyperref so that its macros are defined (and we don't have to redefine
% everything that uses hyperref). So:
\ifgrayscalespec
\RequirePackage[pdftex,breaklinks=true,colorlinks=false,
bookmarksnumbered=true]{hyperref}
\else
\RequirePackage[pdftex,breaklinks=true,colorlinks=true,
pdfhighlight=/O,linkcolor={sbmlblue},citecolor={sbmlblue},
urlcolor={sbmlblue},anchorcolor={sbmlblue},bookmarksnumbered]{hyperref}
\fi
% Although it may seem like we wouldn't need to load xcolor if
% the grayscale option is given, in fact it doesn't affect anything
% to load this and it avoids having to conditionalize other things.
% (The colors aren't actually invoked if grayscale is being used.)
\RequirePackage[pdftex,rgb,dvipsnames,svgnames,hyperref,table]{xcolor}
\else
% Case: not using pdflatex
\RequirePackage{graphicx}
% Test whether we're being run from latex or latex2html
% \latexhtml{
% For latex.
\RequirePackage[breaklinks]{hyperref}
% }{
% For latex2html.
% \RequirePackage[latex2html,breaklinks]{hyperref}
% }
\RequirePackage[rgb,dvipsnames,svgnames,hyperref,table]{xcolor}
\fi
% Load listings package & set some values.
\RequirePackage{listings}
\lstloadlanguages{bash,csh,XML}
% Load draftwatermark if this document is a draft version.
\if@draftspec
\RequirePackage[firstpage]{draftwatermark}
\SetWatermarkLightness{0.92}
\fi
\RequirePackage{overpic}
% We don't need the rotating package in this file, but there is a strange
% interaction between the rotating package and something else in sbmlpkgclass
% (I don't know what). The effect of the interaction is that sidewaystable
% environment contents are shifted left on the page (or from the perspective
% of the rotated table, shiftted up). The solution is to set \rotFPtop, but
% asking users of sbmlpkgclass to know that they have to do this is too much
% to ask. So, to avoid people experiencing the problem and wasting time
% trying to figure out what's causing it, I decided it's better to preload
% rotating. The problem was first reported to me by Maciej Swat in Aug. 2013
% and I found the solution at http://tex.stackexchange.com/a/47879/8318
\RequirePackage{rotating}
\setlength{\rotFPtop}{0pt plus 1fil}
%% ----------------------------------------------------------------------------
%% Font selection.
%% ----------------------------------------------------------------------------
% This sets up Helvetica for headings and TX Typewriter for the tt font.
% The font scaling is because the default Helvetica size is too big.
\RequirePackage{fourier}
\RequirePackage{helvet}
\ifgrayscalespec
% In the grayscale version of the spec, Helvetica bold is used for class
% names in the text, and the width of the words then is too big unless
% we scale down the font even more compared to the regular case below.
\def\Hv@scale{0.814}
\else
\def\Hv@scale{0.87}
\fi
% The following sets up txtt for the typewriter font.
\renewcommand{\ttdefault}{txtt}
\DeclareMathAlphabet{\mathtt}{T1}{txtt}{m}{n}
\SetMathAlphabet{\mathtt}{bold}{T1}{txtt}{b}{n}
% The next bit is an adaption of code from ot1phv.fd and adapted to the txtt
% fonts. The txtt fonts are just a tad too big, so this tries to rescale
% them down a tiny bit. This isn't completely right because I couldn't
% figure out the right syntax when the DeclareFontShape uses ssub below.
% (Notice how the ones with ssub don't have the \Txtt@@scale factor.)
\def\Txtt@scale{0.97}
\edef\Txtt@@scale{s*[\csname Txtt@scale\endcsname]}%
\DeclareFontFamily{T1}{txtt}{\hyphenchar \font\m@ne}
\DeclareFontShape{T1}{txtt}{m}{n}{ %rebular
<-> \Txtt@@scale txtt%
}{}
\DeclareFontShape{T1}{txtt}{m}{sc}{ %cap & small cap
<-> \Txtt@@scale txttsc%
}{}
\DeclareFontShape{T1}{txtt}{m}{sl}{ %slanted
<-> \Txtt@@scale txttsl%
}{}
\DeclareFontShape{T1}{txtt}{m}{it}{ %italic
<-> ssub * txtt/m/sl%
}{}
\DeclareFontShape{T1}{txtt}{m}{ui}{ %unslanted italic
<-> ssub * txtt/m/sl%
}{}
\DeclareFontShape{T1}{txtt}{b}{n}{ %bold
<-> \Txtt@@scale txbtt%
}{}
\DeclareFontShape{T1}{txtt}{b}{sc}{ %bold cap & small cap
<-> \Txtt@@scale txbttsc%
}{}
\DeclareFontShape{T1}{txtt}{b}{sl}{ %bold slanted
<-> \Txtt@@scale txbttsl%
}{}
\DeclareFontShape{T1}{txtt}{b}{it}{ %bold italic
<-> ssub * txtt/b/sl%
}{}
\DeclareFontShape{T1}{txtt}{b}{ui}{ %bold unslanted italic
<-> ssub * txtt/b/sl%
}{}
\DeclareFontShape{T1}{txtt}{bx}{n}{ %bold extended
<-> ssub * txtt/b/n%
}{}
\DeclareFontShape{T1}{txtt}{bx}{sc}{ %bold extended cap & small cap
<-> ssub * txtt/b/sc%
}{}
\DeclareFontShape{T1}{txtt}{bx}{sl}{ %bold extended slanted
<-> ssub * txtt/b/sl%
}{}
\DeclareFontShape{T1}{txtt}{bx}{it}{ %bold extended italic
<-> ssub * txtt/b/sl%
}{}
\DeclareFontShape{T1}{txtt}{bx}{ui}{ %bold extended unslanted italic
<-> ssub * txtt/b/sl%
}{}
% Adjustments due to quirks of the combination of fourier and amsmath:
% Make the \big( braces regular height (default is too short):
\delimiterfactor=1000
\delimitershortfall=1pt
%% ----------------------------------------------------------------------------
%% Main code.
%% ----------------------------------------------------------------------------
\raggedbottom
% Local color definitions.
\definecolor{sbmlblue}{rgb}{0.07,0.50,0.78}
\definecolor{sbmlgray}{gray}{0.7}
\definecolor{sbmlrowgray}{gray}{0.96}
\definecolor{extremelylightgray}{gray}{0.97}
\definecolor{veryverylightgray}{gray}{0.95}
\definecolor{verylightgray}{gray}{0.9}
\definecolor{lightgray}{gray}{0.8}
\definecolor{mediumgray}{gray}{0.5}
\definecolor{darkgray}{gray}{0.3}
\definecolor{almostblack}{gray}{0.23}
\definecolor{normaltextcolor}{gray}{0.23} % Synonym for 'almostblack'
\definecolor{lightyellow}{rgb}{0.98,0.94,0.7}
\definecolor{verylightyellow}{rgb}{0.97,0.95,0.85}
\definecolor{darkblue}{rgb}{0.1,0.4,0.55}
\definecolor{mediumgreen}{rgb}{0.1,0.6,0.3}
% Color for marking changed text, conditional on whether gray scale mode is on.
\ifgrayscalespec
\newcommand{\@sbmlchangedcolor}{normaltextcolor}
\else
\definecolor{sbmlchangedcolor}{rgb}{0.69,0.19,0.376}
\newcommand{\@sbmlchangedcolor}{sbmlchangedcolor}
\fi
% Macros for making consistent font, color, and other selections:
\newcommand{\changed}[1]{\textcolor{\@sbmlchangedcolor}{#1}}
\newenvironment{blockChanged}{\color{\@sbmlchangedcolor}}{\color{normaltextcolor}}
\newcommand{\figureFont}[1]{\textsf{\textbf{#1}}}
\newcommand{\literalFont}[1]{\textcolor{black}{\textup{\ttfamily{#1}}}}
\newcommand{\literalFontNC}[1]{\textup{\ttfamily{#1}}}
\newcommand{\tightspacing}{\renewcommand{\baselinestretch}{0.85}}
\newcommand{\regularspacing}{\renewcommand{\baselinestretch}{\normalbaselinestretch}}
\ifgrayscalespec
\newcommand{\defRef}[2]{\textbf{\class{#1}}\xspace}
\newcommand{\absDefRef}[2]{\textbf{\abstractclass{#1}}\xspace}
\else
\newcommand{\defRef}[2]{\class{\hyperref[#2]{#1}}\xspace}
\newcommand{\absDefRef}[2]{\abstractclass{\hyperref[#2]{#1}}\xspace}
\fi
\renewcommand{\texttt}[1]{\textcolor{black}{\ttfamily #1}}
% Hyperref extras:
\newcommand{\link}[2]{\literalFont{\href{#1}{#2}}}
\newcommand{\mailto}[1]{\link{mailto:#1}{#1}}
% 'lineno' package adjustments.
% The BeginAccSupp business causes the line numbers to be ignored for
% copy-paste operations in the PDF output.
\setlength{\linenumbersep}{2.2em}
\renewcommand{\thelinenumber}{%
\BeginAccSupp{ActualText={}}%
\textcolor{mediumgray}{\parbox[b][\height+1.5pt][c]{10pt}{\arabic{linenumber}}}%
\EndAccSupp{}%
}
% 'booktabs' package adjustments:
\setlength{\cmidrulewidth}{0.3 pt}
\setlength{\lightrulewidth}{0.3 pt}
\setlength{\heavyrulewidth}{0.9 pt}
% Fix placement of figures & tables. This keeps latex from shoving big
% floats to the end of a document when they are somewhat big, which it will
% do even if you put [htb] as the argument.
\setcounter{topnumber}{2} % max num of floats at top of page
\setcounter{bottomnumber}{2} % max num of floats at bottom of page
\renewcommand\topfraction{1.0} % fraction that a top float can cover
\renewcommand\bottomfraction{1.0} % fraction a bottom float can cover
\renewcommand\textfraction{0.0} % >5% of a non-float page must be text
\renewcommand\floatpagefraction{0.9} % float page must be 95% full
% Spacing of floats.
\setlength{\intextsep}{20pt plus 4pt minus 0pt}
% Make floats that appear alone on a page appear at the top, rather than
% (as is the LaTeX default) appearing centered vertically on the page.
\setlength{\@fptop}{5pt}
% Margin adjustments. I've tried using vmargin.sty, but it interacts badly
% with page numbers at the bottom of the page, so I've resorted to hardcoding
% the dimensions like this.
\setlength{\marginparwidth}{0.77in}
\setlength{\marginparsep}{4pt}
\setlength{\oddsidemargin}{0 pt}
\setlength{\evensidemargin}{0 pt}
\setlength{\topmargin}{-0.5 in}
\setlength{\voffset}{0 in}
\setlength{\hoffset}{0 in}
\setlength{\textwidth}{6.5 in}
\setlength{\textheight}{8.95 in}
% Playing games with line spacing.
\newcommand{\normalbaselinestretch}{1.04}
\renewcommand{\baselinestretch}{\normalbaselinestretch}
% Set the table of contents depth
\setcounter{tocdepth}{3}
% Title page macros. Severly hacked from originals in LaTeX's article.cls.
\def\packageTitle#1{\title{#1}\gdef\@packageTitle{#1}}
\def\@packageTitle{\@empty}
\def\packageGeneralURL#1{\gdef\@packageGeneralURL{#1}}
\def\packageThisVersionURL#1{\gdef\@packageThisVersionURL{#1}}
\def\@packageThisVersionURL{\@empty}
\def\packageVersion#1{\gdef\@packageVersion{#1}}
\def\@packageVersion{\@empty}
\def\packageVersionDate#1{\gdef\@packageVersionDate{#1}}
\def\@packageVersionDate{\@empty}
\def\frontNotice#1{\gdef\@frontNotice{#1}}
\def\@puttitle{%
\ifx\@packageGeneralURL\undefined
\relax
\else
\vspace*{-1em}
{\large SBML Level 3 Package Specification}\\[2em]
\fi
\scalebox{1}[0.9]{%
\fcolorbox{black}{mediumgray}{%
\begin{minipage}{\textwidth - 7pt}%
\vspace*{6pt}%
\centering%
\textcolor{white}{\sffamily\bfseries\huge \ifx\@title\@empty\@packageTitle\else\@title\fi}
\vspace*{4pt}%
\end{minipage}}}}
\def\@putauthorinfo{%
\large
\renewcommand{\arraystretch}{0.95}%
{\begin{tabular}[t]{c}%
\@author
\end{tabular}}}
\def\maketableofcontents{%
\thispagestyle{plain}%
\if@notoc
\else
\begingroup
\small%
% Tighten spacing between lines within an entry.
% This assumes 10 pt font!
\setlength{\baselineskip}{10pt}%
% Now adjust inter-entry spacing.
\addtolength{\parskip}{-1.35 ex}%
\if@twocolumntoc
\setlength{\columnsep}{16pt}%
\begin{multicols}{2}
\fi
\tableofcontents%
\if@twocolumntoc
\end{multicols}
\fi
\normalsize%
\addtolength{\parskip}{1.45 ex}%
\endgroup
\clearpage
\fi%
\linenumbers}
% Need redefine \tableofcontents to counter effects of hacking \section below.
\renewcommand\tableofcontents{%
\@startsection{section}{0}{0pt}{-1.8ex \@plus -1ex \@minus -.2ex}%
{0.8ex}{\normalfont\Large\bfseries\sffamily}*% The star fakes a \section*
\contentsname%
\@mkboth{\MakeUppercase\contentsname}{\MakeUppercase\contentsname}%
\@starttoc{toc}%
}
\renewcommand\maketitle{\par
\begingroup
\renewcommand\thefootnote{\@fnsymbol\c@footnote}%
\def\@makefnmark{\rlap{\@textsuperscript{\normalfont\@thefnmark}}}%
\long\def\@makefntext##1{\parindent 1em\noindent
\hb@xt@1.8em{%
\hss\@textsuperscript{\normalfont\@thefnmark}}##1}%
\if@twocolumn
\ifnum \col@number=\@ne
\@maketitle
\else
\twocolumn[\@maketitle]%
\fi
\else
\global\@topnum\z@ % Prevents figures from going at top of page.
\@maketitle
\fi
\thispagestyle{empty}\@thanks
\endgroup
\setcounter{footnote}{0}%
\global\let\thanks\relax
\global\let\maketitle\relax
\global\let\@maketitle\relax
\global\let\@thanks\@empty
\global\let\@author\@empty
\global\let\@date\@empty
\global\let\@title\@empty
\global\let\@authoremail\@empty
\global\let\title\relax
\global\let\author\relax
\global\let\date\relax
\global\let\and\relax
}
\newcommand\maketitlepage{\par
\begingroup
\renewcommand\thefootnote{\@fnsymbol\c@footnote}%
\def\@makefnmark{\rlap{\@textsuperscript{\normalfont\@thefnmark}}}%
\long\def\@makefntext##1{\parindent 1em\noindent
\hb@xt@1.8em{%
\hss\@textsuperscript{\normalfont\@thefnmark}}##1}%
\vskip 2em%
\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{empty}\@thanks
\vfill
\centering%
\ifx\@frontNotice\undefined
\relax
\else
{\cornersize{0.25}\color{DarkRed}\ovalbox{\begin{varwidth}{0.9\textwidth}\centering\@frontNotice\end{varwidth}}}%
\fi
\vfill
\ifx\@packageGeneralURL\undefined
\relax
\else
The latest release, past releases, and other materials related to this specification are available at\\
{\small\url{\@packageGeneralURL}}\\[1em]
\emph{This} release of the specification is available at\\
{\small\url{\@packageThisVersionURL}}\\
\vspace*{2em}
\fi
\vfill
\centerline{\includegraphics[width=2in]{\SBMLbadge}}
\clearpage
\endgroup
\setcounter{footnote}{0}%
\global\let\thanks\relax
\global\let\maketitle\relax
\global\let\@maketitle\relax
\global\let\@thanks\@empty
\global\let\@author\@empty
\global\let\@date\@empty
\global\let\@title\@empty
\global\let\@authoremail\@empty
\global\let\title\relax
\global\let\author\relax
\global\let\date\relax
\global\let\and\relax
}
\def\@maketitle{%
\newpage
\null
\begin{center}%
\let \footnote \thanks
\@puttitle
\vskip 1.8em%
{\lineskip .5em%
\@putauthorinfo
}%
\vskip 2em%
{\large\fbox{\@packageVersion}}%
\vskip 1.5em%
{\large\@packageVersionDate}%
\end{center}%
\par%
\vskip 1.5em%
\ifpdf
\hypersetup{pdftitle={\@title}}
\fi%
}
% Including the logo on the front page. We switch which copy of the logo
% file we use, depending on various factors, and we switch which file format
% is used depending on the output we're producing.
\ifgrayscalespec
\newcommand{\@badgebasefile}{sbol-logo-gray}
\else
\newcommand{\@badgebasefile}{sbol-logo}
\fi
\ifpdf
% Request the JPG format specifically, because the resulting
% quality in the final output is best.
\newcommand{\SBMLbadge}{\@badgebasefile.jpg}%
\else%
\newcommand{\SBMLbadge}{\@badgebasefile.eps}%
\fi
% Graphics adjustments. The path setup is so that the \includegraphics
% in the @puttile definition can find the logo file no matter where the
% document is located (but obviously, it only works for certain path
% combinations -- it's a total hack).
\graphicspath{{./logos/}
{../tex/logos/}
{../project/tex/logos/}
{../../project/tex/logos/}
{../../../project/tex/logos/}
{../../../../project/tex/logos/}}
% Set the page footers.
% Must do this after setting the document title.
\fancyhf{}
\newcommand{\@footchpsection}{Section \nouppercase{\leftmark}}
\newcommand{\@footpage}{Page \thepage\ of \pageref*{LastPage}}
\renewcommand{\footrule}{}
\fancypagestyle{headerandfooter}{%
\renewcommand{\headrulewidth}{0.25pt}
\renewcommand{\headrule}{}
\lhead{}%
\rhead{\color{mediumgray}\small\textsf{Section \nouppercase{\rightmark}}}%
\cfoot{}%
\lfoot{\color{mediumgray}\small\textsf{\@footchpsection}}%
\rfoot{\color{mediumgray}\small\textsf{\@footpage}}%
}
\fancypagestyle{footeronly}{%
\renewcommand{\headrule}{}%
\lhead{}%
\rhead{}%
\lfoot{\color{mediumgray}\small\textsf{\@footchpsection}}%
\rfoot{\color{mediumgray}\small\textsf{\@footpage}}%
}
\fancypagestyle{plain}{%
\renewcommand{\headrule}{}%
\lhead{}%
\rhead{}%
\lfoot{}%
\rfoot{\color{mediumgray}\small\textsf{\@footpage}}%
}
\pagestyle{headerandfooter}
% Definition of paragraph style.
\setlength{\parindent}{0 pt} % Unindented paragraphs, separated ...
\setlength{\parskip}{1.3 ex} % ... by roughly one blank line.
\setlength{\partopsep}{-1ex plus 0.1ex minus -0.2ex}
\setlength{\itemsep}{-0.25ex plus 0.15ex}
% \topsep is supposed to affect list environments like itemize,
% but does nothing there. Instead, it affects environments like tabular.
\setlength{\topsep}{0.3ex plus 0.1ex minus -0.2ex}
\renewcommand{\labelitemi}{\raisebox{0.5pt}{\color{mediumgray}\footnotesize{$\blacksquare$}}}
\renewcommand{\labelitemii}{\raisebox{-1.5pt}{\color{mediumgray}\LARGE$\bullet$}}
\renewcommand{\labelitemiii}{\color{mediumgray}\tiny\DiamondSolid}
\renewcommand{\labelitemiv}{$\diamond$}
% Definition of section heading style.
\renewcommand{\section}{\@startsection%
{section}{1}{0pt \@plus 1ex}{-3.5ex \@plus -2ex \@minus -.2ex}%
{1.2ex}{\clearpage\thispagestyle{footeronly}%
\hspace*{-24.25pt}\color{sbmlgray}{\rule[1.8em]{6.84in}{0.6em}}\color{normaltextcolor}%
\hspace*{-6.84in}\color{sbmlgray}{\rule[-0.8em]{6.84in}{0.1em}}\color{normaltextcolor}%
\noindent\normalfont\LARGE\bfseries\sffamily\hspace*{-6.84in}}}
\renewcommand{\subsection}{\@startsection%
{subsection}{2}{0pt}{-1.25ex \@plus 2ex \@minus -.2ex}%
{0.1ex}{\Large\bfseries\sffamily}}
\renewcommand{\subsubsection}{\@startsection%
{subsubsection}{3}{0pt}{-1ex \@plus 2ex \@minus -.2ex}%
{0.4ex}{\large\bfseries\sffamily\slshape}}
\renewcommand{\paragraph}{\@startsection%
{paragraph}{4}{0pt}{-0.75ex \@plus 2ex \@minus -.2ex}%
{0.4ex}{\normalsize\bfseries\sffamily\slshape}}
% The References heading needs to be fixed up to account for shift
% we apply to section headings. These defs are modified from article.cls.
\bibliographystyle{apalike}
\renewenvironment{thebibliography}[1]%
{\section*{References}%
\pagestyle{plain}%
\addcontentsline{toc}{section}{\protect\numberline{\refname}}%
\list{\@biblabel{\@arabic\c@enumiv}}%
{\settowidth\labelwidth{\@biblabel{#1}}%
\leftmargin\labelwidth
\advance\leftmargin\labelsep
\@openbib@code
\usecounter{enumiv}%
\let\p@enumiv\@empty
\renewcommand\theenumiv{\@arabic\c@enumiv}}%
\sloppy
\clubpenalty4000
\@clubpenalty \clubpenalty
\widowpenalty4000%
\sfcode`\.\@m}
{\def\@noitemerr
{\@latex@warning{Empty `thebibliography' environment}}%
\endlist}
\newcommand{\sectionspecial}{\@startsection%
{section}{1}{0pt}{-1.8ex \@plus -1ex \@minus -.2ex}%
{0.8ex}{\hspace*{-41.1pt}\colorbox{sbmlgray}{\hspace*{6.99in}}\nopagebreak\\%
\hspace*{-20pt}\normalfont\Large\bfseries\sffamily}}
% The following is a modified version of the macro from article.cls.
% It adjusts the vertical spacing in TOC for section lines.
\renewcommand*\l@section[2]{%
\ifnum \c@tocdepth >\z@
\addpenalty\@secpenalty
\addvspace{0.2ex \@plus\p@}%
\setlength\@tempdima{1.5em}%
\begingroup
\parindent \z@ \rightskip \@pnumwidth
\parfillskip -\@pnumwidth
\leavevmode \bfseries\sffamily
\advance\leftskip\@tempdima
\hskip -\leftskip
#1\nobreak\hfil \nobreak\hb@xt@\@pnumwidth{\hss #2}\par
\endgroup
\fi}
\def\@dottedtocline#1#2#3#4#5{%
\ifnum #1>\c@tocdepth \else
\vskip \z@ \@plus.2\p@
{\if@twocolumntoc\else
\leftskip #2
\fi
\relax \rightskip \@tocrmarg \parfillskip -\rightskip
\if@twocolumntoc\else
\parindent #2
\fi
\relax\@afterindenttrue
\interlinepenalty\@M
\leavevmode
\@tempdima #3\relax
\advance\leftskip \@tempdima \null\nobreak\hskip -\leftskip
{\sffamily #4}\nobreak
{\color{mediumgray}
\leaders\hbox{$\m@th
\mkern \@dotsep mu\hbox{.}\mkern \@dotsep
mu$}\hfill
}\nobreak
\hb@xt@\@pnumwidth{\hfil\normalfont\sffamily #5}%
\par}%
\fi}
% The following is modified from natbib.sty, version 1999/05/28 7.0.
% This ensures that the References section gets a TOC entry.
\renewcommand{\bibsection}{%
\addcontentsline{toc}{section}{\protect\textbf{\textsf{\refname}}}%
\section*{\refname}}
% Redefine table & figure to use smaller font, sans serif,
% and to center contents by default.
\renewenvironment{table}[1][] {\@float{table}[#1]\small\sffamily\centering} {\end@float}
\renewenvironment{table*}[1][] {\@dblfloat{table}[#1]\small\sffamily\centering} {\end@dblfloat}
\renewenvironment{figure}[1][] {\@float{figure}[#1]\small\sffamily\centering} {\end@float}
\renewenvironment{figure*}[1][]{\@dblfloat{figure}[#1]\small\sffamily\centering}{\end@dblfloat}
% The following was ripped out of caption.sty, version 1.4b.
% Copyright (C) 1994-95 Harald Axel Sommerfeldt
% The first few lines set up the parameters for the layout created
% by this style file.
\newcommand{\captionsize}{\small}
\newcommand{\captionfont}{\captionsize\sffamily\slshape}
\newcommand{\captionlabelfont}{\captionsize\bfseries\slshape}
\setlength{\abovecaptionskip}{1em}
\newlength{\captionmargin}
\setlength{\captionmargin}{6ex}
\newsavebox{\as@captionbox}
\newlength{\as@captionwidth}
\newcommand{\as@normalcaption}[2]{%
#1 #2\par}
\let\as@caption\as@normalcaption
\newcommand{\as@centercaption}[2]{%
\parbox[t]{\as@captionwidth}{{\centering#1 #2\par}}}
\let\as@shortcaption\as@centercaption
\newcommand{\as@makecaption}[2]{%
\setlength{\leftskip}{\captionmargin}%
\setlength{\rightskip}{\captionmargin}%
\addtolength{\as@captionwidth}{-2\captionmargin}%
\renewcommand{\baselinestretch}{0.9}
\captionfont%
\sbox{\as@captionbox}{{\captionlabelfont #1:} #2}%
\ifdim \wd\as@captionbox >\as@captionwidth
\as@caption{{\captionlabelfont #1:}}{#2}%
\else%
\as@shortcaption{{\captionlabelfont #1:}}{#2}%
\fi}
\renewcommand{\@makecaption}[2]{%
\vskip\abovecaptionskip%
\setlength{\as@captionwidth}{\linewidth}%
\as@makecaption{#1}{#2}%
\vskip\belowcaptionskip}
\ifx\@makerotcaption\undefined
\else
% Adjustment for the "rotating" package.
\renewcommand{\@makerotcaption}[2]{%
\renewcommand{\baselinestretch}{0.9}
\captionfont%
\sbox{\as@captionbox}{{\captionlabelfont #1:} #2}%
\ifdim \wd\as@captionbox > .8\vsize
\rotatebox{90}{%
\setlength{\as@captionwidth}{.8\textheight}%
\begin{minipage}{\as@captionwidth}%
\as@caption{{\captionlabelfont #1:}}{#2}%
\end{minipage}}\par
\else%
\rotatebox{90}{\usebox{\as@captionbox}}%
\fi
\hspace{12pt}}
\fi
\ifx\floatc@plain\undefined
\else
\typeout{\space\space\space\space\space\space\space\space\space
`float' package detected}
\renewcommand\floatc@plain[2]{%
\setlength{\as@captionwidth}{\linewidth}%
\as@makecaption{#1}{#2}}
\ifx\as@ruled\undefined
\else
\renewcommand\floatc@ruled[2]{%
\setlength{\as@captionwidth}{\linewidth}%
\renewcommand{\baselinestretch}{0.9}
\captionfont%
\as@caption{{\captionlabelfont #1:}}{#2}}
\fi
\fi
%
% Additional new commands.
%
% Class and data type formatting macros.
\newcommand{\class}[1]{\figureFont{#1}} % only SBML UML classes
\newcommand{\abstractclass}[1]{\textsl{\figureFont{#1}}} % abstract classes
\newcommand{\primtype}[1]{\literalFont{#1}} % double, SId, SBOTerm, etc.
\newcommand{\primtypeNC}[1]{\literalFontNC{#1}} % same, but without coloring
\newcommand{\token}[1]{\literalFont{#1}} % everything else
\newcommand{\tokenNC}[1]{\literalFontNC{#1}} % everything else, no color
\newcommand{\val}[1]{``\token{#1}''} % a value in XML
\newcommand{\uri}[1]{``\token{#1}''}
% Macros used for defining validation rules.
% First, preliminary internal macros.
\newcommand{\vSymbol}{\textcolor{red}{$\Box\mkern-14mu\checkmark$}}
\newcommand{\vSymbolName}{checked box\xspace}
\newcommand{\cSymbol}{\textcolor{Goldenrod}{\scalefont{0.9}\ding{115}}}
\newcommand{\cSymbolName}{triangle\xspace}
\newcommand{\rSymbol}{\textcolor{blue}{$\medbullet$}}
\newcommand{\rSymbolName}{circle\xspace}
\newcommand{\mSymbol}{\textcolor{Green}{$\bigstar$}}
\newcommand{\mSymbolName}{star\xspace}
% Spacing adjustments when using the symbols inside regular 'description' env.
% Note: *not* used in \sbmlrule below.
\newcommand{\vsp}{\hspace*{4pt}}
\newcommand{\csp}{\hspace*{6.25pt}}
\newcommand{\rsp}{\hspace*{6.25pt}}
\newcommand{\msp}{\hspace*{4.9pt}}
% Now the actual user commands for validation rules.
\newcommand{\sbmlrule}[3]{\begin{enumerate}[labelwidth=8em,leftmargin=10em,align=left]
\item[\textbf{\textsf{#1}}~~#2] #3
\end{enumerate}}
\newcommand{\validRule}[2] {\sbmlrule{#1}{\vSymbol}{#2}}
\newcommand{\consistencyRule}[2]{\sbmlrule{#1}{\cSymbol}{#2}}
\newcommand{\modelingRule}[2] {\sbmlrule{#1}{\mSymbol}{#2}}
\newcommand{\completeRule}[2] {\sbmlrule{#1}{\rSymbol}{#2}}
% Code examples.
\newcommand{\code}[1]{\literalFont{#1}}
\newcommand{\codeNC}[1]{\literalFontNC{#1}}
\lstset{escapechar=|,%
language=XML,%
columns=fullflexible,%
keepspaces=true,%
backgroundcolor=\color{veryverylightgray},%
rulecolor=\color{sbmlgray},%
frame=single,%
numberstyle=\tiny\sffamily,%
basicstyle=\small\ttfamily\color{black},%
keywordstyle=\ttfamily,%
xleftmargin=3.5pt,%
xrightmargin=3.5pt,%
aboveskip=1\baselineskip,%
belowskip=0.4\baselineskip,%
commentstyle=\footnotesize\itshape\color{mediumgray},%
tabsize=2,%
captionpos=b}
\lstdefinestyle{XML}{%
language=XML}
\lstdefinestyle{bash}{%
language=bash}%
\newcommand{\examplespacing}{\renewcommand{\baselinestretch}{0.88}}
\lstnewenvironment{example}[1][]
{\lstset{#1}\examplespacing \csname lst@SetFirstLabel\endcsname}
{\regularspacing \csname lst@SaveFirstLabel\endcsname}
\newcommand{\exampleFile}[2][style=XML]{%
\lstset{#1}\examplespacing\lstinputlisting{#2}\regularspacing}
% Margin note commands.
% The \reversemarginpar is to put notes in the left margin.
\reversemarginpar % Want these be put on the left, not the right.
\newcommand{\notice}{\marginpar{\hspace*{34pt}\raisebox{-0.5ex}{\color{black}\Large\ding{43}}}}
\newcommand{\version}[1]{\marginpar{\hspace*{34pt}\raisebox{-3.0ex}{\color{blue}\small #1}}}
\newcommand{\warning}{\marginpar{\hspace*{34pt}{\color{red}\large\danger}}}
% Margin notes.
%
% Todonotes is nice and offers things like a list of notes, but it uses TikZ,
% and that's a heavy package to load every time. I got annoyed by how much
% it slowed down my latex runs that I created a simple note alternative
% instead. Here's the original todonotes version, for posterity:
%
% \RequirePackage[textsize=scriptsize]{todonotes}
%
% \if@draftspec
% \newcommand{\sbmlshownotes}{}
% \else
% \newcommand{\sbmlshownotes}{disable}
% \fi
%
% \newcommand{\draftnote}[1]{\todo[backgroundcolor=lightyellow,%
% bordercolor=lightgray,linecolor=mediumgray,\sbmlshownotes]{\textit{#1}}}
\newcommand{\draftnoteInternal}[1]{\mbox{}\marginpar{\hspace{0pt}\fcolorbox{Gold}{lightyellow}
{\scriptsize\begin{minipage}[t]{0.65in}\raggedright\textit{#1}\end{minipage}}}}
\if@draftspec
\newcommand{\draftnote}[1]{\draftnoteInternal{#1}}
\else
\newcommand{\draftnote}[1]{}
\fi
% Line numbered environments.
\newenvironment{larray}{%
\begin{linenomath}\setlength{\arraycolsep}{1.5pt}\begin{eqnarray}}%
{\end{eqnarray}\end{linenomath}\par\vspace*{-0.7em}}
\newenvironment{larray*}{%
\begin{linenomath}\setlength{\arraycolsep}{1.5pt}\begin{eqnarray*}}%
{\end{eqnarray*}\end{linenomath}\par\vspace*{-0.7em}}
% Cross-references.
%
% We load the varioref package and define a set of macros for referring to
% floats and sections in a consistent way, such that the entire reference
% ("Section X", "Figure Y", etc.) is made into a hyperlink -- not only "X"