minimap2 0.2.22.0 → 0.2.24.1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (101) hide show
  1. checksums.yaml +4 -4
  2. data/README.md +60 -76
  3. data/ext/Rakefile +55 -0
  4. data/ext/cmappy/cmappy.c +129 -0
  5. data/ext/cmappy/cmappy.h +44 -0
  6. data/ext/minimap2/FAQ.md +46 -0
  7. data/ext/minimap2/LICENSE.txt +24 -0
  8. data/ext/minimap2/MANIFEST.in +10 -0
  9. data/ext/minimap2/Makefile +132 -0
  10. data/ext/minimap2/Makefile.simde +97 -0
  11. data/ext/minimap2/NEWS.md +821 -0
  12. data/ext/minimap2/README.md +403 -0
  13. data/ext/minimap2/align.c +1020 -0
  14. data/ext/minimap2/bseq.c +169 -0
  15. data/ext/minimap2/bseq.h +64 -0
  16. data/ext/minimap2/code_of_conduct.md +30 -0
  17. data/ext/minimap2/cookbook.md +243 -0
  18. data/ext/minimap2/esterr.c +64 -0
  19. data/ext/minimap2/example.c +63 -0
  20. data/ext/minimap2/format.c +559 -0
  21. data/ext/minimap2/hit.c +466 -0
  22. data/ext/minimap2/index.c +775 -0
  23. data/ext/minimap2/kalloc.c +205 -0
  24. data/ext/minimap2/kalloc.h +76 -0
  25. data/ext/minimap2/kdq.h +132 -0
  26. data/ext/minimap2/ketopt.h +120 -0
  27. data/ext/minimap2/khash.h +615 -0
  28. data/ext/minimap2/krmq.h +474 -0
  29. data/ext/minimap2/kseq.h +256 -0
  30. data/ext/minimap2/ksort.h +153 -0
  31. data/ext/minimap2/ksw2.h +184 -0
  32. data/ext/minimap2/ksw2_dispatch.c +96 -0
  33. data/ext/minimap2/ksw2_extd2_sse.c +402 -0
  34. data/ext/minimap2/ksw2_exts2_sse.c +416 -0
  35. data/ext/minimap2/ksw2_extz2_sse.c +313 -0
  36. data/ext/minimap2/ksw2_ll_sse.c +152 -0
  37. data/ext/minimap2/kthread.c +159 -0
  38. data/ext/minimap2/kthread.h +15 -0
  39. data/ext/minimap2/kvec.h +105 -0
  40. data/ext/minimap2/lchain.c +369 -0
  41. data/ext/minimap2/main.c +459 -0
  42. data/ext/minimap2/map.c +714 -0
  43. data/ext/minimap2/minimap.h +410 -0
  44. data/ext/minimap2/minimap2.1 +725 -0
  45. data/ext/minimap2/misc/README.md +179 -0
  46. data/ext/minimap2/misc/mmphase.js +335 -0
  47. data/ext/minimap2/misc/paftools.js +3149 -0
  48. data/ext/minimap2/misc.c +162 -0
  49. data/ext/minimap2/mmpriv.h +132 -0
  50. data/ext/minimap2/options.c +234 -0
  51. data/ext/minimap2/pe.c +177 -0
  52. data/ext/minimap2/python/README.rst +196 -0
  53. data/ext/minimap2/python/cmappy.h +152 -0
  54. data/ext/minimap2/python/cmappy.pxd +153 -0
  55. data/ext/minimap2/python/mappy.pyx +273 -0
  56. data/ext/minimap2/python/minimap2.py +39 -0
  57. data/ext/minimap2/sdust.c +213 -0
  58. data/ext/minimap2/sdust.h +25 -0
  59. data/ext/minimap2/seed.c +131 -0
  60. data/ext/minimap2/setup.py +55 -0
  61. data/ext/minimap2/sketch.c +143 -0
  62. data/ext/minimap2/splitidx.c +84 -0
  63. data/ext/minimap2/sse2neon/emmintrin.h +1689 -0
  64. data/ext/minimap2/test/MT-human.fa +278 -0
  65. data/ext/minimap2/test/MT-orang.fa +276 -0
  66. data/ext/minimap2/test/q-inv.fa +4 -0
  67. data/ext/minimap2/test/q2.fa +2 -0
  68. data/ext/minimap2/test/t-inv.fa +127 -0
  69. data/ext/minimap2/test/t2.fa +2 -0
  70. data/ext/minimap2/tex/Makefile +21 -0
  71. data/ext/minimap2/tex/bioinfo.cls +930 -0
  72. data/ext/minimap2/tex/blasr-mc.eval +17 -0
  73. data/ext/minimap2/tex/bowtie2-s3.sam.eval +28 -0
  74. data/ext/minimap2/tex/bwa-s3.sam.eval +52 -0
  75. data/ext/minimap2/tex/bwa.eval +55 -0
  76. data/ext/minimap2/tex/eval2roc.pl +33 -0
  77. data/ext/minimap2/tex/graphmap.eval +4 -0
  78. data/ext/minimap2/tex/hs38-simu.sh +10 -0
  79. data/ext/minimap2/tex/minialign.eval +49 -0
  80. data/ext/minimap2/tex/minimap2.bib +460 -0
  81. data/ext/minimap2/tex/minimap2.tex +724 -0
  82. data/ext/minimap2/tex/mm2-s3.sam.eval +62 -0
  83. data/ext/minimap2/tex/mm2-update.tex +240 -0
  84. data/ext/minimap2/tex/mm2.approx.eval +12 -0
  85. data/ext/minimap2/tex/mm2.eval +13 -0
  86. data/ext/minimap2/tex/natbib.bst +1288 -0
  87. data/ext/minimap2/tex/natbib.sty +803 -0
  88. data/ext/minimap2/tex/ngmlr.eval +38 -0
  89. data/ext/minimap2/tex/roc.gp +60 -0
  90. data/ext/minimap2/tex/snap-s3.sam.eval +62 -0
  91. data/ext/minimap2.patch +19 -0
  92. data/lib/minimap2/aligner.rb +4 -4
  93. data/lib/minimap2/alignment.rb +11 -11
  94. data/lib/minimap2/ffi/constants.rb +20 -16
  95. data/lib/minimap2/ffi/functions.rb +5 -0
  96. data/lib/minimap2/ffi.rb +4 -5
  97. data/lib/minimap2/version.rb +2 -2
  98. data/lib/minimap2.rb +51 -15
  99. metadata +97 -79
  100. data/lib/minimap2/ffi_helper.rb +0 -53
  101. data/vendor/libminimap2.so +0 -0
@@ -0,0 +1,930 @@
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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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+
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+ % Are we printing crop marks?
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+ \newif\if@cropmarkson \@cropmarksontrue
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+
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+ \NeedsTeXFormat{LaTeX2e}[2001/06/01]
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+ \ProvidesClass{\classname}[\lastmodifieddate\space\versionnumber]
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+
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+ \setlength{\paperheight}{11truein}
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+ \setlength{\paperwidth}{8.5truein}
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+
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+ \newif\if@final
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+
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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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+
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+ \ExecuteOptions{a4paper,nocrop,centre,info}
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+
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+ \ProcessOptions
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+
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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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+ \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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+
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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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+ \itemsep \parsep
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+ \def\scriptsize{\@setfontsize\scriptsize{7pt}{9pt}}
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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\textwidth{42pc} % text measure excluding margins
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+ \addtolength\textheight{\topskip} % including the first
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+ % line on the page
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+
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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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+
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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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+ \addtolength\@tempdima{-\textwidth}
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+ \addtolength\@tempdima{-4.5pc}
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+
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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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+ \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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+ \renewcommand\floatpagefraction{.94}
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+
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+
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+ % Page styles
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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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+
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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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+
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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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+ \gdef\thelastpage{%
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+ \csname @#1\endcsname \@lastpage}%
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+ }
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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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+
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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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+ %
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+ % Sectional units
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+ %
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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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+
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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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+
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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.}
347
+ \newcommand\tablename{Table}
348
+
349
+ % Clearemptydoublepage should really clear the running heads too
350
+ \newcommand{\clearemptydoublepage}{\newpage{\pagestyle{empty}\cleardoublepage}}
351
+
352
+ % Frontmatter, mainmatter and backmatter
353
+
354
+ \newif\if@mainmatter \@mainmattertrue
355
+
356
+ \newcommand\frontmatter{%
357
+ \clearpage
358
+ \@mainmatterfalse
359
+ \pagenumbering{roman}}
360
+
361
+ \newcommand\mainmatter{%
362
+ \clearpage
363
+ \@mainmattertrue
364
+ \pagenumbering{arabic}}
365
+
366
+ \newcommand\backmatter{%
367
+ \clearpage
368
+ \@mainmatterfalse}
369
+
370
+ %%%%%%%%%%%%%%%%%%%%%%%%%%%%%% TITLE %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
371
+ \newlength{\dropfromtop}
372
+ \setlength{\dropfromtop}{\z@}
373
+
374
+ % Application Notes
375
+ \newif\if@appnotes
376
+ \newcommand{\application}{%
377
+ % \setlength{\dropfromtop}{-2.25pc}%
378
+ \global\@appnotestrue}
379
+
380
+ \long\def\title{\@ifnextchar[{\short@title}{\@@title}}
381
+ \def\short@title[#1]{\titlemark{#1}\@@@title}
382
+ \def\@@title#1{\authormark{#1}\@@@title{#1}}
383
+ \long\def\@@@title#1{\gdef\@title{#1}}
384
+
385
+ \long\def\author{\@ifnextchar[{\short@uthor}{\@uthor}}
386
+ \def\short@uthor[#1]{\authormark{#1}\@@author}
387
+ \def\@uthor#1{\authormark{#1}\@@author{#1}}
388
+ \long\def\@@author#1{\gdef\@author{#1}}
389
+
390
+ \def\vol#1{\global\def\@vol{#1}}
391
+ \def\issue#1{\global\def\@issue{#1}}
392
+ \def\address#1{\global\def\@issue{#1}}
393
+ \def\history#1{\global\def\@history{#1}}
394
+ \def\editor#1{\global\def\@editor{#1}}
395
+ \def\pubyear#1{\global\def\@pubyear{#1}}
396
+ \def\copyrightyear#1{\global\def\@copyrightyear{#1}}
397
+ \def\address#1{\global\def\@address{#1}}
398
+ \def\DOI#1{\global\def\@DOI{#1}}
399
+
400
+ \definecolor{gray}{cmyk}{0, 0, 0, 0.15}
401
+ \newlength{\extraspace}
402
+ \setlength{\extraspace}{\z@}
403
+
404
+ \newcommand\maketitle{\par
405
+ \begingroup
406
+ \renewcommand\thefootnote{\@fnsymbol\c@footnote}%
407
+ \def\@makefnmark{\rlap{\@textsuperscript{\normalfont\@thefnmark}}}%
408
+ \long\def\@makefntext##1{\parindent 3mm\noindent
409
+ % \@textsuperscript{\normalfont\@thefnmark}\raggedright##1}%
410
+ \@textsuperscript{\normalfont\@thefnmark}##1}%
411
+ \if@twocolumn
412
+ \ifnum \col@number=\@ne
413
+ \@maketitle
414
+ \else
415
+ \twocolumn[\@maketitle]%
416
+ \fi
417
+ \else
418
+ \newpage
419
+ \global\@topnum\z@ % Prevents figures from going at top of page.
420
+ \@maketitle
421
+ \fi
422
+ \thispagestyle{opening}\@thanks
423
+ \endgroup
424
+ \setcounter{footnote}{0}%
425
+ \global\let\thanks\relax
426
+ \global\let\maketitle\relax
427
+ \global\let\@maketitle\relax
428
+ \global\let\@address\@empty
429
+ \global\let\@history\@empty
430
+ \global\let\@editor\@empty
431
+ \global\let\@thanks\@empty
432
+ \global\let\@author\@empty
433
+ \global\let\@date\@empty
434
+ \global\let\@title\@empty
435
+ \global\let\@pubyear\@empty
436
+ \global\let\address\relax
437
+ \global\let\history\relax
438
+ \global\let\editor\relax
439
+ \global\let\title\relax
440
+ \global\let\author\relax
441
+ \global\let\date\relax
442
+ \global\let\pubyear\relax
443
+ \global\let\@copyrightline\@empty
444
+ \global\let\and\relax
445
+ \@afterindentfalse\@afterheading
446
+ }
447
+
448
+ \newlength{\aboveskipchk}%for checking oddpage or evenpage top skip
449
+ \setlength{\aboveskipchk}{\z@}%
450
+
451
+ \def\@maketitle{%
452
+ \let\footnote\thanks
453
+ \clearemptydoublepage
454
+ \checkoddpage\ifcpoddpage\setlength{\aboveskipchk}{-3pc}\else\setlength{\aboveskipchk}{-5pc}\fi%for checking oddpage or evenpage top skip%%
455
+ \vspace*{\aboveskipchk}%
456
+ \vspace{\dropfromtop}%
457
+ \hbox to \textwidth{%
458
+ {\helvetica\itshape\bfseries\fontsize{19}{12}\selectfont {\color{gray}TECHNICAL REPORT}
459
+ \hfil
460
+ \if@appnotes APPLICATIONS NOTE\hfil\fi
461
+ }%
462
+ \enskip \parbox[b]{11.3pc}{%
463
+ \helvetica
464
+ \flushright\fontsize{8}{10}\fontshape{it}\selectfont
465
+ \hfill
466
+ }}
467
+ \rule{\textwidth}{1\p@}\par%
468
+ \helvetica
469
+ \hbox to \textwidth{%
470
+ \parbox[t]{41pc}{%
471
+ \vspace*{1sp}
472
+ {\helveticabold\fontsize{16}{21}\selectfont\raggedright \@title \par}%
473
+ \vspace{4.5\p@}
474
+ {\authoraffliate\fontsize{11}{13}\selectfont\raggedright \@author \par}%
475
+ \vspace{4\p@}
476
+ {\authoraffliate\fontsize{9}{11}\selectfont\raggedright \@address \par}%
477
+ \vspace{4\p@}
478
+ %{\helvetica\fontsize{8}{10}\selectfont\raggedright \@history \par}
479
+ %\vspace{24\p@}
480
+ %{\helvetica\fontsize{10}{12}\selectfont\raggedright \@editor \par}
481
+ %\vspace{20\p@}
482
+ }%
483
+ }
484
+ \vspace{4.5\p@}%
485
+ \rule{\textwidth}{1\p@}%
486
+ \vspace{12\p@ plus 6\p@ minus 6\p@}%
487
+ \vspace{\extraspace}
488
+ }
489
+ %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
490
+
491
+ %%%%%%%%%%%%%%%%%%%%%%%%%%%% Abstract %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
492
+ \newcommand{\absection}[1]{%
493
+ \par\noindent{\bfseries #1}\space\ignorespaces}
494
+
495
+ \newenvironment{abstract}{%
496
+ \begingroup
497
+ \let\section\absection
498
+ \fontfamily{\sfdefault}\fontsize{8}{11}\sffamily\selectfont
499
+ {\fontseries{b}\selectfont ABSTRACT}\par}
500
+ {\endgroup\bigskip\@afterheading\@afterindentfalse\vskip 12pt plus 3pt minus 1pt}
501
+
502
+ % Section macros
503
+
504
+ % Lowest level heading that takes a number by default
505
+ \setcounter{secnumdepth}{3}
506
+
507
+ \renewcommand{\@seccntformat}[1]{\csname the#1\endcsname\quad}
508
+
509
+ \def\section{%
510
+ \@startsection{section}{1}{\z@}
511
+ {-22\p@ plus -3\p@}{3\p@}
512
+ {\reset@font\raggedright\helveticabold\fontsize{10}{12}\selectfont\MakeUppercase}}
513
+
514
+ \def\subsection{%
515
+ \@startsection{subsection}{2}{\z@}
516
+ {-11\p@ plus -2\p@}{3\p@}
517
+ {\reset@font\raggedright\mathversion{bold}\fontseries{b}\fontsize{10}{12}\selectfont}}
518
+
519
+ \def\subsubsection{%
520
+ \@startsection{subsubsection}{3}{\z@}
521
+ %{-11\p@ plus -1\p@}{-1em}
522
+ {-11\p@ plus -1\p@}{0.001em}
523
+ {\reset@font\normalfont\normalsize\itshape}}
524
+
525
+ \def\textcolon{\text{\rm :}}
526
+
527
+ \def\paragraph{%
528
+ \@startsection{paragraph}{4}{\z@}
529
+ {-6\p@}
530
+ {-.4em}
531
+ {\reset@font\itshape}}
532
+
533
+ % ********************
534
+ % Figures and tables *
535
+ % ********************
536
+
537
+ % Table and array parameters
538
+ \setlength\arraycolsep{.5em}
539
+ \setlength\tabcolsep{.5em}
540
+ \setlength\arrayrulewidth{.5pt}
541
+ \setlength\doublerulesep{2.5pt}
542
+ \setlength\extrarowheight{\z@}
543
+ \renewcommand\arraystretch{1}
544
+
545
+ \newlength{\abovecaptionskip}
546
+ \newlength{\belowcaptionskip}
547
+ \setlength{\abovecaptionskip}{13pt}
548
+ \setlength{\belowcaptionskip}{10.5pt}
549
+
550
+ \long\def\@makecaption#1#2{\vspace{\abovecaptionskip}%
551
+ \begingroup
552
+ \footnotesize
553
+ \textbf{#1.}\enskip{#2}\par
554
+ \endgroup}
555
+
556
+ \long\def\@tablecaption#1#2{%
557
+ \begingroup
558
+ \footnotesize
559
+ \textbf{#1.}\enskip{#2\strut\par}
560
+ \endgroup\vspace{\belowcaptionskip}}
561
+
562
+ % Table rules
563
+ \def\toprule{\noalign{\ifnum0=`}\fi\hrule \@height 0.5pt \hrule \@height 6pt \@width 0pt \futurelet
564
+ \@tempa\@xhline}
565
+ \def\midrule{\noalign{\ifnum0=`}\fi \hrule \@height 6.75pt \@width 0pt \hrule \@height 0.5pt
566
+ \hrule \@height 6pt \@width 0pt \futurelet \@tempa\@xhline}
567
+ \def\botrule{\noalign{\ifnum0=`}\fi \hrule \@height 5.75pt \@width 0pt \hrule \@height 0.5pt \futurelet
568
+ \@tempa\@xhline}
569
+ \def\hrulefill{\leavevmode\leaders\hrule height .5pt\hfill\kern\z@}
570
+
571
+ \def\thefigure{\@arabic\c@figure}
572
+ \def\fps@figure{tbp}
573
+ \def\ftype@figure{1}
574
+ \def\ext@figure{lof}
575
+ \def\fnum@figure{\figurename~\thefigure}
576
+ \def\figure{\@float{figure}}
577
+ \let\endfigure\end@float
578
+ \@namedef{figure*}{\@dblfloat{figure}}
579
+ \@namedef{endfigure*}{\end@dblfloat}
580
+ \def\thetable{\@arabic\c@table}
581
+ \def\fps@table{tbp}
582
+ \def\ftype@table{2}
583
+ \def\ext@table{lot}
584
+ \def\fnum@table{Table~\thetable}
585
+ \def\table{\let\@makecaption\@tablecaption\let\source\tablesource\@float{table}}
586
+ \def\endtable{\end@float}
587
+ \@namedef{table*}{\let\@makecaption\@tablecaption\@dblfloat{table}}
588
+ \@namedef{endtable*}{\end@dblfloat}
589
+
590
+ \newif\if@rotate \@rotatefalse
591
+ \newif\if@rotatecenter \@rotatecenterfalse
592
+ \def\rotatecenter{\global\@rotatecentertrue}
593
+ \def\rotateendcenter{\global\@rotatecenterfalse}
594
+ \def\rotate{\global\@rotatetrue}
595
+ \def\endrotate{\global\@rotatefalse}
596
+ \newdimen\rotdimen
597
+ \def\rotstart#1{\special{ps: gsave currentpoint currentpoint translate
598
+ #1 neg exch neg exch translate}}
599
+ \def\rotfinish{\special{ps: currentpoint grestore moveto}}
600
+ \def\rotl#1{\rotdimen=\ht#1\advance\rotdimen by \dp#1
601
+ \hbox to \rotdimen{\vbox to\wd#1{\vskip \wd#1
602
+ \rotstart{270 rotate}\box #1\vss}\hss}\rotfinish}
603
+ \def\rotr#1{\rotdimen=\ht #1\advance\rotdimen by \dp#1
604
+ \hbox to \rotdimen{\vbox to \wd#1{\vskip \wd#1
605
+ \rotstart{90 rotate}\box #1\vss}\hss}\rotfinish}
606
+
607
+ \newdimen\tempdime
608
+ \newbox\temptbox
609
+
610
+ % From ifmtarg.sty
611
+ % Copyright Peter Wilson and Donald Arseneau, 2000
612
+ \begingroup
613
+ \catcode`\Q=3
614
+ \long\gdef\@ifmtarg#1{\@xifmtarg#1QQ\@secondoftwo\@firstoftwo\@nil}
615
+ \long\gdef\@xifmtarg#1#2Q#3#4#5\@nil{#4}
616
+ \long\gdef\@ifnotmtarg#1{\@xifmtarg#1QQ\@firstofone\@gobble\@nil}
617
+ \endgroup
618
+
619
+ \def\tablesize{\@setfontsize\tablesize{8\p@}{10\p@}}
620
+
621
+ \newenvironment{processtable}[3]{\setbox\temptbox=\hbox{{\tablesize #2}}%
622
+ \tempdime\wd\temptbox\@processtable{#1}{#2}{#3}{\tempdime}}
623
+ {\relax}
624
+
625
+ \newcommand{\@processtable}[4]{%
626
+ \if@rotate
627
+ \setbox4=\vbox to \hsize{\vss\hbox to \textheight{%
628
+ \begin{minipage}{#4}%
629
+ \@ifmtarg{#1}{}{\caption{#1}}{\tablesize #2}%
630
+ \vskip7\p@\noindent
631
+ \parbox{#4}{\fontsize{7}{9}\selectfont #3\par}%
632
+ \end{minipage}}\vss}%
633
+ \rotr{4}
634
+ \else
635
+ \hbox to \hsize{\hss\begin{minipage}[t]{#4}%
636
+ \vskip2.9pt
637
+ \@ifmtarg{#1}{}{\caption{#1}}{\tablesize #2}%
638
+ \vskip6\p@\noindent
639
+ \parbox{#4}{\fontsize{7}{9}\selectfont #3\par}%
640
+ \end{minipage}\hss}\fi}%
641
+
642
+ \newcolumntype{P}[1]{>{\raggedright\let\\\@arraycr\hangindent1em}p{#1}}
643
+
644
+ % ******************************
645
+ % List numbering and lettering *
646
+ % ******************************
647
+ \def\labelenumi{{\rm\arabic{enumi}.}}
648
+ \def\theenumi{\arabic{enumi}}
649
+ \def\labelenumii{{\rm\alph{enumii}.}}
650
+ \def\theenumii{\alph{enumii}}
651
+ \def\p@enumii{\theenumi}
652
+ \def\labelenumiii{{\rm(\arabic{enumiii})}}
653
+ \def\theenumiii{\roman{enumiii}}
654
+ \def\p@enumiii{\theenumi(\theenumii)}
655
+ \def\labelenumiv{{\rm(\arabic{enumiv})}}
656
+ \def\theenumiv{\Alph{enumiv}}
657
+ \def\p@enumiv{\p@enumiii\theenumiii}
658
+ \def\labelitemi{{\small$\bullet$}}
659
+ \def\labelitemii{{\small$\bullet$}}
660
+ \def\labelitemiii{{\small$\bullet$}}
661
+ \def\labelitemiv{{\small$\bullet$}}
662
+
663
+ \def\@listI{\leftmargin\leftmargini \topsep\medskipamount}
664
+ \let\@listi\@listI
665
+ \@listi
666
+ \def\@listii{\topsep\z@\leftmargin\leftmarginii}
667
+ \def\@listiii{\leftmargin\leftmarginiii \topsep\z@}
668
+ \def\@listiv{\leftmargin\leftmarginiv \topsep\z@}
669
+ \def\@listv{\leftmargin\leftmarginv \topsep\z@}
670
+ \def\@listvi{\leftmargin\leftmarginvi \topsep\z@}
671
+
672
+ \setlength{\leftmargini}{3mm}
673
+ \setlength{\leftmarginii}{\z@}
674
+ \setlength{\leftmarginiii}{\z@}
675
+ \setlength{\leftmarginiv}{\z@}
676
+
677
+ % Changes to the list parameters for enumerate
678
+ \def\enumargs{%
679
+ \partopsep \z@
680
+ \itemsep 3\p@
681
+ \parsep \z@
682
+ \labelsep 0.5em
683
+ \listparindent \parindent
684
+ \itemindent \z@
685
+ \topsep 11\p@
686
+ }
687
+
688
+ \def\enumerate{%
689
+ \@ifnextchar[{\@numerate}{\@numerate[0]}}
690
+
691
+ \def\@numerate[#1]{%
692
+ \ifnum \@enumdepth >3 \@toodeep\else
693
+ \advance\@enumdepth \@ne
694
+ \edef\@enumctr{enum\romannumeral\the\@enumdepth}
695
+ \list{\csname label\@enumctr\endcsname}{%
696
+ \enumargs
697
+ \setlength{\leftmargin}{\csname leftmargin\romannumeral\the\@enumdepth\endcsname}
698
+ \usecounter{\@enumctr}
699
+ \settowidth\labelwidth{#1}
700
+ \addtolength{\leftmargin}{\labelwidth}
701
+ \addtolength{\leftmargin}{\labelsep}
702
+ \def\makelabel##1{\hss \llap{##1}}}%
703
+ \fi
704
+ }
705
+ \let\endenumerate\endlist
706
+
707
+ % Changes to the list parameters for itemize
708
+ \def\itemargs{%
709
+ \partopsep \z@
710
+ \itemsep 3\p@
711
+ \parsep \z@
712
+ \labelsep 0.5em
713
+ \rightmargin \z@
714
+ \listparindent \parindent
715
+ \itemindent \z@
716
+ \topsep11\p@
717
+ }
718
+
719
+ \def\itemize{%
720
+ \@ifnextchar[{\@itemize}{\@itemize[$\bullet$]}}
721
+
722
+ \def\@itemize[#1]{%
723
+ \ifnum \@itemdepth >3 \@toodeep\else
724
+ \advance\@itemdepth \@ne
725
+ \edef\@itemctr{item\romannumeral\the\@itemdepth}
726
+ \list{\csname label\@itemctr\endcsname}{%
727
+ \itemargs
728
+ \setlength{\leftmargin}{\csname leftmargin\romannumeral\the\@itemdepth\endcsname}
729
+ \settowidth\labelwidth{#1}
730
+ \addtolength{\leftmargin}{\labelwidth}
731
+ \addtolength{\leftmargin}{\labelsep}
732
+ \def\makelabel##1{\hss \llap{##1}}}%
733
+ \fi
734
+ }
735
+ \let\enditemize\endlist
736
+
737
+ \newenvironment{unlist}{%
738
+ \begin{list}{}%
739
+ {\setlength{\labelwidth}{\z@}%
740
+ \setlength{\labelsep}{\z@}%
741
+ \setlength{\topsep}{\medskipamount}%
742
+ \setlength{\itemsep}{3\p@}%
743
+ \setlength{\leftmargin}{2em}%
744
+ \setlength{\itemindent}{-2em}}}
745
+ {\end{list}}
746
+
747
+
748
+ % ***********************
749
+ % Quotes and Quotations *
750
+ % ***********************
751
+ \def\quotation{\par\begin{list}{}{
752
+ \setlength{\topsep}{\medskipamount}
753
+ \setlength{\leftmargin}{2em}%
754
+ \setlength{\rightmargin}{\z@}%
755
+ \setlength\labelwidth{0pt}%
756
+ \setlength\labelsep{0pt}%
757
+ \listparindent\parindent}%
758
+ \item[]}
759
+ \def\endquotation{\end{list}}
760
+ \let\quote\quotation
761
+ \let\endquote\endquotation
762
+
763
+ \skip\@mpfootins = \skip\footins
764
+ \fboxsep=6\p@
765
+ \fboxrule=1\p@
766
+
767
+ % *******************
768
+ % Table of contents *
769
+ % *******************
770
+ \newcommand\@pnumwidth{4em}
771
+ \newcommand\@tocrmarg{2.55em plus 1fil}
772
+ \newcommand\@dotsep{1000}
773
+ \setcounter{tocdepth}{4}
774
+
775
+ \def\numberline#1{\hbox to \@tempdima{{#1}}}
776
+
777
+ \def\@authortocline#1#2#3#4#5{%
778
+ \vskip 1.5\p@
779
+ \ifnum #1>\c@tocdepth \else
780
+ {\leftskip #2\relax \rightskip \@tocrmarg \parfillskip -\rightskip
781
+ \parindent #2\relax\@afterindenttrue
782
+ \interlinepenalty\@M
783
+ \leavevmode
784
+ \@tempdima #3\relax
785
+ \advance\leftskip \@tempdima \null\nobreak\hskip -\leftskip
786
+ {\itshape #4}\nobreak
787
+ \leaders\hbox{$\m@th
788
+ \mkern \@dotsep mu\hbox{.}\mkern \@dotsep
789
+ mu$}\hfill
790
+ \nobreak
791
+ \hb@xt@\@pnumwidth{\hfil}%
792
+ \par}%
793
+ \fi}
794
+
795
+ \newcommand*\l@author{\@authortocline{2}{0pt}{30pt}}
796
+ \newcommand*\l@section{\@dottedtocline{3}{11pt}{20pt}}
797
+ \newcommand*\l@subsection{\@dottedtocline{4}{31pt}{29pt}}
798
+ \newcommand*\l@subsubsection[2]{}
799
+
800
+
801
+
802
+ % ***********
803
+ % Footnotes *
804
+ % ***********
805
+
806
+ \def\footnoterule{\noindent\rule{\columnwidth}{0.5pt}}
807
+ \def\@makefnmark{\@textsuperscript{\normalfont\@thefnmark}}%
808
+ \newcommand\@makefntext[1]{\noindent{\@makefnmark}\enskip#1}
809
+
810
+ % ***********
811
+ % References *
812
+ % ***********
813
+
814
+ \providecommand{\newblock}{}
815
+ \newenvironment{thebibliography}{%
816
+ \section{\bibname}%
817
+ \begingroup
818
+ \small
819
+ \begin{list}{}{%
820
+ \setlength{\topsep}{\z@}%
821
+ \setlength{\labelsep}{\z@}%
822
+ \settowidth{\labelwidth}{\z@}%
823
+ \setlength{\leftmargin}{4mm}%
824
+ \setlength{\itemindent}{-4mm}}\small}
825
+ {\end{list}\endgroup}
826
+
827
+ \RequirePackage{natbib}
828
+
829
+ % **********
830
+ % Appendix *
831
+ % **********
832
+ \newif\ifappend % Are we in the Appendix?
833
+ \def\appendix{\par
834
+ \setcounter{section}{0}
835
+ \setcounter{subsection}{0}
836
+ \appendtrue
837
+ }
838
+
839
+ %Math parameters
840
+
841
+ \setlength{\jot}{5\p@}
842
+ \mathchardef\@m=1500 % adapted value
843
+
844
+ \def\frenchspacing{\sfcode`\.\@m \sfcode`\?\@m \sfcode`\!\@m
845
+ \sfcode`\:\@m \sfcode`\;\@m \sfcode`\,\@m}
846
+
847
+ % Theorems
848
+ \def\th@plain{%
849
+ %% \let\thm@indent\noindent % no indent
850
+ \thm@headfont{\quad\scshape}% heading font is bold
851
+ \thm@notefont{\upshape\mdseries}% same as heading font
852
+ \thm@headpunct{.}% no period after heading
853
+ \thm@headsep 5\p@ plus\p@ minus\p@\relax
854
+ %% \let\thm@swap\@gobble
855
+ %% \thm@preskip\topsep
856
+ %% \thm@postskip\theorempreskipamount
857
+ \itshape % body font
858
+ }
859
+
860
+ \vbadness=9999
861
+ \tolerance=9999
862
+ \doublehyphendemerits=10000
863
+ \doublehyphendemerits 640000 % corresponds to badness 800
864
+ \finalhyphendemerits 1000000 % corresponds to badness 1000
865
+
866
+ \flushbottom
867
+ \frenchspacing
868
+ \ps@headings
869
+ \twocolumn
870
+
871
+ % Screen PDF compatability
872
+ \newcommand{\medline}[1]{%
873
+ \unskip\unskip\ignorespaces}
874
+
875
+
876
+ %%%%for smaller size text
877
+ \newenvironment{methods}{%
878
+ \begingroup
879
+ \def\section{%
880
+ \@startsection{section}{1}{\z@}
881
+ {-24\p@ plus -3\p@}{4\p@}
882
+ {\reset@font\raggedright\helveticabold\fontsize{10}{12}\selectfont\MakeUppercase}}
883
+ \def\subsection{%
884
+ \@startsection{subsection}{2}{\z@}
885
+ {-5\p@ plus -2\p@}{4\p@}
886
+ {\reset@font\raggedright\mathversion{bold}\fontseries{b}\fontsize{10}{12}\selectfont}}
887
+ \def\subsubsection{%
888
+ \@startsection{subsubsection}{3}{\z@}
889
+ % {-6\p@ plus -1\p@}{-1em}
890
+ {-6\p@ plus -1\p@}{0.001em}
891
+ {\reset@font\normalfont\normalsize\itshape}}
892
+ \footnotesize
893
+ \par}
894
+ {\par\endgroup\bigskip\@afterheading\@afterindentfalse}
895
+
896
+
897
+
898
+ \graphicspath{{g:/artwork/oup/bioinfo/}}
899
+
900
+ \language=2
901
+
902
+ \hyphenation{Figure Table Figures Tables}
903
+
904
+ \newcommand{\href}[2]{#2}
905
+
906
+ \renewenvironment{proof}[1][\proofname]{\par
907
+ \normalfont \topsep6\p@\@plus6\p@\relax
908
+ \labelsep 0.5em
909
+ \trivlist
910
+ \item[\hskip\labelsep\hskip1em\textsc{#1}.]\ignorespaces
911
+ }{\endtrivlist\@endpefalse}
912
+
913
+ %%Different Bonds
914
+
915
+ \def\sbond{\ensuremath{\raise.25ex\hbox{${-}\!\!\!\!{-}$}}\kern -.9pt}
916
+ \def\dbond{\ensuremath{\raise.25ex\hbox{=$\!$=}}}
917
+ \def\tbond{\ensuremath{\raise.20ex\hbox{${\equiv}\!\!\!{\equiv}$}}}
918
+
919
+ % Author queries
920
+ %\fboxsep=4\p@
921
+ %\fboxrule=0.5\p@
922
+ \newcommand{\query}[2][0pt]{}%
923
+ % \marginpar{\vspace*{#1}%
924
+ % {\parbox{\marginparwidth}{%
925
+ % \raggedright\fontsize{6}{8}\selectfont
926
+ % #2}}}}
927
+
928
+ \renewcommand{\dag}{{\mathversion{normal}$^{\dagger}$}}
929
+
930
+ \endinput