summaryrefslogtreecommitdiff
path: root/Master/texmf-dist/source/latex/texshade
diff options
context:
space:
mode:
authorKarl Berry <karl@freefriends.org>2010-03-05 00:29:23 +0000
committerKarl Berry <karl@freefriends.org>2010-03-05 00:29:23 +0000
commit09957f78ef831e10c41f8b12329282e8bcef03e3 (patch)
treedd180f619e1b327904e9b4757a49842469220986 /Master/texmf-dist/source/latex/texshade
parentba5d024e2cd6ca72d404ce6b081797ec9f5f2a6d (diff)
texshade 1.21 (2mar10)
git-svn-id: svn://tug.org/texlive/trunk@17314 c570f23f-e606-0410-a88d-b1316a301751
Diffstat (limited to 'Master/texmf-dist/source/latex/texshade')
-rw-r--r--Master/texmf-dist/source/latex/texshade/texshade.dtx936
-rw-r--r--Master/texmf-dist/source/latex/texshade/texshade.ins4
2 files changed, 792 insertions, 148 deletions
diff --git a/Master/texmf-dist/source/latex/texshade/texshade.dtx b/Master/texmf-dist/source/latex/texshade/texshade.dtx
index d1e9b0e83dd..c5098fdb54b 100644
--- a/Master/texmf-dist/source/latex/texshade/texshade.dtx
+++ b/Master/texmf-dist/source/latex/texshade/texshade.dtx
@@ -358,6 +358,20 @@
% `percentidentity{seq1}{seq2}'.
% }
%
+% \changes{1.20a}{2009-11-30}{%
+% Corrections: identity/similarity tables work now without the need to
+% set a conservation plot in the feature line.
+% }
+%
+% \changes{1.21}{2010-03-01}{%
+% Corrections: `setdomain' ignored a changed `startnumber', corrected;
+% further bug fixes.
+% Introduction: in several commands sequence motifs can be given instead
+% of numeral sequence stretch definitions;
+% new type of sequence emphasis by lowercase characters:
+% `lowerregion' and `lowerblock'.
+% }
+%
%
% \CharacterTable
% {Upper-case \A\B\C\D\E\F\G\H\I\J\K\L\M\N\O\P\Q\R\S\T\U\V\W\X\Y\Z
@@ -396,7 +410,7 @@
% for further information, updates and on-line documentation
% see my homepage at
% \texttt{www.pharmazie.uni-kiel.de/chem/Prof\_Beitz/biotex.html} }}
-% \date{\small v1.20; 2009/10/05\\[2pt] {*** incredible 10 years since first release ***}}
+% \date{\small v1.21; 2010/03/01\\[2pt]}
% \maketitle
% \begin{abstract}
% Setting alignments of nucleotides and peptides for publication
@@ -475,6 +489,30 @@
%
% \subsection{Version History}
%
+% \textbf{v1.21 2010/03/01}
+% \medskip
+%
+% \emph{Corrections:} |\setdomain| now recognizes a changed |\startnumber|.
+%
+% \emph{Introductions:}
+% (a) Sequence motifs (\ref{Lshaderegion}) can be given as a selection pattern
+% in sequence stretch labeling commands, such as |\shaderegion|,
+% |\emphregion| or |\frameblock|, instead of numeral stretch definitions.
+%
+% (b) A new type of sequence emphasis by lowercase letters was implemented:
+% |\lowerregion| and |\lowerblock| (\ref{Llowerregion}).
+% \medskip
+%
+% \textbf{v1.20a 2009/11/30}
+% \medskip
+%
+% \emph{Corrections:} Identity/similarity tables
+% work now without having to set a conservation plot in the feature
+% line.
+% \medskip
+%
+% \newpage
+%
% \textbf{v1.20 2009/10/05}
% \medskip
%
@@ -611,7 +649,6 @@
% by |\hiderelevance|.
% \bigskip
%
-% \newpage
%
% \textbf{v1.13 2006/02/23}
% \medskip
@@ -839,7 +876,6 @@
% works now.
% \bigskip
%
-% \newpage
%
% \textbf{v1.2 1999/6/12}
% \medskip
@@ -1150,7 +1186,7 @@
%
% \begin{texshade}{AQPpro.MSF}
% \setdomain{1}{75..86,103..103,148..148,151..153,155..156,193..195,218..219,222..222}
-% \showruler{1}{top} \rulersteps{1}
+% \showruler{top}{1} \rulersteps{1}
% \hidenumbering
% \hideconsensus
% \end{texshade}
@@ -1161,7 +1197,7 @@
% \begin{verbatim}
% \begin{texshade}{AQPpro.MSF}
% \setdomain{1}{point[8]:1J4N.pdb,81[CA]}
-% \showruler{1}{top} \rulersteps{1}
+% \showruler{top}{1} \rulersteps{1}
% \hidenumbering
% \hideconsensus
% \end{texshade}
@@ -1387,12 +1423,15 @@
% \item [\textbf{hydropathy}:] discrimination between acidic and
% basic, polar uncharged and hydrophobic nonpolar residues
% \label{hydro}
+% \bigskip
%
% \begin{texshade}{AQPpro.MSF}
% \residuesperline*{34}
% \shadingmode[hydropathy]{functional}
% \feature{top}{1}{158..163}{brace}{tinted}
% \tintblock{1}{158..163}
+% \feature{top}{1}{QLVLC}{brace}{lowercased}
+% \lowerblock{1}{QLVLC}
% \setends{1}{138..170}
% \showlegend
% \end{texshade}
@@ -1405,6 +1444,8 @@
% \shadingmode[hydropathy]{functional}
% \feature{top}{1}{158..163}{brace}{tinted}
% \tintblock{1}{158..163}
+% \feature{top}{1}{QLVLC}{brace}{lowercased}
+% \lowerblock{1}{QLVLC}
% \setends{1}{138..170}
% \showlegend
% \end{texshade}
@@ -1414,6 +1455,7 @@
% \item [\textbf{structure}:] displays the potential
% localization within the tertiary structure of
% the protein \label{struc}
+% \bigskip
%
% \begin{texshade}{AQPpro.MSF}
% \residuesperline*{34}
@@ -1423,7 +1465,7 @@
% $\alpha$-helix[Yellow]}{transmembrane domain 4}
% \feature{top}{1}{158..163}{translate[Blue]}{}
% \backtranslabel{oblique}
-% \feature{bottom}{1}{158..163}{brace[Blue]}{loop D [Blue]}
+% \feature{bottom}{1}{[DE]RXXR[DE]}{brace[Blue]}{loop D [Blue]}
% \feature{top}{1}{164..170}{o->[Red]}{trans. dom. 5}
% \showlegend
% \end{texshade}
@@ -1439,7 +1481,7 @@
% $\alpha$-helix[Yellow]}{transmembrane domain 4}
% \feature{top}{1}{158..163}{translate[Blue]}{}
% \backtranslabel{oblique}
-% \feature{bottom}{1}{158..163}{brace[Blue]}{loop D [Blue]}
+% \feature{bottom}{1}{[DE]RXXR[DE]}{brace[Blue]}{loop D [Blue]}
% \feature{top}{1}{164..170}{o->[Red]}{trans. dom. 5}
% \showlegend
% \end{texshade}
@@ -1449,6 +1491,7 @@
% \item [\textbf{chemical}:] residues are shaded due to chemical
% properties of
% their functional groups \label{chem}
+% \bigskip
%
% \begin{texshade}{AQPpro.MSF}
% \residuesperline*{34}
@@ -1473,6 +1516,7 @@
% This is \emph{not} identical to a threshold of 0\%
% where only the majority group would be shaded. See the
% difference:
+% \bigskip
%
% \begin{texshade}{AQPpro.MSF}
% \residuesperline*{34}
@@ -1497,7 +1541,7 @@
% shading following the rasmol
% color scheme \label{ras}
% \bigskip
-%
+% \bigskip
% \bigskip
%
% \begin{texshade}{AQPpro.MSF}
@@ -1534,6 +1578,7 @@
% differences in the surface
% area \label{starea}
% of the different amino acid's sidechains
+% \bigskip
%
% \begin{texshade}{AQPpro.MSF}
% \residuesperline*{34}
@@ -1563,6 +1608,7 @@
% residues), whereas highly accessible
% sidechains are hydrophilic (compare to
% \textbf{hydropathy} and \textbf{structure})
+% \bigskip
%
% \begin{texshade}{AQPpro.MSF}
% \residuesperline*{34}
@@ -3434,20 +3480,22 @@
% within the alignment. The
% foreground and background colors can be set with the last two
% parameters.
-% \meta{selection} can have two different formats
-% depending on whether (a) the user wants to select the positions manually
-% or (b) \TeXshade{} is supposed to select the residues based on 3D
+% \meta{selection} can have three different formats
+% depending on whether (a) the user wants to select the positions manually,
+% (b) the selection should be based on a sequence motif to be found by \TeXshade{},
+% or (c) \TeXshade{} is supposed to select the residues based on 3D
% coordinates provided by a PDB file.
+% \medskip
%
-% To select the residues manually, the user provides a position list of
+% (a) To select the residues manually, the user provides a position list of
% the following format:
% \medskip
%
% \quad|{|\meta{start1}..\meta{stop1}|,|\meta{start2}..\meta{stop2}|,|\ldots|,|\meta{start n}..\meta{stop n}|}|
% \medskip
%
-% Example: in order to shade residue number 13 and the region
-% 20--30 of sequence number 1 in red letters on green ground
+% In order to shade residue number 13 and the region
+% 20--30 of sequence number 1 in red letters on a green background
% type the following command:
% \medskip
%
@@ -3458,7 +3506,23 @@
% \meta{seqref}.
% \medskip
%
-% In order to select positions based on the 3D structure a PDB
+% (b) A sequence motif can be given, which will be found and labeled. A simple
+% example selecting all sequence motifs `NNAD' in sequence `1' would be:
+% \medskip
+%
+% \quad|\shaderegion{1}{NNAD}{Red}{Green}|
+% \medskip
+%
+% The definition can further include `X' for any residue and groups of residues in brackets
+% at uncertain positions. The example below will find all motifs in sequence `1'
+% that start with an asparagine, followed by any two residues, an acidic, a
+% basic residue, again any two residues and finally a glutamine.
+% \medskip
+%
+% \quad|\shaderegion{1}{NXX[DE][KR]XXQ}{Red}{Green}|
+% \medskip
+%
+% (c) In order to select positions based on the 3D structure a PDB
% structure file is required. \TeXshade{} can select residues within
% a given distance in \AA{} around a point, along a line, or above and
% below a plane, which are defined by one to three residues. The points
@@ -3513,7 +3577,7 @@
%
% Both selection formats, i.\,e. a manually given list and the 3D selection,
% can be used with |\shadeblock| (see below),
-% |\tintregion|, |\tintblock|, |\emphregion|, |\emphblock|,
+% |\tintregion|, |\tintblock|, |\emphregion|, |\emphblock|, |\lowerregion|, |\lowerblock|,
% |\frameblock| (all in \ref{Lframeblock}), and |\feature| (\ref{Lfeature}).
%
%
@@ -3529,10 +3593,10 @@
% \medskip
%
%
-% \subsubsection{Emphasizing, tinting, and framing}
+% \subsubsection{Emphasizing, tinting, lowercasing, and framing}
%
% \label{Lemphregion}\label{Lemphblock}
-% If it is prefered to keep the calculated shading colors
+% If it is preferred to keep the calculated shading colors
% but distinct regions or blocks are yet to be emphasized one
% can use the following commands to change the font style of
% such regions:
@@ -3560,6 +3624,7 @@
%
% \label{Ltintregion}\label{Ltintblock}
% Further, it is possible to tint the region or block in question
+% or to switch the characters to lowercase
% by using the commands (for example see hydropathy-figure on page
% \pageref{hydro}):
% \medskip
@@ -3577,6 +3642,18 @@
% The level of tinting in the region in question can be set by
% |\tintdefault{|\meta{level}|}| with |weak|, |normal|, and
% |strong| as possible \meta{level}s.
+% \medskip
+%
+% \label{Llowerregion}\label{Llowerblock}
+% \quad|\lowerregion{|\meta{seqref}|}{|\meta{selection}|}|
+% \medskip
+%
+% and
+% \medskip
+%
+% \quad|\lowerblock{|\meta{seqref}|}{|\meta{selection}|}|
+% \medskip
+%
%
% Another option is to draw a bounding box around the sequence block
% in question (for an example see diversity mode-figure on page
@@ -3630,9 +3707,9 @@
% |\bottomspace{-0.1in}|.
%
% The argument \meta{seqref} and the third
-% parameter containing the selection of the specified residues
+% parameter containing the \meta{selection} of the specified residues
% are identical to the ones described before in several commands, e.\,g.
-% |\ruler| (\ref{ruler}) or |\shaderegion| (\ref{shaderegion}).
+% |\shaderegion| (\ref{shaderegion}).
%
% New is the fourth parameter for the definition of the label style.
% There are many possibilities like braces, helices, boxes, arrows, bars, any
@@ -5919,6 +5996,12 @@
% \quad|\tintdefault{|\meta{effect}|}| \qquad\qquad|weak, normal, strong|
% \hfill[\pageref{Ltintdefault}]
%
+% \quad|\lowerregion{|\meta{seqref}|}{|\meta{selection}|}|
+% \hfill[\pageref{Llowerregion}]
+%
+% \quad|\lowerblock{|\meta{seqref}|}{|\meta{selection}|}|
+% \hfill[\pageref{Llowerblock}]
+%
% \quad|\frameblock{|\meta{seqref}|}{|\meta{selection}|}{|\meta{color}|[|\meta{length}|]}|
% \hfill[\pageref{Lframeblock}]
%
@@ -6019,6 +6102,7 @@
%
% \vspace{1.5\baselineskip}
%
+% \newpage
%
% \textbf{Including secondary structure information}
% \medskip
@@ -6130,6 +6214,8 @@
%
% \vspace{1.5\baselineskip}
%
+% \newpage
+%
% \textbf{Font handling}
% \medskip
%
@@ -6292,8 +6378,8 @@
% \begin{macrocode}
%<*texshade>
\NeedsTeXFormat{LaTeX2e}
-\ProvidesPackage{texshade}[2009/10/05 LaTeX TeXshade (v1.20)]
-\message{Package `texshade', Version 1.20 of 2009/10/05.}
+\ProvidesPackage{texshade}[2010/03/01 LaTeX TeXshade (v1.21)]
+\message{Package `texshade', Version 1.21 of 2010/03/01.}
\PassOptionsToPackage{dvips}{color}
\PassOptionsToPackage{dvips}{graphicx}
@@ -6390,13 +6476,15 @@
\newif\ifttopfeature \newif\ifbbottomfeature
\newif\iftttopfeature \newif\ifbbbottomfeature
\newif\ifttttopfeature\newif\ifbbbbottomfeature
-\newif\ifall@fshade \newif\ifregionalemph
+\newif\ifall@fshade \newif\ifregionalemph
+\newif\ifregionallower
\newif\ifframe@ \newif\ifregionaltint
\newif\ifshow@logo \newif\ifshow@sublogo
\newif\ifhidechar \newif\ifsh@wg@ps
\newif\ifsimmode
\newif\ifregionaltintnow
\newif\ifregionalemphnow
+\newif\ifregionallowernow
\newif\ifregionalshadenow
\newif\iftopfeaturenow
\newif\ifttopfeaturenow
@@ -6417,7 +6505,8 @@
\def\comm@{,} \def\@loc{LOC} \def\@asg{ASG} \def\@t{@} \def\@HP{>HP:}
\def\gre@ter{>} \def\sm@ller{<} \def\N@{N} \def\equ@l{=} \def\H@{H}
\def\gap@char{.} \def\dom@char{{\dom@rule}} \def\yes{yes} \def\y@{y} \def\n@{n}
-\def\o@{o} \def\d@t{.} \def\questi@n{?} \def\st@p@char{*}
+\def\o@{o} \def\d@t{.} \def\questi@n{?} \def\st@p@char{*} \def\semic@n{;}
+\def\br@cket{[}
\def\@TOM{ATOM} \def\C@lpha{CA} \def\@point@{point} \def\@line@{line} \def\@plane@{plane}
\def\gap@rule{\rule[0.3\box@height]{\box@width}{\gap@rulethick}}
\def\dom@rule{\vrule depth\box@depth height\box@height width\domgap@rulethick}
@@ -8576,10 +8665,10 @@
\csname stack@@reg#1\endcsname}
\expandafter\xdef\csname stack@tintreg\the\loopcount\endcsname{%
\csname stack@@tintreg#1\endcsname}
- \expandafter\xdef\csname stack@hidereg\the\loopcount\endcsname{%
- \csname stack@@hidereg#1\endcsname}
\expandafter\xdef\csname stack@emphreg\the\loopcount\endcsname{%
\csname stack@@emphreg#1\endcsname}
+ \expandafter\xdef\csname stack@lowerreg\the\loopcount\endcsname{%
+ \csname stack@@lowerreg#1\endcsname}
\expandafter\xdef\csname stack@framereg\the\loopcount\endcsname{%
\csname stack@@framereg#1\endcsname}
\expandafter\xdef\csname stack@top\the\loopcount\endcsname{%
@@ -8629,10 +8718,10 @@
\csname stack@reg\the\loopcount\endcsname}
\expandafter\xdef\csname stack@@tintreg\the\loopcount\endcsname{%
\csname stack@tintreg\the\loopcount\endcsname}
- \expandafter\xdef\csname stack@@hidereg\the\loopcount\endcsname{%
- \csname stack@hidereg\the\loopcount\endcsname}
\expandafter\xdef\csname stack@@emphreg\the\loopcount\endcsname{%
\csname stack@emphreg\the\loopcount\endcsname}
+ \expandafter\xdef\csname stack@@lowerreg\the\loopcount\endcsname{%
+ \csname stack@lowerreg\the\loopcount\endcsname}
\expandafter\xdef\csname stack@@framereg\the\loopcount\endcsname{%
\csname stack@framereg\the\loopcount\endcsname}
\expandafter\xdef\csname stack@@top\the\loopcount\endcsname{%
@@ -8918,10 +9007,10 @@
\csname stack@reg\the\innerloopcount\endcsname}
\expandafter\xdef\csname stack@tintreg\the\loopcount\endcsname{%
\csname stack@tintreg\the\innerloopcount\endcsname}
- \expandafter\xdef\csname stack@hidereg\the\loopcount\endcsname{%
- \csname stack@hidereg\the\innerloopcount\endcsname}
\expandafter\xdef\csname stack@emphreg\the\loopcount\endcsname{%
\csname stack@emphreg\the\innerloopcount\endcsname}
+ \expandafter\xdef\csname stack@lowerreg\the\loopcount\endcsname{%
+ \csname stack@lowerreg\the\innerloopcount\endcsname}
\expandafter\xdef\csname stack@framereg\the\loopcount\endcsname{%
\csname stack@framereg\the\innerloopcount\endcsname}
\expandafter\xdef\csname stack@top\the\loopcount\endcsname{%
@@ -9189,15 +9278,16 @@
\expandafter\xdef\csname stack@reg\temp@\endcsname{\last@}
}
\def\sort@stack{%
- \expandafter\get@fromstack\last@
- \ifx\first@\ampers@nd
+ \expandafter\get@fromstack\last@
+ \ifx\first@\ampers@nd
\xdef\tmpstack{\tmpstack\the\loopcount;\st@rt;\st@p;\@ll;&;&;&;&;@}
- \else
+ \else
\ifnum\st@rt<\second@
\xdef\tmpstack{\tmpstack\the\loopcount;\st@rt;\st@p;\@ll;%
- \first@;\second@;\third@;\fourth@;\last@}
+ \first@;\second@;\third@;\fourth@;\last@}
\else
- \xdef\tmpstack{\tmpstack\first@;\second@;\third@;\fourth@;} \sort@stack
+ \xdef\tmpstack{\tmpstack\first@;\second@;\third@;\fourth@;}
+ \sort@stack
\fi\fi
}
\def\get@regions#1..#2,#3@{%
@@ -9207,28 +9297,6 @@
\sort@stack
\expandafter\xdef\csname stack@reg\seq@\endcsname{\tmpstack}
}
-\def\getregion@fromhidestack#1{%
- \xdef\temp@{#1}
- \xdef\first@{\csname stack@hidereg\temp@\endcsname}
- \expandafter\get@fromstack\first@
- \expandafter\xdef\csname hidestart\temp@\endcsname{\first@}
- \expandafter\xdef\csname hidestop\temp@\endcsname{\second@}
- \expandafter\xdef\csname hidestyle\temp@\endcsname{\third@}
- \expandafter\xdef\csname hidetext\temp@\endcsname{\fourth@}
- \expandafter\xdef\csname stack@hidereg\temp@\endcsname{\last@}
-}
-\def\sort@hidestack{%
- \expandafter\get@fromstack\last@
- \ifx\first@\ampers@nd
- \xdef\tmpstack{\tmpstack\st@rt;\st@p;\@ll;\text@;&;&;&;&;&;@}
- \else
- \ifnum\st@rt<\second@
- \xdef\tmpstack{\tmpstack\st@rt;\st@p;\@ll;\text@;%
- \first@;\second@;\third@;\fourth@;\last@}
- \else
- \xdef\tmpstack{\tmpstack\first@;\second@;\third@;\fourth@;} \sort@hidestack
- \fi\fi
-}
\def\get@fromemphstack#1;#2;#3;#4@{%
\xdef\first@{#1} \xdef\second@{#2}
\xdef\third@{#3} \xdef\last@{#4@}
@@ -9261,6 +9329,34 @@
\sort@emphstack
\expandafter\xdef\csname stack@emphreg\seq@\endcsname{\tmpstack}
}
+\def\getregion@fromlowerstack#1{%
+ \xdef\temp@{#1}
+ \xdef\first@{\csname stack@lowerreg\temp@\endcsname}
+ \expandafter\get@fromemphstack\first@
+ \expandafter\xdef\csname lowerstart\temp@\endcsname{\first@}
+ \expandafter\xdef\csname lowerstop\temp@\endcsname{\second@}
+ \expandafter\xdef\csname lowerall\temp@\endcsname{\third@}
+ \expandafter\xdef\csname stack@lowerreg\temp@\endcsname{\last@}
+}
+\def\sort@lowerstack{%
+ \expandafter\get@fromemphstack\last@
+ \ifx\first@\ampers@nd
+ \xdef\tmpstack{\tmpstack\st@rt;\st@p;\@ll;&;&;&;@}
+ \else
+ \ifnum\st@rt<\second@
+ \xdef\tmpstack{\tmpstack\st@rt;\st@p;\@ll;\first@;\second@;\third@;\last@}
+ \else
+ \xdef\tmpstack{\tmpstack\first@;\second@;\third@;} \sort@lowerstack
+ \fi\fi
+}
+\def\get@lowerregions#1..#2,#3@{%
+ \regionallowertrue
+ \xdef\st@rt{#1} \xdef\st@p{#2} \xdef\list@{#3}
+ \xdef\last@{\csname stack@lowerreg\seq@\endcsname}
+ \xdef\tmpstack{}
+ \sort@lowerstack
+ \expandafter\xdef\csname stack@lowerreg\seq@\endcsname{\tmpstack}
+}
\def\get@fromdomstack#1;#2;#3@{%
\xdef\first@{#1} \xdef\second@{#2}
\xdef\last@{#3@}
@@ -9304,23 +9400,12 @@
\expandafter\xdef\csname tintall\temp@\endcsname{\third@}
\expandafter\xdef\csname stack@tintreg\temp@\endcsname{\last@}
}
-\def\sort@tintstack{%
- \expandafter\get@fromemphstack\last@
- \ifx\first@\ampers@nd
- \xdef\tmpstack{\tmpstack\st@rt;\st@p;\@ll;&;&;&;@}
- \else
- \ifnum\st@rt<\second@
- \xdef\tmpstack{\tmpstack\st@rt;\st@p;\@ll;\first@;\second@;\third@;\last@}
- \else
- \xdef\tmpstack{\tmpstack\first@;\second@;\third@;} \sort@tintstack
- \fi\fi
-}
\def\get@tintregions#1..#2,#3@{%
\regionaltinttrue
\xdef\st@rt{#1} \xdef\st@p{#2} \xdef\list@{#3}
\xdef\last@{\csname stack@tintreg\seq@\endcsname}
\xdef\tmpstack{}
- \sort@tintstack
+ \sort@emphstack
\expandafter\xdef\csname stack@tintreg\seq@\endcsname{\tmpstack}
}
\def\getregion@fromframestack#1{%
@@ -9466,23 +9551,312 @@
\fi%
\fi%
}
+\def\test@get#1#2@{%
+ \xdef\temp@{#1} \xdef\third@@{#2@}
+ \ifx\temp@\ampers@nd
+ \else
+ \if \temp@ X
+ \xdef\temp@{\second@@}
+ \fi
+ \ifx\temp@\second@@
+ \xdef\third@@{\second@@}
+ \else
+ \expandafter\test@get\third@@
+ \fi
+ \fi
+}
+\def\get@@second@#1#2@{\xdef\second@@{#1}\xdef\first@@{#2@}}
+\def\get@@third@#1]#2@{\xdef\third@@{#1&@}\xdef\fifth@@{#2@}}
+\def\get@third@#1#2@{\xdef\third@@{#1}\xdef\fifth@@{#2@}}
+\def\find@motif{%
+ \expandafter\get@@second@\first@@
+ \ifx\second@@\ampers@nd
+ \else
+ \ifx\second@@\d@t
+ \else
+ \advance\temp@count by 1
+ \if \third@@ X
+ \xdef\third@@{\second@@}
+ \fi
+ \ifx\third@@\br@cket
+ \expandafter\get@@third@\fifth@@
+ \expandafter\test@get\third@@
+ \fi
+ \ifx\second@@\third@@
+ \ifx\nineth@@\n@
+ \xdef\st@rt{\the\temp@count}
+ \xdef\st@p{n}
+ \fi
+ \xdef\nineth@@{y}
+ \expandafter\get@third@\fifth@@
+ \ifx\third@@\ampers@nd
+ \xdef\st@p{\the\temp@count}
+ \xdef\list@{}
+ \xdef\tmpstack{}
+ \xdef\temp@{shade}
+ \ifx\temp@\temp@@
+ \xdef\last@{\csname stack@reg\seq@\endcsname}
+ \loopcount=\style@
+ \sort@stack
+ \expandafter\xdef\csname stack@reg\seq@\endcsname{\tmpstack}
+ \else
+ \xdef\temp@{emph}
+ \ifx\temp@\temp@@
+ \regionalemphtrue
+ \xdef\last@{\csname stack@emphreg\seq@\endcsname}
+ \sort@emphstack
+ \expandafter\xdef\csname stack@emphreg\seq@\endcsname{\tmpstack}
+ \else
+ \xdef\temp@{lower}
+ \ifx\temp@\temp@@
+ \regionallowertrue
+ \xdef\last@{\csname stack@lowerreg\seq@\endcsname}
+ \sort@lowerstack
+ \expandafter\xdef\csname stack@lowerreg\seq@\endcsname{\tmpstack}
+ \else
+ \xdef\temp@{tint}
+ \ifx\temp@\temp@@
+ \regionaltinttrue
+ \xdef\last@{\csname stack@tintreg\seq@\endcsname} \message{((last:\last@))}
+ \sort@emphstack
+ \expandafter\xdef\csname stack@tintreg\seq@\endcsname{\tmpstack} \message{((tmp:\tmpstack))}
+ \else
+ \xdef\temp@{frame}
+ \ifx\temp@\temp@@
+ \frame@true
+ \xdef\last@{\csname stack@framereg\seq@\endcsname}
+ \sort@emphstack
+ \expandafter\xdef\csname stack@framereg\seq@\endcsname{\tmpstack}
+ \else
+ \xdef\temp@{ttttop}
+ \ifx\temp@\temp@@
+ \xdef\last@{\csname stack@ttttop\seq@\endcsname}
+ \sort@fstack
+ \expandafter\xdef\csname stack@ttttop\seq@\endcsname{\tmpstack}
+ \else
+ \xdef\temp@{tttop}
+ \ifx\temp@\temp@@
+ \xdef\last@{\csname stack@tttop\seq@\endcsname}
+ \sort@fstack
+ \expandafter\xdef\csname stack@tttop\seq@\endcsname{\tmpstack}
+ \else
+ \xdef\temp@{ttop}
+ \ifx\temp@\temp@@
+ \xdef\last@{\csname stack@ttop\seq@\endcsname}
+ \sort@fstack
+ \expandafter\xdef\csname stack@ttop\seq@\endcsname{\tmpstack}
+ \else
+ \xdef\temp@{top}
+ \ifx\temp@\temp@@
+ \xdef\last@{\csname stack@top\seq@\endcsname}
+ \sort@fstack
+ \expandafter\xdef\csname stack@top\seq@\endcsname{\tmpstack}
+ \else
+ \xdef\temp@{bottom}
+ \ifx\temp@\temp@@
+ \xdef\last@{\csname stack@bottom\seq@\endcsname}
+ \sort@fstack
+ \expandafter\xdef\csname stack@bottom\seq@\endcsname{\tmpstack}
+ \else
+ \xdef\temp@{bbottom}
+ \ifx\temp@\temp@@
+ \xdef\last@{\csname stack@bbottom\seq@\endcsname}
+ \sort@fstack
+ \expandafter\xdef\csname stack@bbottom\seq@\endcsname{\tmpstack}
+ \else
+ \xdef\temp@{bbbottom}
+ \ifx\temp@\temp@@
+ \xdef\last@{\csname stack@bbbottom\seq@\endcsname}
+ \sort@fstack
+ \expandafter\xdef\csname stack@bbbottom\seq@\endcsname{\tmpstack}
+ \else
+ \xdef\temp@{bbbbottom}
+ \ifx\temp@\temp@@
+ \xdef\last@{\csname stack@bbbbottom\seq@\endcsname}
+ \sort@fstack
+ \expandafter\xdef\csname stack@bbbbottom\seq@\endcsname{\tmpstack}
+ \fi
+ \fi
+ \fi
+ \fi
+ \fi
+ \fi
+ \fi
+ \fi
+ \fi
+ \fi
+ \fi
+ \fi
+ \fi
+ \xdef\fifth@@{\m@tif} \expandafter\get@third@\fifth@@
+ \xdef\nineth@@{n}
+ \fi
+ \else
+ \xdef\nineth@@{n} \xdef\st@p{n}
+ \xdef\fifth@@{\m@tif} \expandafter\get@third@\fifth@@
+ \fi
+ \fi
+ \find@motif
+ \fi
+}
+\def\prep@motif{%
+
+ \def\get@motif@specs##1,##2,##3,##4,##5,&{%
+ \xdef\seq@{##1} \xdef\temp@@{##2} \xdef\@ll{##3} \def\fourth@@{##4} \xdef\fifth@@{##5&@}
+ }
+
+ \loopcount=0
+ \loop
+ \advance\loopcount by 1
+ \expandafter\xdef\csname stack@reg\the\loopcount\endcsname{\csname style\the\loopcount\endcsname;%
+ \csname start\the\loopcount\endcsname;%
+ \csname stop\the\loopcount\endcsname;%
+ \csname all\the\loopcount\endcsname;%
+ \csname stack@reg\the\loopcount\endcsname}
+ \expandafter\xdef\csname stack@emphreg\the\loopcount\endcsname{\csname emphstart\the\loopcount\endcsname;%
+ \csname emphstop\the\loopcount\endcsname;%
+ \csname emphall\the\loopcount\endcsname;%
+ \csname stack@emphreg\the\loopcount\endcsname}
+ \expandafter\xdef\csname stack@lowerreg\the\loopcount\endcsname{\csname lowerstart\the\loopcount\endcsname;%
+ \csname lowerstop\the\loopcount\endcsname;%
+ \csname lowerall\the\loopcount\endcsname;%
+ \csname stack@lowerreg\the\loopcount\endcsname}
+ \expandafter\xdef\csname stack@tintreg\the\loopcount\endcsname{\csname tintstart\the\loopcount\endcsname;%
+ \csname tintstop\the\loopcount\endcsname;%
+ \csname tintall\the\loopcount\endcsname;%
+ \csname stack@tintreg\the\loopcount\endcsname}
+ \expandafter\xdef\csname stack@framereg\the\loopcount\endcsname{\csname framestart\the\loopcount\endcsname;%
+ \csname framestop\the\loopcount\endcsname;%
+ \csname framestyle\the\loopcount\endcsname;%
+ \csname stack@framereg\the\loopcount\endcsname}
+ \expandafter\xdef\csname stack@ttttop\the\loopcount\endcsname{\csname textttttop\the\loopcount\endcsname;%
+ \csname startttttop\the\loopcount\endcsname;%
+ \csname stopttttop\the\loopcount\endcsname;%
+ \csname stylettttop\the\loopcount\endcsname;%
+ \csname stack@ttttop\the\loopcount\endcsname}
+ \expandafter\xdef\csname stack@tttop\the\loopcount\endcsname{\csname texttttop\the\loopcount\endcsname;%
+ \csname starttttop\the\loopcount\endcsname;%
+ \csname stoptttop\the\loopcount\endcsname;%
+ \csname styletttop\the\loopcount\endcsname;%
+ \csname stack@tttop\the\loopcount\endcsname}
+ \expandafter\xdef\csname stack@ttop\the\loopcount\endcsname{\csname textttop\the\loopcount\endcsname;%
+ \csname startttop\the\loopcount\endcsname;%
+ \csname stopttop\the\loopcount\endcsname;%
+ \csname stylettop\the\loopcount\endcsname;%
+ \csname stack@ttop\the\loopcount\endcsname}
+ \expandafter\xdef\csname stack@top\the\loopcount\endcsname{\csname texttop\the\loopcount\endcsname;%
+ \csname starttop\the\loopcount\endcsname;%
+ \csname stoptop\the\loopcount\endcsname;%
+ \csname styletop\the\loopcount\endcsname;%
+ \csname stack@top\the\loopcount\endcsname}
+ \expandafter\xdef\csname stack@bottom\the\loopcount\endcsname{\csname textbottom\the\loopcount\endcsname;%
+ \csname startbottom\the\loopcount\endcsname;%
+ \csname stopbottom\the\loopcount\endcsname;%
+ \csname stylebottom\the\loopcount\endcsname;%
+ \csname stack@bottom\the\loopcount\endcsname}
+ \expandafter\xdef\csname stack@bbottom\the\loopcount\endcsname{\csname textbbottom\the\loopcount\endcsname;%
+ \csname startbbottom\the\loopcount\endcsname;%
+ \csname stopbbottom\the\loopcount\endcsname;%
+ \csname stylebbottom\the\loopcount\endcsname;%
+ \csname stack@bbottom\the\loopcount\endcsname}
+ \expandafter\xdef\csname stack@bbbottom\the\loopcount\endcsname{\csname textbbbottom\the\loopcount\endcsname;%
+ \csname startbbbottom\the\loopcount\endcsname;%
+ \csname stopbbbottom\the\loopcount\endcsname;%
+ \csname stylebbbottom\the\loopcount\endcsname;%
+ \csname stack@bbbottom\the\loopcount\endcsname}
+ \expandafter\xdef\csname stack@bbbbottom\the\loopcount\endcsname{\csname textbbbbottom\the\loopcount\endcsname;%
+ \csname startbbbbottom\the\loopcount\endcsname;%
+ \csname stopbbbbottom\the\loopcount\endcsname;%
+ \csname stylebbbbottom\the\loopcount\endcsname;%
+ \csname stack@bbbbottom\the\loopcount\endcsname}
+ \ifnum\loopcount<\seq@num\repeat
+ \temp@@count=0
+ \loop
+ \advance\temp@@count by 1
+ \xdef\first@@{\csname motif\the\temp@@count\endcsname}
+ \expandafter\get@motif@specs\first@@
+ \xdef\first@@{\csname sequence\seq@\endcsname &@}
+ \temp@count=\csname res@count\seq@\endcsname
+ \xdef\f@text@{\@ll}
+ \xdef\style@{\fourth@@}
+ \xdef\m@tif{\fifth@@} \expandafter\get@third@\fifth@@
+ \xdef\nineth@@{n} \xdef\st@p{n}
+ \find@motif
+ \ifnum\temp@@count<\motif@num\repeat
+ \loopcount=0
+ \loop
+ \advance\loopcount by 1
+ \expandafter\getregion@fromstack{\the\loopcount}
+ \expandafter\getregion@fromtintstack{\the\loopcount}
+ \expandafter\getregion@fromemphstack{\the\loopcount}
+ \expandafter\getregion@fromlowerstack{\the\loopcount}
+ \expandafter\getregion@fromframestack{\the\loopcount}
+ \xdef\bottop@{top} \expandafter\getregion@fromfstack{\the\loopcount}
+ \xdef\bottop@{ttop} \expandafter\getregion@fromfstack{\the\loopcount}
+ \xdef\bottop@{tttop} \expandafter\getregion@fromfstack{\the\loopcount}
+ \xdef\bottop@{ttttop} \expandafter\getregion@fromfstack{\the\loopcount}
+ \xdef\bottop@{bottom} \expandafter\getregion@fromfstack{\the\loopcount}
+ \xdef\bottop@{bbottom} \expandafter\getregion@fromfstack{\the\loopcount}
+ \xdef\bottop@{bbbottom} \expandafter\getregion@fromfstack{\the\loopcount}
+ \xdef\bottop@{bbbbottom} \expandafter\getregion@fromfstack{\the\loopcount}
+ \ifnum\loopcount<\seq@num\repeat
+}
+
+\def\test@motif#1#2@{%
+ \xdef\temp@{shade}
+ \ifx\temp@\temp@@ \xdef\style@{\the\loopcount} \fi
+ \xdef\temp@{emph}
+ \ifx\temp@\temp@@ \xdef\style@{0} \fi
+ \xdef\temp@{lower}
+ \ifx\temp@\temp@@ \xdef\style@{0} \fi
+ \xdef\temp@{tint}
+ \ifx\temp@\temp@@ \xdef\style@{0} \fi
+ \xdef\temp@{frame}
+ \ifx\temp@\temp@@ \xdef\style@{0} \fi
+ \xdef\temp@{#1#2}
+ \xdef\first@{#1}
+ \ifx\first@\br@cket
+ \xdef\label@motif{y}
+ \temp@count=\motif@num
+ \advance\temp@count by 1
+ \xdef\motif@num{\the\temp@count}
+ \expandafter\xdef\csname motif\the\temp@count\endcsname{\seq@,\temp@@,\@ll,\style@,\temp@}
+ \xdef\list@{&}
+ \else
+ \expandafter\check@char\first@
+ \ifletter
+ \xdef\label@motif{y}
+ \temp@count=\motif@num
+ \advance\temp@count by 1
+ \xdef\motif@num{\the\temp@count}
+ \expandafter\xdef\csname motif\the\temp@count\endcsname{\seq@,\temp@@,\@ll,\style@,\temp@}
+ \xdef\list@{&}
+ \fi
+ \fi
+}
\def\test@PDB#1:#2,#3,#4,#5,#6@{%
\xdef\last@{#1[,]&}\expandafter\opt@color\last@
+ \xdef\PDB@distance{no}
\ifx\f@color\comm@
- \xdef\PDB@distance{no}
\else
\xdef\f@color{\f@color .&&@}
\expandafter\coord@get\f@color
- \temp@count=\c@@rd
- \multiply\temp@count by \temp@count
- \xdef\PDB@distance{\the\temp@count}
+ \xdef\temp@{\c@@rd @}
+ \expandafter\check@letter\temp@
+ \ifletter
+ \else
+ \temp@count=\c@@rd
+ \multiply\temp@count by \temp@count
+ \xdef\PDB@distance{\the\temp@count}
+ \fi
\fi
\xdef\PDB@hitpos{0}
\xdef\PDB@stack{}
\xdef\PDB@name{#2}
\xdef\PDB@type{point}
\ifx\fourth@\PDB@type
+ \xdef\PDB@{y}
\xdef\last@{#3[,]&}\expandafter\opt@color\last@
\xdef\PDB@refnum@a{\fourth@}
\ifx\f@color\C@lpha
@@ -9498,6 +9872,7 @@
\else
\xdef\PDB@type{line}
\ifx\fourth@\PDB@type
+ \xdef\PDB@{y}
\xdef\last@{#3[,]&}\expandafter\opt@color\last@
\xdef\PDB@refnum{\fourth@}
\ifx\f@color\C@lpha
@@ -9532,6 +9907,7 @@
\else
\xdef\PDB@type{plane}
\ifx\fourth@\PDB@type
+ \xdef\PDB@{y}
\xdef\last@{#3[,]&}\expandafter\opt@color\last@
\xdef\PDB@refnum{\fourth@}
\ifx\f@color\C@lpha
@@ -9587,6 +9963,9 @@
\ifx\PDB@distance\n@ \xdef\PDB@distance{100}\fi
\load@PDB
\expandafter\get@item\PDB@stack \xdef\list@{\first@@}
+ \else
+ \xdef\temp@{\list@ @}
+ \expandafter\test@motif\temp@
\fi
\fi
\fi
@@ -11245,11 +11624,15 @@
\expandafter\xdef\csname fgseqregion\the\loopcount\endcsname{#3}
\expandafter\xdef\csname bgseqregion\the\loopcount\endcsname{#4}
\xdef\list@{#2,&}
- \xdef\temp@{#2,,,:,,,,@} \expandafter\test@PDB\temp@
- \loop
- \xdef\list@{\list@ @}
- \expandafter\get@regions\list@
- \ifx\list@\ampers@nd\else\repeat
+ \xdef\temp@@{shade}
+ \xdef\temp@{#2,,,:,,,,@} \expandafter\test@PDB\temp@
+ \ifx\list@\ampers@nd
+ \else
+ \loop
+ \xdef\list@{\list@ @}
+ \expandafter\get@regions\list@
+ \ifx\list@\ampers@nd\else\repeat
+ \fi
\fi
}
\def\shadeblock#1#2#3#4{%
@@ -11269,11 +11652,15 @@
\else
\ifx\@ll\yes \xdef\@ll{y}\else \xdef\@ll{n}\fi
\xdef\list@{#2,&}
+ \xdef\temp@@{tint} \loopcount=0
\xdef\temp@{#2,,,:,,,,@} \expandafter\test@PDB\temp@
- \loop
- \xdef\list@{\list@ @}
- \expandafter\get@tintregions\list@
- \ifx\list@\ampers@nd\else\repeat
+ \ifx\list@\ampers@nd
+ \else
+ \loop
+ \xdef\list@{\list@ @}
+ \expandafter\get@tintregions\list@
+ \ifx\list@\ampers@nd\else\repeat
+ \fi
\fi
}
\def\tintblock#1#2{%
@@ -11299,6 +11686,34 @@
\xdef\light@{LightLight}
\fi\fi\fi
}
+\def\lowerregion#1#2{%
+ \xdef\seq@{#1}
+ \xdef\temp@{consensus} \ifx\seq@\temp@ \xdef\seq@{0} \fi
+ \xdef\first@{\seq@ @} \expandafter\check@letter\first@
+ \xdef\first@{\seq@}
+ \ifletter \get@name@number \xdef\seq@{\first@} \fi
+ \ifnum\seq@>\seq@count
+ \message{<Ignored seq `\seq@' in \noexpand\lowerregion or \noexpand\lowerblock>}
+ \else
+ \ifx\@ll\yes \xdef\@ll{y}\else \xdef\@ll{n}\fi
+ \xdef\list@{#2,&}
+ \xdef\temp@@{lower} \loopcount=0
+ \xdef\temp@{#2,,,:,,,,@} \expandafter\test@PDB\temp@
+ \ifx\list@\ampers@nd
+ \else
+ \loop
+ \xdef\list@{\list@ @}
+ \expandafter\get@lowerregions\list@
+ \ifx\list@\ampers@nd\else\repeat
+ \fi
+ \fi
+}
+\def\lowerblock#1#2{%
+ \xdef\seq@{#1}
+ \xdef\@ll{yes}
+ \lowerregion{#1}{#2}
+ \xdef\@ll{}
+}
\def\emphregion#1#2{%
\xdef\seq@{#1}
\xdef\temp@{consensus} \ifx\seq@\temp@ \xdef\seq@{0} \fi
@@ -11310,11 +11725,15 @@
\else
\ifx\@ll\yes \xdef\@ll{y}\else \xdef\@ll{n}\fi
\xdef\list@{#2,&}
+ \xdef\temp@@{emph} \loopcount=0
\xdef\temp@{#2,,,:,,,,@} \expandafter\test@PDB\temp@
- \loop
- \xdef\list@{\list@ @}
- \expandafter\get@emphregions\list@
- \ifx\list@\ampers@nd\else\repeat
+ \ifx\list@\ampers@nd
+ \else
+ \loop
+ \xdef\list@{\list@ @}
+ \expandafter\get@emphregions\list@
+ \ifx\list@\ampers@nd\else\repeat
+ \fi
\fi
}
\def\emphblock#1#2{%
@@ -11335,11 +11754,15 @@
\else
\xdef\@ll{#3}
\xdef\list@{#2,&}
+ \xdef\temp@@{frame} \loopcount=0
\xdef\temp@{#2,,,:,,,,@} \expandafter\test@PDB\temp@
- \loop
- \xdef\list@{\list@ @}
- \expandafter\get@frameregions\list@
- \ifx\list@\ampers@nd\else\repeat
+ \ifx\list@\ampers@nd
+ \else
+ \loop
+ \xdef\list@{\list@ @}
+ \expandafter\get@frameregions\list@
+ \ifx\list@\ampers@nd\else\repeat
+ \fi
\fi
}
\def\bargraphstretch#1{\def\b@r@stretch{#1}}
@@ -11722,8 +12145,6 @@
\do@colorgraph
\else
\xdef\f@@color{\f@color}
- \xdef\list@{#3,&}
- \xdef\temp@{#3,,,:,,,,@} \expandafter\test@PDB\temp@
\def\f@text@{#5}
\xdef\f@color{\f@@color}
\xdef\temp@{#4&}
@@ -11802,13 +12223,20 @@
\fi
\fi
\fi
+ \xdef\list@{#3,&}
+ \xdef\@ll{\f@text@}
+ \xdef\temp@@{\bottop@}
+ \xdef\temp@{#3,,,:,,,,@} \expandafter\test@PDB\temp@
+ \fi
+ \loopcount=0
+ \ifx\list@\ampers@nd
+ \else
+ \loop
+ \advance\loopcount by 1\relax
+ \xdef\list@{\list@ @}
+ \expandafter\get@fregions\list@
+ \ifx\list@\ampers@nd\else\repeat
\fi
- \loopcount=0
- \loop
- \advance\loopcount by 1\relax
- \xdef\list@{\list@ @}
- \expandafter\get@fregions\list@
- \ifx\list@\ampers@nd\else\repeat
\fi\fi\fi
\fi
}
@@ -13764,6 +14192,9 @@
\xdef\first@{\csname res\the\loopcount\endcsname}
\ifx\first@\equ@l
\def\first@{\dom@char} \def\third@{9}
+ \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@
+ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n}
+ \xdef\first@{;\first@}\fi
\expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
\expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
\xdef\first@{=\first@}\fi
@@ -13793,6 +14224,9 @@
\fi
\fi
\fi
+ \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@
+ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n}
+ \xdef\first@{;\first@}\fi
\expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
\expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
\xdef\first@{=\first@}\fi
@@ -13814,6 +14248,9 @@
\def\first@{{}} \def\third@{8}
\fi
\fi
+ \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@
+ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n}
+ \xdef\first@{;\first@}\fi
\expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
\expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
\xdef\first@{=\first@}\fi
@@ -13827,6 +14264,9 @@
\xdef\low@up{lower} \ifx\resn@m@tch\low@up \make@lower \else
\xdef\low@up{upper} \ifx\resn@m@tch\low@up
\else \xdef\first@{\resn@m@tch} \fi\fi\fi
+ \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@
+ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n}
+ \xdef\first@{;\first@}\fi
\expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
\expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
\xdef\first@{=\first@}\fi
@@ -13843,6 +14283,9 @@
\xdef\low@up{lower} \ifx\n@m@tch\low@up \xdef\first@{{ }} \else
\xdef\low@up{upper} \ifx\n@m@tch\low@up \xdef\first@{{ }}
\else \xdef\first@{\n@m@tch} \fi\fi
+ \expandafter\ifx\csname lower@seq0\endcsname\y@
+ \expandafter\xdef\csname lower@seq0\endcsname{n}
+ \xdef\first@{;\first@}\fi
\expandafter\ifx\csname tint@seq0\endcsname\y@
\expandafter\xdef\csname tint@seq0\endcsname{n}
\xdef\first@{=\first@}\fi
@@ -13873,6 +14316,9 @@
\ifx\first@\d@t\def\first@{\gap@char}\fi
\ifx\first@\questi@n\def\first@{\st@p@char}\fi
\ifx\first@\equ@l\def\first@{\dom@char} \xdef\g@p{y} \fi
+ \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@
+ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n}
+ \xdef\first@{;\first@}\fi
\expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
\expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
\xdef\first@{=\first@}\fi
@@ -13937,6 +14383,9 @@
\fi
\fi
\fi
+ \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@
+ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n}
+ \xdef\first@{;\first@}\fi
\expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
\expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
\xdef\first@{=\first@}\fi
@@ -13951,6 +14400,9 @@
\xdef\low@up{lower} \ifx\m@tch\low@up \make@lower \else
\xdef\low@up{upper} \ifx\m@tch\low@up
\else \xdef\first@{\m@tch} \fi\fi
+ \expandafter\ifx\csname lower@seq0\endcsname\y@
+ \expandafter\xdef\csname lower@seq0\endcsname{n}
+ \xdef\first@{;\first@}\fi
\expandafter\ifx\csname tint@seq0\endcsname\y@
\expandafter\xdef\csname tint@seq0\endcsname{n}
\xdef\first@{=\first@}\fi
@@ -13972,6 +14424,9 @@
\xdef\first@{\csname res\the\loopcount\endcsname}
\ifx\first@\equ@l
\def\first@{\dom@char} \def\third@{!} \xdef\g@p{y}
+ \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@
+ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n}
+ \xdef\first@{;\first@}\fi
\expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
\expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
\xdef\first@{=\first@}\fi
@@ -14001,6 +14456,9 @@
\fi
\fi
\fi
+ \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@
+ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n}
+ \xdef\first@{;\first@}\fi
\expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
\expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
\xdef\first@{=\first@}\fi
@@ -14022,6 +14480,9 @@
\def\first@{{}} \def\third@{/}
\fi
\fi
+ \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@
+ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n}
+ \xdef\first@{;\st@p@char}\fi
\expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
\expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
\xdef\first@{=\st@p@char}\fi
@@ -14034,6 +14495,9 @@
\xdef\low@up{lower} \ifx\resn@m@tch\low@up \make@lower \else
\xdef\low@up{upper} \ifx\resn@m@tch\low@up
\else \xdef\first@{\resn@m@tch} \fi\fi
+ \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@
+ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n}
+ \xdef\first@{;\first@}\fi
\expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
\expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
\xdef\first@{=\first@}\fi
@@ -14056,6 +14520,9 @@
\ifx\first@\d@t\def\first@{\gap@char}\fi
\ifx\first@\questi@n\def\first@{\st@p@char}\fi
\ifx\first@\equ@l\def\first@{\dom@char} \xdef\g@p{y} \fi
+ \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@
+ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n}
+ \xdef\first@{;\first@}\fi
\expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
\expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
\xdef\first@{=\first@}\fi
@@ -14069,6 +14536,9 @@
\xdef\first@{\csname res\the\loopcount\endcsname}
\ifx\first@\equ@l
\def\first@{\dom@char} \def\third@{9} \xdef\g@p{y}
+ \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@
+ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n}
+ \xdef\first@{;\first@}\fi
\expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
\expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
\xdef\first@{=\first@}\fi
@@ -14098,6 +14568,9 @@
\fi
\fi
\fi
+ \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@
+ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n}
+ \xdef\first@{;\first@}\fi
\expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
\expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
\xdef\first@{=\first@}\fi
@@ -14119,6 +14592,9 @@
\def\first@{{}} \def\third@{8}
\fi
\fi
+ \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@
+ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n}
+ \xdef\first@{;\first@}\fi
\expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
\expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
\xdef\first@{=\first@}\fi
@@ -14132,6 +14608,9 @@
\xdef\low@up{lower} \ifx\resn@m@tch\low@up \make@lower \else
\xdef\low@up{upper} \ifx\resn@m@tch\low@up
\else \xdef\first@{\resn@m@tch} \fi\fi\fi
+ \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@
+ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n}
+ \xdef\first@{;\first@}\fi
\expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
\expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
\xdef\first@{=\first@}\fi
@@ -14148,6 +14627,9 @@
\xdef\low@up{lower} \ifx\n@m@tch\low@up \xdef\first@{{ }} \else
\xdef\low@up{upper} \ifx\n@m@tch\low@up \xdef\first@{{ }}
\else \xdef\first@{\n@m@tch} \fi\fi
+ \expandafter\ifx\csname lower@seq0\endcsname\y@
+ \expandafter\xdef\csname lower@seq0\endcsname{n}
+ \xdef\first@{;\first@}\fi
\expandafter\ifx\csname tint@seq0\endcsname\y@
\expandafter\xdef\csname tint@seq0\endcsname{n}
\xdef\first@{=\first@}\fi
@@ -14173,6 +14655,9 @@
\ifx\first@\d@t\def\first@{\gap@char}\fi
\ifx\first@\questi@n\def\first@{\st@p@char}\fi
\ifx\first@\equ@l\def\first@{\dom@char} \xdef\g@p{y} \fi
+ \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@
+ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n}
+ \xdef\first@{;\first@}\fi
\expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
\expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
\xdef\first@{=\first@}\fi
@@ -14246,6 +14731,9 @@
\fi
\fi
\fi
+ \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@
+ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n}
+ \xdef\first@{;\first@}\fi
\expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
\expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
\xdef\first@{=\first@}\fi
@@ -14260,6 +14748,9 @@
\xdef\second@{lower} \ifx\m@tch\second@ \make@lower \else
\xdef\second@{upper} \ifx\m@tch\second@
\else \xdef\first@{\m@tch} \fi\fi
+ \expandafter\ifx\csname lower@seq0\endcsname\y@
+ \expandafter\xdef\csname lower@seq0\endcsname{n}
+ \xdef\first@{;\first@}\fi
\expandafter\ifx\csname tint@seq0\endcsname\y@
\expandafter\xdef\csname tint@seq0\endcsname{n}
\xdef\first@{=\first@}\fi
@@ -14284,6 +14775,9 @@
\ifx\first@\d@t\def\first@{\gap@char}\fi
\ifx\first@\questi@n\def\first@{\st@p@char}\fi
\ifx\first@\equ@l\def\first@{\dom@char} \xdef\g@p{y} \fi
+ \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@
+ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n}
+ \xdef\first@{;\first@}\fi
\expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
\expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
\xdef\first@{=\first@}\fi
@@ -14362,6 +14856,9 @@
\fi
\fi
\fi
+ \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@
+ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n}
+ \xdef\first@{;\first@}\fi
\expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
\expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
\xdef\first@{=\first@}\fi
@@ -14376,6 +14873,9 @@
\xdef\second@{lower} \ifx\@llm@tch\second@ \make@lower \else
\xdef\second@{upper} \ifx\@llm@tch\second@
\else \xdef\first@{\@llm@tch} \fi\fi
+ \expandafter\ifx\csname lower@seq0\endcsname\y@
+ \expandafter\xdef\csname lower@seq0\endcsname{n}
+ \xdef\first@{;\first@}\fi
\expandafter\ifx\csname tint@seq0\endcsname\y@
\expandafter\xdef\csname tint@seq0\endcsname{n}
\xdef\first@{=\first@}\fi
@@ -14402,6 +14902,9 @@
\xdef\third@{noshade}
\expandafter\ifx\csname hide@seq\the\loopcount\endcsname\third@
\xdef\first@{\csname res\the\loopcount\endcsname}
+ \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@
+ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n}
+ \xdef\first@{;\first@}\fi
\expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
\expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
\xdef\first@{=\first@}\fi
@@ -14463,6 +14966,9 @@
\fi
\fi
\fi
+ \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@
+ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n}
+ \xdef\first@{;\first@}\fi
\expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
\expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
\xdef\first@{=\first@}\fi
@@ -14521,6 +15027,9 @@
\make@lower \fi
\xdef\third@{noshade}
\expandafter\ifx\csname hide@seq\the\loopcount\endcsname\third@
+ \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@
+ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n}
+ \xdef\first@{;\first@}\fi
\expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
\expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
\xdef\first@{=\first@}\fi
@@ -14531,6 +15040,9 @@
\csname seq\the\loopcount\endcsname%
0\first@}
\else
+ \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@
+ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n}
+ \xdef\first@{;\first@}\fi
\expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
\expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
\xdef\first@{=\first@}\fi
@@ -14586,6 +15098,9 @@
\fi
\xdef\third@{noshade}
\expandafter\ifx\csname hide@seq\the\loopcount\endcsname\third@
+ \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@
+ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n}
+ \xdef\first@{;\first@}\fi
\expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
\expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
\xdef\first@{=\first@}\fi
@@ -14596,6 +15111,9 @@
\csname seq\the\loopcount\endcsname%
*\first@}
\else
+ \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@
+ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n}
+ \xdef\first@{;\first@}\fi
\expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
\expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
\xdef\first@{=\first@}\fi
@@ -14608,6 +15126,9 @@
\fi
\ifnum\loopcount<\seq@count \repeat
\xdef\first@{\csname res0\endcsname}
+ \expandafter\ifx\csname lower@seq0\endcsname\y@
+ \expandafter\xdef\csname lower@seq0\endcsname{n}
+ \xdef\first@{;\first@}\fi
\expandafter\ifx\csname tint@seq0\endcsname\y@
\expandafter\xdef\csname tint@seq0\endcsname{n}
\xdef\first@{=\first@}\fi
@@ -14735,6 +15256,56 @@
\fi
}
+\def\getregion@fromlowerstack@first{%
+ \expandafter\getregion@fromlowerstack{\the\loopcount}
+ \expandafter\ifx\csname lowerstart\the\loopcount\endcsname\ampers@nd
+ \else
+ \expandafter\ifnum\csname lowerstop\the\loopcount\endcsname<\first@@
+ \getregion@fromlowerstack@first
+ \else
+ \expandafter\ifx\csname lowerall\the\loopcount\endcsname\y@
+ \innerloopcount=1
+ \fi
+ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{y}
+ \fi
+ \fi
+}
+
+\def\calc@reglower{%
+ \loopcount=-1 \innerloopcount=0
+ \loop
+ \advance\loopcount by 1
+ \ifnum\loopcount=0 \xdef\first@@{\the\cons@count}
+ \else \xdef\first@@{\csname res@count\the\loopcount\endcsname} \fi
+ \expandafter\ifx\csname lowerstart\the\loopcount\endcsname\ampers@nd
+ \else
+ \expandafter\ifnum\csname lowerstart\the\loopcount\endcsname>\first@@
+ \else
+ \expandafter\ifnum\csname lowerstop\the\loopcount\endcsname<\first@@
+ \getregion@fromlowerstack@first
+ \else
+ \expandafter\ifx\csname lowerall\the\loopcount\endcsname\y@
+ \innerloopcount=1
+ \fi
+ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{y}
+ \expandafter\ifnum\csname lowerstop\the\loopcount\endcsname=\first@@
+ \expandafter\getregion@fromlowerstack{\the\loopcount}
+ \fi
+ \fi
+ \fi\fi
+ \ifnum\loopcount<\seq@count \repeat
+ \loopcount=0
+ \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@
+ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{y}
+ \fi
+ \ifnum\innerloopcount>0
+ \loop
+ \advance\loopcount by 1
+ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{y}
+ \ifnum\loopcount<\seq@count \repeat
+ \fi
+}
+
\def\getregion@fromtintstack@first{%
\expandafter\getregion@fromtintstack{\the\loopcount}
\expandafter\ifx\csname tintstart\the\loopcount\endcsname\ampers@nd
@@ -15024,7 +15595,60 @@
\advance\innerloopcount by 1
\xdef\second@@@{\csname res\the\innerloopcount\endcsname}
\xdef\third@@@{\csname cons\first@@@\second@@@\endcsname}
- \advance\temp@count by \third@@@
+ \advance\temp@count by \third@@@
+ \ifnum\innerloopcount<\seq@count\sum@up\fi
+}
+
+\def\sum@up@cons{%
+ \innerloopcount=\outerloopcount
+ \xdef\first@@@{\csname res\the\outerloopcount\endcsname}
+ \sum@up
+ \advance\outerloopcount by 1\relax
+ \ifnum\outerloopcount<\seq@count
+ \sum@up@cons
+ \else
+ \innerloopcount=\seq@count
+ \advance\innerloopcount by -1
+ \multiply\innerloopcount by \seq@count
+ \multiply\temp@count by 2
+ \multiply\temp@count by \m@trixf@ctor
+ \divide\temp@count by \innerloopcount
+
+ \ifnum\temp@count>100 \temp@count=100 \fi
+ \ifnum\temp@count<0 \temp@count=0 \fi
+ \xdef\cons@val{\the\temp@count}
+ \ifx\first@\equ@l \xdef\cons@val{N} \fi
+
+ \ifx\T@coffee@bcons\y@
+ \xdef\cons@val{\csname TC@num0\endcsname}
+ \if\cons@val *
+ \xdef\cons@val{99}
+ \fi
+ \fi
+ \ifx\T@coffee@ccons\y@
+ \xdef\cons@val{\csname TC@num0\endcsname}
+ \if\cons@val *
+ \xdef\cons@val{99}
+ \fi
+ \fi
+ \fi
+}
+
+\def\collect@cons@res{%
+ \xdef\temp@{\temp@\csname res\the\innerloopcount\endcsname}
+ \advance\innerloopcount by 1
+ \ifnum\innerloopcount>\seq@count\relax
+ \outerloopcount=1\relax
+ \temp@count=0\relax
+ \sum@up@cons
+ \else
+ \collect@cons@res
+ \fi
+}
+
+\def\sum@@up{%
+ \advance\innerloopcount by 1
+ \xdef\second@@@{\csname res\the\innerloopcount\endcsname}
\ifx\first@@@\d@t
\else
@@ -15062,55 +15686,32 @@
\fi
\fi
- \ifnum\innerloopcount<\seq@count\sum@up\fi
+ \ifnum\innerloopcount<\seq@count\sum@@up\fi
}
-\def\sum@up@cons{%
+\def\sum@up@sim{%
\innerloopcount=\outerloopcount
\xdef\first@@@{\csname res\the\outerloopcount\endcsname}
- \sum@up
+ \sum@@up
\advance\outerloopcount by 1\relax
\ifnum\outerloopcount<\seq@count
- \sum@up@cons
- \else
- \innerloopcount=\seq@count
- \advance\innerloopcount by -1
- \multiply\innerloopcount by \seq@count
- \multiply\temp@count by 2
- \multiply\temp@count by \m@trixf@ctor
- \divide\temp@count by \innerloopcount
-
- \ifnum\temp@count>100 \temp@count=100 \fi
- \ifnum\temp@count<0 \temp@count=0 \fi
- \xdef\cons@val{\the\temp@count}
- \ifx\first@\equ@l \xdef\cons@val{N} \fi
-
- \ifx\T@coffee@bcons\y@
- \xdef\cons@val{\csname TC@num0\endcsname}
- \if\cons@val *
- \xdef\cons@val{99}
- \fi
- \fi
- \ifx\T@coffee@ccons\y@
- \xdef\cons@val{\csname TC@num0\endcsname}
- \if\cons@val *
- \xdef\cons@val{99}
- \fi
- \fi
+ \sum@up@sim
\fi
}
-\def\collect@cons@res{%
+\def\collect@similarity{%
\xdef\temp@{\temp@\csname res\the\innerloopcount\endcsname}
\advance\innerloopcount by 1
\ifnum\innerloopcount>\seq@count\relax
\outerloopcount=1\relax
\temp@count=0\relax
- \sum@up@cons
+ \sum@up@sim
\else
- \collect@cons@res
+ \collect@similarity
\fi
}
+
+
\def\sum@up@bits{%
\ifx\first@@@\second@@@
\ifx\first@@@\d@t
@@ -16337,6 +16938,7 @@
\ifregionalshadenow \calc@regshade \fi
\ifregionaltintnow \calc@regtint \fi
\ifregionalemphnow \calc@regemph \fi
+ \ifregionallowernow \calc@reglower \fi
\ifframenow \calc@frame \fi
\iftopfeaturenow \xdef\bottop@{top} \calc@feature \fi
\ifttopfeaturenow \xdef\bottop@{ttop} \calc@feature \fi
@@ -16346,6 +16948,7 @@
\ifbbottomfeaturenow \xdef\bottop@{bbottom} \calc@feature \fi
\ifbbbottomfeaturenow \xdef\bottop@{bbbottom} \calc@feature \fi
\ifbbbbottomfeaturenow \xdef\bottop@{bbbbottom} \calc@feature \fi
+ \ifnum\seq@count>1 \innerloopcount=1 \collect@similarity \fi
\advance\pos@count by 1
\ifshow@logo \calc@logo \fi
\ifall@fshade \all@funcshade
@@ -16495,11 +17098,20 @@
\expandafter\ifnum\csname emphstart\the\loopcount\endcsname>%
\innerloopcount
\else
- \else
\regionalemphnowtrue
\fi
\fi
\fi
+ \ifregionallower
+ \expandafter\ifx\csname lowerstart\the\loopcount\endcsname\ampers@nd
+ \else
+ \expandafter\ifnum\csname lowerstart\the\loopcount\endcsname>%
+ \innerloopcount
+ \else
+ \regionallowernowtrue
+ \fi
+ \fi
+ \fi
\ifframe@
\expandafter\ifx\csname framestart\the\loopcount\endcsname\ampers@nd
\else
@@ -16655,7 +17267,7 @@
\else
\innerloopcount=\csname res@count\the\loopcount\endcsname
\advance\innerloopcount by \res@perline
- \fi %%%%%%%%%%%%%*****
+ \fi
\advance\innerloopcount by 1
\ifregionalshade
\expandafter\ifx\csname start\the\loopcount\endcsname\ampers@nd
@@ -16687,6 +17299,16 @@
\fi
\fi
\fi
+ \ifregionallower
+ \expandafter\ifx\csname lowerstart\the\loopcount\endcsname\ampers@nd
+ \else
+ \expandafter\ifnum\csname lowerstart\the\loopcount\endcsname>%
+ \innerloopcount
+ \else
+ \regionallowernowtrue
+ \fi
+ \fi
+ \fi
\ifframe@
\expandafter\ifx\csname framestart\the\loopcount\endcsname\ampers@nd
\else
@@ -17101,6 +17723,14 @@
\xdef\temp@@{\light@}%
\expandafter\get@second@\first@%
\fi%
+ \ifx\second@\semic@n%
+ \expandafter\get@second@\first@%
+ \xdef\first@@{\first@}%
+ \xdef\first@{\second@}%
+ \make@lower%
+ \xdef\second@{\first@}%
+ \xdef\first@{\first@@}%
+ \fi%
\textcolor{\temp@@\boxc@l@r}{\box@rule}%
\ifhidechar%
\ifx\second@\o@%
@@ -17205,6 +17835,14 @@
\else%
\def\temp@{\csname relax\endcsname}%
\fi%
+ \ifx\second@\semic@n%
+ \expandafter\get@second@\first@%
+ \xdef\first@@{\first@}%
+ \xdef\first@{\second@}%
+ \make@lower%
+ \xdef\second@{\first@}%
+ \xdef\first@{\first@@}%
+ \fi%
\textcolor{\boxc@l@r}{\box@rule}%
\ifhidechar%
\ifx\second@\o@%
@@ -19265,7 +19903,7 @@
\expandafter\xdef\csname sequence\the\loopcount\endcsname{}
\expandafter\xdef\csname dom@num\the\loopcount\endcsname{}
\expandafter\xdef\csname dom@num@break\the\loopcount\endcsname{}
- \expandafter\xdef\csname dom@count\the\loopcount\endcsname{0}
+ \expandafter\xdef\csname dom@count\the\loopcount\endcsname{\csname res@count\the\loopcount\endcsname}
\ifnum\loopcount<\seq@count\repeat
\xdef\domain@num@list{}
\xdef\last@{\stack@dom}
@@ -19314,6 +19952,7 @@
\fi
\ifshow@sublogo \prep@sublogo \fi
\ifshow@logo \prep@logo \fi
+ \ifx\label@motif\y@ \prep@motif \fi
\ifnum\seq@pointer>\res@perline \block@output \fi
\else \read@loop
\fi}
@@ -19365,7 +20004,7 @@
\expandafter\xdef\csname sequence\the\loopcount\endcsname{}
\expandafter\xdef\csname dom@num\the\loopcount\endcsname{}
\expandafter\xdef\csname dom@num@break\the\loopcount\endcsname{}
- \expandafter\xdef\csname dom@count\the\loopcount\endcsname{0}
+ \expandafter\xdef\csname dom@count\the\loopcount\endcsname{\csname res@count\the\loopcount\endcsname}
\ifnum\loopcount<\seq@count\repeat
\xdef\domain@num@list{}
\xdef\last@{\stack@dom}
@@ -19414,6 +20053,7 @@
\fi
\ifshow@sublogo \prep@sublogo \fi
\ifshow@logo \prep@logo \fi
+ \ifx\label@motif\y@ \prep@motif \fi
\ifnum\seq@pointer>\res@perline \block@output \fi
\else
\read@fasta
@@ -19548,8 +20188,8 @@
\expandafter\xdef\csname stack@dom\endcsname{&;&;&;&;@}
\expandafter\xdef\csname stack@reg\the\loopcount\endcsname{&;&;&;&;@}
\expandafter\xdef\csname stack@tintreg\the\loopcount\endcsname{&;&;&;@}
- \expandafter\xdef\csname stack@hidereg\the\loopcount\endcsname{&;&;&;&;@}
\expandafter\xdef\csname stack@emphreg\the\loopcount\endcsname{&;&;&;@}
+ \expandafter\xdef\csname stack@lowerreg\the\loopcount\endcsname{&;&;&;@}
\expandafter\xdef\csname stack@framereg\the\loopcount\endcsname{&;&;&;@}
\expandafter\xdef\csname stack@top\the\loopcount\endcsname{&;&;&;&;@}
\expandafter\xdef\csname stack@ttop\the\loopcount\endcsname{&;&;&;&;@}
@@ -19569,6 +20209,7 @@
\cleanup@name
\expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
\expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n}
+ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n}
\expandafter\xdef\csname hide@seq\the\loopcount\endcsname{false}
\expandafter\xdef\csname hide@@@seq\the\loopcount\endcsname{false}
\expandafter\xdef\csname hide@name\the\loopcount\endcsname{no}
@@ -19577,8 +20218,8 @@
\expandafter\xdef\csname number@col\the\loopcount\endcsname{yes}
\expandafter\xdef\csname stack@reg\the\loopcount\endcsname{&;&;&;&;@}
\expandafter\xdef\csname stack@tintreg\the\loopcount\endcsname{&;&;&;@}
- \expandafter\xdef\csname stack@hidereg\the\loopcount\endcsname{&;&;&;&;@}
\expandafter\xdef\csname stack@emphreg\the\loopcount\endcsname{&;&;&;@}
+ \expandafter\xdef\csname stack@lowerreg\the\loopcount\endcsname{&;&;&;@}
\expandafter\xdef\csname stack@framereg\the\loopcount\endcsname{&;&;&;@}
\expandafter\xdef\csname stack@top\the\loopcount\endcsname{&;&;&;&;@}
\expandafter\xdef\csname stack@ttop\the\loopcount\endcsname{&;&;&;&;@}
@@ -19625,9 +20266,9 @@
\ifshow@cons\setbox1=\hbox{\cons@name}\name@width=\wd1\else\name@width=0pt\fi
\loopcount=0
\expandafter\getregion@fromstack{\the\loopcount}
- \expandafter\getregion@fromhidestack{\the\loopcount}
\expandafter\getregion@fromtintstack{\the\loopcount}
\expandafter\getregion@fromemphstack{\the\loopcount}
+ \expandafter\getregion@fromlowerstack{\the\loopcount}
\expandafter\getregion@fromframestack{\the\loopcount}
\xdef\bottop@{top} \expandafter\getregion@fromfstack{\the\loopcount}
\xdef\bottop@{ttop} \expandafter\getregion@fromfstack{\the\loopcount}
@@ -19676,9 +20317,9 @@
\baselineskip=\box@height \advance\baselineskip by \box@depth
\fi
\expandafter\getregion@fromstack{\the\loopcount}
- \expandafter\getregion@fromhidestack{\the\loopcount}
\expandafter\getregion@fromtintstack{\the\loopcount}
\expandafter\getregion@fromemphstack{\the\loopcount}
+ \expandafter\getregion@fromlowerstack{\the\loopcount}
\expandafter\getregion@fromframestack{\the\loopcount}
\xdef\bottop@{top} \expandafter\getregion@fromfstack{\the\loopcount}
\xdef\bottop@{ttop} \expandafter\getregion@fromfstack{\the\loopcount}
@@ -19910,7 +20551,7 @@
\cons@count=0
\expandafter\xdef\csname res@count0\endcsname{0}
\xdef\allow@zero{n} \xdef\c@ns@shift{0}
-\regionalshadefalse\regionalemphfalse\regionaltintfalse
+\regionalshadefalse\regionalemphfalse\regionallowerfalse\regionaltintfalse
\frame@false
\xdef\ruler@rot{0}
\topfeaturefalse \bottomfeaturefalse
@@ -20019,7 +20660,8 @@
\xdef\all@thresh@ld{100} \all@shadefalse
\hidefeaturenames \hidefeaturestylenames
\xdef\T@coffee@ccons{n} \xdef\T@coffee@bcons{n}
-\xdef\dom@in{no}
+\xdef\dom@in{no} \xdef\label@motif{no}
+\xdef\motif@num{0}
\hfuzz9999pt
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -20282,7 +20924,7 @@
\medsepline % Medium height if separation line is on
\medblockskip % Medium skip between sequence blocks
\flexblockspace % Use optimized space between blocks
-\featurerule{0.5ex} % Set feature rule thickness to 1/5 ex
+\featurerule{0.5ex} % Set feature rule thickness to 1/2 ex
\bargraphstretch{1} % Do not stretch bars in feature graphs
\colorscalestretch{1} % Do not stretch color scales in features
\backtranstext{horizontal} % Horizontal triplets in feature texts
@@ -20311,6 +20953,10 @@
\setseries{features}{md} % Use normal series for feature texts
\setshape {features}{it} % Use italics shape for feature texts
\setsize {features}{normalsize} % Use normal size for feature texts
+\setfamily{featurestyles}{tt} % Use typewriter family for feature styles
+\setseries{featurestyles}{md} % Use normal series for feature styles
+\setshape {featurestyles}{up} % Use upright shape for feature styles
+\setsize {featurestyles}{normalsize}% Use normal size for feature styles
\setfamily{legend}{tt} % Use typewriter family for legend texts
\setseries{legend}{md} % Use normal series for legend texts
\setshape {legend}{up} % Use upright shape for legend texts
@@ -20333,10 +20979,10 @@
\appearance{PHDtopo}{TM}{top} % |
{box[LightGray]:TM\numcount}{} % |
\appearance{HMMTOP}{internal} % |
- {bottom}{---} % |
+ {bottom}{'-'} % |
{int.\ \Alphacount} % |
\appearance{HMMTOP}{external} % |
- {top}{---} % |
+ {top}{,-,} % |
{ext.\ \Alphacount} % |
\appearance{HMMTOP}{TM}{top} % |
{helix}{TM\numcount} % |
@@ -20370,7 +21016,6 @@
{top}{,-,}{turn} % |
\appearance{DSSP}{bend}{top} % /
{fill:$\diamond$}{} % /
-
\pepgroups{FYW,ILVM,RK,DE,GA,ST,NQ} % Amino acid grouping due to similarity
@@ -20397,7 +21042,6 @@
\pepsims{N}{QD} % Q and D (but not E) are similar to N
\pepsims{Q}{NE} % N and E (but not D) are similar to Q
-
\DNAgroups{GAR,CTY} % Nucleotide grouping due to similarity
\DNAsims{A}{GR} % G and R are similar to A
diff --git a/Master/texmf-dist/source/latex/texshade/texshade.ins b/Master/texmf-dist/source/latex/texshade/texshade.ins
index 51f043c8d20..b45ae964513 100644
--- a/Master/texmf-dist/source/latex/texshade/texshade.ins
+++ b/Master/texmf-dist/source/latex/texshade/texshade.ins
@@ -1,7 +1,7 @@
%%
%% docstrip install file for texshade.sty
%%
-%% Copyright 1999-2009 Eric Beitz
+%% Copyright 1999-2010 Eric Beitz
%%
\def\batchfile{texshade.ins}
@@ -14,7 +14,7 @@
LaTeX package for typesetting nucleotide and peptide alignments
-Copyright (C) 1999-2009 Eric Beitz
+Copyright (C) 1999-2010 Eric Beitz
See the file texshade.txt
\endpreamble