From 09957f78ef831e10c41f8b12329282e8bcef03e3 Mon Sep 17 00:00:00 2001 From: Karl Berry Date: Fri, 5 Mar 2010 00:29:23 +0000 Subject: texshade 1.21 (2mar10) git-svn-id: svn://tug.org/texlive/trunk@17314 c570f23f-e606-0410-a88d-b1316a301751 --- .../texmf-dist/source/latex/texshade/texshade.dtx | 936 +++++++++++++++++---- .../texmf-dist/source/latex/texshade/texshade.ins | 4 +- 2 files changed, 792 insertions(+), 148 deletions(-) (limited to 'Master/texmf-dist/source/latex/texshade') 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{} + \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 @@ -16494,12 +17097,21 @@ \else \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 -- cgit v1.2.3