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authorKarl Berry <karl@freefriends.org>2010-10-12 00:14:10 +0000
committerKarl Berry <karl@freefriends.org>2010-10-12 00:14:10 +0000
commitd514da93f0c807683bc53dab573bc0900c64b3c9 (patch)
treebffd4d97992ba34a75243ff7e521653a20d3db70 /Master/texmf-dist
parent789dbe837b7d397424aa86d0c0439fdb2d5a9703 (diff)
texshade (11oct10)
git-svn-id: svn://tug.org/texlive/trunk@20065 c570f23f-e606-0410-a88d-b1316a301751
Diffstat (limited to 'Master/texmf-dist')
-rw-r--r--Master/texmf-dist/doc/latex/texshade/README2
-rw-r--r--Master/texmf-dist/doc/latex/texshade/texshade.pdfbin692481 -> 760478 bytes
-rw-r--r--Master/texmf-dist/source/latex/texshade/texshade.dtx320
-rw-r--r--Master/texmf-dist/tex/latex/texshade/texshade.sty256
4 files changed, 509 insertions, 69 deletions
diff --git a/Master/texmf-dist/doc/latex/texshade/README b/Master/texmf-dist/doc/latex/texshade/README
index 6cb21a49fb5..4bfb071ff50 100644
--- a/Master/texmf-dist/doc/latex/texshade/README
+++ b/Master/texmf-dist/doc/latex/texshade/README
@@ -1,4 +1,4 @@
- TeXshade v1.21
+ TeXshade v1.22
>>
>> A LaTeX package for setting nucleotide and peptide alignments.
>>
diff --git a/Master/texmf-dist/doc/latex/texshade/texshade.pdf b/Master/texmf-dist/doc/latex/texshade/texshade.pdf
index 78bc44f0b78..fe59789d182 100644
--- a/Master/texmf-dist/doc/latex/texshade/texshade.pdf
+++ b/Master/texmf-dist/doc/latex/texshade/texshade.pdf
Binary files differ
diff --git a/Master/texmf-dist/source/latex/texshade/texshade.dtx b/Master/texmf-dist/source/latex/texshade/texshade.dtx
index c5098fdb54b..bcfd2b97ea3 100644
--- a/Master/texmf-dist/source/latex/texshade/texshade.dtx
+++ b/Master/texmf-dist/source/latex/texshade/texshade.dtx
@@ -10,7 +10,7 @@
% `README.txt' for further information!
%
%
-% Copyright (C) 1999-2009 Eric Beitz
+% Copyright (C) 1999-2010 Eric Beitz
% See the file texshade.txt
%
% \fi
@@ -372,6 +372,15 @@
% `lowerregion' and `lowerblock'.
% }
%
+% \changes{1.22}{2010-10-11}{%
+% Corrections: minor bug fixes.
+% Introduction: `defshadingcolors' defines and names sets of shading
+% colors for later re-use within the alignment;
+% `changeshadingcolors' allows one to use different sets
+% of shading colors in different sequence blocks.
+% }
+%
+%
%
% \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
@@ -410,7 +419,7 @@
% 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 v1.21; 2010/03/01\\[2pt]}
+% \date{\small v1.22; 2010/10/11\\[2pt]}
% \maketitle
% \begin{abstract}
% Setting alignments of nucleotides and peptides for publication
@@ -489,6 +498,16 @@
%
% \subsection{Version History}
%
+% \textbf{v1.22 2010/10/11}
+% \medskip
+%
+% \emph{Introductions:}
+% Sets of shading colors can be defined and named using
+% |\defshadingcolors| (p.\ \pageref{Ldefshadingcolors}) and different
+% sets of colors can be selected for different sequence blocks by
+% |\changeshadingcolors| (\ref{Lchangeshadingcolors}).
+% \medskip
+%
% \textbf{v1.21 2010/03/01}
% \medskip
%
@@ -511,7 +530,6 @@
% line.
% \medskip
%
-% \newpage
%
% \textbf{v1.20 2009/10/05}
% \medskip
@@ -2325,7 +2343,7 @@
%
% \item |\shadingmode[|\meta{allmatchspecial/number}|]{identical}|
%
-% There is not much to explain here (see \ref{ident}). Use the
+% See \ref{ident} for examples. Use the
% option |allmatchspecial| to shade positions with a special color
% where all residues are identical. Or use a percentage number
% (0--100) as an option to set an additional threshold for highly
@@ -2396,6 +2414,11 @@
% Note the double curly braces which make \TeXshade{}
% interpret this complex symbol description as one single
% character.
+%
+% Once a set of shading colors is redefined, it can be saved using
+% |\defshadingcolors{|\meta{name}|}|\label{Ldefshadingcolors} for
+% later use in the document (see \ref{shaderegion}).
+%
% \bigskip
%
%
@@ -3593,6 +3616,25 @@
% \medskip
%
%
+% Another option is to change the whole set of shading colors for certain
+% sequence blocks, e.\,g.\ from |blues| to |reds| or self-defined color sets (see \ref{Lshadingmode}).
+% Therefore, the following command was implemented:
+% \medskip
+%
+% \quad |\changeshadingcolors{|\meta{seqref}|}{|\meta{selection}|}{|\meta{name}|}|
+% \medskip \label{Lchangeshadingcolors}
+%
+% Examples:
+% \medskip
+%
+% \quad |\changeshadingcolors{1}{10..50}{reds}|
+% \medskip
+%
+% \quad |\changeshadingcolors{AQP1}{[AS]NKD}{my_set}|
+% \medskip
+%
+% etc.
+%
% \subsubsection{Emphasizing, tinting, lowercasing, and framing}
%
% \label{Lemphregion}\label{Lemphblock}
@@ -4119,8 +4161,12 @@
%
% See section \ref{colors} for how to select colors in \TeX{}shade.
%
-% Font styles can be set as usual, e.\,g.\ |\setsize{featurenames}{large}| or
-% |\featurestylenamesrm| etc. (see section \ref{Lsetfamily}).
+% Font styles can be set as usual (see section \ref{Lsetfamily}), e.\,g.\
+% \medskip
+%
+% |\setsize{featurenames}{large}| or |\featurestylenamesrm| etc.
+% \medskip
+%
%
%
% Examples for the appearance of features are given in the
@@ -5594,6 +5640,8 @@
% \quad|\conservedresidues{|\meta{res.col.}|}{|\meta{shad.col.}|}{|\meta{case}|}{|\meta{style}|}|
%
% \quad|\allmatchresidues{|\meta{res.col.}|}{|\meta{shad.col.}|}{|\meta{case}|}{|\meta{style}|}|
+%
+% \quad|\defshadingcolors{|\meta{name}|}|
% \newpage
%
% \quad|\funcshadingstyle{|\meta{residue}|}{|\meta{res.col.}|}{|\meta{shad.color}|}|
@@ -5975,8 +6023,8 @@
% \quad|\shadeblock{|\meta{seqref}|}{|\meta{selection}|}{|\meta{res.col.}|}{|\meta{shad.col.}|}|
% \hfill[\pageref{Lshadeblock}]
%
-% \quad|\shadeblock{|\meta{seqref}|}{|\meta{selection}|}{|\meta{res.col.}|}{|\meta{shad.col.}|}|
-% \hfill[\pageref{Lshadeblock}]
+% \quad|\changeshadingcolors{|\meta{seqref}|}{|\meta{selection}|}{|\meta{name}|}|
+% \hfill[\pageref{Lchangeshadingcolors}]
%
% \quad|\emphregion{|\meta{seqref}|}{|\meta{selection}|}|
% \hfill[\pageref{Lemphregion}]
@@ -6378,8 +6426,8 @@
% \begin{macrocode}
%<*texshade>
\NeedsTeXFormat{LaTeX2e}
-\ProvidesPackage{texshade}[2010/03/01 LaTeX TeXshade (v1.21)]
-\message{Package `texshade', Version 1.21 of 2010/03/01.}
+\ProvidesPackage{texshade}[2010/10/11 LaTeX TeXshade (v1.22)]
+\message{Package `texshade', Version 1.22 of 2010/10/11.}
\PassOptionsToPackage{dvips}{color}
\PassOptionsToPackage{dvips}{graphicx}
@@ -6479,6 +6527,7 @@
\newif\ifall@fshade \newif\ifregionalemph
\newif\ifregionallower
\newif\ifframe@ \newif\ifregionaltint
+\newif\ifshading@
\newif\ifshow@logo \newif\ifshow@sublogo
\newif\ifhidechar \newif\ifsh@wg@ps
\newif\ifsimmode
@@ -6495,6 +6544,7 @@
\newif\ifbbbottomfeaturenow
\newif\ifbbbbottomfeaturenow
\newif\ifframenow
+\newif\ifshadingnow
\newif\iffix@
\expandafter\ifx\csname mdqon\endcsname\relax
@@ -6506,7 +6556,7 @@
\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\semic@n{;}
-\def\br@cket{[}
+\def\br@cket{[} \def\p@r@gr@ph{¤}
\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}
@@ -8671,6 +8721,8 @@
\csname stack@@lowerreg#1\endcsname}
\expandafter\xdef\csname stack@framereg\the\loopcount\endcsname{%
\csname stack@@framereg#1\endcsname}
+ \expandafter\xdef\csname stack@shadingreg\the\loopcount\endcsname{%
+ \csname stack@@shadingreg#1\endcsname}
\expandafter\xdef\csname stack@top\the\loopcount\endcsname{%
\csname stack@@top#1\endcsname}
\expandafter\xdef\csname stack@ttop\the\loopcount\endcsname{%
@@ -8724,6 +8776,8 @@
\csname stack@lowerreg\the\loopcount\endcsname}
\expandafter\xdef\csname stack@@framereg\the\loopcount\endcsname{%
\csname stack@framereg\the\loopcount\endcsname}
+ \expandafter\xdef\csname stack@@shadingreg\the\loopcount\endcsname{%
+ \csname stack@shadingreg\the\loopcount\endcsname}
\expandafter\xdef\csname stack@@top\the\loopcount\endcsname{%
\csname stack@top\the\loopcount\endcsname}
\expandafter\xdef\csname stack@@ttop\the\loopcount\endcsname{%
@@ -9013,6 +9067,8 @@
\csname stack@lowerreg\the\innerloopcount\endcsname}
\expandafter\xdef\csname stack@framereg\the\loopcount\endcsname{%
\csname stack@framereg\the\innerloopcount\endcsname}
+ \expandafter\xdef\csname stack@shadingreg\the\loopcount\endcsname{%
+ \csname stack@shadingreg\the\innerloopcount\endcsname}
\expandafter\xdef\csname stack@top\the\loopcount\endcsname{%
\csname stack@top\the\innerloopcount\endcsname}
\expandafter\xdef\csname stack@ttop\the\loopcount\endcsname{%
@@ -9425,6 +9481,23 @@
\sort@emphstack
\expandafter\xdef\csname stack@framereg\seq@\endcsname{\tmpstack}
}
+\def\getregion@fromshadingstack#1{%
+ \xdef\temp@{#1}
+ \xdef\first@{\csname stack@shadingreg\temp@\endcsname}
+ \expandafter\get@fromemphstack\first@
+ \expandafter\xdef\csname shadingstart\temp@\endcsname{\first@}
+ \expandafter\xdef\csname shadingstop\temp@\endcsname{\second@}
+ \expandafter\xdef\csname shadingstyle\temp@\endcsname{\third@}
+ \expandafter\xdef\csname stack@shadingreg\temp@\endcsname{\last@}
+}
+\def\get@shadingregions#1..#2,#3@{%
+ \shading@true
+ \xdef\st@rt{#1} \xdef\st@p{#2} \xdef\list@{#3}
+ \xdef\last@{\csname stack@shadingreg\seq@\endcsname}
+ \xdef\tmpstack{}
+ \sort@emphstack
+ \expandafter\xdef\csname stack@shadingreg\seq@\endcsname{\tmpstack}
+}
\def\getregion@fromfstack#1{%
\xdef\temp@{#1}
\xdef\first@{\csname stack@\bottop@\temp@\endcsname}
@@ -9462,14 +9535,6 @@
\sort@fstack
\expandafter\xdef\csname stack@\bottop@\seq@\endcsname{\tmpstack}
}
-\def\get@frameregions#1..#2,#3@{%
- \frame@true
- \xdef\st@rt{#1} \xdef\st@p{#2} \xdef\list@{#3}
- \xdef\last@{\csname stack@framereg\seq@\endcsname}
- \xdef\tmpstack{}
- \sort@emphstack
- \expandafter\xdef\csname stack@framereg\seq@\endcsname{\tmpstack}
-}
\def\getarrow@shape#1#2#3#4&{%
\xdef\first@@{#1}\xdef\second@@{#2}\xdef\third@@{#3}
\if\first@@ v
@@ -9617,9 +9682,9 @@
\xdef\temp@{tint}
\ifx\temp@\temp@@
\regionaltinttrue
- \xdef\last@{\csname stack@tintreg\seq@\endcsname} \message{((last:\last@))}
+ \xdef\last@{\csname stack@tintreg\seq@\endcsname}
\sort@emphstack
- \expandafter\xdef\csname stack@tintreg\seq@\endcsname{\tmpstack} \message{((tmp:\tmpstack))}
+ \expandafter\xdef\csname stack@tintreg\seq@\endcsname{\tmpstack}
\else
\xdef\temp@{frame}
\ifx\temp@\temp@@
@@ -9628,6 +9693,13 @@
\sort@emphstack
\expandafter\xdef\csname stack@framereg\seq@\endcsname{\tmpstack}
\else
+ \xdef\temp@{shading}
+ \ifx\temp@\temp@@
+ \shading@true
+ \xdef\last@{\csname stack@shadingreg\seq@\endcsname}
+ \sort@emphstack
+ \expandafter\xdef\csname stack@shadingreg\seq@\endcsname{\tmpstack}
+ \else
\xdef\temp@{ttttop}
\ifx\temp@\temp@@
\xdef\last@{\csname stack@ttttop\seq@\endcsname}
@@ -9688,10 +9760,15 @@
\fi
\fi
\fi
+ \fi
\xdef\fifth@@{\m@tif} \expandafter\get@third@\fifth@@
\xdef\nineth@@{n}
\fi
\else
+ \ifx\nineth@@\y@
+ \xdef\first@@{\second@@\first@@}
+ \advance\temp@count by -1
+ \fi
\xdef\nineth@@{n} \xdef\st@p{n}
\xdef\fifth@@{\m@tif} \expandafter\get@third@\fifth@@
\fi
@@ -9729,6 +9806,10 @@
\csname framestop\the\loopcount\endcsname;%
\csname framestyle\the\loopcount\endcsname;%
\csname stack@framereg\the\loopcount\endcsname}
+ \expandafter\xdef\csname stack@shadingreg\the\loopcount\endcsname{\csname shadingstart\the\loopcount\endcsname;%
+ \csname shadingstop\the\loopcount\endcsname;%
+ \csname shadingstyle\the\loopcount\endcsname;%
+ \csname stack@shadingreg\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;%
@@ -9791,6 +9872,7 @@
\expandafter\getregion@fromemphstack{\the\loopcount}
\expandafter\getregion@fromlowerstack{\the\loopcount}
\expandafter\getregion@fromframestack{\the\loopcount}
+ \expandafter\getregion@fromshadingstack{\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}
@@ -9813,6 +9895,8 @@
\ifx\temp@\temp@@ \xdef\style@{0} \fi
\xdef\temp@{frame}
\ifx\temp@\temp@@ \xdef\style@{0} \fi
+ \xdef\temp@{shading}
+ \ifx\temp@\temp@@ \xdef\style@{0} \fi
\xdef\temp@{#1#2}
\xdef\first@{#1}
\ifx\first@\br@cket
@@ -11765,6 +11849,28 @@
\fi
\fi
}
+\def\changeshadingcolors#1#2#3{%
+ \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\changeshadingcolors>}
+ \else
+ \xdef\@ll{#3}
+ \xdef\list@{#2,&}
+ \xdef\temp@@{shading} \loopcount=0
+ \xdef\temp@{#2,,,:,,,,@} \expandafter\test@PDB\temp@
+ \ifx\list@\ampers@nd
+ \else
+ \loop
+ \xdef\list@{\list@ @}
+ \expandafter\get@shadingregions\list@
+ \ifx\list@\ampers@nd\else\repeat
+ \fi
+ \fi
+}
\def\bargraphstretch#1{\def\b@r@stretch{#1}}
\def\colorscalestretch#1{\def\sc@le@stretch{#1}}
\def\rm@@measure#1#2@{%
@@ -12149,7 +12255,9 @@
\xdef\f@color{\f@@color}
\xdef\temp@{#4&}
\ifx\temp@\ampers@nd
+ \xdef\list@{#3,&}
\xdef\style@{&}
+ \def\f@text@{#5}
\else
\xdef\last@{restriction}
\ifx\second@@\last@
@@ -13310,6 +13418,27 @@
\expandafter\xdef\csname funcm@tch\first@\endcsname{#4}
\expandafter\def\csname func@style\first@\endcsname{\csname text#5\endcsname}
\fi}
+\def\defshadingcolors#1{%
+ \expandafter\xdef\csname TextNomatch@#1\endcsname{\TextNomatch}
+ \expandafter\xdef\csname Nomatch@#1\endcsname{\Nomatch}
+ \expandafter\xdef\csname resn@m@tch@#1\endcsname{\resn@m@tch}
+
+ \expandafter\xdef\csname TextSimilar@#1\endcsname{\TextSimilar}
+ \expandafter\xdef\csname Similar@#1\endcsname{\Similar}
+ \expandafter\xdef\csname ressimm@tch@#1\endcsname{\ressimm@tch}
+
+ \expandafter\xdef\csname TextIdentical@#1\endcsname{\TextIdentical}
+ \expandafter\xdef\csname Identical@#1\endcsname{\Identical}
+ \expandafter\xdef\csname resm@tch@#1\endcsname{\resm@tch}
+
+ \expandafter\xdef\csname TextAllmatch@#1\endcsname{\TextAllmatch}
+ \expandafter\xdef\csname Allmatch@#1\endcsname{\Allmatch}
+ \expandafter\xdef\csname res@llm@tch@#1\endcsname{\res@llm@tch}
+
+ \expandafter\xdef\csname gap@fg@#1\endcsname{\gap@fg}
+ \expandafter\xdef\csname gap@bg@#1\endcsname{\gap@bg}
+
+}
\def\shadingcolors#1{%
\gapcolors{Black}{White}
\nomatchresidues{Black}{White}{upper}{up}
@@ -13335,12 +13464,30 @@
\allmatchresidues{White}{Black}{upper}{sl}
\else \xdef\second@{grays}
\ifx\first@\second@
- \else \message{<Undefined color set - using `grays'>} \xdef\first@{grays}\fi
- \ifx\first@\second@
\similarresidues{Black}{LightGray}{upper}{up}
\conservedresidues{White}{DarkGray}{upper}{up}
\allmatchresidues{White}{Black}{upper}{up}
- \fi\fi\fi\fi\fi}
+ \else
+ \xdef\TextNomatch{\csname TextNomatch@#1\endcsname}
+ \xdef\Nomatch {\csname Nomatch@#1\endcsname}
+ \xdef\resn@m@tch {\csname resn@m@tch@#1\endcsname}
+ \xdef\TextSimilar{\csname TextSimilar@#1\endcsname}
+ \xdef\Similar {\csname Similar@#1\endcsname}
+ \xdef\ressimm@tch{\csname ressimm@tch@#1\endcsname}
+ \xdef\TextIdentical{\csname TextIdentical@#1\endcsname}
+ \xdef\Identical {\csname Identical@#1\endcsname}
+ \xdef\resm@tch {\csname resm@tch@#1\endcsname}
+ \xdef\TextAllmatch{\csname TextAllmatch@#1\endcsname}
+ \xdef\Allmatch {\csname Allmatch@#1\endcsname}
+ \xdef\res@llm@tch {\csname res@llm@tch@#1\endcsname}
+ \xdef\gap@fg {\csname gap@fg@#1\endcsname}
+ \xdef\gap@bg {\csname gap@bg@#1\endcsname}
+ \xdef\domgap@fg {\csname domgap@fg@#1\endcsname}
+ \xdef\domgap@bg {\csname domgap@bg@#1\endcsname}
+ \fi\fi\fi\fi\fi
+ \xdef\first@{#1}
+ \expandafter\defshadingcolors{\first@}
+}
\def\nomatchresidues#1#2#3#4 {\xdef\first@{#1&}\xdef\second@{#2&}\xdef\third@{#3&}
\xdef\last@{\ampers@nd}
\ifx\first@\last@\else\def\TextNomatch{#1}
@@ -15206,6 +15353,48 @@
\ifnum\loopcount<\seq@count \repeat
}
+\def\getregion@fromshadingstack@first{%
+ \expandafter\getregion@fromshadingstack{\the\loopcount}
+ \expandafter\ifx\csname shadingstart\the\loopcount\endcsname\ampers@nd
+ \else
+ \expandafter\ifnum\csname shadingstop\the\loopcount\endcsname<\first@@
+ \getregion@fromshadingstack@first
+ \fi
+ \fi
+}
+
+\def\calc@shading{%
+ \xdef\shading@style{&}
+ \loopcount=-1
+ \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 shadingstart\the\loopcount\endcsname\ampers@nd
+ \else
+ \expandafter\ifnum\csname shadingstart\the\loopcount\endcsname>\first@@
+ \else
+ \expandafter\ifnum\csname shadingstop\the\loopcount\endcsname<\first@@
+ \getregion@fromshadingstack@first
+ \else
+ \xdef\shading@style{\csname shadingstyle\the\loopcount\endcsname}
+ \expandafter\ifnum\csname shadingstop\the\loopcount\endcsname=\first@@
+ \expandafter\getregion@fromshadingstack{\the\loopcount}
+ \fi
+ \fi
+ \fi\fi
+ \ifnum\loopcount<\seq@count \repeat
+ \loopcount=0
+ \loop
+ \advance\loopcount by 1
+ \ifx\shading@style\ampers@nd
+ \else
+ \expandafter\xdef\csname seq\the\loopcount\endcsname{%
+ \csname seq\the\loopcount\endcsname¤\shading@style)}
+ \fi
+ \ifnum\loopcount<\seq@count \repeat
+}
+
\def\getregion@fromemphstack@first{%
\expandafter\getregion@fromemphstack{\the\loopcount}
\expandafter\ifx\csname emphstart\the\loopcount\endcsname\ampers@nd
@@ -16940,6 +17129,7 @@
\ifregionalemphnow \calc@regemph \fi
\ifregionallowernow \calc@reglower \fi
\ifframenow \calc@frame \fi
+ \ifshadingnow\iffuncmode\else\ifT@coffee\else \calc@shading \fi\fi\fi
\iftopfeaturenow \xdef\bottop@{top} \calc@feature \fi
\ifttopfeaturenow \xdef\bottop@{ttop} \calc@feature \fi
\iftttopfeaturenow \xdef\bottop@{tttop} \calc@feature \fi
@@ -17122,6 +17312,16 @@
\fi
\fi
\fi
+ \ifshading@
+ \expandafter\ifx\csname shadingstart\the\loopcount\endcsname\ampers@nd
+ \else
+ \expandafter\ifnum\csname shadingstart\the\loopcount\endcsname>%
+ \innerloopcount
+ \else
+ \shadingnowtrue
+ \fi
+ \fi
+ \fi
\iftopfeature
\xdef\bottop@{top}
\expandafter\ifx\csname start\bottop@\the\loopcount\endcsname\ampers@nd
@@ -17319,6 +17519,16 @@
\fi
\fi
\fi
+ \ifshading@
+ \expandafter\ifx\csname shadingstart\the\loopcount\endcsname\ampers@nd
+ \else
+ \expandafter\ifnum\csname shadingstart\the\loopcount\endcsname>%
+ \innerloopcount
+ \else
+ \shadingnowtrue
+ \fi
+ \fi
+ \fi
\iftopfeature
\xdef\bottop@{top}
\expandafter\ifx\csname start\bottop@\the\loopcount\endcsname\ampers@nd
@@ -17660,6 +17870,14 @@
\hbox to \number@width{\hss\numbertext@size{\temp@}\@kern}}\fi%
\xdef\first@{#2@}%
}
+\def\special@shading#1)#2#3#4@{%
+ \xdef\second@{@\second@#1}%
+ \xdef\third@{\second@}%
+ \xdef\first@{#4@}%
+ \xdef\second@{#3}%
+ \xdef\last@{#2}%
+ \def\res@@style{\csname relax\endcsname}%
+}
\def\special@shade#1)#2#3#4@{%
\xdef\second@{\second@#1}%
\xdef\boxc@l@r{\csname bgseqregion\second@\endcsname}%
@@ -17674,6 +17892,8 @@
\xdef\second@{#2}%
\xdef\last@{#1}%
\xdef\temp@@{}%
+ \xdef\third@{}%
+ \ifx\last@\p@r@gr@ph\expandafter\special@shading\first@\fi%
\ifx\last@\ampers@nd\def\last@{0}\expandafter\special@shade\first@%
\else%
\ifT@coffee%
@@ -17692,25 +17912,34 @@
\if\last@ /\def\last@{10}\fi
\if\last@ !\def\last@{11}\fi
\else%
- \ifcase\last@\xdef\boxc@l@r{\Allmatch}\xdef\textc@l@r{\TextAllmatch}%
+ \ifcase\last@\xdef\boxc@l@r{\csname Allmatch\third@\endcsname}%
+ \xdef\textc@l@r{\csname TextAllmatch\third@\endcsname}%
\def\res@@style{\all@style}%
- \or\xdef\boxc@l@r{\Identical}\xdef\textc@l@r{\TextIdentical}%
+ \or\xdef\boxc@l@r{\csname Identical\third@\endcsname}%
+ \xdef\textc@l@r{\csname TextIdentical\third@\endcsname}%
\def\res@@style{\id@style}%
- \or\xdef\boxc@l@r{\Similar}\xdef\textc@l@r{\TextSimilar}%
+ \or\xdef\boxc@l@r{\csname Similar\third@\endcsname}%
+ \xdef\textc@l@r{\csname TextSimilar\third@\endcsname}%
\def\res@@style{\sim@style}%
- \or\xdef\boxc@l@r{\Nomatch}\xdef\textc@l@r{\TextNomatch}%
+ \or\xdef\boxc@l@r{\csname Nomatch\third@\endcsname}%
+ \xdef\textc@l@r{\csname TextNomatch\third@\endcsname}%
\def\res@@style{\no@style}%
- \or\xdef\boxc@l@r{\ConsNomatch}\xdef\textc@l@r{\ConsTextNomatch}%
+ \or\xdef\boxc@l@r{\csname ConsNomatch\third@\endcsname}%
+ \xdef\textc@l@r{\csname ConsTextNomatch\third@\endcsname}%
\def\res@@style{\csname relax\endcsname}%
- \or\xdef\boxc@l@r{\ConsMatch}\xdef\textc@l@r{\ConsTextMatch}%
+ \or\xdef\boxc@l@r{\csname ConsMatch\third@\endcsname}%
+ \xdef\textc@l@r{\csnam ConsTextMatch\third@\endcsname}%
\def\res@@style{\csname relax\endcsname}%
- \or\xdef\boxc@l@r{\ConsAllmatch}\xdef\textc@l@r{\ConsTextAllmatch}%
+ \or\xdef\boxc@l@r{\csname ConsAllmatch\third@\endcsname}%
+ \xdef\textc@l@r{\csname ConsTextAllmatch\third@\endcsname}%
\def\res@@style{\csname relax\endcsname}%
- \or\xdef\boxc@l@r{\gap@bg}\xdef\textc@l@r{\gap@fg}%
+ \or\xdef\boxc@l@r{\csname gap@bg\third@\endcsname}%
+ \xdef\textc@l@r{\csname gap@fg\third@\endcsname}%
\def\res@@style{\csname relax\endcsname}%
\or\xdef\boxc@l@r{White}\xdef\textc@l@r{White}%
\def\res@@style{\csname relax\endcsname}%
- \else\xdef\boxc@l@r{\domgap@bg}\xdef\textc@l@r{\domgap@fg}%
+ \else\xdef\boxc@l@r{\csname domgap@bg\endcsname}%
+ \xdef\textc@l@r{\csname domgap@fg\endcsname}%
\def\res@@style{\csname relax\endcsname}%
\fi\fi\fi\fi%
\ifx\second@\comm@%
@@ -17754,6 +17983,8 @@
\fi}
\def\next@cons#1#2#3@{%
\xdef\last@{#1}%
+ \xdef\third@{}%
+ \ifx\last@\p@r@gr@ph\expandafter\special@shading\first@\fi%
\ifx\last@\ampers@nd\def\last@{0}\expandafter\special@shade\first@%
\else%
\ifx\collect@cons@colors\y@%
@@ -17806,13 +18037,17 @@
\fi%
\fi%
\else%
- \ifcase#1\xdef\boxc@l@r{\Allmatch}\xdef\textc@l@r{\TextAllmatch}%
+ \ifcase#1\xdef\boxc@l@r{\csname Allmatch\third@\endcsname}%
+ \xdef\textc@l@r{\csname TextAllmatch\third@\endcsname}%
\def\res@@style{\all@style}%
- \or\xdef\boxc@l@r{\Identical}\xdef\textc@l@r{\TextIdentical}%
+ \or\xdef\boxc@l@r{\csname Identical\third@\endcsname}%
+ \xdef\textc@l@r{\csname TextIdentical\third@\endcsname}%
\def\res@@style{\id@style}%
- \or\xdef\boxc@l@r{\Similar}\xdef\textc@l@r{\TextSimilar}%
+ \or\xdef\boxc@l@r{\csname Similar\third@\endcsname}%
+ \xdef\textc@l@r{\csname TextSimilar\third@\endcsname}%
\def\res@@style{\sim@style}%
- \or\xdef\boxc@l@r{\Nomatch}\xdef\textc@l@r{\TextNomatch}%
+ \or\xdef\boxc@l@r{\csname Nomatch\third@\endcsname}%
+ \xdef\textc@l@r{\csname TextNomatch\third@\endcsname}%
\def\res@@style{\no@style}%
\or\xdef\boxc@l@r{\ConsNomatch}\xdef\textc@l@r{\ConsTextNomatch}%
\def\res@@style{\csname relax\endcsname}%
@@ -20191,6 +20426,7 @@
\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@shadingreg\the\loopcount\endcsname{&;&;&;@}
\expandafter\xdef\csname stack@top\the\loopcount\endcsname{&;&;&;&;@}
\expandafter\xdef\csname stack@ttop\the\loopcount\endcsname{&;&;&;&;@}
\expandafter\xdef\csname stack@tttop\the\loopcount\endcsname{&;&;&;&;@}
@@ -20221,6 +20457,7 @@
\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@shadingreg\the\loopcount\endcsname{&;&;&;@}
\expandafter\xdef\csname stack@top\the\loopcount\endcsname{&;&;&;&;@}
\expandafter\xdef\csname stack@ttop\the\loopcount\endcsname{&;&;&;&;@}
\expandafter\xdef\csname stack@tttop\the\loopcount\endcsname{&;&;&;&;@}
@@ -20270,6 +20507,7 @@
\expandafter\getregion@fromemphstack{\the\loopcount}
\expandafter\getregion@fromlowerstack{\the\loopcount}
\expandafter\getregion@fromframestack{\the\loopcount}
+ \expandafter\getregion@fromshadingstack{\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}
@@ -20321,6 +20559,7 @@
\expandafter\getregion@fromemphstack{\the\loopcount}
\expandafter\getregion@fromlowerstack{\the\loopcount}
\expandafter\getregion@fromframestack{\the\loopcount}
+ \expandafter\getregion@fromshadingstack{\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}
@@ -20543,6 +20782,11 @@
\xdef\prfx{DNA}\clear@groups\clear@sims
\clearfuncgroups
\clear@simpairs
+\shadingcolors{blues}
+\shadingcolors{reds}
+\shadingcolors{greens}
+\shadingcolors{grays}
+\shadingcolors{black}
\loopcount=\@lign@count
\advance\loopcount by 1\relax
\xdef\@lign@count{\the\loopcount}
@@ -20552,7 +20796,7 @@
\expandafter\xdef\csname res@count0\endcsname{0}
\xdef\allow@zero{n} \xdef\c@ns@shift{0}
\regionalshadefalse\regionalemphfalse\regionallowerfalse\regionaltintfalse
-\frame@false
+\frame@false\shading@false
\xdef\ruler@rot{0}
\topfeaturefalse \bottomfeaturefalse
\ttopfeaturefalse \bbottomfeaturefalse
diff --git a/Master/texmf-dist/tex/latex/texshade/texshade.sty b/Master/texmf-dist/tex/latex/texshade/texshade.sty
index d8ab1cccdc6..03c74861193 100644
--- a/Master/texmf-dist/tex/latex/texshade/texshade.sty
+++ b/Master/texmf-dist/tex/latex/texshade/texshade.sty
@@ -13,8 +13,8 @@
%%
\NeedsTeXFormat{LaTeX2e}
-\ProvidesPackage{texshade}[2010/03/01 LaTeX TeXshade (v1.21)]
-\message{Package `texshade', Version 1.21 of 2010/03/01.}
+\ProvidesPackage{texshade}[2010/10/11 LaTeX TeXshade (v1.22)]
+\message{Package `texshade', Version 1.22 of 2010/10/11.}
\PassOptionsToPackage{dvips}{color}
\PassOptionsToPackage{dvips}{graphicx}
@@ -114,6 +114,7 @@
\newif\ifall@fshade \newif\ifregionalemph
\newif\ifregionallower
\newif\ifframe@ \newif\ifregionaltint
+\newif\ifshading@
\newif\ifshow@logo \newif\ifshow@sublogo
\newif\ifhidechar \newif\ifsh@wg@ps
\newif\ifsimmode
@@ -130,6 +131,7 @@
\newif\ifbbbottomfeaturenow
\newif\ifbbbbottomfeaturenow
\newif\ifframenow
+\newif\ifshadingnow
\newif\iffix@
\expandafter\ifx\csname mdqon\endcsname\relax
@@ -141,7 +143,7 @@
\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\semic@n{;}
-\def\br@cket{[}
+\def\br@cket{[} \def\p@r@gr@ph{¤}
\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}
@@ -2297,6 +2299,8 @@
\csname stack@@lowerreg#1\endcsname}
\expandafter\xdef\csname stack@framereg\the\loopcount\endcsname{%
\csname stack@@framereg#1\endcsname}
+ \expandafter\xdef\csname stack@shadingreg\the\loopcount\endcsname{%
+ \csname stack@@shadingreg#1\endcsname}
\expandafter\xdef\csname stack@top\the\loopcount\endcsname{%
\csname stack@@top#1\endcsname}
\expandafter\xdef\csname stack@ttop\the\loopcount\endcsname{%
@@ -2350,6 +2354,8 @@
\csname stack@lowerreg\the\loopcount\endcsname}
\expandafter\xdef\csname stack@@framereg\the\loopcount\endcsname{%
\csname stack@framereg\the\loopcount\endcsname}
+ \expandafter\xdef\csname stack@@shadingreg\the\loopcount\endcsname{%
+ \csname stack@shadingreg\the\loopcount\endcsname}
\expandafter\xdef\csname stack@@top\the\loopcount\endcsname{%
\csname stack@top\the\loopcount\endcsname}
\expandafter\xdef\csname stack@@ttop\the\loopcount\endcsname{%
@@ -2639,6 +2645,8 @@
\csname stack@lowerreg\the\innerloopcount\endcsname}
\expandafter\xdef\csname stack@framereg\the\loopcount\endcsname{%
\csname stack@framereg\the\innerloopcount\endcsname}
+ \expandafter\xdef\csname stack@shadingreg\the\loopcount\endcsname{%
+ \csname stack@shadingreg\the\innerloopcount\endcsname}
\expandafter\xdef\csname stack@top\the\loopcount\endcsname{%
\csname stack@top\the\innerloopcount\endcsname}
\expandafter\xdef\csname stack@ttop\the\loopcount\endcsname{%
@@ -3051,6 +3059,23 @@
\sort@emphstack
\expandafter\xdef\csname stack@framereg\seq@\endcsname{\tmpstack}
}
+\def\getregion@fromshadingstack#1{%
+ \xdef\temp@{#1}
+ \xdef\first@{\csname stack@shadingreg\temp@\endcsname}
+ \expandafter\get@fromemphstack\first@
+ \expandafter\xdef\csname shadingstart\temp@\endcsname{\first@}
+ \expandafter\xdef\csname shadingstop\temp@\endcsname{\second@}
+ \expandafter\xdef\csname shadingstyle\temp@\endcsname{\third@}
+ \expandafter\xdef\csname stack@shadingreg\temp@\endcsname{\last@}
+}
+\def\get@shadingregions#1..#2,#3@{%
+ \shading@true
+ \xdef\st@rt{#1} \xdef\st@p{#2} \xdef\list@{#3}
+ \xdef\last@{\csname stack@shadingreg\seq@\endcsname}
+ \xdef\tmpstack{}
+ \sort@emphstack
+ \expandafter\xdef\csname stack@shadingreg\seq@\endcsname{\tmpstack}
+}
\def\getregion@fromfstack#1{%
\xdef\temp@{#1}
\xdef\first@{\csname stack@\bottop@\temp@\endcsname}
@@ -3088,14 +3113,6 @@
\sort@fstack
\expandafter\xdef\csname stack@\bottop@\seq@\endcsname{\tmpstack}
}
-\def\get@frameregions#1..#2,#3@{%
- \frame@true
- \xdef\st@rt{#1} \xdef\st@p{#2} \xdef\list@{#3}
- \xdef\last@{\csname stack@framereg\seq@\endcsname}
- \xdef\tmpstack{}
- \sort@emphstack
- \expandafter\xdef\csname stack@framereg\seq@\endcsname{\tmpstack}
-}
\def\getarrow@shape#1#2#3#4&{%
\xdef\first@@{#1}\xdef\second@@{#2}\xdef\third@@{#3}
\if\first@@ v
@@ -3243,9 +3260,9 @@
\xdef\temp@{tint}
\ifx\temp@\temp@@
\regionaltinttrue
- \xdef\last@{\csname stack@tintreg\seq@\endcsname} \message{((last:\last@))}
+ \xdef\last@{\csname stack@tintreg\seq@\endcsname}
\sort@emphstack
- \expandafter\xdef\csname stack@tintreg\seq@\endcsname{\tmpstack} \message{((tmp:\tmpstack))}
+ \expandafter\xdef\csname stack@tintreg\seq@\endcsname{\tmpstack}
\else
\xdef\temp@{frame}
\ifx\temp@\temp@@
@@ -3254,6 +3271,13 @@
\sort@emphstack
\expandafter\xdef\csname stack@framereg\seq@\endcsname{\tmpstack}
\else
+ \xdef\temp@{shading}
+ \ifx\temp@\temp@@
+ \shading@true
+ \xdef\last@{\csname stack@shadingreg\seq@\endcsname}
+ \sort@emphstack
+ \expandafter\xdef\csname stack@shadingreg\seq@\endcsname{\tmpstack}
+ \else
\xdef\temp@{ttttop}
\ifx\temp@\temp@@
\xdef\last@{\csname stack@ttttop\seq@\endcsname}
@@ -3314,10 +3338,15 @@
\fi
\fi
\fi
+ \fi
\xdef\fifth@@{\m@tif} \expandafter\get@third@\fifth@@
\xdef\nineth@@{n}
\fi
\else
+ \ifx\nineth@@\y@
+ \xdef\first@@{\second@@\first@@}
+ \advance\temp@count by -1
+ \fi
\xdef\nineth@@{n} \xdef\st@p{n}
\xdef\fifth@@{\m@tif} \expandafter\get@third@\fifth@@
\fi
@@ -3355,6 +3384,10 @@
\csname framestop\the\loopcount\endcsname;%
\csname framestyle\the\loopcount\endcsname;%
\csname stack@framereg\the\loopcount\endcsname}
+ \expandafter\xdef\csname stack@shadingreg\the\loopcount\endcsname{\csname shadingstart\the\loopcount\endcsname;%
+ \csname shadingstop\the\loopcount\endcsname;%
+ \csname shadingstyle\the\loopcount\endcsname;%
+ \csname stack@shadingreg\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;%
@@ -3417,6 +3450,7 @@
\expandafter\getregion@fromemphstack{\the\loopcount}
\expandafter\getregion@fromlowerstack{\the\loopcount}
\expandafter\getregion@fromframestack{\the\loopcount}
+ \expandafter\getregion@fromshadingstack{\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}
@@ -3439,6 +3473,8 @@
\ifx\temp@\temp@@ \xdef\style@{0} \fi
\xdef\temp@{frame}
\ifx\temp@\temp@@ \xdef\style@{0} \fi
+ \xdef\temp@{shading}
+ \ifx\temp@\temp@@ \xdef\style@{0} \fi
\xdef\temp@{#1#2}
\xdef\first@{#1}
\ifx\first@\br@cket
@@ -5386,6 +5422,28 @@
\fi
\fi
}
+\def\changeshadingcolors#1#2#3{%
+ \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\changeshadingcolors>}
+ \else
+ \xdef\@ll{#3}
+ \xdef\list@{#2,&}
+ \xdef\temp@@{shading} \loopcount=0
+ \xdef\temp@{#2,,,:,,,,@} \expandafter\test@PDB\temp@
+ \ifx\list@\ampers@nd
+ \else
+ \loop
+ \xdef\list@{\list@ @}
+ \expandafter\get@shadingregions\list@
+ \ifx\list@\ampers@nd\else\repeat
+ \fi
+ \fi
+}
\def\bargraphstretch#1{\def\b@r@stretch{#1}}
\def\colorscalestretch#1{\def\sc@le@stretch{#1}}
\def\rm@@measure#1#2@{%
@@ -5770,7 +5828,9 @@
\xdef\f@color{\f@@color}
\xdef\temp@{#4&}
\ifx\temp@\ampers@nd
+ \xdef\list@{#3,&}
\xdef\style@{&}
+ \def\f@text@{#5}
\else
\xdef\last@{restriction}
\ifx\second@@\last@
@@ -6931,6 +6991,27 @@
\expandafter\xdef\csname funcm@tch\first@\endcsname{#4}
\expandafter\def\csname func@style\first@\endcsname{\csname text#5\endcsname}
\fi}
+\def\defshadingcolors#1{%
+ \expandafter\xdef\csname TextNomatch@#1\endcsname{\TextNomatch}
+ \expandafter\xdef\csname Nomatch@#1\endcsname{\Nomatch}
+ \expandafter\xdef\csname resn@m@tch@#1\endcsname{\resn@m@tch}
+
+ \expandafter\xdef\csname TextSimilar@#1\endcsname{\TextSimilar}
+ \expandafter\xdef\csname Similar@#1\endcsname{\Similar}
+ \expandafter\xdef\csname ressimm@tch@#1\endcsname{\ressimm@tch}
+
+ \expandafter\xdef\csname TextIdentical@#1\endcsname{\TextIdentical}
+ \expandafter\xdef\csname Identical@#1\endcsname{\Identical}
+ \expandafter\xdef\csname resm@tch@#1\endcsname{\resm@tch}
+
+ \expandafter\xdef\csname TextAllmatch@#1\endcsname{\TextAllmatch}
+ \expandafter\xdef\csname Allmatch@#1\endcsname{\Allmatch}
+ \expandafter\xdef\csname res@llm@tch@#1\endcsname{\res@llm@tch}
+
+ \expandafter\xdef\csname gap@fg@#1\endcsname{\gap@fg}
+ \expandafter\xdef\csname gap@bg@#1\endcsname{\gap@bg}
+
+}
\def\shadingcolors#1{%
\gapcolors{Black}{White}
\nomatchresidues{Black}{White}{upper}{up}
@@ -6956,12 +7037,30 @@
\allmatchresidues{White}{Black}{upper}{sl}
\else \xdef\second@{grays}
\ifx\first@\second@
- \else \message{<Undefined color set - using `grays'>} \xdef\first@{grays}\fi
- \ifx\first@\second@
\similarresidues{Black}{LightGray}{upper}{up}
\conservedresidues{White}{DarkGray}{upper}{up}
\allmatchresidues{White}{Black}{upper}{up}
- \fi\fi\fi\fi\fi}
+ \else
+ \xdef\TextNomatch{\csname TextNomatch@#1\endcsname}
+ \xdef\Nomatch {\csname Nomatch@#1\endcsname}
+ \xdef\resn@m@tch {\csname resn@m@tch@#1\endcsname}
+ \xdef\TextSimilar{\csname TextSimilar@#1\endcsname}
+ \xdef\Similar {\csname Similar@#1\endcsname}
+ \xdef\ressimm@tch{\csname ressimm@tch@#1\endcsname}
+ \xdef\TextIdentical{\csname TextIdentical@#1\endcsname}
+ \xdef\Identical {\csname Identical@#1\endcsname}
+ \xdef\resm@tch {\csname resm@tch@#1\endcsname}
+ \xdef\TextAllmatch{\csname TextAllmatch@#1\endcsname}
+ \xdef\Allmatch {\csname Allmatch@#1\endcsname}
+ \xdef\res@llm@tch {\csname res@llm@tch@#1\endcsname}
+ \xdef\gap@fg {\csname gap@fg@#1\endcsname}
+ \xdef\gap@bg {\csname gap@bg@#1\endcsname}
+ \xdef\domgap@fg {\csname domgap@fg@#1\endcsname}
+ \xdef\domgap@bg {\csname domgap@bg@#1\endcsname}
+ \fi\fi\fi\fi\fi
+ \xdef\first@{#1}
+ \expandafter\defshadingcolors{\first@}
+}
\def\nomatchresidues#1#2#3#4 {\xdef\first@{#1&}\xdef\second@{#2&}\xdef\third@{#3&}
\xdef\last@{\ampers@nd}
\ifx\first@\last@\else\def\TextNomatch{#1}
@@ -8826,6 +8925,48 @@
\ifnum\loopcount<\seq@count \repeat
}
+\def\getregion@fromshadingstack@first{%
+ \expandafter\getregion@fromshadingstack{\the\loopcount}
+ \expandafter\ifx\csname shadingstart\the\loopcount\endcsname\ampers@nd
+ \else
+ \expandafter\ifnum\csname shadingstop\the\loopcount\endcsname<\first@@
+ \getregion@fromshadingstack@first
+ \fi
+ \fi
+}
+
+\def\calc@shading{%
+ \xdef\shading@style{&}
+ \loopcount=-1
+ \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 shadingstart\the\loopcount\endcsname\ampers@nd
+ \else
+ \expandafter\ifnum\csname shadingstart\the\loopcount\endcsname>\first@@
+ \else
+ \expandafter\ifnum\csname shadingstop\the\loopcount\endcsname<\first@@
+ \getregion@fromshadingstack@first
+ \else
+ \xdef\shading@style{\csname shadingstyle\the\loopcount\endcsname}
+ \expandafter\ifnum\csname shadingstop\the\loopcount\endcsname=\first@@
+ \expandafter\getregion@fromshadingstack{\the\loopcount}
+ \fi
+ \fi
+ \fi\fi
+ \ifnum\loopcount<\seq@count \repeat
+ \loopcount=0
+ \loop
+ \advance\loopcount by 1
+ \ifx\shading@style\ampers@nd
+ \else
+ \expandafter\xdef\csname seq\the\loopcount\endcsname{%
+ \csname seq\the\loopcount\endcsname¤\shading@style)}
+ \fi
+ \ifnum\loopcount<\seq@count \repeat
+}
+
\def\getregion@fromemphstack@first{%
\expandafter\getregion@fromemphstack{\the\loopcount}
\expandafter\ifx\csname emphstart\the\loopcount\endcsname\ampers@nd
@@ -10551,6 +10692,7 @@
\ifregionalemphnow \calc@regemph \fi
\ifregionallowernow \calc@reglower \fi
\ifframenow \calc@frame \fi
+ \ifshadingnow\iffuncmode\else\ifT@coffee\else \calc@shading \fi\fi\fi
\iftopfeaturenow \xdef\bottop@{top} \calc@feature \fi
\ifttopfeaturenow \xdef\bottop@{ttop} \calc@feature \fi
\iftttopfeaturenow \xdef\bottop@{tttop} \calc@feature \fi
@@ -10733,6 +10875,16 @@
\fi
\fi
\fi
+ \ifshading@
+ \expandafter\ifx\csname shadingstart\the\loopcount\endcsname\ampers@nd
+ \else
+ \expandafter\ifnum\csname shadingstart\the\loopcount\endcsname>%
+ \innerloopcount
+ \else
+ \shadingnowtrue
+ \fi
+ \fi
+ \fi
\iftopfeature
\xdef\bottop@{top}
\expandafter\ifx\csname start\bottop@\the\loopcount\endcsname\ampers@nd
@@ -10930,6 +11082,16 @@
\fi
\fi
\fi
+ \ifshading@
+ \expandafter\ifx\csname shadingstart\the\loopcount\endcsname\ampers@nd
+ \else
+ \expandafter\ifnum\csname shadingstart\the\loopcount\endcsname>%
+ \innerloopcount
+ \else
+ \shadingnowtrue
+ \fi
+ \fi
+ \fi
\iftopfeature
\xdef\bottop@{top}
\expandafter\ifx\csname start\bottop@\the\loopcount\endcsname\ampers@nd
@@ -11271,6 +11433,14 @@
\hbox to \number@width{\hss\numbertext@size{\temp@}\@kern}}\fi%
\xdef\first@{#2@}%
}
+\def\special@shading#1)#2#3#4@{%
+ \xdef\second@{@\second@#1}%
+ \xdef\third@{\second@}%
+ \xdef\first@{#4@}%
+ \xdef\second@{#3}%
+ \xdef\last@{#2}%
+ \def\res@@style{\csname relax\endcsname}%
+}
\def\special@shade#1)#2#3#4@{%
\xdef\second@{\second@#1}%
\xdef\boxc@l@r{\csname bgseqregion\second@\endcsname}%
@@ -11285,6 +11455,8 @@
\xdef\second@{#2}%
\xdef\last@{#1}%
\xdef\temp@@{}%
+ \xdef\third@{}%
+ \ifx\last@\p@r@gr@ph\expandafter\special@shading\first@\fi%
\ifx\last@\ampers@nd\def\last@{0}\expandafter\special@shade\first@%
\else%
\ifT@coffee%
@@ -11303,25 +11475,34 @@
\if\last@ /\def\last@{10}\fi
\if\last@ !\def\last@{11}\fi
\else%
- \ifcase\last@\xdef\boxc@l@r{\Allmatch}\xdef\textc@l@r{\TextAllmatch}%
+ \ifcase\last@\xdef\boxc@l@r{\csname Allmatch\third@\endcsname}%
+ \xdef\textc@l@r{\csname TextAllmatch\third@\endcsname}%
\def\res@@style{\all@style}%
- \or\xdef\boxc@l@r{\Identical}\xdef\textc@l@r{\TextIdentical}%
+ \or\xdef\boxc@l@r{\csname Identical\third@\endcsname}%
+ \xdef\textc@l@r{\csname TextIdentical\third@\endcsname}%
\def\res@@style{\id@style}%
- \or\xdef\boxc@l@r{\Similar}\xdef\textc@l@r{\TextSimilar}%
+ \or\xdef\boxc@l@r{\csname Similar\third@\endcsname}%
+ \xdef\textc@l@r{\csname TextSimilar\third@\endcsname}%
\def\res@@style{\sim@style}%
- \or\xdef\boxc@l@r{\Nomatch}\xdef\textc@l@r{\TextNomatch}%
+ \or\xdef\boxc@l@r{\csname Nomatch\third@\endcsname}%
+ \xdef\textc@l@r{\csname TextNomatch\third@\endcsname}%
\def\res@@style{\no@style}%
- \or\xdef\boxc@l@r{\ConsNomatch}\xdef\textc@l@r{\ConsTextNomatch}%
+ \or\xdef\boxc@l@r{\csname ConsNomatch\third@\endcsname}%
+ \xdef\textc@l@r{\csname ConsTextNomatch\third@\endcsname}%
\def\res@@style{\csname relax\endcsname}%
- \or\xdef\boxc@l@r{\ConsMatch}\xdef\textc@l@r{\ConsTextMatch}%
+ \or\xdef\boxc@l@r{\csname ConsMatch\third@\endcsname}%
+ \xdef\textc@l@r{\csnam ConsTextMatch\third@\endcsname}%
\def\res@@style{\csname relax\endcsname}%
- \or\xdef\boxc@l@r{\ConsAllmatch}\xdef\textc@l@r{\ConsTextAllmatch}%
+ \or\xdef\boxc@l@r{\csname ConsAllmatch\third@\endcsname}%
+ \xdef\textc@l@r{\csname ConsTextAllmatch\third@\endcsname}%
\def\res@@style{\csname relax\endcsname}%
- \or\xdef\boxc@l@r{\gap@bg}\xdef\textc@l@r{\gap@fg}%
+ \or\xdef\boxc@l@r{\csname gap@bg\third@\endcsname}%
+ \xdef\textc@l@r{\csname gap@fg\third@\endcsname}%
\def\res@@style{\csname relax\endcsname}%
\or\xdef\boxc@l@r{White}\xdef\textc@l@r{White}%
\def\res@@style{\csname relax\endcsname}%
- \else\xdef\boxc@l@r{\domgap@bg}\xdef\textc@l@r{\domgap@fg}%
+ \else\xdef\boxc@l@r{\csname domgap@bg\endcsname}%
+ \xdef\textc@l@r{\csname domgap@fg\endcsname}%
\def\res@@style{\csname relax\endcsname}%
\fi\fi\fi\fi%
\ifx\second@\comm@%
@@ -11365,6 +11546,8 @@
\fi}
\def\next@cons#1#2#3@{%
\xdef\last@{#1}%
+ \xdef\third@{}%
+ \ifx\last@\p@r@gr@ph\expandafter\special@shading\first@\fi%
\ifx\last@\ampers@nd\def\last@{0}\expandafter\special@shade\first@%
\else%
\ifx\collect@cons@colors\y@%
@@ -11417,13 +11600,17 @@
\fi%
\fi%
\else%
- \ifcase#1\xdef\boxc@l@r{\Allmatch}\xdef\textc@l@r{\TextAllmatch}%
+ \ifcase#1\xdef\boxc@l@r{\csname Allmatch\third@\endcsname}%
+ \xdef\textc@l@r{\csname TextAllmatch\third@\endcsname}%
\def\res@@style{\all@style}%
- \or\xdef\boxc@l@r{\Identical}\xdef\textc@l@r{\TextIdentical}%
+ \or\xdef\boxc@l@r{\csname Identical\third@\endcsname}%
+ \xdef\textc@l@r{\csname TextIdentical\third@\endcsname}%
\def\res@@style{\id@style}%
- \or\xdef\boxc@l@r{\Similar}\xdef\textc@l@r{\TextSimilar}%
+ \or\xdef\boxc@l@r{\csname Similar\third@\endcsname}%
+ \xdef\textc@l@r{\csname TextSimilar\third@\endcsname}%
\def\res@@style{\sim@style}%
- \or\xdef\boxc@l@r{\Nomatch}\xdef\textc@l@r{\TextNomatch}%
+ \or\xdef\boxc@l@r{\csname Nomatch\third@\endcsname}%
+ \xdef\textc@l@r{\csname TextNomatch\third@\endcsname}%
\def\res@@style{\no@style}%
\or\xdef\boxc@l@r{\ConsNomatch}\xdef\textc@l@r{\ConsTextNomatch}%
\def\res@@style{\csname relax\endcsname}%
@@ -13801,6 +13988,7 @@
\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@shadingreg\the\loopcount\endcsname{&;&;&;@}
\expandafter\xdef\csname stack@top\the\loopcount\endcsname{&;&;&;&;@}
\expandafter\xdef\csname stack@ttop\the\loopcount\endcsname{&;&;&;&;@}
\expandafter\xdef\csname stack@tttop\the\loopcount\endcsname{&;&;&;&;@}
@@ -13831,6 +14019,7 @@
\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@shadingreg\the\loopcount\endcsname{&;&;&;@}
\expandafter\xdef\csname stack@top\the\loopcount\endcsname{&;&;&;&;@}
\expandafter\xdef\csname stack@ttop\the\loopcount\endcsname{&;&;&;&;@}
\expandafter\xdef\csname stack@tttop\the\loopcount\endcsname{&;&;&;&;@}
@@ -13880,6 +14069,7 @@
\expandafter\getregion@fromemphstack{\the\loopcount}
\expandafter\getregion@fromlowerstack{\the\loopcount}
\expandafter\getregion@fromframestack{\the\loopcount}
+ \expandafter\getregion@fromshadingstack{\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}
@@ -13931,6 +14121,7 @@
\expandafter\getregion@fromemphstack{\the\loopcount}
\expandafter\getregion@fromlowerstack{\the\loopcount}
\expandafter\getregion@fromframestack{\the\loopcount}
+ \expandafter\getregion@fromshadingstack{\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}
@@ -14153,6 +14344,11 @@
\xdef\prfx{DNA}\clear@groups\clear@sims
\clearfuncgroups
\clear@simpairs
+\shadingcolors{blues}
+\shadingcolors{reds}
+\shadingcolors{greens}
+\shadingcolors{grays}
+\shadingcolors{black}
\loopcount=\@lign@count
\advance\loopcount by 1\relax
\xdef\@lign@count{\the\loopcount}
@@ -14162,7 +14358,7 @@
\expandafter\xdef\csname res@count0\endcsname{0}
\xdef\allow@zero{n} \xdef\c@ns@shift{0}
\regionalshadefalse\regionalemphfalse\regionallowerfalse\regionaltintfalse
-\frame@false
+\frame@false\shading@false
\xdef\ruler@rot{0}
\topfeaturefalse \bottomfeaturefalse
\ttopfeaturefalse \bbottomfeaturefalse