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-rw-r--r--Master/texmf-dist/doc/latex/textopo/textopo.pdfbin352722 -> 486686 bytes
-rw-r--r--Master/texmf-dist/doc/latex/textopo/textopo.txt12
-rw-r--r--Master/texmf-dist/source/latex/textopo/textopo.dtx91
-rw-r--r--Master/texmf-dist/tex/latex/textopo/textopo.sty60
4 files changed, 127 insertions, 36 deletions
diff --git a/Master/texmf-dist/doc/latex/textopo/textopo.pdf b/Master/texmf-dist/doc/latex/textopo/textopo.pdf
index a60d0eb7e34..38027a65dfd 100644
--- a/Master/texmf-dist/doc/latex/textopo/textopo.pdf
+++ b/Master/texmf-dist/doc/latex/textopo/textopo.pdf
Binary files differ
diff --git a/Master/texmf-dist/doc/latex/textopo/textopo.txt b/Master/texmf-dist/doc/latex/textopo/textopo.txt
index 5c19de110cc..ff9bd4b8722 100644
--- a/Master/texmf-dist/doc/latex/textopo/textopo.txt
+++ b/Master/texmf-dist/doc/latex/textopo/textopo.txt
@@ -1,4 +1,4 @@
- TeXtopo v1.4
+ TeXtopo v1.5
>>
>> A LaTeX package for shaded membrane protein topology plots.
>>
@@ -24,7 +24,7 @@
>> allows one to apply calculated shading based on sequence con-
>> servation and functional aspects of the residue sidechains.
>>
- Copyright (C) 2000-2005 Eric Beitz
+ Copyright (C) 2000-2011 Eric Beitz
@@ -115,11 +115,11 @@
3 - CONTACT
- E-Mail: eric.beitz@uni-tuebingen.de
- WWW: http://homepages.uni-tuebingen.de/beitz/
+ E-Mail: ebeitz@pharmazie.uni-kiel.de
+ WWW: http://www.pharmazie.uni-kiel.de/chem/
(On-line documentation and updates)
- Address: Eric Beitz, Universit"at T"ubingen, Pharmazeutische Chemie,
- Auf der Morgenstelle 8, D-72076 T"ubingen (Germany)
+ Address: Eric Beitz, University of Kiel, Pharmaceutical Chemistry,
+ Gutenbergstrasse 76, D-24118 Kiel (Germany)
diff --git a/Master/texmf-dist/source/latex/textopo/textopo.dtx b/Master/texmf-dist/source/latex/textopo/textopo.dtx
index 2e0c448db9f..ebb8bbd6c46 100644
--- a/Master/texmf-dist/source/latex/textopo/textopo.dtx
+++ b/Master/texmf-dist/source/latex/textopo/textopo.dtx
@@ -9,7 +9,7 @@
% files. See the file `textopo.txt' for further information!
%
%
-% Copyright (C) 2000-2005 Eric Beitz
+% Copyright (C) 2000-2011 Eric Beitz
% See the file textopo.txt
%
% \fi
@@ -76,6 +76,12 @@
% - new input format `HMMTOP' for `getsequence'.
% }
%
+% \changes{1.5}{2011-06-02}{%
+% Corrections:
+% - compatibility issues with the current TeXshade
+% version solved.
+% }
+%
%
% \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
@@ -101,14 +107,14 @@
% Eric Beitz (2000), \TeX{}topo:
% shaded membrane protein topology plots in \LaTeXe.
% \textit{Bioinformatics} \textbf{16}: 1050--1051.}}
-% \author{Eric Beitz\footnote{University of T\"ubingen,
-% Pharmaceutical Chemistry, Morgenstelle 8,
-% D-72076 T\"ubingen, Germany;
-% send electronic mail to \texttt{eric.beitz@uni-tuebingen.de};
+% \author{Eric Beitz\footnote{University of Kiel,
+% Pharmaceutical Chemistry, Gutenbergstrasse 8,
+% D-24118 Kiel, Germany;
+% send electronic mail to \texttt{ebeitz@pharmazie.uni-kiel.de};
% for further information, updates and on-line documentation
% see my homepage at
-% \texttt{http://homepages.uni-tuebingen.de/beitz/}}}
-% \date{v1.4; 2005/02/14\\}
+% \texttt{www.pharmazie.uni-kiel.de/chem/Prof\_Beitz/biotex.html} }}
+% \date{v1.5; 2011/06/02\\}
% \maketitle
% \begin{textopo}
% \getsequence{PHD}{AQP1.PHD}
@@ -167,6 +173,13 @@
%
% \subsection{Version History}
%
+% \textbf{v1.5 2011/06/02}
+% \medskip
+%
+% Compatibility with the current \TeXshade{} version was
+% re-established.
+% \medskip
+%
% \textbf{v1.4 2005/02/14}
% \medskip
%
@@ -176,6 +189,8 @@
% and some minor bugs have been fixed.
% \bigskip
%
+% \newpage
+%
% \textbf{v1.3 2002/04/15}
% \medskip
%
@@ -700,7 +715,7 @@
% named \textit{filename}|.htp|.
% \medskip
%
-% Syntax: |\getsequence[make new]{HMMTOP}{|\meta{HMMTOP-file}|}| \label{mgetsequence}
+% Syntax: |\getsequence[make new]{HMMTOP}{|\meta{HMMTOP-file}|}|
% \medskip
%
%
@@ -2858,8 +2873,8 @@
% \begin{macrocode}
%<*textpo>
\NeedsTeXFormat{LaTeX2e}
-\ProvidesPackage{textopo}[2001/03/09 LaTeX TeXtopo (v1.4)]
-\message{Package `textopo', Version 1.4 of 05/02/14.}
+\ProvidesPackage{textopo}[2011/06/02 LaTeX TeXtopo (v1.5)]
+\message{Package `textopo', Version 1.5 of 2011/06/02.}
\PassOptionsToPackage{dvips}{color}
\PassOptionsToPackage{dvips}{graphicx}
@@ -8744,14 +8759,14 @@
\@tempdima=0.1\dimen@
\multiply\dimen@\@tempdima
\dimen@0.65536\dimen@
- \xdef\first@{\expandafter\noPT\the\dimen@ @}
+ \xdef\first@{\expandafter\noPT\the\dimen@ 000@}
\expandafter\get@numnum\first@
\x@pos=\first@
\dimen@=\y@pos\s@
\@tempdima=0.1\dimen@
\multiply\dimen@\@tempdima
\dimen@0.65536\dimen@
- \xdef\first@{\expandafter\noPT\the\dimen@ @}
+ \xdef\first@{\expandafter\noPT\the\dimen@ 000@}
\expandafter\get@numnum\first@
\y@pos=\first@\relax
\advance\x@pos by \y@pos\relax
@@ -8874,8 +8889,8 @@
{Undefined file type demanded}
{\MessageBreak
The type of file you demanded is undefined or you have \MessageBreak
- misspelled it. Currently `PHD', `SwissProt' and `alignment'\MessageBreak
- are known to TeXtopo.\MessageBreak\MessageBreak
+ misspelled it. Currently `PHD', `SwissProt', `alignment',\MessageBreak
+ and `HMMTOP' are known to TeXtopo.\MessageBreak\MessageBreak
Stop here, otherwise you're likely getting in trouble. \MessageBreak
Type X <return> to quit. \MessageBreak
}
@@ -9383,7 +9398,7 @@
\expandafter\xdef\csname ins@n\insert@num\endcsname{#1}
\expandafter\xdef\csname ins@x\insert@num\endcsname{\directi@n}
\expandafter\xdef\csname ins@y\insert@num\endcsname{\length@}
- \expandafter\xdef\csname ins@z\insert@num\endcsname{#3}
+ \expandafter\def\csname ins@z\insert@num\endcsname{#3}
}
\def\remodel#1#2{%
@@ -9471,6 +9486,12 @@
\else
\xdef\third@{\second@}
\fi\fi\fi
+ \xdef\temp@{featurenames}
+ \ifx\first@\temp@ \xdef\ftext@family{\third@}
+ \else
+ \xdef\temp@{featurestylenames}
+ \ifx\first@\temp@ \xdef\fstyles@family{\third@}
+ \else
\xdef\temp@{features}
\ifx\first@\temp@ \xdef\featuretext@family{\third@}
\else
@@ -9501,8 +9522,13 @@
\xdef\temp@{TMlabels}
\ifx\first@\temp@ \xdef\TMlabel@family{\third@}
\else
+ \xdef\temp@{ruler}
+ \ifx\first@\temp@ \xdef\ruler@family{\second@}
+ \else
\xdef\temp@{all}
\ifx\first@\temp@
+ \xdef\ftext@family{\third@}
+ \xdef\fstyles@family{\third@}
\xdef\featuretext@family{\third@}
\xdef\featurestyles@family{\third@}
\xdef\numbertext@family{\third@}
@@ -9512,7 +9538,8 @@
\xdef\label@family{\third@}
\xdef\looplabel@family{\third@}
\xdef\TMlabel@family{\third@}
- \fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi
+ \xdef\ruler@family{\second@}
+ \fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi
\fi
}
\def\setseries#1#2{%
@@ -9531,6 +9558,12 @@
\else
\xdef\third@{\second@}
\fi\fi
+ \xdef\temp@{featurenames}
+ \ifx\first@\temp@ \xdef\ftext@series{\third@}
+ \else
+ \xdef\temp@{featurestylenames}
+ \ifx\first@\temp@ \xdef\fstyles@series{\third@}
+ \else
\xdef\temp@{features}
\ifx\first@\temp@ \xdef\featuretext@series{\third@}
\else
@@ -9563,6 +9596,8 @@
\else
\xdef\temp@{all}
\ifx\first@\temp@
+ \xdef\ftext@series{\third@}
+ \xdef\fstyles@series{\third@}
\xdef\featuretext@series{\third@}
\xdef\featurestyles@series{\third@}
\xdef\numbertext@series{\third@}
@@ -9572,7 +9607,7 @@
\xdef\label@series{\third@}
\xdef\looplabel@series{\third@}
\xdef\TMlabel@series{\third@}
- \fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi
+ \fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi
\fi
}
\def\setshape#1#2{%
@@ -9599,6 +9634,12 @@
\else
\xdef\third@{\second@}
\fi\fi\fi\fi
+ \xdef\temp@{featurenames}
+ \ifx\first@\temp@ \xdef\ftext@shape{\third@}
+ \else
+ \xdef\temp@{featurestylenames}
+ \ifx\first@\temp@ \xdef\fstyles@shape{\third@}
+ \else
\xdef\temp@{features}
\ifx\first@\temp@ \xdef\featuretext@shape{\third@}
\else
@@ -9631,6 +9672,8 @@
\else
\xdef\temp@{all}
\ifx\first@\temp@
+ \xdef\ftext@shape{\third@}
+ \xdef\fstyles@shape{\third@}
\xdef\featuretext@shape{\third@}
\xdef\featurestyles@shape{\third@}
\xdef\numbertext@shape{\third@}
@@ -9640,7 +9683,7 @@
\xdef\label@shape{\third@}
\xdef\looplabel@shape{\third@}
\xdef\TMlabel@shape{\third@}
- \fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi
+ \fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi
\fi
}
\def\setsize#1#2{%
@@ -9656,6 +9699,14 @@
\ifx\first@\temp@
\def\featurestyles@size{\csname #2\endcsname}
\else
+ \xdef\temp@{featurenames}
+ \ifx\first@\temp@
+ \def\ftext@size{\csname #2\endcsname}
+ \else
+ \xdef\temp@{featurestylenames}
+ \ifx\first@\temp@
+ \def\fstyles@size{\csname #2\endcsname}
+ \else
\xdef\temp@{numbering}
\ifx\first@\temp@
\def\numbertext@size{\csname #2\endcsname}
@@ -9693,6 +9744,8 @@
\ifx\first@\temp@
\def\featuretext@size{\csname #2\endcsname}
\def\featurestyles@size{\csname #2\endcsname}
+ \def\ftext@size{\csname #2\endcsname}
+ \def\fstyles@size{\csname #2\endcsname}
\def\numbertext@size{\csname #2\endcsname}
\def\namestext@size{\csname #2\endcsname}
\def\legend@size{\csname #2\endcsname} \def\l@size{#2}
@@ -9701,7 +9754,7 @@
\def\TMlabel@size{\csname #2\endcsname}
\def\residues@size{\csname #2\endcsname}
\xdef\res@size{#2}
- \fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi
+ \fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi
\xdef\temp@{Huge}
\ifx\temp@\res@size
\def\bottomruler@size{\csname Large\endcsname}
diff --git a/Master/texmf-dist/tex/latex/textopo/textopo.sty b/Master/texmf-dist/tex/latex/textopo/textopo.sty
index 11e92431b4b..456fd7ecd4a 100644
--- a/Master/texmf-dist/tex/latex/textopo/textopo.sty
+++ b/Master/texmf-dist/tex/latex/textopo/textopo.sty
@@ -12,8 +12,8 @@
%% See the file textopo.txt
%%
\NeedsTeXFormat{LaTeX2e}
-\ProvidesPackage{textopo}[2001/03/09 LaTeX TeXtopo (v1.4)]
-\message{Package `textopo', Version 1.4 of 05/02/14.}
+\ProvidesPackage{textopo}[2011/06/02 LaTeX TeXtopo (v1.5)]
+\message{Package `textopo', Version 1.5 of 2011/06/02.}
\PassOptionsToPackage{dvips}{color}
\PassOptionsToPackage{dvips}{graphicx}
@@ -5895,14 +5895,14 @@
\@tempdima=0.1\dimen@
\multiply\dimen@\@tempdima
\dimen@0.65536\dimen@
- \xdef\first@{\expandafter\noPT\the\dimen@ @}
+ \xdef\first@{\expandafter\noPT\the\dimen@ 000@}
\expandafter\get@numnum\first@
\x@pos=\first@
\dimen@=\y@pos\s@
\@tempdima=0.1\dimen@
\multiply\dimen@\@tempdima
\dimen@0.65536\dimen@
- \xdef\first@{\expandafter\noPT\the\dimen@ @}
+ \xdef\first@{\expandafter\noPT\the\dimen@ 000@}
\expandafter\get@numnum\first@
\y@pos=\first@\relax
\advance\x@pos by \y@pos\relax
@@ -6025,8 +6025,8 @@
{Undefined file type demanded}
{\MessageBreak
The type of file you demanded is undefined or you have \MessageBreak
- misspelled it. Currently `PHD', `SwissProt' and `alignment'\MessageBreak
- are known to TeXtopo.\MessageBreak\MessageBreak
+ misspelled it. Currently `PHD', `SwissProt', `alignment',\MessageBreak
+ and `HMMTOP' are known to TeXtopo.\MessageBreak\MessageBreak
Stop here, otherwise you're likely getting in trouble. \MessageBreak
Type X <return> to quit. \MessageBreak
}
@@ -6534,7 +6534,7 @@
\expandafter\xdef\csname ins@n\insert@num\endcsname{#1}
\expandafter\xdef\csname ins@x\insert@num\endcsname{\directi@n}
\expandafter\xdef\csname ins@y\insert@num\endcsname{\length@}
- \expandafter\xdef\csname ins@z\insert@num\endcsname{#3}
+ \expandafter\def\csname ins@z\insert@num\endcsname{#3}
}
\def\remodel#1#2{%
@@ -6621,6 +6621,12 @@
\else
\xdef\third@{\second@}
\fi\fi\fi
+ \xdef\temp@{featurenames}
+ \ifx\first@\temp@ \xdef\ftext@family{\third@}
+ \else
+ \xdef\temp@{featurestylenames}
+ \ifx\first@\temp@ \xdef\fstyles@family{\third@}
+ \else
\xdef\temp@{features}
\ifx\first@\temp@ \xdef\featuretext@family{\third@}
\else
@@ -6651,8 +6657,13 @@
\xdef\temp@{TMlabels}
\ifx\first@\temp@ \xdef\TMlabel@family{\third@}
\else
+ \xdef\temp@{ruler}
+ \ifx\first@\temp@ \xdef\ruler@family{\second@}
+ \else
\xdef\temp@{all}
\ifx\first@\temp@
+ \xdef\ftext@family{\third@}
+ \xdef\fstyles@family{\third@}
\xdef\featuretext@family{\third@}
\xdef\featurestyles@family{\third@}
\xdef\numbertext@family{\third@}
@@ -6662,7 +6673,8 @@
\xdef\label@family{\third@}
\xdef\looplabel@family{\third@}
\xdef\TMlabel@family{\third@}
- \fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi
+ \xdef\ruler@family{\second@}
+ \fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi
\fi
}
\def\setseries#1#2{%
@@ -6681,6 +6693,12 @@
\else
\xdef\third@{\second@}
\fi\fi
+ \xdef\temp@{featurenames}
+ \ifx\first@\temp@ \xdef\ftext@series{\third@}
+ \else
+ \xdef\temp@{featurestylenames}
+ \ifx\first@\temp@ \xdef\fstyles@series{\third@}
+ \else
\xdef\temp@{features}
\ifx\first@\temp@ \xdef\featuretext@series{\third@}
\else
@@ -6713,6 +6731,8 @@
\else
\xdef\temp@{all}
\ifx\first@\temp@
+ \xdef\ftext@series{\third@}
+ \xdef\fstyles@series{\third@}
\xdef\featuretext@series{\third@}
\xdef\featurestyles@series{\third@}
\xdef\numbertext@series{\third@}
@@ -6722,7 +6742,7 @@
\xdef\label@series{\third@}
\xdef\looplabel@series{\third@}
\xdef\TMlabel@series{\third@}
- \fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi
+ \fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi
\fi
}
\def\setshape#1#2{%
@@ -6749,6 +6769,12 @@
\else
\xdef\third@{\second@}
\fi\fi\fi\fi
+ \xdef\temp@{featurenames}
+ \ifx\first@\temp@ \xdef\ftext@shape{\third@}
+ \else
+ \xdef\temp@{featurestylenames}
+ \ifx\first@\temp@ \xdef\fstyles@shape{\third@}
+ \else
\xdef\temp@{features}
\ifx\first@\temp@ \xdef\featuretext@shape{\third@}
\else
@@ -6781,6 +6807,8 @@
\else
\xdef\temp@{all}
\ifx\first@\temp@
+ \xdef\ftext@shape{\third@}
+ \xdef\fstyles@shape{\third@}
\xdef\featuretext@shape{\third@}
\xdef\featurestyles@shape{\third@}
\xdef\numbertext@shape{\third@}
@@ -6790,7 +6818,7 @@
\xdef\label@shape{\third@}
\xdef\looplabel@shape{\third@}
\xdef\TMlabel@shape{\third@}
- \fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi
+ \fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi
\fi
}
\def\setsize#1#2{%
@@ -6806,6 +6834,14 @@
\ifx\first@\temp@
\def\featurestyles@size{\csname #2\endcsname}
\else
+ \xdef\temp@{featurenames}
+ \ifx\first@\temp@
+ \def\ftext@size{\csname #2\endcsname}
+ \else
+ \xdef\temp@{featurestylenames}
+ \ifx\first@\temp@
+ \def\fstyles@size{\csname #2\endcsname}
+ \else
\xdef\temp@{numbering}
\ifx\first@\temp@
\def\numbertext@size{\csname #2\endcsname}
@@ -6843,6 +6879,8 @@
\ifx\first@\temp@
\def\featuretext@size{\csname #2\endcsname}
\def\featurestyles@size{\csname #2\endcsname}
+ \def\ftext@size{\csname #2\endcsname}
+ \def\fstyles@size{\csname #2\endcsname}
\def\numbertext@size{\csname #2\endcsname}
\def\namestext@size{\csname #2\endcsname}
\def\legend@size{\csname #2\endcsname} \def\l@size{#2}
@@ -6851,7 +6889,7 @@
\def\TMlabel@size{\csname #2\endcsname}
\def\residues@size{\csname #2\endcsname}
\xdef\res@size{#2}
- \fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi
+ \fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi
\xdef\temp@{Huge}
\ifx\temp@\res@size
\def\bottomruler@size{\csname Large\endcsname}