diff options
| -rw-r--r-- | Master/texmf-dist/doc/latex/textopo/textopo.pdf | bin | 352722 -> 486686 bytes | |||
| -rw-r--r-- | Master/texmf-dist/doc/latex/textopo/textopo.txt | 12 | ||||
| -rw-r--r-- | Master/texmf-dist/source/latex/textopo/textopo.dtx | 91 | ||||
| -rw-r--r-- | Master/texmf-dist/tex/latex/textopo/textopo.sty | 60 |
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 Binary files differindex a60d0eb7e34..38027a65dfd 100644 --- a/Master/texmf-dist/doc/latex/textopo/textopo.pdf +++ b/Master/texmf-dist/doc/latex/textopo/textopo.pdf 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} |