TeXtopo v1.5

git-svn-id: svn://tug.org/texlive/trunk@23337 c570f23f-e606-0410-a88d-b1316a301751

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
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}