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-rw-r--r--Master/texmf-dist/tex/latex/texshade/texshade.sty112
1 files changed, 108 insertions, 4 deletions
diff --git a/Master/texmf-dist/tex/latex/texshade/texshade.sty b/Master/texmf-dist/tex/latex/texshade/texshade.sty
index 03c74861193..f447d59ef2f 100644
--- a/Master/texmf-dist/tex/latex/texshade/texshade.sty
+++ b/Master/texmf-dist/tex/latex/texshade/texshade.sty
@@ -8,13 +8,13 @@
%%
%% LaTeX package for typesetting nucleotide and peptide alignments
%%
-%% Copyright (C) 1999-2010 Eric Beitz
+%% Copyright (C) 1999-2011 Eric Beitz
%% See the file texshade.txt
%%
\NeedsTeXFormat{LaTeX2e}
-\ProvidesPackage{texshade}[2010/10/11 LaTeX TeXshade (v1.22)]
-\message{Package `texshade', Version 1.22 of 2010/10/11.}
+\ProvidesPackage{texshade}[2011/05/13 LaTeX TeXshade (v1.23)]
+\message{Package `texshade', Version 1.23 of 2011/05/13.}
\PassOptionsToPackage{dvips}{color}
\PassOptionsToPackage{dvips}{graphicx}
@@ -6104,6 +6104,8 @@
\message{<Unknown shading mode - using `similar'>}
\simmodetrue \funcmodefalse
\fi\fi\fi\fi\fi}
+\def\hideallmatchpositions{\xdef\all@out{y}}
+\def\showallmatchpositions{\xdef\all@out{n}}
\newcommand\allmatchspecial[1][100]{%
\ifnum#1<0
\xdef\all@thresh@ld{0}
@@ -13444,6 +13446,80 @@
\xdef\stylefeaturebbbbottom{}}
\def\guess@protein{\seqtype{P}\message{<Seqtype guess: protein>}}
\def\guess@DNA{\seqtype{N}\message{<Seqtype guess: nucleotide>}}
+\def\allmatch@out{%
+ \xdef\leave@in{n}
+ \loopcount=1
+ \xdef\seq@line{\csname seq\the\loopcount\endcsname}
+ \expandafter\res@get\seq@line
+ \expandafter\xdef\csname seq\the\loopcount\endcsname{\seq@line}
+ \ifnum\loopcount=\start@seq\relax
+ \expandafter\check@char\first@
+ \ifletter
+ \advance\temp@@count by 1
+ \ifnum\temp@@count=\end@num\relax
+ \advance\temp@count by 1
+ \xdef\second@{\the\temp@count}
+ \advance\temp@count by -1
+ \fi
+ \fi
+ \fi
+ \ifx\first@\ampers@nd
+ \ifx\domain@active\y@
+ \xdef\stack@dom{\stack@dom\the\temp@count;}
+ \fi
+ \xdef\stack@dom{\stack@dom &;&;@}
+ \else
+ \xdef\first@@{\first@}
+ \advance\temp@count by 1
+ \loop
+ \advance\loopcount by 1
+ \xdef\seq@line{\csname seq\the\loopcount\endcsname}
+ \expandafter\res@get\seq@line
+ \expandafter\xdef\csname seq\the\loopcount\endcsname{\seq@line}
+ \ifx\first@@\first@\else\xdef\leave@in{y}\fi
+ \ifnum\loopcount=\start@seq\relax
+ \expandafter\check@char\first@
+ \ifletter
+ \advance\temp@@count by 1
+ \ifnum\temp@@count=\end@num\relax \xdef\second@{\the\temp@count}\fi
+ \fi
+ \fi
+ \ifnum\loopcount<\seq@count\repeat
+ \ifx\leave@in\y@
+ \ifx\domain@active\n@
+ \ifnum\start@seq=0
+ \xdef\domain@active{y}
+ \xdef\stack@dom{\stack@dom\the\temp@count;}
+ \else
+ \ifnum\temp@@count<\start@num\relax
+ \else
+ \ifnum\temp@@count>\end@num\relax
+ \else
+ \xdef\domain@active{y}
+ \xdef\stack@dom{\stack@dom\the\temp@count;}
+ \fi
+ \fi
+ \fi
+ \else
+ \ifnum\start@seq>0
+ \ifnum\temp@@count<\end@num\relax
+ \else
+ \xdef\domain@active{n}
+ \xdef\stack@dom{\stack@dom\second@;}
+ \fi
+ \fi
+ \fi
+ \else
+ \ifx\domain@active\y@
+ \xdef\domain@active{n}
+ \advance\temp@count by -1
+ \xdef\stack@dom{\stack@dom\the\temp@count;}
+ \advance\temp@count by 1
+ \fi
+ \fi
+ \allmatch@out
+ \fi
+}
\def\domain@count{%
\xdef\@ddg@p{n}
\loopcount=0
@@ -13680,6 +13756,20 @@
\fi
\fi
\ifeof\alignfile
+ \ifx\all@out\y@
+ \xdef\domain@seq{0}
+ \loopcount=0
+ \loop
+ \advance\loopcount by 1
+ \expandafter\xdef\csname seq\the\loopcount\endcsname{\csname sequence\the\loopcount\endcsname &@}
+ \ifnum\loopcount<\seq@count\repeat
+ \xdef\domain@active{n}
+ \xdef\stack@dom{}
+ \temp@count=0
+ \temp@@count=0
+ \allmatch@out
+ \xdef\dom@in{y}
+ \fi
\ifx\dom@in\y@
\loopcount=0
\ifT@coffee
@@ -13781,6 +13871,20 @@
\fi
\fi
\ifeof\alignfile
+ \ifx\all@out\y@
+ \xdef\domain@seq{0}
+ \loopcount=0
+ \loop
+ \advance\loopcount by 1
+ \expandafter\xdef\csname seq\the\loopcount\endcsname{\csname sequence\the\loopcount\endcsname &@}
+ \ifnum\loopcount<\seq@count\repeat
+ \xdef\domain@active{n}
+ \xdef\stack@dom{}
+ \temp@count=0
+ \temp@@count=0
+ \allmatch@out
+ \xdef\dom@in{y}
+ \fi
\ifx\dom@in\y@
\loopcount=0
\ifT@coffee
@@ -14467,7 +14571,7 @@
\hidefeaturenames \hidefeaturestylenames
\xdef\T@coffee@ccons{n} \xdef\T@coffee@bcons{n}
\xdef\dom@in{no} \xdef\label@motif{no}
-\xdef\motif@num{0}
+\xdef\motif@num{0} \xdef\all@out{n}
\hfuzz9999pt
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