diff options
Diffstat (limited to 'Master/texmf-dist/tex/latex/texshade')
| -rw-r--r-- | Master/texmf-dist/tex/latex/texshade/texshade.sty | 112 |
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 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |