diff options
Diffstat (limited to 'Master/texmf-dist')
| -rw-r--r-- | Master/texmf-dist/doc/latex/texshade/README | 4 | ||||
| -rw-r--r-- | Master/texmf-dist/doc/latex/texshade/texshade.pdf | bin | 760478 -> 763706 bytes | |||
| -rw-r--r-- | Master/texmf-dist/source/latex/texshade/texshade.dtx | 153 | ||||
| -rw-r--r-- | Master/texmf-dist/source/latex/texshade/texshade.ins | 4 | ||||
| -rw-r--r-- | Master/texmf-dist/tex/latex/texshade/texshade.sty | 112 |
5 files changed, 259 insertions, 14 deletions
diff --git a/Master/texmf-dist/doc/latex/texshade/README b/Master/texmf-dist/doc/latex/texshade/README index 4bfb071ff50..e44157d204e 100644 --- a/Master/texmf-dist/doc/latex/texshade/README +++ b/Master/texmf-dist/doc/latex/texshade/README @@ -1,4 +1,4 @@ - TeXshade v1.22 + TeXshade v1.23 >> >> A LaTeX package for setting nucleotide and peptide alignments. >> @@ -26,7 +26,7 @@ >> ding modes. TeXshade combines highest flexibility and the >> habitual TeX output quality--with reasonable time expenditure. >> - Copyright (C) 1999 - 2010 Eric Beitz + Copyright (C) 1999 - 2011 Eric Beitz diff --git a/Master/texmf-dist/doc/latex/texshade/texshade.pdf b/Master/texmf-dist/doc/latex/texshade/texshade.pdf Binary files differindex fe59789d182..509af83e324 100644 --- a/Master/texmf-dist/doc/latex/texshade/texshade.pdf +++ b/Master/texmf-dist/doc/latex/texshade/texshade.pdf diff --git a/Master/texmf-dist/source/latex/texshade/texshade.dtx b/Master/texmf-dist/source/latex/texshade/texshade.dtx index bcfd2b97ea3..f7590eea074 100644 --- a/Master/texmf-dist/source/latex/texshade/texshade.dtx +++ b/Master/texmf-dist/source/latex/texshade/texshade.dtx @@ -10,7 +10,7 @@ % `README.txt' for further information! % % -% Copyright (C) 1999-2010 Eric Beitz +% Copyright (C) 1999-2011 Eric Beitz % See the file texshade.txt % % \fi @@ -380,6 +380,11 @@ % of shading colors in different sequence blocks. % } % +% \changes{1.23}{2011-05-13}{% +% Introduction: `hideallmatchpositions' removes all positions in the +% alignment where all residues match, i.e. a handy feature for +% diverse mode to condense the output to the relevant sites. +% } % % % \CharacterTable @@ -419,7 +424,7 @@ % for further information, updates and on-line documentation % see my homepage at % \texttt{www.pharmazie.uni-kiel.de/chem/Prof\_Beitz/biotex.html} }} -% \date{\small v1.22; 2010/10/11\\[2pt]} +% \date{\small v1.23; 2011/05/13\\[2pt]} % \maketitle % \begin{abstract} % Setting alignments of nucleotides and peptides for publication @@ -498,6 +503,17 @@ % % \subsection{Version History} % +% \textbf{v1.23 2011/05/13} +% \medskip +% +% \emph{Introductions:} +% In diverse mode sequence positions where all residues match do not +% contain much information. A new command, +% |\hideallmatchpositions|, \footnote{Requested by Matt Russell.} +% will remove all such positions from the alignment and hence condense +% the output considerably. +% \medskip +% % \textbf{v1.22 2010/10/11} % \medskip % @@ -508,6 +524,8 @@ % |\changeshadingcolors| (\ref{Lchangeshadingcolors}). % \medskip % +% \newpage +% % \textbf{v1.21 2010/03/01} % \medskip % @@ -627,6 +645,8 @@ % \bigskip % % +% \newpage +% % % \textbf{v1.16 2007/02/18} % \medskip @@ -915,6 +935,8 @@ % `|\Alphacount|'. All commands are described in \ref{structure}. % \bigskip % +% \newpage +% % \textbf{v1.1 1999/5/26} % \medskip % @@ -2549,6 +2571,18 @@ % used to redefine the |diverse| mode settings (mind the double % curly braces around the dot-symbol!). % +% \label{Lhideallmatchpositions} +% Since alignment positions where all residues match do not contain +% much information, those sites can be blanked out using +% Ê|\hideallmatchpositions|. The resulting break in the alignment is +% indicated by a gap and a vertical line. See the |\setdomain| +% command (\ref{Lsetdomain}) +% for further information on how to change the gap and ruler colors. +% A single-stepped ruler is also recommended (\ref{Lshowruler}). +% Ê|\hideallmatchpositions| can be combined with |\setends| +% (\ref{Lsetends}). +% +% % \item |\shadingmode[|\meta{type}|]{functional}|\label{funcdef} % There are seven different functional shading modes available for % peptide sequences; nucleotide sequences can not be shaded due @@ -2567,7 +2601,7 @@ % \item \meta{type} = |hydropathy|\quad Acidic and basic (as % above), polar uncharged (C, G, N, Q, S, % T, Y) and hydrophobic nonpolar (A, F, I, L, M, -% P, V, W), see also \textsc{Kyte} and +% P, V, W), see also \textsc{Kyte} \& % \textsc{Doolittle} [3]. % % \item \meta{type} = |structure|\quad External (D, E, H, K, N, Q, R), @@ -5622,6 +5656,9 @@ % \quad|\allmatchspecial[|\meta{percentage}|]| % \hfill[\pageref{Lallmatchspecial}] % +% \quad|\hideallmatchpositions| +% \hfill[\pageref{Lhideallmatchpositions}] +% % \quad|\shadeallresidues| % \hfill[\pageref{Lshadeallresidues}] % @@ -6426,8 +6463,8 @@ % \begin{macrocode} %<*texshade> \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} @@ -12531,6 +12568,8 @@ \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} @@ -19881,6 +19920,80 @@ \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 @@ -20117,6 +20230,20 @@ \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 @@ -20218,6 +20345,20 @@ \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 @@ -20905,7 +21046,7 @@ \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 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% diff --git a/Master/texmf-dist/source/latex/texshade/texshade.ins b/Master/texmf-dist/source/latex/texshade/texshade.ins index b45ae964513..73f08c8f6de 100644 --- a/Master/texmf-dist/source/latex/texshade/texshade.ins +++ b/Master/texmf-dist/source/latex/texshade/texshade.ins @@ -1,7 +1,7 @@ %% %% docstrip install file for texshade.sty %% -%% Copyright 1999-2010 Eric Beitz +%% Copyright 1999-2011 Eric Beitz %% \def\batchfile{texshade.ins} @@ -14,7 +14,7 @@ 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 \endpreamble 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 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |