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-rw-r--r--Master/texmf-dist/doc/latex/texshade/README4
-rw-r--r--Master/texmf-dist/doc/latex/texshade/texshade.pdfbin760478 -> 763706 bytes
-rw-r--r--Master/texmf-dist/source/latex/texshade/texshade.dtx153
-rw-r--r--Master/texmf-dist/source/latex/texshade/texshade.ins4
-rw-r--r--Master/texmf-dist/tex/latex/texshade/texshade.sty112
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
index fe59789d182..509af83e324 100644
--- a/Master/texmf-dist/doc/latex/texshade/texshade.pdf
+++ b/Master/texmf-dist/doc/latex/texshade/texshade.pdf
Binary files differ
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
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%