texlive[67243] Master/texmf-dist: texshade (29may23)
commits+karl at tug.org
commits+karl at tug.org
Mon May 29 21:07:17 CEST 2023
Revision: 67243
http://tug.org/svn/texlive?view=revision&revision=67243
Author: karl
Date: 2023-05-29 21:07:17 +0200 (Mon, 29 May 2023)
Log Message:
-----------
texshade (29may23)
Modified Paths:
--------------
trunk/Master/texmf-dist/doc/latex/texshade/README
trunk/Master/texmf-dist/doc/latex/texshade/texshade.pdf
trunk/Master/texmf-dist/source/latex/texshade/texshade.dtx
trunk/Master/texmf-dist/source/latex/texshade/texshade.ins
trunk/Master/texmf-dist/tex/latex/texshade/texshade.sty
Modified: trunk/Master/texmf-dist/doc/latex/texshade/README
===================================================================
--- trunk/Master/texmf-dist/doc/latex/texshade/README 2023-05-28 23:43:08 UTC (rev 67242)
+++ trunk/Master/texmf-dist/doc/latex/texshade/README 2023-05-29 19:07:17 UTC (rev 67243)
@@ -1,4 +1,4 @@
- TeXshade v1.26a
+ TeXshade v1.26b
>>
>> 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 - 2022 Eric Beitz
+ Copyright (C) 1999 - 2023 Eric Beitz
Modified: trunk/Master/texmf-dist/doc/latex/texshade/texshade.pdf
===================================================================
(Binary files differ)
Modified: trunk/Master/texmf-dist/source/latex/texshade/texshade.dtx
===================================================================
--- trunk/Master/texmf-dist/source/latex/texshade/texshade.dtx 2023-05-28 23:43:08 UTC (rev 67242)
+++ trunk/Master/texmf-dist/source/latex/texshade/texshade.dtx 2023-05-29 19:07:17 UTC (rev 67243)
@@ -10,8 +10,7 @@
% `README.txt' for further information!
%
%
-% Copyright (C) 1999-2021 Eric Beitz
-% See the file texshade.txt
+% Copyright (C) 1999-2023 Eric Beitz
%
% \fi
%
@@ -419,8 +418,12 @@
% structure meme paper was added;
% `par' line endings now treated correctly.}
%
+% \changes{1.26b}{2023-05-28}{%
+% Corrections: shading, tinting, emphasizing, lower casing
+% of motifs now works with set domains.}
%
%
+%
% \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
% Lower-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
@@ -458,7 +461,7 @@
% 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 v1.26a; 2022/08/29\\[2pt]}
+% \date{\small v1.26b; 2023/05/28\\[2pt]}
% \maketitle
% \begin{abstract}
% Setting alignments of nucleotides and peptides for publication
@@ -542,12 +545,12 @@
%
% \subsection{Version History}
%
-% \textbf{v1.26(a) 2021/04/01 (2022/08/29)}
+% \textbf{v1.26(a, b) 2021/04/01 (2022/08/29, 2023/05/28)}
% \medskip
%
% \emph{Corrections}: Frames at line ends remain open to indicate
% continuity of the marked region, and |\par| line endings are now treated
-% correctly.
+% correctly; motifs are now properly located in set domains for shading etc.
%
% \emph{Introductions:}
% Chimera command file export option for 'structure memes'
@@ -6611,8 +6614,8 @@
% \begin{macrocode}
%<*texshade>
\NeedsTeXFormat{LaTeX2e}
-\ProvidesPackage{texshade}[2022/08/29 LaTeX TeXshade (v1.26a)]
-\message{Package `texshade', Version 1.26a of 2022/08/29.}
+\ProvidesPackage{texshade}[2023/05/28 LaTeX TeXshade (v1.26b)]
+\message{Package `texshade', Version 1.26b of 2023/05/28.}
\PassOptionsToPackage{dvips}{color}
\PassOptionsToPackage{dvips}{graphicx}
@@ -10073,7 +10076,11 @@
\advance\temp@@count by 1
\xdef\first@@{\csname motif\the\temp@@count\endcsname}
\expandafter\get at motif@specs\first@@
- \xdef\first@@{\csname sequence\seq@\endcsname &@}
+ \if\dom at in\y@
+ \xdef\first@@{\csname seq at dom\seq@\endcsname &@}
+ \else
+ \xdef\first@@{\csname sequence\seq@\endcsname &@}
+ \fi
\temp at count=\csname res at count\seq@\endcsname
\expandafter\ifnum\csname seq at start\seq@\endcsname<0 \ifx\allow at zero\n@ \advance\temp at count by 1 \fi\fi
\xdef\f at text@{\@ll}
@@ -21371,6 +21378,7 @@
\expandafter\xdef\csname T at cof\the\loopcount\endcsname{\temp@ &@}
\expandafter\xdef\csname T at coffee\the\loopcount\endcsname{}
\fi
+ \expandafter\xdef\csname seq at dom\the\loopcount\endcsname{\csname sequence\the\loopcount\endcsname}
\expandafter\xdef\csname seq\the\loopcount\endcsname{\csname sequence\the\loopcount\endcsname &@}
\expandafter\xdef\csname sequence\the\loopcount\endcsname{}
\expandafter\xdef\csname dom at num\the\loopcount\endcsname{}
@@ -21486,6 +21494,7 @@
\expandafter\xdef\csname T at cof\the\loopcount\endcsname{\temp@ &@}
\expandafter\xdef\csname T at coffee\the\loopcount\endcsname{}
\fi
+ \expandafter\xdef\csname seq at dom\the\loopcount\endcsname{\csname sequence\the\loopcount\endcsname}
\expandafter\xdef\csname seq\the\loopcount\endcsname{\csname sequence\the\loopcount\endcsname &@}
\expandafter\xdef\csname sequence\the\loopcount\endcsname{}
\expandafter\xdef\csname dom at num\the\loopcount\endcsname{}
Modified: trunk/Master/texmf-dist/source/latex/texshade/texshade.ins
===================================================================
--- trunk/Master/texmf-dist/source/latex/texshade/texshade.ins 2023-05-28 23:43:08 UTC (rev 67242)
+++ trunk/Master/texmf-dist/source/latex/texshade/texshade.ins 2023-05-29 19:07:17 UTC (rev 67243)
@@ -1,7 +1,7 @@
%%
%% docstrip install file for texshade.sty
%%
-%% Copyright 1999-2021 Eric Beitz
+%% Copyright 1999-2023 Eric Beitz
%%
\def\batchfile{texshade.ins}
@@ -14,8 +14,8 @@
LaTeX package for typesetting nucleotide and peptide alignments
-Copyright (C) 1999-2021 Eric Beitz
-See the file texshade.txt
+Copyright (C) 1999-2023 Eric Beitz
+See the file README
\endpreamble
Modified: trunk/Master/texmf-dist/tex/latex/texshade/texshade.sty
===================================================================
--- trunk/Master/texmf-dist/tex/latex/texshade/texshade.sty 2023-05-28 23:43:08 UTC (rev 67242)
+++ trunk/Master/texmf-dist/tex/latex/texshade/texshade.sty 2023-05-29 19:07:17 UTC (rev 67243)
@@ -8,13 +8,13 @@
%%
%% LaTeX package for typesetting nucleotide and peptide alignments
%%
-%% Copyright (C) 1999-2021 Eric Beitz
-%% See the file texshade.txt
+%% Copyright (C) 1999-2023 Eric Beitz
+%% See the file README
%%
\NeedsTeXFormat{LaTeX2e}
-\ProvidesPackage{texshade}[2022/08/29 LaTeX TeXshade (v1.26a)]
-\message{Package `texshade', Version 1.26a of 2022/08/29.}
+\ProvidesPackage{texshade}[2023/05/28 LaTeX TeXshade (v1.26b)]
+\message{Package `texshade', Version 1.26b of 2023/05/28.}
\PassOptionsToPackage{dvips}{color}
\PassOptionsToPackage{dvips}{graphicx}
@@ -3464,7 +3464,11 @@
\advance\temp@@count by 1
\xdef\first@@{\csname motif\the\temp@@count\endcsname}
\expandafter\get at motif@specs\first@@
- \xdef\first@@{\csname sequence\seq@\endcsname &@}
+ \if\dom at in\y@
+ \xdef\first@@{\csname seq at dom\seq@\endcsname &@}
+ \else
+ \xdef\first@@{\csname sequence\seq@\endcsname &@}
+ \fi
\temp at count=\csname res at count\seq@\endcsname
\expandafter\ifnum\csname seq at start\seq@\endcsname<0 \ifx\allow at zero\n@ \advance\temp at count by 1 \fi\fi
\xdef\f at text@{\@ll}
@@ -14664,6 +14668,7 @@
\expandafter\xdef\csname T at cof\the\loopcount\endcsname{\temp@ &@}
\expandafter\xdef\csname T at coffee\the\loopcount\endcsname{}
\fi
+ \expandafter\xdef\csname seq at dom\the\loopcount\endcsname{\csname sequence\the\loopcount\endcsname}
\expandafter\xdef\csname seq\the\loopcount\endcsname{\csname sequence\the\loopcount\endcsname &@}
\expandafter\xdef\csname sequence\the\loopcount\endcsname{}
\expandafter\xdef\csname dom at num\the\loopcount\endcsname{}
@@ -14779,6 +14784,7 @@
\expandafter\xdef\csname T at cof\the\loopcount\endcsname{\temp@ &@}
\expandafter\xdef\csname T at coffee\the\loopcount\endcsname{}
\fi
+ \expandafter\xdef\csname seq at dom\the\loopcount\endcsname{\csname sequence\the\loopcount\endcsname}
\expandafter\xdef\csname seq\the\loopcount\endcsname{\csname sequence\the\loopcount\endcsname &@}
\expandafter\xdef\csname sequence\the\loopcount\endcsname{}
\expandafter\xdef\csname dom at num\the\loopcount\endcsname{}
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