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-rw-r--r--Master/texmf-dist/doc/latex/texshade/README4
-rw-r--r--Master/texmf-dist/doc/latex/texshade/texshade.pdfbin1235875 -> 1565024 bytes
-rw-r--r--Master/texmf-dist/source/latex/texshade/texshade.dtx25
-rw-r--r--Master/texmf-dist/source/latex/texshade/texshade.ins6
-rw-r--r--Master/texmf-dist/tex/latex/texshade/texshade.sty16
5 files changed, 33 insertions, 18 deletions
diff --git a/Master/texmf-dist/doc/latex/texshade/README b/Master/texmf-dist/doc/latex/texshade/README
index ef3b5d56e06..f6063602bff 100644
--- a/Master/texmf-dist/doc/latex/texshade/README
+++ b/Master/texmf-dist/doc/latex/texshade/README
@@ -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
diff --git a/Master/texmf-dist/doc/latex/texshade/texshade.pdf b/Master/texmf-dist/doc/latex/texshade/texshade.pdf
index 01730abc593..d2088ac9b29 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 2f14d416530..44fad1c38f8 100644
--- a/Master/texmf-dist/source/latex/texshade/texshade.dtx
+++ b/Master/texmf-dist/source/latex/texshade/texshade.dtx
@@ -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
%
@@ -419,6 +418,10 @@
% 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
@@ -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@motif@specs\first@@
- \xdef\first@@{\csname sequence\seq@\endcsname &@}
+ \if\dom@in\y@
+ \xdef\first@@{\csname seq@dom\seq@\endcsname &@}
+ \else
+ \xdef\first@@{\csname sequence\seq@\endcsname &@}
+ \fi
\temp@count=\csname res@count\seq@\endcsname
\expandafter\ifnum\csname seq@start\seq@\endcsname<0 \ifx\allow@zero\n@ \advance\temp@count by 1 \fi\fi
\xdef\f@text@{\@ll}
@@ -21371,6 +21378,7 @@
\expandafter\xdef\csname T@cof\the\loopcount\endcsname{\temp@ &@}
\expandafter\xdef\csname T@coffee\the\loopcount\endcsname{}
\fi
+ \expandafter\xdef\csname seq@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@num\the\loopcount\endcsname{}
@@ -21486,6 +21494,7 @@
\expandafter\xdef\csname T@cof\the\loopcount\endcsname{\temp@ &@}
\expandafter\xdef\csname T@coffee\the\loopcount\endcsname{}
\fi
+ \expandafter\xdef\csname seq@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@num\the\loopcount\endcsname{}
diff --git a/Master/texmf-dist/source/latex/texshade/texshade.ins b/Master/texmf-dist/source/latex/texshade/texshade.ins
index 75dce91652b..47130a06994 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 1999-2021 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
diff --git a/Master/texmf-dist/tex/latex/texshade/texshade.sty b/Master/texmf-dist/tex/latex/texshade/texshade.sty
index 0254bd5c4ff..b14e9f3d877 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) 1999-2021 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@motif@specs\first@@
- \xdef\first@@{\csname sequence\seq@\endcsname &@}
+ \if\dom@in\y@
+ \xdef\first@@{\csname seq@dom\seq@\endcsname &@}
+ \else
+ \xdef\first@@{\csname sequence\seq@\endcsname &@}
+ \fi
\temp@count=\csname res@count\seq@\endcsname
\expandafter\ifnum\csname seq@start\seq@\endcsname<0 \ifx\allow@zero\n@ \advance\temp@count by 1 \fi\fi
\xdef\f@text@{\@ll}
@@ -14664,6 +14668,7 @@
\expandafter\xdef\csname T@cof\the\loopcount\endcsname{\temp@ &@}
\expandafter\xdef\csname T@coffee\the\loopcount\endcsname{}
\fi
+ \expandafter\xdef\csname seq@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@num\the\loopcount\endcsname{}
@@ -14779,6 +14784,7 @@
\expandafter\xdef\csname T@cof\the\loopcount\endcsname{\temp@ &@}
\expandafter\xdef\csname T@coffee\the\loopcount\endcsname{}
\fi
+ \expandafter\xdef\csname seq@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@num\the\loopcount\endcsname{}
generated by cgit v1.2.3 (git 2.39.1) at 2024-11-13 12:01:56 +0000