TeXshade v1.23

git-svn-id: svn://tug.org/texlive/trunk@23321 c570f23f-e606-0410-a88d-b1316a301751

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
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%