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authorKarl Berry <karl@freefriends.org>2010-03-05 00:29:23 +0000
committerKarl Berry <karl@freefriends.org>2010-03-05 00:29:23 +0000
commit09957f78ef831e10c41f8b12329282e8bcef03e3 (patch)
treedd180f619e1b327904e9b4757a49842469220986 /Master/texmf-dist/tex
parentba5d024e2cd6ca72d404ce6b081797ec9f5f2a6d (diff)
texshade 1.21 (2mar10)
git-svn-id: svn://tug.org/texlive/trunk@17314 c570f23f-e606-0410-a88d-b1316a301751
Diffstat (limited to 'Master/texmf-dist/tex')
-rw-r--r--Master/texmf-dist/tex/latex/texshade/texshade.def10
-rw-r--r--Master/texmf-dist/tex/latex/texshade/texshade.sty783
2 files changed, 676 insertions, 117 deletions
diff --git a/Master/texmf-dist/tex/latex/texshade/texshade.def b/Master/texmf-dist/tex/latex/texshade/texshade.def
index a69d64f5d23..0f1931a541e 100644
--- a/Master/texmf-dist/tex/latex/texshade/texshade.def
+++ b/Master/texmf-dist/tex/latex/texshade/texshade.def
@@ -62,7 +62,7 @@
\medsepline % Medium height if separation line is on
\medblockskip % Medium skip between sequence blocks
\flexblockspace % Use optimized space between blocks
-\featurerule{0.5ex} % Set feature rule thickness to 1/5 ex
+\featurerule{0.5ex} % Set feature rule thickness to 1/2 ex
\bargraphstretch{1} % Do not stretch bars in feature graphs
\colorscalestretch{1} % Do not stretch color scales in features
\backtranstext{horizontal} % Horizontal triplets in feature texts
@@ -91,6 +91,10 @@
\setseries{features}{md} % Use normal series for feature texts
\setshape {features}{it} % Use italics shape for feature texts
\setsize {features}{normalsize} % Use normal size for feature texts
+\setfamily{featurestyles}{tt} % Use typewriter family for feature styles
+\setseries{featurestyles}{md} % Use normal series for feature styles
+\setshape {featurestyles}{up} % Use upright shape for feature styles
+\setsize {featurestyles}{normalsize}% Use normal size for feature styles
\setfamily{legend}{tt} % Use typewriter family for legend texts
\setseries{legend}{md} % Use normal series for legend texts
\setshape {legend}{up} % Use upright shape for legend texts
@@ -113,10 +117,10 @@
\appearance{PHDtopo}{TM}{top} % |
{box[LightGray]:TM\numcount}{} % |
\appearance{HMMTOP}{internal} % |
- {bottom}{---} % |
+ {bottom}{'-'} % |
{int.\ \Alphacount} % |
\appearance{HMMTOP}{external} % |
- {top}{---} % |
+ {top}{,-,} % |
{ext.\ \Alphacount} % |
\appearance{HMMTOP}{TM}{top} % |
{helix}{TM\numcount} % |
diff --git a/Master/texmf-dist/tex/latex/texshade/texshade.sty b/Master/texmf-dist/tex/latex/texshade/texshade.sty
index 646ce2b077e..d8ab1cccdc6 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) 1999-2009 Eric Beitz
+%% Copyright (C) 1999-2010 Eric Beitz
%% See the file texshade.txt
%%
\NeedsTeXFormat{LaTeX2e}
-\ProvidesPackage{texshade}[2009/10/05 LaTeX TeXshade (v1.20)]
-\message{Package `texshade', Version 1.20 of 2009/10/05.}
+\ProvidesPackage{texshade}[2010/03/01 LaTeX TeXshade (v1.21)]
+\message{Package `texshade', Version 1.21 of 2010/03/01.}
\PassOptionsToPackage{dvips}{color}
\PassOptionsToPackage{dvips}{graphicx}
@@ -112,12 +112,14 @@
\newif\iftttopfeature \newif\ifbbbottomfeature
\newif\ifttttopfeature\newif\ifbbbbottomfeature
\newif\ifall@fshade \newif\ifregionalemph
+\newif\ifregionallower
\newif\ifframe@ \newif\ifregionaltint
\newif\ifshow@logo \newif\ifshow@sublogo
\newif\ifhidechar \newif\ifsh@wg@ps
\newif\ifsimmode
\newif\ifregionaltintnow
\newif\ifregionalemphnow
+\newif\ifregionallowernow
\newif\ifregionalshadenow
\newif\iftopfeaturenow
\newif\ifttopfeaturenow
@@ -138,7 +140,8 @@
\def\comm@{,} \def\@loc{LOC} \def\@asg{ASG} \def\@t{@} \def\@HP{>HP:}
\def\gre@ter{>} \def\sm@ller{<} \def\N@{N} \def\equ@l{=} \def\H@{H}
\def\gap@char{.} \def\dom@char{{\dom@rule}} \def\yes{yes} \def\y@{y} \def\n@{n}
-\def\o@{o} \def\d@t{.} \def\questi@n{?} \def\st@p@char{*}
+\def\o@{o} \def\d@t{.} \def\questi@n{?} \def\st@p@char{*} \def\semic@n{;}
+\def\br@cket{[}
\def\@TOM{ATOM} \def\C@lpha{CA} \def\@point@{point} \def\@line@{line} \def\@plane@{plane}
\def\gap@rule{\rule[0.3\box@height]{\box@width}{\gap@rulethick}}
\def\dom@rule{\vrule depth\box@depth height\box@height width\domgap@rulethick}
@@ -2288,10 +2291,10 @@
\csname stack@@reg#1\endcsname}
\expandafter\xdef\csname stack@tintreg\the\loopcount\endcsname{%
\csname stack@@tintreg#1\endcsname}
- \expandafter\xdef\csname stack@hidereg\the\loopcount\endcsname{%
- \csname stack@@hidereg#1\endcsname}
\expandafter\xdef\csname stack@emphreg\the\loopcount\endcsname{%
\csname stack@@emphreg#1\endcsname}
+ \expandafter\xdef\csname stack@lowerreg\the\loopcount\endcsname{%
+ \csname stack@@lowerreg#1\endcsname}
\expandafter\xdef\csname stack@framereg\the\loopcount\endcsname{%
\csname stack@@framereg#1\endcsname}
\expandafter\xdef\csname stack@top\the\loopcount\endcsname{%
@@ -2341,10 +2344,10 @@
\csname stack@reg\the\loopcount\endcsname}
\expandafter\xdef\csname stack@@tintreg\the\loopcount\endcsname{%
\csname stack@tintreg\the\loopcount\endcsname}
- \expandafter\xdef\csname stack@@hidereg\the\loopcount\endcsname{%
- \csname stack@hidereg\the\loopcount\endcsname}
\expandafter\xdef\csname stack@@emphreg\the\loopcount\endcsname{%
\csname stack@emphreg\the\loopcount\endcsname}
+ \expandafter\xdef\csname stack@@lowerreg\the\loopcount\endcsname{%
+ \csname stack@lowerreg\the\loopcount\endcsname}
\expandafter\xdef\csname stack@@framereg\the\loopcount\endcsname{%
\csname stack@framereg\the\loopcount\endcsname}
\expandafter\xdef\csname stack@@top\the\loopcount\endcsname{%
@@ -2630,10 +2633,10 @@
\csname stack@reg\the\innerloopcount\endcsname}
\expandafter\xdef\csname stack@tintreg\the\loopcount\endcsname{%
\csname stack@tintreg\the\innerloopcount\endcsname}
- \expandafter\xdef\csname stack@hidereg\the\loopcount\endcsname{%
- \csname stack@hidereg\the\innerloopcount\endcsname}
\expandafter\xdef\csname stack@emphreg\the\loopcount\endcsname{%
\csname stack@emphreg\the\innerloopcount\endcsname}
+ \expandafter\xdef\csname stack@lowerreg\the\loopcount\endcsname{%
+ \csname stack@lowerreg\the\innerloopcount\endcsname}
\expandafter\xdef\csname stack@framereg\the\loopcount\endcsname{%
\csname stack@framereg\the\innerloopcount\endcsname}
\expandafter\xdef\csname stack@top\the\loopcount\endcsname{%
@@ -2909,7 +2912,8 @@
\xdef\tmpstack{\tmpstack\the\loopcount;\st@rt;\st@p;\@ll;%
\first@;\second@;\third@;\fourth@;\last@}
\else
- \xdef\tmpstack{\tmpstack\first@;\second@;\third@;\fourth@;} \sort@stack
+ \xdef\tmpstack{\tmpstack\first@;\second@;\third@;\fourth@;}
+ \sort@stack
\fi\fi
}
\def\get@regions#1..#2,#3@{%
@@ -2919,28 +2923,6 @@
\sort@stack
\expandafter\xdef\csname stack@reg\seq@\endcsname{\tmpstack}
}
-\def\getregion@fromhidestack#1{%
- \xdef\temp@{#1}
- \xdef\first@{\csname stack@hidereg\temp@\endcsname}
- \expandafter\get@fromstack\first@
- \expandafter\xdef\csname hidestart\temp@\endcsname{\first@}
- \expandafter\xdef\csname hidestop\temp@\endcsname{\second@}
- \expandafter\xdef\csname hidestyle\temp@\endcsname{\third@}
- \expandafter\xdef\csname hidetext\temp@\endcsname{\fourth@}
- \expandafter\xdef\csname stack@hidereg\temp@\endcsname{\last@}
-}
-\def\sort@hidestack{%
- \expandafter\get@fromstack\last@
- \ifx\first@\ampers@nd
- \xdef\tmpstack{\tmpstack\st@rt;\st@p;\@ll;\text@;&;&;&;&;&;@}
- \else
- \ifnum\st@rt<\second@
- \xdef\tmpstack{\tmpstack\st@rt;\st@p;\@ll;\text@;%
- \first@;\second@;\third@;\fourth@;\last@}
- \else
- \xdef\tmpstack{\tmpstack\first@;\second@;\third@;\fourth@;} \sort@hidestack
- \fi\fi
-}
\def\get@fromemphstack#1;#2;#3;#4@{%
\xdef\first@{#1} \xdef\second@{#2}
\xdef\third@{#3} \xdef\last@{#4@}
@@ -2973,6 +2955,34 @@
\sort@emphstack
\expandafter\xdef\csname stack@emphreg\seq@\endcsname{\tmpstack}
}
+\def\getregion@fromlowerstack#1{%
+ \xdef\temp@{#1}
+ \xdef\first@{\csname stack@lowerreg\temp@\endcsname}
+ \expandafter\get@fromemphstack\first@
+ \expandafter\xdef\csname lowerstart\temp@\endcsname{\first@}
+ \expandafter\xdef\csname lowerstop\temp@\endcsname{\second@}
+ \expandafter\xdef\csname lowerall\temp@\endcsname{\third@}
+ \expandafter\xdef\csname stack@lowerreg\temp@\endcsname{\last@}
+}
+\def\sort@lowerstack{%
+ \expandafter\get@fromemphstack\last@
+ \ifx\first@\ampers@nd
+ \xdef\tmpstack{\tmpstack\st@rt;\st@p;\@ll;&;&;&;@}
+ \else
+ \ifnum\st@rt<\second@
+ \xdef\tmpstack{\tmpstack\st@rt;\st@p;\@ll;\first@;\second@;\third@;\last@}
+ \else
+ \xdef\tmpstack{\tmpstack\first@;\second@;\third@;} \sort@lowerstack
+ \fi\fi
+}
+\def\get@lowerregions#1..#2,#3@{%
+ \regionallowertrue
+ \xdef\st@rt{#1} \xdef\st@p{#2} \xdef\list@{#3}
+ \xdef\last@{\csname stack@lowerreg\seq@\endcsname}
+ \xdef\tmpstack{}
+ \sort@lowerstack
+ \expandafter\xdef\csname stack@lowerreg\seq@\endcsname{\tmpstack}
+}
\def\get@fromdomstack#1;#2;#3@{%
\xdef\first@{#1} \xdef\second@{#2}
\xdef\last@{#3@}
@@ -3016,23 +3026,12 @@
\expandafter\xdef\csname tintall\temp@\endcsname{\third@}
\expandafter\xdef\csname stack@tintreg\temp@\endcsname{\last@}
}
-\def\sort@tintstack{%
- \expandafter\get@fromemphstack\last@
- \ifx\first@\ampers@nd
- \xdef\tmpstack{\tmpstack\st@rt;\st@p;\@ll;&;&;&;@}
- \else
- \ifnum\st@rt<\second@
- \xdef\tmpstack{\tmpstack\st@rt;\st@p;\@ll;\first@;\second@;\third@;\last@}
- \else
- \xdef\tmpstack{\tmpstack\first@;\second@;\third@;} \sort@tintstack
- \fi\fi
-}
\def\get@tintregions#1..#2,#3@{%
\regionaltinttrue
\xdef\st@rt{#1} \xdef\st@p{#2} \xdef\list@{#3}
\xdef\last@{\csname stack@tintreg\seq@\endcsname}
\xdef\tmpstack{}
- \sort@tintstack
+ \sort@emphstack
\expandafter\xdef\csname stack@tintreg\seq@\endcsname{\tmpstack}
}
\def\getregion@fromframestack#1{%
@@ -3178,23 +3177,312 @@
\fi%
\fi%
}
+\def\test@get#1#2@{%
+ \xdef\temp@{#1} \xdef\third@@{#2@}
+ \ifx\temp@\ampers@nd
+ \else
+ \if \temp@ X
+ \xdef\temp@{\second@@}
+ \fi
+ \ifx\temp@\second@@
+ \xdef\third@@{\second@@}
+ \else
+ \expandafter\test@get\third@@
+ \fi
+ \fi
+}
+\def\get@@second@#1#2@{\xdef\second@@{#1}\xdef\first@@{#2@}}
+\def\get@@third@#1]#2@{\xdef\third@@{#1&@}\xdef\fifth@@{#2@}}
+\def\get@third@#1#2@{\xdef\third@@{#1}\xdef\fifth@@{#2@}}
+\def\find@motif{%
+ \expandafter\get@@second@\first@@
+ \ifx\second@@\ampers@nd
+ \else
+ \ifx\second@@\d@t
+ \else
+ \advance\temp@count by 1
+ \if \third@@ X
+ \xdef\third@@{\second@@}
+ \fi
+ \ifx\third@@\br@cket
+ \expandafter\get@@third@\fifth@@
+ \expandafter\test@get\third@@
+ \fi
+ \ifx\second@@\third@@
+ \ifx\nineth@@\n@
+ \xdef\st@rt{\the\temp@count}
+ \xdef\st@p{n}
+ \fi
+ \xdef\nineth@@{y}
+ \expandafter\get@third@\fifth@@
+ \ifx\third@@\ampers@nd
+ \xdef\st@p{\the\temp@count}
+ \xdef\list@{}
+ \xdef\tmpstack{}
+ \xdef\temp@{shade}
+ \ifx\temp@\temp@@
+ \xdef\last@{\csname stack@reg\seq@\endcsname}
+ \loopcount=\style@
+ \sort@stack
+ \expandafter\xdef\csname stack@reg\seq@\endcsname{\tmpstack}
+ \else
+ \xdef\temp@{emph}
+ \ifx\temp@\temp@@
+ \regionalemphtrue
+ \xdef\last@{\csname stack@emphreg\seq@\endcsname}
+ \sort@emphstack
+ \expandafter\xdef\csname stack@emphreg\seq@\endcsname{\tmpstack}
+ \else
+ \xdef\temp@{lower}
+ \ifx\temp@\temp@@
+ \regionallowertrue
+ \xdef\last@{\csname stack@lowerreg\seq@\endcsname}
+ \sort@lowerstack
+ \expandafter\xdef\csname stack@lowerreg\seq@\endcsname{\tmpstack}
+ \else
+ \xdef\temp@{tint}
+ \ifx\temp@\temp@@
+ \regionaltinttrue
+ \xdef\last@{\csname stack@tintreg\seq@\endcsname} \message{((last:\last@))}
+ \sort@emphstack
+ \expandafter\xdef\csname stack@tintreg\seq@\endcsname{\tmpstack} \message{((tmp:\tmpstack))}
+ \else
+ \xdef\temp@{frame}
+ \ifx\temp@\temp@@
+ \frame@true
+ \xdef\last@{\csname stack@framereg\seq@\endcsname}
+ \sort@emphstack
+ \expandafter\xdef\csname stack@framereg\seq@\endcsname{\tmpstack}
+ \else
+ \xdef\temp@{ttttop}
+ \ifx\temp@\temp@@
+ \xdef\last@{\csname stack@ttttop\seq@\endcsname}
+ \sort@fstack
+ \expandafter\xdef\csname stack@ttttop\seq@\endcsname{\tmpstack}
+ \else
+ \xdef\temp@{tttop}
+ \ifx\temp@\temp@@
+ \xdef\last@{\csname stack@tttop\seq@\endcsname}
+ \sort@fstack
+ \expandafter\xdef\csname stack@tttop\seq@\endcsname{\tmpstack}
+ \else
+ \xdef\temp@{ttop}
+ \ifx\temp@\temp@@
+ \xdef\last@{\csname stack@ttop\seq@\endcsname}
+ \sort@fstack
+ \expandafter\xdef\csname stack@ttop\seq@\endcsname{\tmpstack}
+ \else
+ \xdef\temp@{top}
+ \ifx\temp@\temp@@
+ \xdef\last@{\csname stack@top\seq@\endcsname}
+ \sort@fstack
+ \expandafter\xdef\csname stack@top\seq@\endcsname{\tmpstack}
+ \else
+ \xdef\temp@{bottom}
+ \ifx\temp@\temp@@
+ \xdef\last@{\csname stack@bottom\seq@\endcsname}
+ \sort@fstack
+ \expandafter\xdef\csname stack@bottom\seq@\endcsname{\tmpstack}
+ \else
+ \xdef\temp@{bbottom}
+ \ifx\temp@\temp@@
+ \xdef\last@{\csname stack@bbottom\seq@\endcsname}
+ \sort@fstack
+ \expandafter\xdef\csname stack@bbottom\seq@\endcsname{\tmpstack}
+ \else
+ \xdef\temp@{bbbottom}
+ \ifx\temp@\temp@@
+ \xdef\last@{\csname stack@bbbottom\seq@\endcsname}
+ \sort@fstack
+ \expandafter\xdef\csname stack@bbbottom\seq@\endcsname{\tmpstack}
+ \else
+ \xdef\temp@{bbbbottom}
+ \ifx\temp@\temp@@
+ \xdef\last@{\csname stack@bbbbottom\seq@\endcsname}
+ \sort@fstack
+ \expandafter\xdef\csname stack@bbbbottom\seq@\endcsname{\tmpstack}
+ \fi
+ \fi
+ \fi
+ \fi
+ \fi
+ \fi
+ \fi
+ \fi
+ \fi
+ \fi
+ \fi
+ \fi
+ \fi
+ \xdef\fifth@@{\m@tif} \expandafter\get@third@\fifth@@
+ \xdef\nineth@@{n}
+ \fi
+ \else
+ \xdef\nineth@@{n} \xdef\st@p{n}
+ \xdef\fifth@@{\m@tif} \expandafter\get@third@\fifth@@
+ \fi
+ \fi
+ \find@motif
+ \fi
+}
+\def\prep@motif{%
+
+ \def\get@motif@specs##1,##2,##3,##4,##5,&{%
+ \xdef\seq@{##1} \xdef\temp@@{##2} \xdef\@ll{##3} \def\fourth@@{##4} \xdef\fifth@@{##5&@}
+ }
+
+ \loopcount=0
+ \loop
+ \advance\loopcount by 1
+ \expandafter\xdef\csname stack@reg\the\loopcount\endcsname{\csname style\the\loopcount\endcsname;%
+ \csname start\the\loopcount\endcsname;%
+ \csname stop\the\loopcount\endcsname;%
+ \csname all\the\loopcount\endcsname;%
+ \csname stack@reg\the\loopcount\endcsname}
+ \expandafter\xdef\csname stack@emphreg\the\loopcount\endcsname{\csname emphstart\the\loopcount\endcsname;%
+ \csname emphstop\the\loopcount\endcsname;%
+ \csname emphall\the\loopcount\endcsname;%
+ \csname stack@emphreg\the\loopcount\endcsname}
+ \expandafter\xdef\csname stack@lowerreg\the\loopcount\endcsname{\csname lowerstart\the\loopcount\endcsname;%
+ \csname lowerstop\the\loopcount\endcsname;%
+ \csname lowerall\the\loopcount\endcsname;%
+ \csname stack@lowerreg\the\loopcount\endcsname}
+ \expandafter\xdef\csname stack@tintreg\the\loopcount\endcsname{\csname tintstart\the\loopcount\endcsname;%
+ \csname tintstop\the\loopcount\endcsname;%
+ \csname tintall\the\loopcount\endcsname;%
+ \csname stack@tintreg\the\loopcount\endcsname}
+ \expandafter\xdef\csname stack@framereg\the\loopcount\endcsname{\csname framestart\the\loopcount\endcsname;%
+ \csname framestop\the\loopcount\endcsname;%
+ \csname framestyle\the\loopcount\endcsname;%
+ \csname stack@framereg\the\loopcount\endcsname}
+ \expandafter\xdef\csname stack@ttttop\the\loopcount\endcsname{\csname textttttop\the\loopcount\endcsname;%
+ \csname startttttop\the\loopcount\endcsname;%
+ \csname stopttttop\the\loopcount\endcsname;%
+ \csname stylettttop\the\loopcount\endcsname;%
+ \csname stack@ttttop\the\loopcount\endcsname}
+ \expandafter\xdef\csname stack@tttop\the\loopcount\endcsname{\csname texttttop\the\loopcount\endcsname;%
+ \csname starttttop\the\loopcount\endcsname;%
+ \csname stoptttop\the\loopcount\endcsname;%
+ \csname styletttop\the\loopcount\endcsname;%
+ \csname stack@tttop\the\loopcount\endcsname}
+ \expandafter\xdef\csname stack@ttop\the\loopcount\endcsname{\csname textttop\the\loopcount\endcsname;%
+ \csname startttop\the\loopcount\endcsname;%
+ \csname stopttop\the\loopcount\endcsname;%
+ \csname stylettop\the\loopcount\endcsname;%
+ \csname stack@ttop\the\loopcount\endcsname}
+ \expandafter\xdef\csname stack@top\the\loopcount\endcsname{\csname texttop\the\loopcount\endcsname;%
+ \csname starttop\the\loopcount\endcsname;%
+ \csname stoptop\the\loopcount\endcsname;%
+ \csname styletop\the\loopcount\endcsname;%
+ \csname stack@top\the\loopcount\endcsname}
+ \expandafter\xdef\csname stack@bottom\the\loopcount\endcsname{\csname textbottom\the\loopcount\endcsname;%
+ \csname startbottom\the\loopcount\endcsname;%
+ \csname stopbottom\the\loopcount\endcsname;%
+ \csname stylebottom\the\loopcount\endcsname;%
+ \csname stack@bottom\the\loopcount\endcsname}
+ \expandafter\xdef\csname stack@bbottom\the\loopcount\endcsname{\csname textbbottom\the\loopcount\endcsname;%
+ \csname startbbottom\the\loopcount\endcsname;%
+ \csname stopbbottom\the\loopcount\endcsname;%
+ \csname stylebbottom\the\loopcount\endcsname;%
+ \csname stack@bbottom\the\loopcount\endcsname}
+ \expandafter\xdef\csname stack@bbbottom\the\loopcount\endcsname{\csname textbbbottom\the\loopcount\endcsname;%
+ \csname startbbbottom\the\loopcount\endcsname;%
+ \csname stopbbbottom\the\loopcount\endcsname;%
+ \csname stylebbbottom\the\loopcount\endcsname;%
+ \csname stack@bbbottom\the\loopcount\endcsname}
+ \expandafter\xdef\csname stack@bbbbottom\the\loopcount\endcsname{\csname textbbbbottom\the\loopcount\endcsname;%
+ \csname startbbbbottom\the\loopcount\endcsname;%
+ \csname stopbbbbottom\the\loopcount\endcsname;%
+ \csname stylebbbbottom\the\loopcount\endcsname;%
+ \csname stack@bbbbottom\the\loopcount\endcsname}
+ \ifnum\loopcount<\seq@num\repeat
+ \temp@@count=0
+ \loop
+ \advance\temp@@count by 1
+ \xdef\first@@{\csname motif\the\temp@@count\endcsname}
+ \expandafter\get@motif@specs\first@@
+ \xdef\first@@{\csname sequence\seq@\endcsname &@}
+ \temp@count=\csname res@count\seq@\endcsname
+ \xdef\f@text@{\@ll}
+ \xdef\style@{\fourth@@}
+ \xdef\m@tif{\fifth@@} \expandafter\get@third@\fifth@@
+ \xdef\nineth@@{n} \xdef\st@p{n}
+ \find@motif
+ \ifnum\temp@@count<\motif@num\repeat
+ \loopcount=0
+ \loop
+ \advance\loopcount by 1
+ \expandafter\getregion@fromstack{\the\loopcount}
+ \expandafter\getregion@fromtintstack{\the\loopcount}
+ \expandafter\getregion@fromemphstack{\the\loopcount}
+ \expandafter\getregion@fromlowerstack{\the\loopcount}
+ \expandafter\getregion@fromframestack{\the\loopcount}
+ \xdef\bottop@{top} \expandafter\getregion@fromfstack{\the\loopcount}
+ \xdef\bottop@{ttop} \expandafter\getregion@fromfstack{\the\loopcount}
+ \xdef\bottop@{tttop} \expandafter\getregion@fromfstack{\the\loopcount}
+ \xdef\bottop@{ttttop} \expandafter\getregion@fromfstack{\the\loopcount}
+ \xdef\bottop@{bottom} \expandafter\getregion@fromfstack{\the\loopcount}
+ \xdef\bottop@{bbottom} \expandafter\getregion@fromfstack{\the\loopcount}
+ \xdef\bottop@{bbbottom} \expandafter\getregion@fromfstack{\the\loopcount}
+ \xdef\bottop@{bbbbottom} \expandafter\getregion@fromfstack{\the\loopcount}
+ \ifnum\loopcount<\seq@num\repeat
+}
+
+\def\test@motif#1#2@{%
+ \xdef\temp@{shade}
+ \ifx\temp@\temp@@ \xdef\style@{\the\loopcount} \fi
+ \xdef\temp@{emph}
+ \ifx\temp@\temp@@ \xdef\style@{0} \fi
+ \xdef\temp@{lower}
+ \ifx\temp@\temp@@ \xdef\style@{0} \fi
+ \xdef\temp@{tint}
+ \ifx\temp@\temp@@ \xdef\style@{0} \fi
+ \xdef\temp@{frame}
+ \ifx\temp@\temp@@ \xdef\style@{0} \fi
+ \xdef\temp@{#1#2}
+ \xdef\first@{#1}
+ \ifx\first@\br@cket
+ \xdef\label@motif{y}
+ \temp@count=\motif@num
+ \advance\temp@count by 1
+ \xdef\motif@num{\the\temp@count}
+ \expandafter\xdef\csname motif\the\temp@count\endcsname{\seq@,\temp@@,\@ll,\style@,\temp@}
+ \xdef\list@{&}
+ \else
+ \expandafter\check@char\first@
+ \ifletter
+ \xdef\label@motif{y}
+ \temp@count=\motif@num
+ \advance\temp@count by 1
+ \xdef\motif@num{\the\temp@count}
+ \expandafter\xdef\csname motif\the\temp@count\endcsname{\seq@,\temp@@,\@ll,\style@,\temp@}
+ \xdef\list@{&}
+ \fi
+ \fi
+}
\def\test@PDB#1:#2,#3,#4,#5,#6@{%
\xdef\last@{#1[,]&}\expandafter\opt@color\last@
+ \xdef\PDB@distance{no}
\ifx\f@color\comm@
- \xdef\PDB@distance{no}
\else
\xdef\f@color{\f@color .&&@}
\expandafter\coord@get\f@color
- \temp@count=\c@@rd
- \multiply\temp@count by \temp@count
- \xdef\PDB@distance{\the\temp@count}
+ \xdef\temp@{\c@@rd @}
+ \expandafter\check@letter\temp@
+ \ifletter
+ \else
+ \temp@count=\c@@rd
+ \multiply\temp@count by \temp@count
+ \xdef\PDB@distance{\the\temp@count}
+ \fi
\fi
\xdef\PDB@hitpos{0}
\xdef\PDB@stack{}
\xdef\PDB@name{#2}
\xdef\PDB@type{point}
\ifx\fourth@\PDB@type
+ \xdef\PDB@{y}
\xdef\last@{#3[,]&}\expandafter\opt@color\last@
\xdef\PDB@refnum@a{\fourth@}
\ifx\f@color\C@lpha
@@ -3210,6 +3498,7 @@
\else
\xdef\PDB@type{line}
\ifx\fourth@\PDB@type
+ \xdef\PDB@{y}
\xdef\last@{#3[,]&}\expandafter\opt@color\last@
\xdef\PDB@refnum{\fourth@}
\ifx\f@color\C@lpha
@@ -3244,6 +3533,7 @@
\else
\xdef\PDB@type{plane}
\ifx\fourth@\PDB@type
+ \xdef\PDB@{y}
\xdef\last@{#3[,]&}\expandafter\opt@color\last@
\xdef\PDB@refnum{\fourth@}
\ifx\f@color\C@lpha
@@ -3299,6 +3589,9 @@
\ifx\PDB@distance\n@ \xdef\PDB@distance{100}\fi
\load@PDB
\expandafter\get@item\PDB@stack \xdef\list@{\first@@}
+ \else
+ \xdef\temp@{\list@ @}
+ \expandafter\test@motif\temp@
\fi
\fi
\fi
@@ -4952,11 +5245,15 @@
\expandafter\xdef\csname fgseqregion\the\loopcount\endcsname{#3}
\expandafter\xdef\csname bgseqregion\the\loopcount\endcsname{#4}
\xdef\list@{#2,&}
+ \xdef\temp@@{shade}
\xdef\temp@{#2,,,:,,,,@} \expandafter\test@PDB\temp@
- \loop
- \xdef\list@{\list@ @}
- \expandafter\get@regions\list@
- \ifx\list@\ampers@nd\else\repeat
+ \ifx\list@\ampers@nd
+ \else
+ \loop
+ \xdef\list@{\list@ @}
+ \expandafter\get@regions\list@
+ \ifx\list@\ampers@nd\else\repeat
+ \fi
\fi
}
\def\shadeblock#1#2#3#4{%
@@ -4976,11 +5273,15 @@
\else
\ifx\@ll\yes \xdef\@ll{y}\else \xdef\@ll{n}\fi
\xdef\list@{#2,&}
+ \xdef\temp@@{tint} \loopcount=0
\xdef\temp@{#2,,,:,,,,@} \expandafter\test@PDB\temp@
- \loop
- \xdef\list@{\list@ @}
- \expandafter\get@tintregions\list@
- \ifx\list@\ampers@nd\else\repeat
+ \ifx\list@\ampers@nd
+ \else
+ \loop
+ \xdef\list@{\list@ @}
+ \expandafter\get@tintregions\list@
+ \ifx\list@\ampers@nd\else\repeat
+ \fi
\fi
}
\def\tintblock#1#2{%
@@ -5006,6 +5307,34 @@
\xdef\light@{LightLight}
\fi\fi\fi
}
+\def\lowerregion#1#2{%
+ \xdef\seq@{#1}
+ \xdef\temp@{consensus} \ifx\seq@\temp@ \xdef\seq@{0} \fi
+ \xdef\first@{\seq@ @} \expandafter\check@letter\first@
+ \xdef\first@{\seq@}
+ \ifletter \get@name@number \xdef\seq@{\first@} \fi
+ \ifnum\seq@>\seq@count
+ \message{<Ignored seq `\seq@' in \noexpand\lowerregion or \noexpand\lowerblock>}
+ \else
+ \ifx\@ll\yes \xdef\@ll{y}\else \xdef\@ll{n}\fi
+ \xdef\list@{#2,&}
+ \xdef\temp@@{lower} \loopcount=0
+ \xdef\temp@{#2,,,:,,,,@} \expandafter\test@PDB\temp@
+ \ifx\list@\ampers@nd
+ \else
+ \loop
+ \xdef\list@{\list@ @}
+ \expandafter\get@lowerregions\list@
+ \ifx\list@\ampers@nd\else\repeat
+ \fi
+ \fi
+}
+\def\lowerblock#1#2{%
+ \xdef\seq@{#1}
+ \xdef\@ll{yes}
+ \lowerregion{#1}{#2}
+ \xdef\@ll{}
+}
\def\emphregion#1#2{%
\xdef\seq@{#1}
\xdef\temp@{consensus} \ifx\seq@\temp@ \xdef\seq@{0} \fi
@@ -5017,11 +5346,15 @@
\else
\ifx\@ll\yes \xdef\@ll{y}\else \xdef\@ll{n}\fi
\xdef\list@{#2,&}
+ \xdef\temp@@{emph} \loopcount=0
\xdef\temp@{#2,,,:,,,,@} \expandafter\test@PDB\temp@
- \loop
- \xdef\list@{\list@ @}
- \expandafter\get@emphregions\list@
- \ifx\list@\ampers@nd\else\repeat
+ \ifx\list@\ampers@nd
+ \else
+ \loop
+ \xdef\list@{\list@ @}
+ \expandafter\get@emphregions\list@
+ \ifx\list@\ampers@nd\else\repeat
+ \fi
\fi
}
\def\emphblock#1#2{%
@@ -5042,11 +5375,15 @@
\else
\xdef\@ll{#3}
\xdef\list@{#2,&}
+ \xdef\temp@@{frame} \loopcount=0
\xdef\temp@{#2,,,:,,,,@} \expandafter\test@PDB\temp@
- \loop
- \xdef\list@{\list@ @}
- \expandafter\get@frameregions\list@
- \ifx\list@\ampers@nd\else\repeat
+ \ifx\list@\ampers@nd
+ \else
+ \loop
+ \xdef\list@{\list@ @}
+ \expandafter\get@frameregions\list@
+ \ifx\list@\ampers@nd\else\repeat
+ \fi
\fi
}
\def\bargraphstretch#1{\def\b@r@stretch{#1}}
@@ -5429,8 +5766,6 @@
\do@colorgraph
\else
\xdef\f@@color{\f@color}
- \xdef\list@{#3,&}
- \xdef\temp@{#3,,,:,,,,@} \expandafter\test@PDB\temp@
\def\f@text@{#5}
\xdef\f@color{\f@@color}
\xdef\temp@{#4&}
@@ -5509,13 +5844,20 @@
\fi
\fi
\fi
+ \xdef\list@{#3,&}
+ \xdef\@ll{\f@text@}
+ \xdef\temp@@{\bottop@}
+ \xdef\temp@{#3,,,:,,,,@} \expandafter\test@PDB\temp@
\fi
\loopcount=0
- \loop
- \advance\loopcount by 1\relax
- \xdef\list@{\list@ @}
- \expandafter\get@fregions\list@
- \ifx\list@\ampers@nd\else\repeat
+ \ifx\list@\ampers@nd
+ \else
+ \loop
+ \advance\loopcount by 1\relax
+ \xdef\list@{\list@ @}
+ \expandafter\get@fregions\list@
+ \ifx\list@\ampers@nd\else\repeat
+ \fi
\fi\fi\fi
\fi
}
@@ -7470,6 +7812,9 @@
\xdef\first@{\csname res\the\loopcount\endcsname}
\ifx\first@\equ@l
\def\first@{\dom@char} \def\third@{9}
+ \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@
+ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n}
+ \xdef\first@{;\first@}\fi
\expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
\expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
\xdef\first@{=\first@}\fi
@@ -7499,6 +7844,9 @@
\fi
\fi
\fi
+ \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@
+ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n}
+ \xdef\first@{;\first@}\fi
\expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
\expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
\xdef\first@{=\first@}\fi
@@ -7520,6 +7868,9 @@
\def\first@{{}} \def\third@{8}
\fi
\fi
+ \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@
+ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n}
+ \xdef\first@{;\first@}\fi
\expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
\expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
\xdef\first@{=\first@}\fi
@@ -7533,6 +7884,9 @@
\xdef\low@up{lower} \ifx\resn@m@tch\low@up \make@lower \else
\xdef\low@up{upper} \ifx\resn@m@tch\low@up
\else \xdef\first@{\resn@m@tch} \fi\fi\fi
+ \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@
+ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n}
+ \xdef\first@{;\first@}\fi
\expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
\expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
\xdef\first@{=\first@}\fi
@@ -7549,6 +7903,9 @@
\xdef\low@up{lower} \ifx\n@m@tch\low@up \xdef\first@{{ }} \else
\xdef\low@up{upper} \ifx\n@m@tch\low@up \xdef\first@{{ }}
\else \xdef\first@{\n@m@tch} \fi\fi
+ \expandafter\ifx\csname lower@seq0\endcsname\y@
+ \expandafter\xdef\csname lower@seq0\endcsname{n}
+ \xdef\first@{;\first@}\fi
\expandafter\ifx\csname tint@seq0\endcsname\y@
\expandafter\xdef\csname tint@seq0\endcsname{n}
\xdef\first@{=\first@}\fi
@@ -7579,6 +7936,9 @@
\ifx\first@\d@t\def\first@{\gap@char}\fi
\ifx\first@\questi@n\def\first@{\st@p@char}\fi
\ifx\first@\equ@l\def\first@{\dom@char} \xdef\g@p{y} \fi
+ \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@
+ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n}
+ \xdef\first@{;\first@}\fi
\expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
\expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
\xdef\first@{=\first@}\fi
@@ -7643,6 +8003,9 @@
\fi
\fi
\fi
+ \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@
+ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n}
+ \xdef\first@{;\first@}\fi
\expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
\expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
\xdef\first@{=\first@}\fi
@@ -7657,6 +8020,9 @@
\xdef\low@up{lower} \ifx\m@tch\low@up \make@lower \else
\xdef\low@up{upper} \ifx\m@tch\low@up
\else \xdef\first@{\m@tch} \fi\fi
+ \expandafter\ifx\csname lower@seq0\endcsname\y@
+ \expandafter\xdef\csname lower@seq0\endcsname{n}
+ \xdef\first@{;\first@}\fi
\expandafter\ifx\csname tint@seq0\endcsname\y@
\expandafter\xdef\csname tint@seq0\endcsname{n}
\xdef\first@{=\first@}\fi
@@ -7678,6 +8044,9 @@
\xdef\first@{\csname res\the\loopcount\endcsname}
\ifx\first@\equ@l
\def\first@{\dom@char} \def\third@{!} \xdef\g@p{y}
+ \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@
+ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n}
+ \xdef\first@{;\first@}\fi
\expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
\expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
\xdef\first@{=\first@}\fi
@@ -7707,6 +8076,9 @@
\fi
\fi
\fi
+ \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@
+ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n}
+ \xdef\first@{;\first@}\fi
\expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
\expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
\xdef\first@{=\first@}\fi
@@ -7728,6 +8100,9 @@
\def\first@{{}} \def\third@{/}
\fi
\fi
+ \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@
+ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n}
+ \xdef\first@{;\st@p@char}\fi
\expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
\expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
\xdef\first@{=\st@p@char}\fi
@@ -7740,6 +8115,9 @@
\xdef\low@up{lower} \ifx\resn@m@tch\low@up \make@lower \else
\xdef\low@up{upper} \ifx\resn@m@tch\low@up
\else \xdef\first@{\resn@m@tch} \fi\fi
+ \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@
+ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n}
+ \xdef\first@{;\first@}\fi
\expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
\expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
\xdef\first@{=\first@}\fi
@@ -7762,6 +8140,9 @@
\ifx\first@\d@t\def\first@{\gap@char}\fi
\ifx\first@\questi@n\def\first@{\st@p@char}\fi
\ifx\first@\equ@l\def\first@{\dom@char} \xdef\g@p{y} \fi
+ \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@
+ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n}
+ \xdef\first@{;\first@}\fi
\expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
\expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
\xdef\first@{=\first@}\fi
@@ -7775,6 +8156,9 @@
\xdef\first@{\csname res\the\loopcount\endcsname}
\ifx\first@\equ@l
\def\first@{\dom@char} \def\third@{9} \xdef\g@p{y}
+ \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@
+ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n}
+ \xdef\first@{;\first@}\fi
\expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
\expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
\xdef\first@{=\first@}\fi
@@ -7804,6 +8188,9 @@
\fi
\fi
\fi
+ \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@
+ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n}
+ \xdef\first@{;\first@}\fi
\expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
\expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
\xdef\first@{=\first@}\fi
@@ -7825,6 +8212,9 @@
\def\first@{{}} \def\third@{8}
\fi
\fi
+ \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@
+ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n}
+ \xdef\first@{;\first@}\fi
\expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
\expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
\xdef\first@{=\first@}\fi
@@ -7838,6 +8228,9 @@
\xdef\low@up{lower} \ifx\resn@m@tch\low@up \make@lower \else
\xdef\low@up{upper} \ifx\resn@m@tch\low@up
\else \xdef\first@{\resn@m@tch} \fi\fi\fi
+ \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@
+ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n}
+ \xdef\first@{;\first@}\fi
\expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
\expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
\xdef\first@{=\first@}\fi
@@ -7854,6 +8247,9 @@
\xdef\low@up{lower} \ifx\n@m@tch\low@up \xdef\first@{{ }} \else
\xdef\low@up{upper} \ifx\n@m@tch\low@up \xdef\first@{{ }}
\else \xdef\first@{\n@m@tch} \fi\fi
+ \expandafter\ifx\csname lower@seq0\endcsname\y@
+ \expandafter\xdef\csname lower@seq0\endcsname{n}
+ \xdef\first@{;\first@}\fi
\expandafter\ifx\csname tint@seq0\endcsname\y@
\expandafter\xdef\csname tint@seq0\endcsname{n}
\xdef\first@{=\first@}\fi
@@ -7879,6 +8275,9 @@
\ifx\first@\d@t\def\first@{\gap@char}\fi
\ifx\first@\questi@n\def\first@{\st@p@char}\fi
\ifx\first@\equ@l\def\first@{\dom@char} \xdef\g@p{y} \fi
+ \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@
+ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n}
+ \xdef\first@{;\first@}\fi
\expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
\expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
\xdef\first@{=\first@}\fi
@@ -7952,6 +8351,9 @@
\fi
\fi
\fi
+ \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@
+ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n}
+ \xdef\first@{;\first@}\fi
\expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
\expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
\xdef\first@{=\first@}\fi
@@ -7966,6 +8368,9 @@
\xdef\second@{lower} \ifx\m@tch\second@ \make@lower \else
\xdef\second@{upper} \ifx\m@tch\second@
\else \xdef\first@{\m@tch} \fi\fi
+ \expandafter\ifx\csname lower@seq0\endcsname\y@
+ \expandafter\xdef\csname lower@seq0\endcsname{n}
+ \xdef\first@{;\first@}\fi
\expandafter\ifx\csname tint@seq0\endcsname\y@
\expandafter\xdef\csname tint@seq0\endcsname{n}
\xdef\first@{=\first@}\fi
@@ -7990,6 +8395,9 @@
\ifx\first@\d@t\def\first@{\gap@char}\fi
\ifx\first@\questi@n\def\first@{\st@p@char}\fi
\ifx\first@\equ@l\def\first@{\dom@char} \xdef\g@p{y} \fi
+ \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@
+ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n}
+ \xdef\first@{;\first@}\fi
\expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
\expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
\xdef\first@{=\first@}\fi
@@ -8068,6 +8476,9 @@
\fi
\fi
\fi
+ \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@
+ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n}
+ \xdef\first@{;\first@}\fi
\expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
\expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
\xdef\first@{=\first@}\fi
@@ -8082,6 +8493,9 @@
\xdef\second@{lower} \ifx\@llm@tch\second@ \make@lower \else
\xdef\second@{upper} \ifx\@llm@tch\second@
\else \xdef\first@{\@llm@tch} \fi\fi
+ \expandafter\ifx\csname lower@seq0\endcsname\y@
+ \expandafter\xdef\csname lower@seq0\endcsname{n}
+ \xdef\first@{;\first@}\fi
\expandafter\ifx\csname tint@seq0\endcsname\y@
\expandafter\xdef\csname tint@seq0\endcsname{n}
\xdef\first@{=\first@}\fi
@@ -8108,6 +8522,9 @@
\xdef\third@{noshade}
\expandafter\ifx\csname hide@seq\the\loopcount\endcsname\third@
\xdef\first@{\csname res\the\loopcount\endcsname}
+ \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@
+ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n}
+ \xdef\first@{;\first@}\fi
\expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
\expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
\xdef\first@{=\first@}\fi
@@ -8169,6 +8586,9 @@
\fi
\fi
\fi
+ \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@
+ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n}
+ \xdef\first@{;\first@}\fi
\expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
\expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
\xdef\first@{=\first@}\fi
@@ -8227,6 +8647,9 @@
\make@lower \fi
\xdef\third@{noshade}
\expandafter\ifx\csname hide@seq\the\loopcount\endcsname\third@
+ \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@
+ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n}
+ \xdef\first@{;\first@}\fi
\expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
\expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
\xdef\first@{=\first@}\fi
@@ -8237,6 +8660,9 @@
\csname seq\the\loopcount\endcsname%
0\first@}
\else
+ \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@
+ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n}
+ \xdef\first@{;\first@}\fi
\expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
\expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
\xdef\first@{=\first@}\fi
@@ -8292,6 +8718,9 @@
\fi
\xdef\third@{noshade}
\expandafter\ifx\csname hide@seq\the\loopcount\endcsname\third@
+ \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@
+ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n}
+ \xdef\first@{;\first@}\fi
\expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
\expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
\xdef\first@{=\first@}\fi
@@ -8302,6 +8731,9 @@
\csname seq\the\loopcount\endcsname%
*\first@}
\else
+ \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@
+ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n}
+ \xdef\first@{;\first@}\fi
\expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
\expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
\xdef\first@{=\first@}\fi
@@ -8314,6 +8746,9 @@
\fi
\ifnum\loopcount<\seq@count \repeat
\xdef\first@{\csname res0\endcsname}
+ \expandafter\ifx\csname lower@seq0\endcsname\y@
+ \expandafter\xdef\csname lower@seq0\endcsname{n}
+ \xdef\first@{;\first@}\fi
\expandafter\ifx\csname tint@seq0\endcsname\y@
\expandafter\xdef\csname tint@seq0\endcsname{n}
\xdef\first@{=\first@}\fi
@@ -8441,6 +8876,56 @@
\fi
}
+\def\getregion@fromlowerstack@first{%
+ \expandafter\getregion@fromlowerstack{\the\loopcount}
+ \expandafter\ifx\csname lowerstart\the\loopcount\endcsname\ampers@nd
+ \else
+ \expandafter\ifnum\csname lowerstop\the\loopcount\endcsname<\first@@
+ \getregion@fromlowerstack@first
+ \else
+ \expandafter\ifx\csname lowerall\the\loopcount\endcsname\y@
+ \innerloopcount=1
+ \fi
+ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{y}
+ \fi
+ \fi
+}
+
+\def\calc@reglower{%
+ \loopcount=-1 \innerloopcount=0
+ \loop
+ \advance\loopcount by 1
+ \ifnum\loopcount=0 \xdef\first@@{\the\cons@count}
+ \else \xdef\first@@{\csname res@count\the\loopcount\endcsname} \fi
+ \expandafter\ifx\csname lowerstart\the\loopcount\endcsname\ampers@nd
+ \else
+ \expandafter\ifnum\csname lowerstart\the\loopcount\endcsname>\first@@
+ \else
+ \expandafter\ifnum\csname lowerstop\the\loopcount\endcsname<\first@@
+ \getregion@fromlowerstack@first
+ \else
+ \expandafter\ifx\csname lowerall\the\loopcount\endcsname\y@
+ \innerloopcount=1
+ \fi
+ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{y}
+ \expandafter\ifnum\csname lowerstop\the\loopcount\endcsname=\first@@
+ \expandafter\getregion@fromlowerstack{\the\loopcount}
+ \fi
+ \fi
+ \fi\fi
+ \ifnum\loopcount<\seq@count \repeat
+ \loopcount=0
+ \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@
+ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{y}
+ \fi
+ \ifnum\innerloopcount>0
+ \loop
+ \advance\loopcount by 1
+ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{y}
+ \ifnum\loopcount<\seq@count \repeat
+ \fi
+}
+
\def\getregion@fromtintstack@first{%
\expandafter\getregion@fromtintstack{\the\loopcount}
\expandafter\ifx\csname tintstart\the\loopcount\endcsname\ampers@nd
@@ -8728,6 +9213,59 @@
\xdef\second@@@{\csname res\the\innerloopcount\endcsname}
\xdef\third@@@{\csname cons\first@@@\second@@@\endcsname}
\advance\temp@count by \third@@@
+ \ifnum\innerloopcount<\seq@count\sum@up\fi
+}
+
+\def\sum@up@cons{%
+ \innerloopcount=\outerloopcount
+ \xdef\first@@@{\csname res\the\outerloopcount\endcsname}
+ \sum@up
+ \advance\outerloopcount by 1\relax
+ \ifnum\outerloopcount<\seq@count
+ \sum@up@cons
+ \else
+ \innerloopcount=\seq@count
+ \advance\innerloopcount by -1
+ \multiply\innerloopcount by \seq@count
+ \multiply\temp@count by 2
+ \multiply\temp@count by \m@trixf@ctor
+ \divide\temp@count by \innerloopcount
+
+ \ifnum\temp@count>100 \temp@count=100 \fi
+ \ifnum\temp@count<0 \temp@count=0 \fi
+ \xdef\cons@val{\the\temp@count}
+ \ifx\first@\equ@l \xdef\cons@val{N} \fi
+
+ \ifx\T@coffee@bcons\y@
+ \xdef\cons@val{\csname TC@num0\endcsname}
+ \if\cons@val *
+ \xdef\cons@val{99}
+ \fi
+ \fi
+ \ifx\T@coffee@ccons\y@
+ \xdef\cons@val{\csname TC@num0\endcsname}
+ \if\cons@val *
+ \xdef\cons@val{99}
+ \fi
+ \fi
+ \fi
+}
+
+\def\collect@cons@res{%
+ \xdef\temp@{\temp@\csname res\the\innerloopcount\endcsname}
+ \advance\innerloopcount by 1
+ \ifnum\innerloopcount>\seq@count\relax
+ \outerloopcount=1\relax
+ \temp@count=0\relax
+ \sum@up@cons
+ \else
+ \collect@cons@res
+ \fi
+}
+
+\def\sum@@up{%
+ \advance\innerloopcount by 1
+ \xdef\second@@@{\csname res\the\innerloopcount\endcsname}
\ifx\first@@@\d@t
\else
@@ -8765,55 +9303,31 @@
\fi
\fi
- \ifnum\innerloopcount<\seq@count\sum@up\fi
+ \ifnum\innerloopcount<\seq@count\sum@@up\fi
}
-\def\sum@up@cons{%
+\def\sum@up@sim{%
\innerloopcount=\outerloopcount
\xdef\first@@@{\csname res\the\outerloopcount\endcsname}
- \sum@up
+ \sum@@up
\advance\outerloopcount by 1\relax
\ifnum\outerloopcount<\seq@count
- \sum@up@cons
- \else
- \innerloopcount=\seq@count
- \advance\innerloopcount by -1
- \multiply\innerloopcount by \seq@count
- \multiply\temp@count by 2
- \multiply\temp@count by \m@trixf@ctor
- \divide\temp@count by \innerloopcount
-
- \ifnum\temp@count>100 \temp@count=100 \fi
- \ifnum\temp@count<0 \temp@count=0 \fi
- \xdef\cons@val{\the\temp@count}
- \ifx\first@\equ@l \xdef\cons@val{N} \fi
-
- \ifx\T@coffee@bcons\y@
- \xdef\cons@val{\csname TC@num0\endcsname}
- \if\cons@val *
- \xdef\cons@val{99}
- \fi
- \fi
- \ifx\T@coffee@ccons\y@
- \xdef\cons@val{\csname TC@num0\endcsname}
- \if\cons@val *
- \xdef\cons@val{99}
- \fi
- \fi
+ \sum@up@sim
\fi
}
-\def\collect@cons@res{%
+\def\collect@similarity{%
\xdef\temp@{\temp@\csname res\the\innerloopcount\endcsname}
\advance\innerloopcount by 1
\ifnum\innerloopcount>\seq@count\relax
\outerloopcount=1\relax
\temp@count=0\relax
- \sum@up@cons
+ \sum@up@sim
\else
- \collect@cons@res
+ \collect@similarity
\fi
}
+
\def\sum@up@bits{%
\ifx\first@@@\second@@@
\ifx\first@@@\d@t
@@ -10035,6 +10549,7 @@
\ifregionalshadenow \calc@regshade \fi
\ifregionaltintnow \calc@regtint \fi
\ifregionalemphnow \calc@regemph \fi
+ \ifregionallowernow \calc@reglower \fi
\ifframenow \calc@frame \fi
\iftopfeaturenow \xdef\bottop@{top} \calc@feature \fi
\ifttopfeaturenow \xdef\bottop@{ttop} \calc@feature \fi
@@ -10044,6 +10559,7 @@
\ifbbottomfeaturenow \xdef\bottop@{bbottom} \calc@feature \fi
\ifbbbottomfeaturenow \xdef\bottop@{bbbottom} \calc@feature \fi
\ifbbbbottomfeaturenow \xdef\bottop@{bbbbottom} \calc@feature \fi
+ \ifnum\seq@count>1 \innerloopcount=1 \collect@similarity \fi
\advance\pos@count by 1
\ifshow@logo \calc@logo \fi
\ifall@fshade \all@funcshade
@@ -10193,11 +10709,20 @@
\expandafter\ifnum\csname emphstart\the\loopcount\endcsname>%
\innerloopcount
\else
- \else
\regionalemphnowtrue
\fi
\fi
\fi
+ \ifregionallower
+ \expandafter\ifx\csname lowerstart\the\loopcount\endcsname\ampers@nd
+ \else
+ \expandafter\ifnum\csname lowerstart\the\loopcount\endcsname>%
+ \innerloopcount
+ \else
+ \regionallowernowtrue
+ \fi
+ \fi
+ \fi
\ifframe@
\expandafter\ifx\csname framestart\the\loopcount\endcsname\ampers@nd
\else
@@ -10353,7 +10878,7 @@
\else
\innerloopcount=\csname res@count\the\loopcount\endcsname
\advance\innerloopcount by \res@perline
- \fi %%%%%%%%%%%%%*****
+ \fi
\advance\innerloopcount by 1
\ifregionalshade
\expandafter\ifx\csname start\the\loopcount\endcsname\ampers@nd
@@ -10385,6 +10910,16 @@
\fi
\fi
\fi
+ \ifregionallower
+ \expandafter\ifx\csname lowerstart\the\loopcount\endcsname\ampers@nd
+ \else
+ \expandafter\ifnum\csname lowerstart\the\loopcount\endcsname>%
+ \innerloopcount
+ \else
+ \regionallowernowtrue
+ \fi
+ \fi
+ \fi
\ifframe@
\expandafter\ifx\csname framestart\the\loopcount\endcsname\ampers@nd
\else
@@ -10799,6 +11334,14 @@
\xdef\temp@@{\light@}%
\expandafter\get@second@\first@%
\fi%
+ \ifx\second@\semic@n%
+ \expandafter\get@second@\first@%
+ \xdef\first@@{\first@}%
+ \xdef\first@{\second@}%
+ \make@lower%
+ \xdef\second@{\first@}%
+ \xdef\first@{\first@@}%
+ \fi%
\textcolor{\temp@@\boxc@l@r}{\box@rule}%
\ifhidechar%
\ifx\second@\o@%
@@ -10903,6 +11446,14 @@
\else%
\def\temp@{\csname relax\endcsname}%
\fi%
+ \ifx\second@\semic@n%
+ \expandafter\get@second@\first@%
+ \xdef\first@@{\first@}%
+ \xdef\first@{\second@}%
+ \make@lower%
+ \xdef\second@{\first@}%
+ \xdef\first@{\first@@}%
+ \fi%
\textcolor{\boxc@l@r}{\box@rule}%
\ifhidechar%
\ifx\second@\o@%
@@ -12963,7 +13514,7 @@
\expandafter\xdef\csname sequence\the\loopcount\endcsname{}
\expandafter\xdef\csname dom@num\the\loopcount\endcsname{}
\expandafter\xdef\csname dom@num@break\the\loopcount\endcsname{}
- \expandafter\xdef\csname dom@count\the\loopcount\endcsname{0}
+ \expandafter\xdef\csname dom@count\the\loopcount\endcsname{\csname res@count\the\loopcount\endcsname}
\ifnum\loopcount<\seq@count\repeat
\xdef\domain@num@list{}
\xdef\last@{\stack@dom}
@@ -13012,6 +13563,7 @@
\fi
\ifshow@sublogo \prep@sublogo \fi
\ifshow@logo \prep@logo \fi
+ \ifx\label@motif\y@ \prep@motif \fi
\ifnum\seq@pointer>\res@perline \block@output \fi
\else \read@loop
\fi}
@@ -13063,7 +13615,7 @@
\expandafter\xdef\csname sequence\the\loopcount\endcsname{}
\expandafter\xdef\csname dom@num\the\loopcount\endcsname{}
\expandafter\xdef\csname dom@num@break\the\loopcount\endcsname{}
- \expandafter\xdef\csname dom@count\the\loopcount\endcsname{0}
+ \expandafter\xdef\csname dom@count\the\loopcount\endcsname{\csname res@count\the\loopcount\endcsname}
\ifnum\loopcount<\seq@count\repeat
\xdef\domain@num@list{}
\xdef\last@{\stack@dom}
@@ -13112,6 +13664,7 @@
\fi
\ifshow@sublogo \prep@sublogo \fi
\ifshow@logo \prep@logo \fi
+ \ifx\label@motif\y@ \prep@motif \fi
\ifnum\seq@pointer>\res@perline \block@output \fi
\else
\read@fasta
@@ -13245,8 +13798,8 @@
\expandafter\xdef\csname stack@dom\endcsname{&;&;&;&;@}
\expandafter\xdef\csname stack@reg\the\loopcount\endcsname{&;&;&;&;@}
\expandafter\xdef\csname stack@tintreg\the\loopcount\endcsname{&;&;&;@}
- \expandafter\xdef\csname stack@hidereg\the\loopcount\endcsname{&;&;&;&;@}
\expandafter\xdef\csname stack@emphreg\the\loopcount\endcsname{&;&;&;@}
+ \expandafter\xdef\csname stack@lowerreg\the\loopcount\endcsname{&;&;&;@}
\expandafter\xdef\csname stack@framereg\the\loopcount\endcsname{&;&;&;@}
\expandafter\xdef\csname stack@top\the\loopcount\endcsname{&;&;&;&;@}
\expandafter\xdef\csname stack@ttop\the\loopcount\endcsname{&;&;&;&;@}
@@ -13266,6 +13819,7 @@
\cleanup@name
\expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
\expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n}
+ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n}
\expandafter\xdef\csname hide@seq\the\loopcount\endcsname{false}
\expandafter\xdef\csname hide@@@seq\the\loopcount\endcsname{false}
\expandafter\xdef\csname hide@name\the\loopcount\endcsname{no}
@@ -13274,8 +13828,8 @@
\expandafter\xdef\csname number@col\the\loopcount\endcsname{yes}
\expandafter\xdef\csname stack@reg\the\loopcount\endcsname{&;&;&;&;@}
\expandafter\xdef\csname stack@tintreg\the\loopcount\endcsname{&;&;&;@}
- \expandafter\xdef\csname stack@hidereg\the\loopcount\endcsname{&;&;&;&;@}
\expandafter\xdef\csname stack@emphreg\the\loopcount\endcsname{&;&;&;@}
+ \expandafter\xdef\csname stack@lowerreg\the\loopcount\endcsname{&;&;&;@}
\expandafter\xdef\csname stack@framereg\the\loopcount\endcsname{&;&;&;@}
\expandafter\xdef\csname stack@top\the\loopcount\endcsname{&;&;&;&;@}
\expandafter\xdef\csname stack@ttop\the\loopcount\endcsname{&;&;&;&;@}
@@ -13322,9 +13876,9 @@
\ifshow@cons\setbox1=\hbox{\cons@name}\name@width=\wd1\else\name@width=0pt\fi
\loopcount=0
\expandafter\getregion@fromstack{\the\loopcount}
- \expandafter\getregion@fromhidestack{\the\loopcount}
\expandafter\getregion@fromtintstack{\the\loopcount}
\expandafter\getregion@fromemphstack{\the\loopcount}
+ \expandafter\getregion@fromlowerstack{\the\loopcount}
\expandafter\getregion@fromframestack{\the\loopcount}
\xdef\bottop@{top} \expandafter\getregion@fromfstack{\the\loopcount}
\xdef\bottop@{ttop} \expandafter\getregion@fromfstack{\the\loopcount}
@@ -13373,9 +13927,9 @@
\baselineskip=\box@height \advance\baselineskip by \box@depth
\fi
\expandafter\getregion@fromstack{\the\loopcount}
- \expandafter\getregion@fromhidestack{\the\loopcount}
\expandafter\getregion@fromtintstack{\the\loopcount}
\expandafter\getregion@fromemphstack{\the\loopcount}
+ \expandafter\getregion@fromlowerstack{\the\loopcount}
\expandafter\getregion@fromframestack{\the\loopcount}
\xdef\bottop@{top} \expandafter\getregion@fromfstack{\the\loopcount}
\xdef\bottop@{ttop} \expandafter\getregion@fromfstack{\the\loopcount}
@@ -13607,7 +14161,7 @@
\cons@count=0
\expandafter\xdef\csname res@count0\endcsname{0}
\xdef\allow@zero{n} \xdef\c@ns@shift{0}
-\regionalshadefalse\regionalemphfalse\regionaltintfalse
+\regionalshadefalse\regionalemphfalse\regionallowerfalse\regionaltintfalse
\frame@false
\xdef\ruler@rot{0}
\topfeaturefalse \bottomfeaturefalse
@@ -13716,7 +14270,8 @@
\xdef\all@thresh@ld{100} \all@shadefalse
\hidefeaturenames \hidefeaturestylenames
\xdef\T@coffee@ccons{n} \xdef\T@coffee@bcons{n}
-\xdef\dom@in{no}
+\xdef\dom@in{no} \xdef\label@motif{no}
+\xdef\motif@num{0}
\hfuzz9999pt
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%