diff options
Diffstat (limited to 'Master/texmf-dist/tex/latex/texshade')
| -rw-r--r-- | Master/texmf-dist/tex/latex/texshade/texshade.sty | 1106 |
1 files changed, 999 insertions, 107 deletions
diff --git a/Master/texmf-dist/tex/latex/texshade/texshade.sty b/Master/texmf-dist/tex/latex/texshade/texshade.sty index 77a390d1fc3..a3cd5b24ade 100644 --- a/Master/texmf-dist/tex/latex/texshade/texshade.sty +++ b/Master/texmf-dist/tex/latex/texshade/texshade.sty @@ -101,6 +101,7 @@ \newif\ifnumbers@left \newif\ifnumbers@right \newif\ifhide@cons \newif\ifshow@cons \newif\iffuncmode \newif\iflegend@ +\newif\ifT@coffee \newif\ifnumbers@ \newif\ifnames@ \newif\ifgerm@n \newif\ifsp@nish \newif\ifrpl@fix @@ -108,6 +109,8 @@ \newif\ifstart@ \newif\ifstop@ \newif\iftopfeature \newif\ifbottomfeature \newif\ifttopfeature \newif\ifbbottomfeature +\newif\iftttopfeature \newif\ifbbbottomfeature +\newif\ifttttopfeature\newif\ifbbbbottomfeature \newif\ifall@fshade \newif\ifregionalemph \newif\ifframe@ \newif\ifregionaltint \newif\ifshow@logo \newif\ifshow@sublogo @@ -118,8 +121,12 @@ \newif\ifregionalshadenow \newif\iftopfeaturenow \newif\ifttopfeaturenow +\newif\iftttopfeaturenow +\newif\ifttttopfeaturenow \newif\ifbottomfeaturenow \newif\ifbbottomfeaturenow +\newif\ifbbbottomfeaturenow +\newif\ifbbbbottomfeaturenow \newif\ifframenow \newif\iffix@ @@ -816,6 +823,17 @@ \definecolor{Gray95} {cmyk}{0,0,0,0.95} \definecolor{Black} {cmyk}{0,0,0,1} \definecolor{Gray100} {cmyk}{0,0,0,1} +\definecolor{TC0} {cmyk}{0.4,0.4,0,0} +\definecolor{TC1} {cmyk}{0.6,0,0.7,0} +\definecolor{TC2} {cmyk}{0.4,0,0.7,0} +\definecolor{TC3} {cmyk}{0.2,0,1,0} +\definecolor{TC4} {cmyk}{0,0,1,0} +\definecolor{TC5} {cmyk}{0,0.2,1,0} +\definecolor{TC6} {cmyk}{0,0.4,1,0} +\definecolor{TC7} {cmyk}{0,0.6,1,0} +\definecolor{TC8} {cmyk}{0,0.8,1,0} +\definecolor{TC9} {cmyk}{0,0.875,1,0} +\definecolor{TC99} {cmyk}{0,0,0,0} \definecolor{LightGreenYellow} {cmyk}{0.08,0,0.35,0} \definecolor{LightYellow} {cmyk}{0,0,0.50,0} \definecolor{LightGoldenrod} {cmyk}{0,0.05,0.42,0} @@ -907,6 +925,16 @@ \definecolor{LightGray95} {cmyk}{0,0,0,0.47} \definecolor{LightBlack} {cmyk}{0,0,0,0.50} \definecolor{LightGray100} {cmyk}{0,0,0,0.50} +\definecolor{LightTC0} {cmyk}{0.2,0.2,0,0} +\definecolor{LightTC1} {cmyk}{0.3,0,0.35,0} +\definecolor{LightTC2} {cmyk}{0.2,0,0.35,0} +\definecolor{LightTC3} {cmyk}{0.1,0,0.5,0} +\definecolor{LightTC4} {cmyk}{0,0,0.5,0} +\definecolor{LightTC5} {cmyk}{0,0.1,0.5,0} +\definecolor{LightTC6} {cmyk}{0,0.2,0.5,0} +\definecolor{LightTC7} {cmyk}{0,0.3,0.5,0} +\definecolor{LightTC8} {cmyk}{0,0.4,0.5,0} +\definecolor{LightTC99} {cmyk}{0,0,0,0} \definecolor{LightLightGreenYellow} {cmyk}{0.04,0,0.17,0} \definecolor{LightLightYellow} {cmyk}{0,0,0.25,0} \definecolor{LightLightGoldenrod} {cmyk}{0,0.02,0.21,0} @@ -998,6 +1026,16 @@ \definecolor{LightLightGray95} {cmyk}{0,0,0,0.23} \definecolor{LightLightBlack} {cmyk}{0,0,0,0.25} \definecolor{LightLightGray100} {cmyk}{0,0,0,0.25} +\definecolor{LightLightTC0} {cmyk}{0.1,0.1,0,0} +\definecolor{LightLightTC1} {cmyk}{0.15,0,0.175,0} +\definecolor{LightLightTC2} {cmyk}{0.1,0,0.175,0} +\definecolor{LightLightTC3} {cmyk}{0.05,0,0.25,0} +\definecolor{LightLightTC4} {cmyk}{0,0,0.25,0} +\definecolor{LightLightTC5} {cmyk}{0,0.05,0.25,0} +\definecolor{LightLightTC6} {cmyk}{0,0.1,0.25,0} +\definecolor{LightLightTC7} {cmyk}{0,0.15,0.25,0} +\definecolor{LightLightTC8} {cmyk}{0,0.2,0.25,0} +\definecolor{LightLightTC99} {cmyk}{0,0,0,0} \definecolor{LightLightLightGreenYellow} {cmyk}{0.02,0,0.08,0} \definecolor{LightLightLightYellow} {cmyk}{0,0,0.12,0} \definecolor{LightLightLightGoldenrod} {cmyk}{0,0.01,0.10,0} @@ -1090,6 +1128,16 @@ \definecolor{LightLightLightGray95} {cmyk}{0,0,0,0.115} \definecolor{LightLightLightBlack} {cmyk}{0,0,0,0.12} \definecolor{LightLightLightGray100} {cmyk}{0,0,0,0.125} +\definecolor{LightLightLightTC0} {cmyk}{0.05,0.05,0,0} +\definecolor{LightLightLightTC1} {cmyk}{0.075,0,0.086,0} +\definecolor{LightLightLightTC2} {cmyk}{0.05,0,0.086,0} +\definecolor{LightLightLightTC3} {cmyk}{0.025,0,0.125,0} +\definecolor{LightLightLightTC4} {cmyk}{0,0,0.125,0} +\definecolor{LightLightLightTC5} {cmyk}{0,0.025,0.125,0} +\definecolor{LightLightLightTC6} {cmyk}{0,0.05,0.125,0} +\definecolor{LightLightLightTC7} {cmyk}{0,0.0175,0.125,0} +\definecolor{LightLightLightTC8} {cmyk}{0,0.1,0.125,0} +\definecolor{LightLightLightTC99} {cmyk}{0,0,0,0} \definecolor{BlueRed5} {rgb} {0.15,0.17,0.55} \definecolor{BlueRed10} {rgb} {0.20,0.23,0.57} \definecolor{BlueRed15} {rgb} {0.24,0.29,0.60} @@ -1404,6 +1452,16 @@ \expandafter\xdef\csname res\the\loopcount\endcsname{\first@} \expandafter\xdef\csname sequence\the\loopcount\endcsname{#2@}} \def\remove@fromseq#1@{\expandafter\xdef\csname sequence\the\loopcount\endcsname{#1}} +\def\TC@get#1#2@{\xdef\char@num{`#1} + \ifnum\char@num=45 \xdef\TC@first@{*} + \else + \ifnum\char@num>57 \xdef\TC@first@{*} + \else + \xdef\TC@first@{#1} + \fi + \fi + \expandafter\xdef\csname TC@num\the\loopcount\endcsname{\TC@first@} + \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{#2@}} \def\sublogo@get#1 @{\xdef\first@{#1}} \def\re@write#1,#2@{% \xdef\third@{#2,@} @@ -1455,10 +1513,18 @@ \csname stack@@top#1\endcsname} \expandafter\xdef\csname stack@ttop\the\loopcount\endcsname{% \csname stack@@ttop#1\endcsname} + \expandafter\xdef\csname stack@tttop\the\loopcount\endcsname{% + \csname stack@@tttop#1\endcsname} + \expandafter\xdef\csname stack@ttttop\the\loopcount\endcsname{% + \csname stack@@ttttop#1\endcsname} \expandafter\xdef\csname stack@bottom\the\loopcount\endcsname{% \csname stack@@bottom#1\endcsname} \expandafter\xdef\csname stack@bbottom\the\loopcount\endcsname{% \csname stack@@bbottom#1\endcsname} + \expandafter\xdef\csname stack@bbbottom\the\loopcount\endcsname{% + \csname stack@@bbbottom#1\endcsname} + \expandafter\xdef\csname stack@bbbbottom\the\loopcount\endcsname{% + \csname stack@@bbbbottom#1\endcsname} } \def\reorder@seqs#1{% \loopcount=0 @@ -1500,10 +1566,18 @@ \csname stack@top\the\loopcount\endcsname} \expandafter\xdef\csname stack@@ttop\the\loopcount\endcsname{% \csname stack@ttop\the\loopcount\endcsname} + \expandafter\xdef\csname stack@@tttop\the\loopcount\endcsname{% + \csname stack@tttop\the\loopcount\endcsname} + \expandafter\xdef\csname stack@@ttttop\the\loopcount\endcsname{% + \csname stack@ttttop\the\loopcount\endcsname} \expandafter\xdef\csname stack@@bottom\the\loopcount\endcsname{% \csname stack@bottom\the\loopcount\endcsname} \expandafter\xdef\csname stack@@bbottom\the\loopcount\endcsname{% \csname stack@bbottom\the\loopcount\endcsname} + \expandafter\xdef\csname stack@@bbbottom\the\loopcount\endcsname{% + \csname stack@bbbottom\the\loopcount\endcsname} + \expandafter\xdef\csname stack@@bbbbottom\the\loopcount\endcsname{% + \csname stack@bbbbottom\the\loopcount\endcsname} \ifnum\loopcount<\killseq@count \repeat \xdef\third@{#1} \loopcount=0 \innerloopcount=0 \xdef\last@{kill} \xdef\second@{e} @@ -1779,10 +1853,18 @@ \csname stack@top\the\innerloopcount\endcsname} \expandafter\xdef\csname stack@ttop\the\loopcount\endcsname{% \csname stack@ttop\the\innerloopcount\endcsname} + \expandafter\xdef\csname stack@tttop\the\loopcount\endcsname{% + \csname stack@tttop\the\innerloopcount\endcsname} + \expandafter\xdef\csname stack@ttttop\the\loopcount\endcsname{% + \csname stack@ttttop\the\innerloopcount\endcsname} \expandafter\xdef\csname stack@bottom\the\loopcount\endcsname{% \csname stack@bottom\the\innerloopcount\endcsname} \expandafter\xdef\csname stack@bbottom\the\loopcount\endcsname{% \csname stack@bbottom\the\innerloopcount\endcsname} + \expandafter\xdef\csname stack@bbbottom\the\loopcount\endcsname{% + \csname stack@bbbottom\the\innerloopcount\endcsname} + \expandafter\xdef\csname stack@bbbbottom\the\loopcount\endcsname{% + \csname stack@bbbbottom\the\innerloopcount\endcsname} \expandafter\xdef\csname res@count\the\loopcount\endcsname{% \csname res@count\the\innerloopcount\endcsname} \expandafter\xdef\csname hide@seq\the\innerloopcount\endcsname{kill} @@ -2586,6 +2668,97 @@ \fi \ifx\sim@char\ampers@nd\else\write@PHDtopo\fi } +\def\include@T@coffee{% + \bgroup + \immediate\openin\structurefile = \TC@first@\relax + \ifeof\structurefile + \PackageError{TeXshade} + {File `\TC@first@' not found} + {\MessageBreak + The file you specified is missing or you have \MessageBreak + misspelled it. \MessageBreak\MessageBreak + No T-Coffee shading will be displayed (using "similar"). \MessageBreak + Type <return> to proceed. \MessageBreak + Type X <return> to quit. \MessageBreak +} + \immediate\closein\structurefile\egroup + \simmodetrue \funcmodefalse \T@coffeefalse + \else + \message{<T-Coffee shading>} + \xdef\first@{} \xdef\temp@{*} + \loop + \read\structurefile to \readline + \xdef\test@{\expandafter\string\readline} + \ifx\test@\par@ + \else + \xdef\structureline{\readline & & & & & & & & &@} + \expandafter\struc@get\structureline + \ifx\first@\temp@ \xdef\temp@{y} + \read\structurefile to \readline + \read\structurefile to \readline + \fi + \fi + \ifx\temp@\y@ \else\repeat + \loopcount=0 + \xdef\temp@{cons} + \loop + \read\structurefile to \readline + \xdef\test@{\expandafter\string\readline} + \ifx\test@\par@ + \else + \xdef\structureline{\readline & & & & & & & & &@} + \expandafter\struc@get\structureline + \if\second@ : + \advance\loopcount by 1\relax + \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{} + \fi + \fi + \ifx\first@\temp@\expandafter\xdef\csname T@coffee0\endcsname{} \else\repeat + \xdef\temp@{\the\loopcount} + \loopcount=0 + \loop + \read\structurefile to \readline + \xdef\test@{\expandafter\string\readline} + \ifx\test@\par@ + \else + \xdef\structureline{\readline & & & & & & & & &@} + \expandafter\struc@get\structureline + \advance\loopcount by 1 + \ifnum\loopcount=\temp@ \loopcount=0 \fi + \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{\csname T@coffee\the\loopcount\endcsname \third@} + \fi + \ifeof\structurefile \else\repeat + \closein\structurefile + \loopcount=0 + \loop + \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{\csname T@coffee\the\loopcount\endcsname @} + \advance\loopcount by 1 + \ifnum\loopcount=\temp@ \else\repeat + \egroup + \def\n@m@tch{{$\bullet$}} + \expandafter\def\csname fg@color0\endcsname{TC0} + \expandafter\def\csname fg@color1\endcsname{TC1} + \expandafter\def\csname fg@color2\endcsname{TC2} + \expandafter\def\csname fg@color3\endcsname{TC3} + \expandafter\def\csname fg@color4\endcsname{TC4} + \expandafter\def\csname fg@color5\endcsname{TC5} + \expandafter\def\csname fg@color6\endcsname{TC6} + \expandafter\def\csname fg@color7\endcsname{TC7} + \expandafter\def\csname fg@color8\endcsname{TC8} + \expandafter\def\csname fg@color9\endcsname{TC9} + \expandafter\def\csname fg@textcolor0\endcsname{Black} + \expandafter\def\csname fg@textcolor1\endcsname{Black} + \expandafter\def\csname fg@textcolor2\endcsname{Black} + \expandafter\def\csname fg@textcolor3\endcsname{Black} + \expandafter\def\csname fg@textcolor4\endcsname{Black} + \expandafter\def\csname fg@textcolor5\endcsname{Black} + \expandafter\def\csname fg@textcolor6\endcsname{Black} + \expandafter\def\csname fg@textcolor7\endcsname{Black} + \expandafter\def\csname fg@textcolor8\endcsname{Black} + \expandafter\def\csname fg@textcolor9\endcsname{Black} + \fi + } + \def\include@DSSP{% \xdef\first@{\csname optiondssp\the\loopcount\endcsname} \xdef\bottop@{\csname bottopdssp\the\loopcount\endcsname} @@ -3875,10 +4048,18 @@ \ifx\bottop@\temp@ \topfeaturetrue\fi \xdef\temp@{ttop} \ifx\bottop@\temp@ \ttopfeaturetrue\fi + \xdef\temp@{tttop} + \ifx\bottop@\temp@ \tttopfeaturetrue\fi + \xdef\temp@{ttttop} + \ifx\bottop@\temp@ \ttttopfeaturetrue\fi \xdef\temp@{bottom} \ifx\bottop@\temp@ \bottomfeaturetrue\fi \xdef\temp@{bbottom} \ifx\bottop@\temp@ \bbottomfeaturetrue\fi + \xdef\temp@{bbbottom} + \ifx\bottop@\temp@ \bbbottomfeaturetrue\fi + \xdef\temp@{bbbbottom} + \ifx\bottop@\temp@ \bbbbottomfeaturetrue\fi \xdef\seq@{#2} \xdef\temp@{consensus} \ifx\seq@\temp@ \xdef\seq@{0} \fi \xdef\first@{\seq@ @} \expandafter\check@letter\first@ @@ -3943,6 +4124,10 @@ \ifx\bottop@\temp@ \xdef\bottom@stretch{y}\fi \xdef\temp@{bbottom} \ifx\bottop@\temp@ \xdef\bbottom@stretch{y}\fi + \xdef\temp@{bbbottom} + \ifx\bottop@\temp@ \xdef\bbbottom@stretch{y}\fi + \xdef\temp@{bbbbottom} + \ifx\bottop@\temp@ \xdef\bbbbottom@stretch{y}\fi \else \xdef\last@{color} \ifx\second@@\last@ @@ -3987,6 +4172,11 @@ \xdef\last@{bcons} \ifx\second@@\last@ \ifx\f@color\gr@ydef@ult\xdef\f@color{Gray50}\fi + \xdef\last@{T-Coffee} + \ifx\f@color\last@ + \xdef\T@coffee@bcons{y} + \xdef\f@color{Gray50} + \fi \xdef\style@{cons[bar]:cons[\f@color][0]} \else \xdef\last@{ch} @@ -4007,6 +4197,11 @@ \xdef\last@{ccons} \ifx\second@@\last@ \ifx\f@color\gr@ydef@ult\xdef\f@color{ColdHot}\fi + \xdef\last@{T-Coffee} + \ifx\f@color\last@ + \xdef\T@coffee@ccons{y} + \xdef\f@color{TC} + \fi \xdef\style@{cons[color]:cons[\f@color][0]} \else \xdef\style@{#4} \expandafter\getarrow@shape\temp@ @@ -4030,9 +4225,11 @@ \def\showfeaturename#1#2{\expandafter\xdef\csname featuretextn@me#1\endcsname{#2}} \def\showfeaturestylename#1#2{\expandafter\xdef\csname featurestylesn@me#1\endcsname{#2}} \def\hidefeaturename#1{\expandafter\xdef\csname featuretextn@me#1\endcsname{}} -\def\hidefeaturenames{\xdef\featuretextn@mettop{}\xdef\featuretextn@metop{}\xdef\featuretextn@mebottom{}\xdef\featuretextn@mebbottom{}} +\def\hidefeaturenames{\xdef\featuretextn@mettop{}\xdef\featuretextn@metop{}\xdef\featuretextn@mebottom{}\xdef\featuretextn@mebbottom{} + \xdef\featuretextn@metttop{}\xdef\featuretextn@mettttop{}\xdef\featuretextn@mebbbbottom{}\xdef\featuretextn@mebbbottom{}} \def\hidefeaturestylename#1{\expandafter\xdef\csname featurestylesn@me#1\endcsname{}} -\def\hidefeaturestylenames{\xdef\featurestylesn@mettop{}\xdef\featurestylesn@metop{}\xdef\featurestylesn@mebottom{}\xdef\featurestylesn@mebbottom{}} +\def\hidefeaturestylenames{\xdef\featurestylesn@mettop{}\xdef\featurestylesn@metop{}\xdef\featurestylesn@mebottom{}\xdef\featurestylesn@mebbottom{} + \xdef\featurestylesn@metttop{}\xdef\featurestylesn@mettttop{}\xdef\featurestylesn@mebbbbottom{}\xdef\featurestylesn@mebbbottom{}} \def\seqtype#1{\xdef\seq@type{#1} \if\seq@type P \xdef\prefix@{pep} \else \if\seq@type p \xdef\seq@type{P} \xdef\prefix@{pep} @@ -4092,8 +4289,12 @@ \def\vblockspace#1{\def\block@skip{\vspace{#1}}} \def\topspace#1{\def\t@sp@ce{#1}} \def\ttopspace#1{\def\tt@sp@ce{#1}} +\def\tttopspace#1{\def\ttt@sp@ce{#1}} +\def\ttttopspace#1{\def\tttt@sp@ce{#1}} \def\bottomspace#1{\def\b@sp@ce{#1}} \def\bbottomspace#1{\def\bb@sp@ce{#1}} +\def\bbbottomspace#1{\def\bbb@sp@ce{#1}} +\def\bbbbottomspace#1{\def\bbbb@sp@ce{#1}} \def\fixblockspace{\fix@true} \def\flexblockspace{\fix@false} \def\nosepline{\def\seq@skip{\relax}} @@ -4117,6 +4318,7 @@ \fi \fi} \newcommand{\shadingmode}[2][-1]{% + \T@coffeefalse \xdef\last@{#2} \xdef\first@{identical} \ifx\first@\last@ @@ -4162,6 +4364,12 @@ \else \simmodefalse \funcmodetrue \func@shading{#1} \xdef\seq@type{P} \xdef\prefix@{pep} \fi \else + \xdef\first@{T-Coffee} + \ifx\first@\last@ + \simmodefalse \funcmodefalse \T@coffeetrue + \xdef\second@{#1 @} \expandafter\check@letter\second@ + \ifletter \xdef\TC@first@{#1}\include@T@coffee\fi + \else \xdef\first@{diverse} \ifx\first@\last@ \xdef\last@{#1} @@ -4180,7 +4388,7 @@ \else \message{<Unknown shading mode - using `similar'>} \simmodetrue \funcmodefalse - \fi\fi\fi\fi} + \fi\fi\fi\fi\fi} \newcommand\allmatchspecial[1][100]{% \ifnum#1<0 \xdef\all@thresh@ld{0} @@ -4197,8 +4405,8 @@ \ifx\first@\second@\def\gap@char{o} \else\def\gap@char{#1}\fi} \def\gaprule#1{\def\gap@rulethick{#1}} -\def\setends#1#2{% - \xdef\start@seq{#1} +\newcommand{\setends}[3][&]{% + \xdef\start@seq{#2} \xdef\temp@{consensus} \ifx\start@seq\temp@ \message{<\noexpand\setends does not accept `consensus'>} @@ -4208,14 +4416,14 @@ \xdef\first@{\start@seq} \ifletter \get@name@number \xdef\start@seq{\first@} \fi \ifnum\start@seq>\seq@count - \message{<\noexpand\setends{} error: sequence `#1' not defined>} + \message{<\noexpand\setends{} error: sequence `#2' not defined>} \xdef\start@seq{0} \else \ifnum\start@seq<1 - \message{<\noexpand\setends{} error: sequence `#1' not defined>} + \message{<\noexpand\setends{} error: sequence `#2' not defined>} \xdef\start@seq{0} \else - \xdef\second@{#2@} \expandafter\get@nums\second@ + \xdef\second@{#3@} \expandafter\get@nums\second@ \xdef\start@num{\first@} \xdef\end@num{\second@} \ifnum\start@num=0 \xdef\allow@zero{y}\fi \ifnum\end@num=0 \xdef\allow@zero{y}\fi @@ -4223,20 +4431,21 @@ \fi \fi \fi + \xdef\first@{#1}\ifx\first@\ampers@nd\else\startnumber{#2}{#1}\fi } -\def\startnumber#1#2{% - \xdef\first@{#1} \xdef\second@{consensus} +\newcommand{\startnumber}[3][&]{% + \xdef\first@{#2} \xdef\second@{consensus} \ifx\first@\second@ - \ifnum#2=0 \xdef\allow@zero{y} \fi + \ifnum#3=0 \xdef\allow@zero{y} \fi \expandafter\xdef\csname seq@start0\endcsname{#2} - \cons@count=#2 \advance\cons@count by -1\relax + \cons@count=#3 \advance\cons@count by -1\relax \expandafter\xdef\csname res@count0\endcsname{\the\cons@count} \else - \xdef\first@{#1 @} \expandafter\check@letter\first@ - \xdef\first@{#1} \ifletter \get@name@number \fi - \ifnum\first@>\seq@count \message{<Ignored seq `#1' in \noexpand\startnumber>} + \xdef\first@{#2 @} \expandafter\check@letter\first@ + \xdef\first@{#2} \ifletter \get@name@number \fi + \ifnum\first@>\seq@count \message{<Ignored seq `#2' in \noexpand\startnumber>} \else - \xdef\second@{#2} + \xdef\second@{#3} \ifnum\second@=0 \xdef\allow@zero{y} \fi \expandafter\xdef\csname seq@start\first@\endcsname{\second@} \res@count=\second@ @@ -4244,6 +4453,7 @@ \expandafter\xdef\csname res@count\first@\endcsname{\the\res@count} \fi \fi + \xdef\first@{#1}\ifx\first@\ampers@nd\else\setends{#2}{#1}\fi } \def\seqlength#1#2{% \xdef\first@{#1 @} \expandafter\check@letter\first@ @@ -5208,16 +5418,24 @@ \ifx\third@\first@\white@box\else\textcolor{\third@}{\box@rule}\fi \fi\fi\fi\fi} \def\featurenamescolor#1{% + \expandafter\xdef\csname ftext@fg@ttttop\endcsname{#1} + \expandafter\xdef\csname ftext@fg@tttop\endcsname{#1} \expandafter\xdef\csname ftext@fg@ttop\endcsname{#1} \expandafter\xdef\csname ftext@fg@top\endcsname{#1} \expandafter\xdef\csname ftext@fg@bottom\endcsname{#1} \expandafter\xdef\csname ftext@fg@bbottom\endcsname{#1} + \expandafter\xdef\csname ftext@fg@bbbottom\endcsname{#1} + \expandafter\xdef\csname ftext@fg@bbbbottom\endcsname{#1} } \def\featurestylenamescolor#1{% + \expandafter\xdef\csname fstyles@fg@ttttop\endcsname{#1} + \expandafter\xdef\csname fstyles@fg@tttop\endcsname{#1} \expandafter\xdef\csname fstyles@fg@ttop\endcsname{#1} \expandafter\xdef\csname fstyles@fg@top\endcsname{#1} \expandafter\xdef\csname fstyles@fg@bottom\endcsname{#1} \expandafter\xdef\csname fstyles@fg@bbottom\endcsname{#1} + \expandafter\xdef\csname fstyles@fg@bbbottom\endcsname{#1} + \expandafter\xdef\csname fstyles@fg@bbbbottom\endcsname{#1} } \def\featurenamecolor#1#2{\expandafter\xdef\csname ftext@fg@#1\endcsname{#2}} \def\featurestylenamecolor#1#2{\expandafter\xdef\csname fstyles@fg@#1\endcsname{#2}} @@ -5328,6 +5546,9 @@ \logo@rule\kern-\wd1\textcolor{White}{\texttt{d}}% \texttt{e}} +\def\includeTCoffee#1{% + \xdef\TC@first@{#1}\include@T@coffee} + \def\firstcolumnDSSP{\xdef\fc@DSSP{y}} \def\secondcolumnDSSP{\xdef\fc@DSSP{n}} @@ -6386,6 +6607,66 @@ \fi \ifnum\loopcount<\seq@count \repeat} +\def\T@coffee@shade{% + \loopcount=0 + \expandafter\ifx\csname tint@seq0\endcsname\y@ + \expandafter\xdef\csname tint@seq0\endcsname{n} + \xdef\first@{=\first@}\fi + \expandafter\ifx\csname emph@seq0\endcsname\y@ + \expandafter\xdef\csname emph@seq0\endcsname{n} + \xdef\first@{,\first@}\fi + \xdef\second@{\csname TC@num0\endcsname} + \xdef\consensus{\consensus\second@\n@m@tch} + \xdef\constopo{\constopo\second@} + \loop + \advance\loopcount by 1 + \xdef\first@{\csname res\the\loopcount\endcsname} + \xdef\second@{\csname TC@num\the\loopcount\endcsname} + \ifx\first@\d@t + \expandafter\ifnum\csname res@count\the\loopcount\endcsname% + <\csname seq@start\the\loopcount\endcsname + \ifsh@wg@ps + \def\first@{\gap@char}\def\second@{*} + \else + \def\first@{{}} \def\second@{/} + \fi + \else + \expandafter\ifnum\csname res@count\the\loopcount\endcsname% + <\csname seq@len\the\loopcount\endcsname + \def\first@{\gap@char}\def\second@{*} + \else + \ifsh@wg@ps + \def\first@{\gap@char}\def\second@{*} + \else + \def\first@{{}} \def\second@{/} + \fi + \fi + \fi + \fi + \xdef\third@{noshade} + \expandafter\ifx\csname hide@seq\the\loopcount\endcsname\third@ + \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} + \xdef\first@{=\first@}\fi + \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n} + \xdef\first@{,\first@}\fi + \expandafter\xdef\csname seq\the\loopcount\endcsname{% + \csname seq\the\loopcount\endcsname% + *\first@} + \else + \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} + \xdef\first@{=\first@}\fi + \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n} + \xdef\first@{,\first@}\fi + \expandafter\xdef\csname seq\the\loopcount\endcsname{% + \csname seq\the\loopcount\endcsname% + \second@\first@} + \fi + \ifnum\loopcount<\seq@count \repeat} + \def\getregion@fromstack@first{% \expandafter\getregion@fromstack{\the\loopcount} \expandafter\ifx\csname start\the\loopcount\endcsname\ampers@nd @@ -6804,6 +7085,18 @@ \multiply\temp@count by 2 \divide\temp@count by \innerloopcount \xdef\cons@val{\the\temp@count} + \ifx\T@coffee@bcons\y@ + \xdef\cons@val{\csname TC@num0\endcsname} + \if\cons@val * + \xdef\cons@val{99} + \fi \message{(b(\cons@val)b)} + \fi + \ifx\T@coffee@ccons\y@ + \xdef\cons@val{\csname TC@num0\endcsname} + \if\cons@val * + \xdef\cons@val{99} + \fi \message{(c(\cons@val)c)} + \fi \fi } @@ -7700,10 +7993,15 @@ \def\c@nsensus{% \ifnum\pos@count>\res@perline \else + \loopcount=0 \global\advance\cons@count by 1\relax \ifnum\cons@count=0\relax \ifx\allow@zero\n@ \global\advance\cons@count by 1 \fi \fi + \ifT@coffee + \xdef\TC@line{\csname T@coffee0\endcsname} + \expandafter\TC@get\TC@line + \fi \expandafter\xdef\csname res@count0\endcsname{\the\cons@count} \ifx\hide@true\y@ \expandafter\ifx\csname hidestart0\endcsname\ampers@nd @@ -7720,9 +8018,13 @@ \fi \fi \fi - \loopcount=0 \loop \advance\loopcount by 1 + \ifT@coffee + \xdef\TC@line{\csname T@coffee\the\loopcount\endcsname} + \expandafter\TC@get\TC@line + \xdef\TC@first@{\csname TC@num\the\loopcount\endcsname} + \fi \xdef\seq@line{\csname sequence\the\loopcount\endcsname} \expandafter\residue@get\seq@line \xdef\first@{\csname res\the\loopcount\endcsname} @@ -7786,6 +8088,14 @@ \ifnum\v@lseqttop=\loopcount \xdef\v@lttop{\v@lttop,\csname \ffourth@ttop\first@\endcsname} \fi\fi + \ifx\collect@valtttop\yes + \ifnum\v@lseqtttop=\loopcount + \xdef\v@ltttop{\v@ltttop,\csname \ffourth@tttop\first@\endcsname} + \fi\fi + \ifx\collect@valttttop\yes + \ifnum\v@lseqttttop=\loopcount + \xdef\v@lttttop{\v@lttttop,\csname \ffourth@ttttop\first@\endcsname} + \fi\fi \ifx\collect@valbottom\yes \ifnum\v@lseqbottom=\loopcount \xdef\v@lbottom{\v@lbottom,\csname \ffourth@bottom\first@\endcsname} @@ -7794,6 +8104,14 @@ \ifnum\v@lseqbbottom=\loopcount \xdef\v@lbbottom{\v@lbbottom,\csname \ffourth@bbottom\first@\endcsname} \fi\fi + \ifx\collect@valbbbottom\yes + \ifnum\v@lseqbbbottom=\loopcount + \xdef\v@lbbbottom{\v@lbbbottom,\csname \ffourth@bbbottom\first@\endcsname} + \fi\fi + \ifx\collect@valbbbbottom\yes + \ifnum\v@lseqbbbbottom=\loopcount + \xdef\v@lbbbbottom{\v@lbbbbottom,\csname \ffourth@bbbbottom\first@\endcsname} + \fi\fi \fi \ifx\collect@restop\yes \ifnum\tr@nsseqtop=\loopcount @@ -7819,6 +8137,30 @@ \ifnum\innerloopcount>3 \innerloopcount=1 \fi \xdef\triple@countttop{\the\innerloopcount} \fi\fi + \ifx\collect@restttop\yes + \ifnum\tr@nsseqtttop=\loopcount + \xdef\last@restttop{\last@@restttop} + \xdef\last@@restttop{\first@} + \ifx\hide@now\n@ + \xdef\tr@nslatetttop{\tr@nslatetttop\first@} + \fi + \innerloopcount=\triple@counttttop + \advance\innerloopcount by 1 + \ifnum\innerloopcount>3 \innerloopcount=1 \fi + \xdef\triple@counttttop{\the\innerloopcount} + \fi\fi + \ifx\collect@resttttop\yes + \ifnum\tr@nsseqttttop=\loopcount + \xdef\last@resttttop{\last@@resttttop} + \xdef\last@@resttttop{\first@} + \ifx\hide@now\n@ + \xdef\tr@nslatettttop{\tr@nslatettttop\first@} + \fi + \innerloopcount=\triple@countttttop + \advance\innerloopcount by 1 + \ifnum\innerloopcount>3 \innerloopcount=1 \fi + \xdef\triple@countttttop{\the\innerloopcount} + \fi\fi \ifx\collect@resbottom\yes \ifnum\tr@nsseqbottom=\loopcount \xdef\last@resbottom{\last@@resbottom} @@ -7843,6 +8185,30 @@ \ifnum\innerloopcount>3 \innerloopcount=1 \fi \xdef\triple@countbbottom{\the\innerloopcount} \fi\fi + \ifx\collect@resbbbottom\yes + \ifnum\tr@nsseqbbbottom=\loopcount + \xdef\last@resbbbottom{\last@@resbbbottom} + \xdef\last@@resbbbottom{\first@} + \ifx\hide@now\n@ + \xdef\tr@nslatebbbottom{\tr@nslatebbbottom\first@} + \fi + \innerloopcount=\triple@countbbbottom + \advance\innerloopcount by 1 + \ifnum\innerloopcount>3 \innerloopcount=1 \fi + \xdef\triple@countbbbottom{\the\innerloopcount} + \fi\fi + \ifx\collect@resbbbbottom\yes + \ifnum\tr@nsseqbbbbottom=\loopcount + \xdef\last@resbbbbottom{\last@@resbbbbottom} + \xdef\last@@resbbbbottom{\first@} + \ifx\hide@now\n@ + \xdef\tr@nslatebbbbottom{\tr@nslatebbbbottom\first@} + \fi + \innerloopcount=\triple@countbbbbottom + \advance\innerloopcount by 1 + \ifnum\innerloopcount>3 \innerloopcount=1 \fi + \xdef\triple@countbbbbottom{\the\innerloopcount} + \fi\fi \innerloopcount=\csname mol@weight\the\loopcount\endcsname \advance\innerloopcount by \csname \prefix@ mw\first@\endcsname \expandafter\xdef\csname mol@weight\the\loopcount\endcsname{% @@ -7862,6 +8228,14 @@ \ifnum\v@lseqttop=\loopcount \xdef\v@lttop{\v@lttop,N} \fi\fi + \ifx\collect@valtttop\yes + \ifnum\v@lseqtttop=\loopcount + \xdef\v@ltttop{\v@ltttop,N} + \fi\fi + \ifx\collect@valttttop\yes + \ifnum\v@lseqttttop=\loopcount + \xdef\v@lttttop{\v@lttttop,N} + \fi\fi \ifx\collect@valbottom\yes \ifnum\v@lseqbottom=\loopcount \xdef\v@lbottom{\v@lbottom,N} @@ -7870,6 +8244,14 @@ \ifnum\v@lseqbbottom=\loopcount \xdef\v@lbbottom{\v@lbbottom,N} \fi\fi + \ifx\collect@valbbbottom\yes + \ifnum\v@lseqbbbottom=\loopcount + \xdef\v@lbbbottom{\v@lbbbottom,N} + \fi\fi + \ifx\collect@valbbbbottom\yes + \ifnum\v@lseqbbbbottom=\loopcount + \xdef\v@lbbbbottom{\v@lbbbbottom,N} + \fi\fi \ifx\collect@restop\yes \ifnum\tr@nsseqtop=\loopcount \xdef\tr@nslatetop{\tr@nslatetop -} @@ -7878,6 +8260,14 @@ \ifnum\tr@nsseqttop=\loopcount \xdef\tr@nslatettop{\tr@nslatettop -} \fi\fi + \ifx\collect@restttop\yes + \ifnum\tr@nsseqtttop=\loopcount + \xdef\tr@nslatetttop{\tr@nslatetttop -} + \fi\fi + \ifx\collect@resttttop\yes + \ifnum\tr@nsseqttttop=\loopcount + \xdef\tr@nslatettttop{\tr@nslatettttop -} + \fi\fi \ifx\collect@resbottom\yes \ifnum\tr@nsseqbottom=\loopcount \xdef\tr@nslatebottom{\tr@nslatebottom -} @@ -7886,6 +8276,14 @@ \ifnum\tr@nsseqbbottom=\loopcount \xdef\tr@nslatebbottom{\tr@nslatebbottom -} \fi\fi + \ifx\collect@resbbbottom\yes + \ifnum\tr@nsseqbbbottom=\loopcount + \xdef\tr@nslatebbbottom{\tr@nslatebbbottom -} + \fi\fi + \ifx\collect@resbbbbottom\yes + \ifnum\tr@nsseqbbbbottom=\loopcount + \xdef\tr@nslatebbbbottom{\tr@nslatebbbbottom -} + \fi\fi \fi \fi \ifnum\loopcount<\seq@count \repeat @@ -7923,6 +8321,18 @@ \sum@up@cons \xdef\v@lttop{\v@lttop,\cons@val} \fi + \ifx\collect@cons@graphtttop\yes + \outerloopcount=1\relax + \temp@count=0\relax + \sum@up@cons + \xdef\v@ltttop{\v@ltttop,\cons@val} + \fi + \ifx\collect@cons@graphttttop\yes + \outerloopcount=1\relax + \temp@count=0\relax + \sum@up@cons + \xdef\v@lttttop{\v@lttttop,\cons@val} + \fi \ifx\collect@cons@graphbottom\yes \outerloopcount=1\relax \temp@count=0\relax @@ -7935,6 +8345,18 @@ \sum@up@cons \xdef\v@lbbottom{\v@lbbottom,\cons@val} \fi + \ifx\collect@cons@graphbbbottom\yes + \outerloopcount=1\relax + \temp@count=0\relax + \sum@up@cons + \xdef\v@lbbbottom{\v@lbbbottom,\cons@val} + \fi + \ifx\collect@cons@graphbbbbottom\yes + \outerloopcount=1\relax + \temp@count=0\relax + \sum@up@cons + \xdef\v@lbbbbottom{\v@lbbbbottom,\cons@val} + \fi \ifx\collect@cons@colors\y@ \outerloopcount=1\relax \temp@count=0\relax @@ -7971,10 +8393,14 @@ \ifregionaltintnow \calc@regtint \fi \ifregionalemphnow \calc@regemph \fi \ifframenow \calc@frame \fi - \iftopfeaturenow \xdef\bottop@{top} \calc@feature \fi - \ifttopfeaturenow \xdef\bottop@{ttop} \calc@feature \fi - \ifbottomfeaturenow \xdef\bottop@{bottom} \calc@feature \fi - \ifbbottomfeaturenow \xdef\bottop@{bbottom} \calc@feature \fi + \iftopfeaturenow \xdef\bottop@{top} \calc@feature \fi + \ifttopfeaturenow \xdef\bottop@{ttop} \calc@feature \fi + \iftttopfeaturenow \xdef\bottop@{tttop} \calc@feature \fi + \ifttttopfeaturenow \xdef\bottop@{ttttop} \calc@feature \fi + \ifbottomfeaturenow \xdef\bottop@{bottom} \calc@feature \fi + \ifbbottomfeaturenow \xdef\bottop@{bbottom} \calc@feature \fi + \ifbbbottomfeaturenow \xdef\bottop@{bbbottom} \calc@feature \fi + \ifbbbbottomfeaturenow \xdef\bottop@{bbbbottom} \calc@feature \fi \ifx\hide@now\y@ \xdef\hidebar@on{1} \ifnum\pos@count=\bar@pos @@ -7990,13 +8416,16 @@ \ifshow@logo \calc@logo \fi \ifall@fshade \all@funcshade \else - \ifnum\cons@num>0 \loopcount=\cons@num \else \loopcount=\seq@count \fi - \xdef\match@case{0} \xdef\m@x{1} - \iffuncmode - \xdef\prfx{\prefix@} \xdef\prefix@{func} \xdef\c@se{3} \check@sim - \xdef\prefix@{\prfx} - \else \xdef\c@se{1} \check@ident \fi - \ifcase\match@case \unc@nserved \or \c@nserved \or \allm@tch \else \functi@nal \fi + \ifT@coffee \T@coffee@shade + \else + \ifnum\cons@num>0 \loopcount=\cons@num \else \loopcount=\seq@count \fi + \xdef\match@case{0} \xdef\m@x{1} + \iffuncmode + \xdef\prfx{\prefix@} \xdef\prefix@{func} \xdef\c@se{3} \check@sim + \xdef\prefix@{\prfx} + \else \xdef\c@se{1} \check@ident \fi + \ifcase\match@case \unc@nserved \or \c@nserved \or \allm@tch \else \functi@nal \fi + \fi \fi %%%%%%%% \fi @@ -8008,10 +8437,14 @@ \global\stop@true \loopcount=\pos@count \advance\loopcount by -1 \relax \res@perline=\loopcount - \iftopfeature \xdef\bottop@{top} \calc@feature \fi - \ifttopfeature \xdef\bottop@{ttop} \calc@feature \fi - \ifbottomfeature \xdef\bottop@{bottom} \calc@feature \fi - \ifbbottomfeature \xdef\bottop@{bbottom} \calc@feature \fi + \iftopfeature \xdef\bottop@{top} \calc@feature \fi + \ifttopfeature \xdef\bottop@{ttop} \calc@feature \fi + \iftttopfeature \xdef\bottop@{tttop} \calc@feature \fi + \ifttttopfeature \xdef\bottop@{ttttop} \calc@feature \fi + \ifbottomfeature \xdef\bottop@{bottom} \calc@feature \fi + \ifbbottomfeature \xdef\bottop@{bbottom} \calc@feature \fi + \ifbbbottomfeature \xdef\bottop@{bbbottom} \calc@feature \fi + \ifbbbbottomfeature \xdef\bottop@{bbbbottom} \calc@feature \fi \pos@count=0 \fi \fi} @@ -8026,6 +8459,10 @@ \def\c@unt{% \advance\loopcount by 1 + \ifT@coffee + \xdef\seq@line{\csname T@coffee\the\loopcount\endcsname} + \expandafter\TC@get\seq@line + \fi \xdef\seq@line{\csname sequence\the\loopcount\endcsname} \expandafter\residue@get\seq@line \xdef\first@{\csname res\the\loopcount\endcsname} @@ -8050,6 +8487,10 @@ \advance\end@count by 1 \ifnum\end@count<\start@number \loopcount=0 + \ifT@coffee + \xdef\seq@line{\csname T@coffee\the\loopcount\endcsname} + \expandafter\TC@get\seq@line + \fi \c@unt \count@first \fi} @@ -8065,8 +8506,10 @@ \regionalshadenowfalse \regionalemphnowfalse \regionaltintnowfalse \framenowfalse \fi - \topfeaturenowfalse \bottomfeaturenowfalse - \ttopfeaturenowfalse \bbottomfeaturenowfalse + \topfeaturenowfalse \bottomfeaturenowfalse + \ttopfeaturenowfalse \bbottomfeaturenowfalse + \tttopfeaturenowfalse \bbbottomfeaturenowfalse + \ttttopfeaturenowfalse \bbbbottomfeaturenowfalse \innerloopcount=\cons@count \advance\innerloopcount by \res@perline \advance\innerloopcount by 1 \loopcount=0 @@ -8133,6 +8576,28 @@ \fi \fi \fi + \iftttopfeature + \xdef\bottop@{tttop} + \expandafter\ifx\csname start\bottop@\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname start\bottop@\the\loopcount\endcsname>% + \innerloopcount + \else + \tttopfeaturenowtrue + \fi + \fi + \fi + \ifttttopfeature + \xdef\bottop@{ttttop} + \expandafter\ifx\csname start\bottop@\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname start\bottop@\the\loopcount\endcsname>% + \innerloopcount + \else + \ttttopfeaturenowtrue + \fi + \fi + \fi \ifbottomfeature \xdef\bottop@{bottom} \expandafter\ifx\csname start\bottop@\the\loopcount\endcsname\ampers@nd @@ -8155,12 +8620,35 @@ \fi \fi \fi + \ifbbbottomfeature + \xdef\bottop@{bbbottom} + \expandafter\ifx\csname start\bottop@\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname start\bottop@\the\loopcount\endcsname>% + \innerloopcount + \else + \bbbottomfeaturenowtrue + \fi + \fi + \fi + \ifbbbbottomfeature + \xdef\bottop@{bbbbottom} + \expandafter\ifx\csname start\bottop@\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname start\bottop@\the\loopcount\endcsname>% + \innerloopcount + \else + \bbbbottomfeaturenowtrue + \fi + \fi + \fi \loop \advance\loopcount by 1 \ifnumbers@left - \innerloopcount=\csname seq@len\the\loopcount\endcsname + \innerloopcount=\csname seq@len\the\loopcount\endcsname\relax \expandafter\ifnum\csname res@count\the\loopcount\endcsname=% \innerloopcount + \res@count=\innerloopcount \else \res@count=\csname res@count\the\loopcount\endcsname \advance\res@count by 1 @@ -8259,6 +8747,28 @@ \fi \fi \fi + \iftttopfeature + \xdef\bottop@{tttop} + \expandafter\ifx\csname start\bottop@\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname start\bottop@\the\loopcount\endcsname>% + \innerloopcount + \else + \tttopfeaturenowtrue + \fi + \fi + \fi + \ifttttopfeature + \xdef\bottop@{ttttop} + \expandafter\ifx\csname start\bottop@\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname start\bottop@\the\loopcount\endcsname>% + \innerloopcount + \else + \ttttopfeaturenowtrue + \fi + \fi + \fi \ifbottomfeature \xdef\bottop@{bottom} \expandafter\ifx\csname start\bottop@\the\loopcount\endcsname\ampers@nd @@ -8281,6 +8791,28 @@ \fi \fi \fi + \ifbbbottomfeature + \xdef\bottop@{bbbottom} + \expandafter\ifx\csname start\bottop@\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname start\bottop@\the\loopcount\endcsname>% + \innerloopcount + \else + \bbbottomfeaturenowtrue + \fi + \fi + \fi + \ifbbbbottomfeature + \xdef\bottop@{bbbbottom} + \expandafter\ifx\csname start\bottop@\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname start\bottop@\the\loopcount\endcsname>% + \innerloopcount + \else + \bbbbottomfeaturenowtrue + \fi + \fi + \fi \ifnum\loopcount<\seq@count \repeat \c@nsensus} @@ -8299,6 +8831,115 @@ \fontfamily{\legend@family}% \fontseries{\legend@series}% \fontshape{\legend@shape}% + \ifT@coffee + \noindent% + \ifnames@\ifnames@right\else\hbox to \name@width{\hss}\fi\fi% + \ifnumbers@\ifnumbers@left\hbox to \number@width{\hss}\fi\fi% + \hbox to \hspace@legend{\hss}% + \def\res@@style{\csname no@style\endcsname}% + \def\temp@{X}\xdef\low@up{lower}% + \expandafter\ifx\csname n@m@tch\the\loopcount\endcsname\low@up% + \def\temp@{x}\fi% + \ifhidechar\xdef\temp@{}\fi% + \textcolor{TC0}{\box@rule}% + \kern-\box@width\textcolor{Black}{\hbox to \box@width{% + \legend@size{\res@@style{\hss\temp@\hss}}}}% + \kern2ex\textcolor{\legend@fg}{% + \ifgerm@n\kern2ex\legend@size{schlecht}% + \else\ifsp@nish\kern2ex\legend@size{mala}% + \else\kern2ex\legend@size{bad}\fi\fi} + \newline\hbox{}% + \noindent% + \ifnames@\ifnames@right\else\hbox to \name@width{\hss}\fi\fi% + \ifnumbers@\ifnumbers@left\hbox to \number@width{\hss}\fi\fi% + \hbox to \hspace@legend{\hss}% + \textcolor{TC1}{\box@rule}% + \kern-\box@width\textcolor{Black}{\hbox to \box@width{% + \legend@size{\res@@style{\hss\temp@\hss}}}}% + \kern2ex\textcolor{\legend@fg}{\legend@size{}} + \newline\hbox{}% + \noindent% + \ifnames@\ifnames@right\else\hbox to \name@width{\hss}\fi\fi% + \ifnumbers@\ifnumbers@left\hbox to \number@width{\hss}\fi\fi% + \hbox to \hspace@legend{\hss}% + \textcolor{TC2}{\box@rule}% + \kern-\box@width\textcolor{Black}{\hbox to \box@width{% + \legend@size{\res@@style{\hss\temp@\hss}}}}% + \kern2ex\textcolor{\legend@fg}{\legend@size{}} + \newline\hbox{}% + \noindent% + \ifnames@\ifnames@right\else\hbox to \name@width{\hss}\fi\fi% + \ifnumbers@\ifnumbers@left\hbox to \number@width{\hss}\fi\fi% + \hbox to \hspace@legend{\hss}% + \textcolor{TC3}{\box@rule}% + \kern-\box@width\textcolor{Black}{\hbox to \box@width{% + \legend@size{\res@@style{\hss\temp@\hss}}}}% + \kern2ex\textcolor{\legend@fg}{\legend@size{}} + \newline\hbox{}% + \noindent% + \ifnames@\ifnames@right\else\hbox to \name@width{\hss}\fi\fi% + \ifnumbers@\ifnumbers@left\hbox to \number@width{\hss}\fi\fi% + \hbox to \hspace@legend{\hss}% + \textcolor{TC4}{\box@rule}% + \kern-\box@width\textcolor{Black}{\hbox to \box@width{% + \legend@size{\res@@style{\hss\temp@\hss}}}}% + \kern2ex\textcolor{\legend@fg}{% + \ifgerm@n\kern2ex\legend@size{Grad der}% + \else\ifsp@nish\kern2ex\legend@size{conservaci\'on}% + \else\kern2ex\legend@size{level of}\fi\fi} + \newline\hbox{}% + \noindent% + \ifnames@\ifnames@right\else\hbox to \name@width{\hss}\fi\fi% + \ifnumbers@\ifnumbers@left\hbox to \number@width{\hss}\fi\fi% + \hbox to \hspace@legend{\hss}% + \textcolor{TC5}{\box@rule}% + \kern-\box@width\textcolor{Black}{\hbox to \box@width{% + \legend@size{\res@@style{\hss\temp@\hss}}}}% + \kern2ex\textcolor{\legend@fg}{% + \ifgerm@n\kern2ex\legend@size{Konservierung}% + \else\ifsp@nish\kern2ex\legend@size{}% + \else\kern2ex\legend@size{conservation}\fi\fi} + \newline\hbox{}% + \noindent% + \ifnames@\ifnames@right\else\hbox to \name@width{\hss}\fi\fi% + \ifnumbers@\ifnumbers@left\hbox to \number@width{\hss}\fi\fi% + \hbox to \hspace@legend{\hss}% + \textcolor{TC6}{\box@rule}% + \kern-\box@width\textcolor{Black}{\hbox to \box@width{% + \legend@size{\res@@style{\hss\temp@\hss}}}}% + \kern2ex\textcolor{\legend@fg}{\legend@size{}} + \newline\hbox{}% + \noindent% + \ifnames@\ifnames@right\else\hbox to \name@width{\hss}\fi\fi% + \ifnumbers@\ifnumbers@left\hbox to \number@width{\hss}\fi\fi% + \hbox to \hspace@legend{\hss}% + \textcolor{TC7}{\box@rule}% + \kern-\box@width\textcolor{Black}{\hbox to \box@width{% + \legend@size{\res@@style{\hss\temp@\hss}}}}% + \kern2ex\textcolor{\legend@fg}{\legend@size{}} + \newline\hbox{}% + \noindent% + \ifnames@\ifnames@right\else\hbox to \name@width{\hss}\fi\fi% + \ifnumbers@\ifnumbers@left\hbox to \number@width{\hss}\fi\fi% + \hbox to \hspace@legend{\hss}% + \textcolor{TC8}{\box@rule}% + \kern-\box@width\textcolor{Black}{\hbox to \box@width{% + \legend@size{\res@@style{\hss\temp@\hss}}}}% + \kern2ex\textcolor{\legend@fg}{\legend@size{}} + \newline\hbox{}% + \noindent% + \ifnames@\ifnames@right\else\hbox to \name@width{\hss}\fi\fi% + \ifnumbers@\ifnumbers@left\hbox to \number@width{\hss}\fi\fi% + \hbox to \hspace@legend{\hss}% + \textcolor{TC9}{\box@rule}% + \kern-\box@width\textcolor{Black}{\hbox to \box@width{% + \legend@size{\res@@style{\hss\temp@\hss}}}}% + \kern2ex\textcolor{\legend@fg}{% + \ifgerm@n\kern2ex\legend@size{gut}% + \else\ifsp@nish\kern2ex\legend@size{buena}% + \else\kern2ex\legend@size{good}\fi\fi} + \newline\hbox{}% + \else \iffuncmode \ifnum\fgroup@num>0 \loopcount=0 @@ -8393,6 +9034,7 @@ \newline\hbox{}\noindent \fi \fi + \fi } \def\put@name<#1>#2@{% \ifnames@% @@ -8440,6 +9082,13 @@ \xdef\temp@@{}% \ifx\last@\ampers@nd\def\last@{0}\expandafter\special@shade\first@% \else% + \ifT@coffee% + \xdef\boxc@l@r{\csname fg@color#1\endcsname}% + \xdef\textc@l@r{\csname fg@textcolor#1\endcsname}% + \def\res@@style{\csname func@style#1\endcsname}% + \if\last@ *\def\last@{0}\fi + \if\last@ /\def\last@{10}\fi + \else% \iffuncmode% \xdef\boxc@l@r{\csname fg@color#1\endcsname}% \xdef\textc@l@r{\csname fg@textcolor#1\endcsname}% @@ -8465,7 +9114,7 @@ \def\res@@style{\csname relax\endcsname}% \else\xdef\boxc@l@r{White}\xdef\textc@l@r{White}% \def\res@@style{\csname relax\endcsname}% - \fi\fi\fi% + \fi\fi\fi\fi% \ifx\second@\comm@% \def\temp@{\res@style}% \expandafter\get@second@\first@% @@ -8502,20 +9151,48 @@ \ifx\last@\ampers@nd\def\last@{0}\expandafter\special@shade\first@% \else% \ifx\collect@cons@colors\y@% + \if\last@ *% + \xdef\boxc@l@r{\gap@bg}\xdef\textc@l@r{\gap@bg}% + \else% + \if\last@ /% + \xdef\boxc@l@r{White}\xdef\textc@l@r{White}% + \else% \expandafter\get@item\first@@@% \xdef\first@@@{\first@}% \ifx\box@scale\y@% \xdef\boxc@l@r{\c@nssc@le\fourth@}% \else% - \xdef\boxc@l@r{\c@nssc@le}% + \xdef\first@{T-Coffee}% + \ifx\first@\c@nssc@le% + \xdef\boxc@l@r{TC\last@}% + \else + \xdef\boxc@l@r{\c@nssc@le}% + \fi% \fi% \ifx\text@scale\y@% \xdef\textc@l@r{\c@nsc@l\fourth@}% \else% - \xdef\textc@l@r{\c@nsc@l}% - \fi% + \xdef\first@{T-Coffee}% + \ifx\first@\c@nsc@l% + \xdef\textc@l@r{TC\last@}% + \else + \xdef\textc@l@r{\c@nsc@l}% + \fi% + \fi\fi\fi% \def\res@@style{\csname relax\endcsname}% \else% + \ifT@coffee% + \if\last@ *% + \xdef\boxc@l@r{\gap@bg}\xdef\textc@l@r{\gap@bg}% + \else% + \if\last@ /% + \xdef\boxc@l@r{White}\xdef\textc@l@r{White}% + \else% + \xdef\boxc@l@r{White}\xdef\textc@l@r{TC\last@}% + \def\res@@style{\csname relax\endcsname}% + \fi% + \fi% + \else% \ifcase#1\xdef\boxc@l@r{\Allmatch}\xdef\textc@l@r{\TextAllmatch}% \def\res@@style{\all@style}% \or\xdef\boxc@l@r{\Identical}\xdef\textc@l@r{\TextIdentical}% @@ -8534,7 +9211,7 @@ \def\res@@style{\csname relax\endcsname}% \else\xdef\boxc@l@r{White}\xdef\textc@l@r{White}% \def\res@@style{\csname relax\endcsname}% - \fi\fi\fi% + \fi\fi\fi\fi% \xdef\first@{#3@}% \xdef\second@{#2}% \ifx\second@\comm@% @@ -8813,9 +9490,19 @@ \ensuremath{\overbrace{\hbox to \second@\box@width{\hss% \rule[0.2\arrow@height]{0pt}{0pt}\hss}}}% \else% + \xdef\last@{tttop}% + \ifx\bottop@\last@% + \ensuremath{\overbrace{\hbox to \second@\box@width{\hss% + \rule[0.2\arrow@height]{0pt}{0pt}\hss}}}% + \else% + \xdef\last@{ttttop}% + \ifx\bottop@\last@% + \ensuremath{\overbrace{\hbox to \second@\box@width{\hss% + \rule[0.2\arrow@height]{0pt}{0pt}\hss}}}% + \else% \raisebox{1.75\arrow@height}{\ensuremath{\underbrace{\hbox to % \second@\box@width{}}}}% - \fi\fi}% + \fi\fi\fi\fi}% \else% \xdef\last@{fill}% \ifx\second@@\last@% @@ -8880,12 +9567,15 @@ \ifx\second@@\N@\hbox to \box@width{\hss}% \else \loopcount=\second@@% - \advance\loopcount by -\pm@shift% - \advance\loopcount by 4% - \divide\loopcount by 5% - \multiply\loopcount by 5% - \ifnum\loopcount>100\loopcount=100\fi% - \ifnum\loopcount<5\loopcount=5\fi% + \ifx\T@coffee@ccons\y@% + \else% + \advance\loopcount by -\pm@shift% + \advance\loopcount by 4% + \divide\loopcount by 5% + \multiply\loopcount by 5% + \ifnum\loopcount>100\loopcount=100\fi% + \ifnum\loopcount<5\loopcount=5\fi% + \fi% \setlength\arrow@height{50\box@height}% \divide\arrow@height by 100\relax% \setlength\arrow@height{\sc@le@stretch\arrow@height}% @@ -8915,7 +9605,13 @@ {\vrule height\arrow@height width\box@width}}\hss}% \kern-\box@width% \fi% + \ifx\T@coffee@bcons\y@% + \ifnum\second@@=99 \xdef\second@@{0}\fi% + \fi \setlength\arrow@height{\second@@\box@height}% + \ifx\T@coffee@bcons\y@% + \setlength\arrow@height{11\arrow@height}% + \fi \divide\arrow@height by 100\relax% \setlength\arrow@height{\b@r@stretch\arrow@height}% \ifdim\arrow@height<0pt% @@ -9050,7 +9746,13 @@ \xdef\temp@{ttop}% \ifx\bottop@\temp@ \xdef\last@{0.25}% \else% - \xdef\last@{-0.25}\fi\fi% + \xdef\temp@{tttop}% + \ifx\bottop@\temp@ \xdef\last@{0.25}% + \else% + \xdef\temp@{ttttop}% + \ifx\bottop@\temp@ \xdef\last@{0.25}% + \else% + \xdef\last@{-0.25}\fi\fi\fi\fi% \textcolor{\f@color}{% \raisebox{\last@\arrow@height}{% \if\first@@ ,% @@ -9279,12 +9981,46 @@ \def\put@feature{% \vspace{-\baselineskip}% \newline\hbox{}% + \xdef\temp@{ttttop}% + \ifx\temp@\bottop@% + \ifnames@right\else\ifnames@% + \fontfamily{\ftext@family}\fontseries{\ftext@series}\fontshape{\ftext@shape}% + \selectfont% + \textcolor{\csname ftext@fg@\bottop@\endcsname}{\hbox to \name@width{\ftext@size\csname featuretextn@me\bottop@\endcsname\hss}}\fi\fi% + \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi% + \xdef\first@{\csname textfeature\bottop@\endcsname @}% + \loopcount=\res@perline% + \put@featuretext% + \ifnumbers@right\ifnumbers@\hbox to \number@width{\hss}\fi\fi% + \ifnames@right\ifnames@% + \fontfamily{\ftext@family}\fontseries{\ftext@series}\fontshape{\ftext@shape}% + \selectfont% + \kern1em\hbox to \loopcount\box@width{\hss}% + \textcolor{\csname ftext@fg@\bottop@\endcsname}{\hbox to \name@width{\ftext@size\csname featuretextn@me\bottop@\endcsname\hss}}\fi\fi% + \else% + \xdef\temp@{tttop}% + \ifx\temp@\bottop@% + \ifnames@right\else\ifnames@% + \fontfamily{\ftext@family}\fontseries{\ftext@series}\fontshape{\ftext@shape}% + \selectfont% + \textcolor{\csname ftext@fg@\bottop@\endcsname}{\hbox to \name@width{\ftext@size\csname featuretextn@me\bottop@\endcsname\hss}}\fi\fi% + \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi% + \xdef\first@{\csname textfeature\bottop@\endcsname @}% + \loopcount=\res@perline% + \put@featuretext% + \ifnumbers@right\ifnumbers@\hbox to \number@width{\hss}\fi\fi% + \ifnames@right\ifnames@% + \fontfamily{\ftext@family}\fontseries{\ftext@series}\fontshape{\ftext@shape}% + \selectfont% + \kern1em\hbox to \loopcount\box@width{\hss}% + \textcolor{\csname ftext@fg@\bottop@\endcsname}{\hbox to \name@width{\ftext@size\csname featuretextn@me\bottop@\endcsname\hss}}\fi\fi% + \else% \xdef\temp@{ttop}% \ifx\temp@\bottop@% \ifnames@right\else\ifnames@% \fontfamily{\ftext@family}\fontseries{\ftext@series}\fontshape{\ftext@shape}% \selectfont% - \textcolor{\csname ftext@fg@\bottop@\endcsname}{\hbox to \name@width{\csname featuretextn@me\bottop@\endcsname\hss}}\fi\fi% + \textcolor{\csname ftext@fg@\bottop@\endcsname}{\hbox to \name@width{\ftext@size\csname featuretextn@me\bottop@\endcsname\hss}}\fi\fi% \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi% \xdef\first@{\csname textfeature\bottop@\endcsname @}% \loopcount=\res@perline% @@ -9294,14 +10030,14 @@ \fontfamily{\ftext@family}\fontseries{\ftext@series}\fontshape{\ftext@shape}% \selectfont% \kern1em\hbox to \loopcount\box@width{\hss}% - \textcolor{\csname ftext@fg@\bottop@\endcsname}{\hbox to \name@width{\csname featuretextn@me\bottop@\endcsname\hss}}\fi\fi% + \textcolor{\csname ftext@fg@\bottop@\endcsname}{\hbox to \name@width{\ftext@size\csname featuretextn@me\bottop@\endcsname\hss}}\fi\fi% \else% \xdef\temp@{top}% \ifx\temp@\bottop@% \ifnames@right\else\ifnames@% \fontfamily{\ftext@family}\fontseries{\ftext@series}\fontshape{\ftext@shape}% \selectfont% - \textcolor{\csname ftext@fg@\bottop@\endcsname}{\hbox to \name@width{\csname featuretextn@me\bottop@\endcsname\hss}}\fi\fi% + \textcolor{\csname ftext@fg@\bottop@\endcsname}{\hbox to \name@width{\ftext@size\csname featuretextn@me\bottop@\endcsname\hss}}\fi\fi% \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi% \xdef\first@{\csname textfeature\bottop@\endcsname @}% \loopcount=\res@perline% @@ -9311,12 +10047,12 @@ \fontfamily{\ftext@family}\fontseries{\ftext@series}\fontshape{\ftext@shape}% \selectfont% \kern1em\hbox to \loopcount\box@width{\hss}% - \textcolor{\csname ftext@fg@\bottop@\endcsname}{\hbox to \name@width{\csname featuretextn@me\bottop@\endcsname\hss}}\fi\fi% + \textcolor{\csname ftext@fg@\bottop@\endcsname}{\hbox to \name@width{\ftext@size\csname featuretextn@me\bottop@\endcsname\hss}}\fi\fi% \else \ifnames@right\else\ifnames@% \fontfamily{\fstyles@family}\fontseries{\fstyles@series}\fontshape{\fstyles@shape}% \selectfont% - \textcolor{\csname fstyles@fg@\bottop@\endcsname}{\hbox to \name@width{\csname featurestylesn@me\bottop@\endcsname\hss}}\fi\fi% + \textcolor{\csname fstyles@fg@\bottop@\endcsname}{\hbox to \name@width{\fstyles@size\csname featurestylesn@me\bottop@\endcsname\hss}}\fi\fi% \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi% \xdef\first@{\csname stylefeature\bottop@\endcsname @}% \loopcount=\res@perline% @@ -9326,14 +10062,14 @@ \fontfamily{\fstyles@family}\fontseries{\fstyles@series}\fontshape{\fstyles@shape}% \selectfont% \kern1em\hbox to \loopcount\box@width{\hss}% - \textcolor{\csname fstyles@fg@\bottop@\endcsname}{\hbox to \name@width{\csname featurestylesn@me\bottop@\endcsname\hss}}\fi\fi% - \fi\fi% + \textcolor{\csname fstyles@fg@\bottop@\endcsname}{\hbox to \name@width{\fstyles@size\csname featurestylesn@me\bottop@\endcsname\hss}}\fi\fi% + \fi\fi\fi\fi% \newline\hbox{}% \ifx\temp@\bottop@% \ifnames@right\else\ifnames@% \fontfamily{\fstyles@family}\fontseries{\fstyles@series}\fontshape{\fstyles@shape}% \selectfont% - \textcolor{\csname fstyles@fg@\bottop@\endcsname}{\hbox to \name@width{\csname featurestylesn@me\bottop@\endcsname\hss}}\fi\fi% + \textcolor{\csname fstyles@fg@\bottop@\endcsname}{\hbox to \name@width{\fstyles@size\csname featurestylesn@me\bottop@\endcsname\hss}}\fi\fi% \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi% \xdef\first@{\csname stylefeature\bottop@\endcsname @}% \loopcount=\res@perline% @@ -9343,14 +10079,31 @@ \fontfamily{\fstyles@family}\fontseries{\fstyles@series}\fontshape{\fstyles@shape}% \selectfont% \kern1em\hbox to \loopcount\box@width{\hss}% - \textcolor{\csname fstyles@fg@\bottop@\endcsname}{\hbox to \name@width{\csname featurestylesn@me\bottop@\endcsname\hss}}\fi\fi% + \textcolor{\csname fstyles@fg@\bottop@\endcsname}{\hbox to \name@width{\fstyles@size\csname featurestylesn@me\bottop@\endcsname\hss}}\fi\fi% \else% \xdef\temp@{ttop}% \ifx\temp@\bottop@% \ifnames@right\else\ifnames@% \fontfamily{\fstyles@family}\fontseries{\fstyles@series}\fontshape{\fstyles@shape}% \selectfont% - \textcolor{\csname fstyles@fg@\bottop@\endcsname}{\hbox to \name@width{\csname featurestylesn@me\bottop@\endcsname\hss}}\fi\fi% + \textcolor{\csname fstyles@fg@\bottop@\endcsname}{\hbox to \name@width{\fstyles@size\csname featurestylesn@me\bottop@\endcsname\hss}}\fi\fi% + \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi% + \xdef\first@{\csname stylefeature\bottop@\endcsname @}% + \loopcount=\res@perline% + \put@featurestyle% + \ifnumbers@right\ifnumbers@\hbox to \number@width{\hss}\fi\fi% + \ifnames@right\ifnames@% + \fontfamily{\fstyles@family}\fontseries{\fstyles@series}\fontshape{\fstyles@shape}% + \selectfont% + \kern1em\hbox to \loopcount\box@width{\hss}% + \textcolor{\csname fstyles@fg@\bottop@\endcsname}{\hbox to \name@width{\fstyles@size\csname featurestylesn@me\bottop@\endcsname\hss}}\fi\fi% + \else + \xdef\temp@{tttop}% + \ifx\temp@\bottop@% + \ifnames@right\else\ifnames@% + \fontfamily{\fstyles@family}\fontseries{\fstyles@series}\fontshape{\fstyles@shape}% + \selectfont% + \textcolor{\csname fstyles@fg@\bottop@\endcsname}{\hbox to \name@width{\fstyles@size\csname featurestylesn@me\bottop@\endcsname\hss}}\fi\fi% \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi% \xdef\first@{\csname stylefeature\bottop@\endcsname @}% \loopcount=\res@perline% @@ -9360,12 +10113,29 @@ \fontfamily{\fstyles@family}\fontseries{\fstyles@series}\fontshape{\fstyles@shape}% \selectfont% \kern1em\hbox to \loopcount\box@width{\hss}% - \textcolor{\csname fstyles@fg@\bottop@\endcsname}{\hbox to \name@width{\csname featurestylesn@me\bottop@\endcsname\hss}}\fi\fi% + \textcolor{\csname fstyles@fg@\bottop@\endcsname}{\hbox to \name@width{\fstyles@size\csname featurestylesn@me\bottop@\endcsname\hss}}\fi\fi% + \else + \xdef\temp@{ttttop}% + \ifx\temp@\bottop@% + \ifnames@right\else\ifnames@% + \fontfamily{\fstyles@family}\fontseries{\fstyles@series}\fontshape{\fstyles@shape}% + \selectfont% + \textcolor{\csname fstyles@fg@\bottop@\endcsname}{\hbox to \name@width{\fstyles@size\csname featurestylesn@me\bottop@\endcsname\hss}}\fi\fi% + \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi% + \xdef\first@{\csname stylefeature\bottop@\endcsname @}% + \loopcount=\res@perline% + \put@featurestyle% + \ifnumbers@right\ifnumbers@\hbox to \number@width{\hss}\fi\fi% + \ifnames@right\ifnames@% + \fontfamily{\fstyles@family}\fontseries{\fstyles@series}\fontshape{\fstyles@shape}% + \selectfont% + \kern1em\hbox to \loopcount\box@width{\hss}% + \textcolor{\csname fstyles@fg@\bottop@\endcsname}{\hbox to \name@width{\fstyles@size\csname featurestylesn@me\bottop@\endcsname\hss}}\fi\fi% \else \ifnames@right\else\ifnames@% \fontfamily{\ftext@family}\fontseries{\ftext@series}\fontshape{\ftext@shape}% \selectfont% - \textcolor{\csname ftext@fg@\bottop@\endcsname}{\hbox to \name@width{\csname featuretextn@me\bottop@\endcsname\hss}}\fi\fi% + \textcolor{\csname ftext@fg@\bottop@\endcsname}{\hbox to \name@width{\ftext@size\csname featuretextn@me\bottop@\endcsname\hss}}\fi\fi% \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi% \xdef\first@{\csname textfeature\bottop@\endcsname @}% \xdef\first@{\csname textfeature\bottop@\endcsname @}% @@ -9376,8 +10146,8 @@ \fontfamily{\ftext@family}\fontseries{\ftext@series}\fontshape{\ftext@shape}% \selectfont% \kern1em\hbox to \loopcount\box@width{\hss}% - \textcolor{\csname ftext@fg@\bottop@\endcsname}{\hbox to \name@width{\csname featuretextn@me\bottop@\endcsname\hss}}\fi\fi% - \fi\fi% + \textcolor{\csname ftext@fg@\bottop@\endcsname}{\hbox to \name@width{\ftext@size\csname featuretextn@me\bottop@\endcsname\hss}}\fi\fi% + \fi\fi\fi\fi% \newline\hbox{}% } \def\put@@@frame#1{% @@ -10009,10 +10779,32 @@ \def\set@lines{% \pos@count=1 \xdef\frame@pos{1}\xdef\bar@pos{0}\xdef\hidebar@on{0}% - \xdef\featurepostop{1}\xdef\featureposbottom{1}% - \xdef\featureposttop{1}\xdef\featureposbbottom{1}% + \xdef\featurepostop{1} \xdef\featureposbottom{1}% + \xdef\featureposttop{1} \xdef\featureposbbottom{1}% + \xdef\featurepostttop{1} \xdef\featureposbbbottom{1}% + \xdef\featureposttttop{1} \xdef\featureposbbbbottom{1}% \findc@nsensus% \noindent% + \ifnum\feature@ttttop=1 + \ifnum\featureonttttop=0 \xdef\feature@ttttop{0} \fi + \xdef\bottop@{ttttop}% + \put@feature% + \vspace{\tttt@sp@ce}% + \vspace{-\baselineskip}% + \newline\hbox{}% + \else + \iffix@\ifttttopfeature \vspace{\tttt@sp@ce}\newline\hbox{}\newline\hbox{}\fi\fi + \fi + \ifnum\feature@tttop=1 + \ifnum\featureontttop=0 \xdef\feature@tttop{0} \fi + \xdef\bottop@{tttop}% + \put@feature% + \vspace{\ttt@sp@ce}% + \vspace{-\baselineskip}% + \newline\hbox{}% + \else + \iffix@\iftttopfeature \vspace{\ttt@sp@ce}\newline\hbox{}\newline\hbox{}\fi\fi + \fi \ifnum\feature@ttop=1 \ifnum\featureonttop=0 \xdef\feature@ttop{0} \fi \xdef\bottop@{ttop}% @@ -10175,12 +10967,56 @@ \fi \fi \fi + \ifnum\feature@bbbottom=1 % + \ifnum\featureonbbbottom=0 \xdef\feature@bbbottom{0}\fi% + \xdef\bottop@{bbbottom}% + \vspace{\bbb@sp@ce}% + \if\bbbottom@stretch y% + \vspace{-\box@height}% + \vspace{\b@r@stretch\box@height}% + \fi% + \put@feature% + \else + \iffix@ + \if\bbbottom@stretch y% + \vspace{-\box@height}% + \vspace{\b@r@stretch\box@height}% + \fi% + \ifbbbottomfeature + \vspace{\bbb@sp@ce}\newline\hbox{}\newline\hbox{}% + \fi + \fi + \fi + \ifnum\feature@bbbbottom=1 % + \ifnum\featureonbbbbottom=0 \xdef\feature@bbbbottom{0}\fi% + \xdef\bottop@{bbbbottom}% + \vspace{\bbbb@sp@ce}% + \if\bbbbottom@stretch y% + \vspace{-\box@height}% + \vspace{\b@r@stretch\box@height}% + \fi% + \put@feature% + \else + \iffix@ + \if\bbbbottom@stretch y% + \vspace{-\box@height}% + \vspace{\b@r@stretch\box@height}% + \fi% + \ifbbbbottomfeature + \vspace{\bbbb@sp@ce}\newline\hbox{}\newline\hbox{}% + \fi + \fi + \fi \xdef\consensus{} \xdef\ruler@{} - \xdef\styleframe{} \xdef\stylehidebar{} - \xdef\textfeaturetop{} \xdef\textfeaturebottom{} - \xdef\textfeaturettop{} \xdef\textfeaturebbottom{} - \xdef\stylefeaturetop{} \xdef\stylefeaturebottom{} - \xdef\stylefeaturettop{} \xdef\stylefeaturebbottom{} + \xdef\styleframe{} \xdef\stylehidebar{} + \xdef\textfeaturetop{} \xdef\textfeaturebottom{} + \xdef\textfeaturettop{} \xdef\textfeaturebbottom{} + \xdef\textfeaturetttop{} \xdef\textfeaturebbbottom{} + \xdef\textfeaturettttop{} \xdef\textfeaturebbbbottom{} + \xdef\stylefeaturetop{} \xdef\stylefeaturebottom{} + \xdef\stylefeaturettop{} \xdef\stylefeaturebbottom{} + \xdef\stylefeaturetttop{} \xdef\stylefeaturebbbottom{} + \xdef\stylefeaturettttop{} \xdef\stylefeaturebbbbottom{} \loopcount=0 \loop \advance\loopcount by 1 @@ -10202,6 +11038,10 @@ \advance\loopcount by 1\relax \xdef\seq@line{\csname sequence\the\loopcount\endcsname} \expandafter\remove@fromseq\seq@line + \ifT@coffee + \xdef\TC@cons{\csname TC0\endcsname} + \expandafter\remove@fromTC\TC@cons + \fi \ifnum\loopcount<\seq@count \repeat \fi \ifstop@ @@ -10284,15 +11124,23 @@ \xdef\consensus{} \xdef\constopo{} \xdef\frame@on{0} - \xdef\textfeaturetop{} \xdef\featureontop{0} - \xdef\textfeaturettop{} \xdef\featureonttop{0} - \xdef\textfeaturebottom{} \xdef\featureonbottom{0} - \xdef\textfeaturebbottom{}\xdef\featureonbbottom{0} + \xdef\textfeaturetop{} \xdef\featureontop{0} + \xdef\textfeaturettop{} \xdef\featureonttop{0} + \xdef\textfeaturetttop{} \xdef\featureontttop{0} + \xdef\textfeaturettttop{} \xdef\featureonttttop{0} + \xdef\textfeaturebottom{} \xdef\featureonbottom{0} + \xdef\textfeaturebbottom{} \xdef\featureonbbottom{0} + \xdef\textfeaturebbbottom{} \xdef\featureonbbbottom{0} + \xdef\textfeaturebbbbottom{} \xdef\featureonbbbbottom{0} \xdef\styleframe{} \xdef\stylehidebar{} \xdef\stylefeaturetop{} \xdef\stylefeaturettop{} + \xdef\stylefeaturetttop{} + \xdef\stylefeaturettttop{} \xdef\stylefeaturebottom{} - \xdef\stylefeaturebbottom{}} + \xdef\stylefeaturebbottom{} + \xdef\stylefeaturebbbottom{} + \xdef\stylefeaturebbbbottom{}} \def\guess@protein{\seqtype{P}\message{<Seqtype guess: protein>}} \def\guess@DNA{\seqtype{N}\message{<Seqtype guess: nucleotide>}} \def\residue@count{% @@ -10384,7 +11232,12 @@ \if\seq@type A \guess@DNA \fi \advance\seq@pointer by \res@count\relax \xdef\total@pos{\the\total@count} - \ifnum\end@num>\end@count\relax\xdef\end@num{\the\end@count}\fi + \ifx\end@num\n@\xdef\end@num{\the\end@count}\fi + \total@count=\end@count\relax + \xdef\first@{\csname res@count\start@seq\endcsname} + \advance\total@count by \first@\relax + \xdef\first@{\the\total@count} + \ifnum\end@num>\total@count\xdef\end@num{\the\total@count}\fi \ifshow@sublogo \prep@sublogo \fi \ifshow@logo \prep@logo \fi \ifnum\seq@pointer>\res@perline \block@output \fi @@ -10428,7 +11281,12 @@ \if\seq@type A \guess@DNA \fi \advance\seq@pointer by \res@count \xdef\total@pos{\the\total@count} - \ifnum\end@num>\end@count\relax\xdef\end@num{\the\end@count}\fi + \ifx\end@num\n@\xdef\end@num{\the\end@count}\fi + \total@count=\end@count\relax + \xdef\first@{\csname res@count\start@seq\endcsname} + \advance\total@count by \first@\relax + \xdef\first@{\the\total@count} + \ifnum\end@num>\total@count\xdef\end@num{\the\total@count}\fi \ifshow@sublogo \prep@sublogo \fi \ifshow@logo \prep@logo \fi \ifnum\seq@pointer>\res@perline \block@output \fi @@ -10568,8 +11426,12 @@ \expandafter\xdef\csname stack@framereg\the\loopcount\endcsname{&;&;&;@} \expandafter\xdef\csname stack@top\the\loopcount\endcsname{&;&;&;&;@} \expandafter\xdef\csname stack@ttop\the\loopcount\endcsname{&;&;&;&;@} + \expandafter\xdef\csname stack@tttop\the\loopcount\endcsname{&;&;&;&;@} + \expandafter\xdef\csname stack@ttttop\the\loopcount\endcsname{&;&;&;&;@} \expandafter\xdef\csname stack@bottom\the\loopcount\endcsname{&;&;&;&;@} \expandafter\xdef\csname stack@bbottom\the\loopcount\endcsname{&;&;&;&;@} + \expandafter\xdef\csname stack@bbbottom\the\loopcount\endcsname{&;&;&;&;@} + \expandafter\xdef\csname stack@bbbbottom\the\loopcount\endcsname{&;&;&;&;@} \expandafter\xdef\csname seq@start\the\loopcount\endcsname{1} \expandafter\xdef\csname name@col\the\loopcount\endcsname{yes} \expandafter\xdef\csname number@col\the\loopcount\endcsname{yes} @@ -10581,6 +11443,7 @@ \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} \expandafter\xdef\csname emph@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} \expandafter\xdef\csname name@col\the\loopcount\endcsname{yes} \expandafter\xdef\csname hide@number\the\loopcount\endcsname{no} @@ -10592,8 +11455,12 @@ \expandafter\xdef\csname stack@framereg\the\loopcount\endcsname{&;&;&;@} \expandafter\xdef\csname stack@top\the\loopcount\endcsname{&;&;&;&;@} \expandafter\xdef\csname stack@ttop\the\loopcount\endcsname{&;&;&;&;@} + \expandafter\xdef\csname stack@tttop\the\loopcount\endcsname{&;&;&;&;@} + \expandafter\xdef\csname stack@ttttop\the\loopcount\endcsname{&;&;&;&;@} \expandafter\xdef\csname stack@bottom\the\loopcount\endcsname{&;&;&;&;@} \expandafter\xdef\csname stack@bbottom\the\loopcount\endcsname{&;&;&;&;@} + \expandafter\xdef\csname stack@bbbottom\the\loopcount\endcsname{&;&;&;&;@} + \expandafter\xdef\csname stack@bbbbottom\the\loopcount\endcsname{&;&;&;&;@} \expandafter\xdef\csname seq@gap\the\loopcount\endcsname{no} \expandafter\xdef\csname seq@start\the\loopcount\endcsname{1} \expandafter\xdef\csname mol@weight\the\loopcount\endcsname{0} @@ -10635,10 +11502,14 @@ \expandafter\getregion@fromtintstack{\the\loopcount} \expandafter\getregion@fromemphstack{\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@{bottom} \expandafter\getregion@fromfstack{\the\loopcount} - \xdef\bottop@{bbottom}\expandafter\getregion@fromfstack{\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} \fontfamily{\namestext@family} \fontseries{\namestext@series} \fontshape{\namestext@shape} @@ -10682,17 +11553,18 @@ \expandafter\getregion@fromtintstack{\the\loopcount} \expandafter\getregion@fromemphstack{\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@{bottom} \expandafter\getregion@fromfstack{\the\loopcount} - \xdef\bottop@{bbottom}\expandafter\getregion@fromfstack{\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} \innerloopcount = \csname seq@len\the\loopcount\endcsname \advance\innerloopcount by \csname seq@start\the\loopcount\endcsname \advance\innerloopcount by -1 \expandafter\xdef\csname seq@len\the\loopcount\endcsname{\the\innerloopcount} - \ifsh@wg@ps - \expandafter\xdef\csname seq@len\the\loopcount\endcsname{99999999} - \fi \advance\loopcount by 1 \ifnum\loopcount>\seq@count \else \repeat \advance\name@width by 1em @@ -10902,23 +11774,29 @@ \advance\loopcount by 1\relax \xdef\@lign@count{\the\loopcount} \start@true \xdef\start@num{1} \xdef\start@seq{0} -\stop@false \xdef\end@num{99999999} \xdef\seq@regions{0} +\stop@false \xdef\end@num{n} \xdef\seq@regions{0} \cons@count=0 \expandafter\xdef\csname res@count0\endcsname{0} \xdef\allow@zero{n} \xdef\c@ns@shift{0} \regionalshadefalse\regionalemphfalse\regionaltintfalse \frame@false \xdef\ruler@rot{0} -\topfeaturefalse\bottomfeaturefalse -\ttopfeaturefalse\bbottomfeaturefalse +\topfeaturefalse \bottomfeaturefalse +\ttopfeaturefalse \bbottomfeaturefalse +\tttopfeaturefalse \bbbottomfeaturefalse +\ttttopfeaturefalse \bbbbottomfeaturefalse \all@fshadefalse\hidecharfalse \xdef\finger@linenum{0} \xdef\hide@seqs{n} \xdef\dssp@num{0} \xdef\stride@num{0} \xdef\PHD@num{0} \xdef\HMMTOP@num{0} -\xdef\bottop@{top} \expandafter\xdef\csname feature@\bottop@\endcsname{0} -\xdef\bottop@{ttop} \expandafter\xdef\csname feature@\bottop@\endcsname{0} -\xdef\bottop@{bottom} \expandafter\xdef\csname feature@\bottop@\endcsname{0} -\xdef\bottop@{bbottom}\expandafter\xdef\csname feature@\bottop@\endcsname{0} +\xdef\bottop@{top} \expandafter\xdef\csname feature@\bottop@\endcsname{0} +\xdef\bottop@{ttop} \expandafter\xdef\csname feature@\bottop@\endcsname{0} +\xdef\bottop@{tttop} \expandafter\xdef\csname feature@\bottop@\endcsname{0} +\xdef\bottop@{ttttop} \expandafter\xdef\csname feature@\bottop@\endcsname{0} +\xdef\bottop@{bottom} \expandafter\xdef\csname feature@\bottop@\endcsname{0} +\xdef\bottop@{bbottom} \expandafter\xdef\csname feature@\bottop@\endcsname{0} +\xdef\bottop@{bbbottom} \expandafter\xdef\csname feature@\bottop@\endcsname{0} +\xdef\bottop@{bbbbottom}\expandafter\xdef\csname feature@\bottop@\endcsname{0} \xdef\frame@{0} \xdef\show@Hdssp{no} \xdef\show@Gdssp{no} \xdef\show@Idssp{no} \xdef\show@Edssp{no} \xdef\show@Bdssp{no} \xdef\show@Tdssp{no} @@ -10928,23 +11806,36 @@ \xdef\show@itop{no} \xdef\show@etop{no} \xdef\show@TMtop{no} \xdef\show@i@HMMTOP{no} \xdef\show@e@HMMTOP{no} \xdef\show@TM@HMMTOP{no} \xdef\show@Hsec{no} \xdef\show@Esec{no} -\xdef\collect@restop{no} \xdef\collect@resttop{no} -\xdef\collect@resbottom{no} \xdef\collect@resbbottom{no} -\xdef\tr@nslatetop{} \xdef\tr@nslatettop{} -\xdef\tr@nslatebottom{} \xdef\tr@nslatebbottom{} -\xdef\tr@nsseqtop{0} \xdef\tr@nsseqttop{0} -\xdef\tr@nsseqbottom{0} \xdef\tr@nsseqbbottom{0} -\xdef\triple@counttop{0} \xdef\triple@countttop{0} -\xdef\triple@countbottom{0} \xdef\triple@countbbottom{0} -\xdef\last@@restop{} \xdef\last@@resttop{} -\xdef\last@@resbottom{} \xdef\last@@resbbottom{} -\xdef\out@put{y} \xdef\m@p{no} -\xdef\t@sp@ce{0mm} \xdef\tt@sp@ce{0mm} -\xdef\b@sp@ce{0mm} \xdef\bb@sp@ce{0mm} +\xdef\collect@restop{no} \xdef\collect@resttop{no} +\xdef\collect@restttop{no} \xdef\collect@resttttop{no} +\xdef\collect@resbottom{no} \xdef\collect@resbbottom{no} +\xdef\collect@resbbbottom{no}\xdef\collect@resbbbbottom{no} +\xdef\tr@nslatetop{} \xdef\tr@nslatettop{} +\xdef\tr@nslatetttop{} \xdef\tr@nslatettttop{} +\xdef\tr@nslatebottom{} \xdef\tr@nslatebbottom{} +\xdef\tr@nslatebbbottom{} \xdef\tr@nslatebbbbottom{} +\xdef\tr@nsseqtop{0} \xdef\tr@nsseqttop{0} +\xdef\tr@nsseqtttop{0} \xdef\tr@nsseqttttop{0} +\xdef\tr@nsseqbottom{0} \xdef\tr@nsseqbbottom{0} +\xdef\tr@nsseqbbbottom{0} \xdef\tr@nsseqbbbbottom{0} +\xdef\triple@counttop{0} \xdef\triple@countttop{0} +\xdef\triple@counttttop{0} \xdef\triple@countttttop{0} +\xdef\triple@countbottom{0} \xdef\triple@countbbottom{0} +\xdef\triple@countbbbottom{0}\xdef\triple@countbbbbottom{0} +\xdef\last@@restop{} \xdef\last@@resttop{} +\xdef\last@@restttop{} \xdef\last@@resttttop{} +\xdef\last@@resbottom{} \xdef\last@@resbbottom{} +\xdef\last@@resbbbottom{} \xdef\last@@resbbbbottom{} +\xdef\out@put{y} \xdef\m@p{no} +\xdef\t@sp@ce{0mm} \xdef\tt@sp@ce{0mm} +\xdef\ttt@sp@ce{0mm} \xdef\tttt@sp@ce{0mm} +\xdef\b@sp@ce{0mm} \xdef\bb@sp@ce{0mm} +\xdef\bbb@sp@ce{0mm} \xdef\bbbb@sp@ce{0mm} \xdef\seq@gap@num{0} \xdef\h@ndalign{no} \xdef\sep@space{0pt} \xdef\c@pshort{n} \xdef\bottom@stretch{n} \xdef\bbottom@stretch{n} +\xdef\bbbottom@stretch{n} \xdef\bbbbottom@stretch{n} \xdef\c@nscol{} \xdef\c@nssc@le{ColdHot} \xdef\collect@cons@colors{no} \xdef\cons@now{no} \xdef\res@numA{0} \xdef\res@numB{0} @@ -10993,6 +11884,7 @@ \xdef\divref@{0} \xdef\all@thresh@ld{100} \all@shadefalse \hidefeaturenames \hidefeaturestylenames +\xdef\T@coffee@ccons{n} \xdef\T@coffee@bcons{n} %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%% %%%%% |