texshade 1.18

git-svn-id: svn://tug.org/texlive/trunk@7474 c570f23f-e606-0410-a88d-b1316a301751

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}
 
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