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authorKarl Berry <karl@freefriends.org>2008-04-17 15:21:19 +0000
committerKarl Berry <karl@freefriends.org>2008-04-17 15:21:19 +0000
commit679b379df816aa8af46fd18bd199c5ade5cb9662 (patch)
tree894b060f76780a0b99c8dd4c044efed3913e7ea5 /Master/texmf-dist/source/latex/texshade
parent8a1fed7bea2318d80390919b2c106509e4efceef (diff)
texshade 1.18
git-svn-id: svn://tug.org/texlive/trunk@7474 c570f23f-e606-0410-a88d-b1316a301751
Diffstat (limited to 'Master/texmf-dist/source/latex/texshade')
-rw-r--r--Master/texmf-dist/source/latex/texshade/texshade.dtx1406
-rw-r--r--Master/texmf-dist/source/latex/texshade/texshade.ins3
2 files changed, 1252 insertions, 157 deletions
diff --git a/Master/texmf-dist/source/latex/texshade/texshade.dtx b/Master/texmf-dist/source/latex/texshade/texshade.dtx
index 67f26d001a0..61e88ddf8d0 100644
--- a/Master/texmf-dist/source/latex/texshade/texshade.dtx
+++ b/Master/texmf-dist/source/latex/texshade/texshade.dtx
@@ -10,7 +10,7 @@
% `texshade.txt' for further information!
%
%
-% Copyright (C) 1999-2007 Eric Beitz
+% Copyright (C) 1999-2008 Eric Beitz
% See the file texshade.txt
%
% \fi
@@ -280,10 +280,11 @@
% `hideblock' allows one to hide parts of the
% alignment (still in experimental stage!).
% New home: TeXshade, TeXtopo, and BioTeX have a new home:
-% `www.pharmazie.uni-kiel.de/chem/' - click on `Beitz'
+% `www.pharmazie.uni-kiel.de/chem/Prof_Beitz/biotex.html'
% }
%
% \changes{1.17}{2007-06-19}{%
+% Corrections: .
% Introduction: `allmatchspecial' now accepts an optional threshold
% percentage allowing one to set two levels off
% conservation;
@@ -306,6 +307,23 @@
% }
%
%
+% \changes{1.18}{2008-04-15}{%
+% Corrections: bug fixes concerning:
+% featurenames, ordering, numbering, setends.
+% Introduction: T-Coffee shading can be imported and displayed
+% in the alignment, in the consensus,
+% in feature color scales and bar graphs by
+% `shadingmode[ASCII-file]{T-Coffee}' and
+% `includeTCoffee';
+% two more feature lines on top and at bottom:
+% `ttttop', `tttop', `bbbottom', and `bbbbottom';
+% fusion of the `startnumber' and `setends' commands
+% via optional parameters.
+% }
+%
+%
+%
+%
% \CharacterTable
% {Upper-case \A\B\C\D\E\F\G\H\I\J\K\L\M\N\O\P\Q\R\S\T\U\V\W\X\Y\Z
% Lower-case \a\b\c\d\e\f\g\h\i\j\k\l\m\n\o\p\q\r\s\t\u\v\w\x\y\z
@@ -342,8 +360,8 @@
% send electronic mail to \texttt{ebeitz@pharmazie.uni-kiel.de};
% for further information, updates and on-line documentation
% see my homepage at
-% \texttt{www.pharmazie.uni-kiel.de/chem/} -- click on `Beitz'}}
-% \date{v1.17; 2007/06/19\\}
+% \texttt{www.pharmazie.uni-kiel.de/chem/Prof\_Beitz/biotex.html} }}
+% \date{v1.18; 2008/04/15\\}
% \maketitle
% \begin{abstract}
% Setting alignments of nucleotides and peptides for publication
@@ -395,6 +413,8 @@
% (MSF-format)\\
% \quad|AQPpro.MSF| \> an example protein alignment
% (MSF-format)\\
+% \quad|AQP_TC.asc| \> an example T-Coffee shading file
+% (|score_ascii|-format)\\
% \quad|AQP2spec.ALN|\> a further protein alignment
% (minimal ALN-file)\\
% \quad|AQP1.phd|\> secondary structure information
@@ -420,6 +440,26 @@
%
% \subsection{Version History}
%
+% \textbf{v1.18 2008/04/15}
+% \medskip
+%
+% \emph{Correction:} several bug fixed concerning featurename
+% display, sequence ordering and numbering.
+%
+% \emph{Introduction:}
+% (a) T-Coffee shading information can be loaded and put on the
+% alignment.\footnote{Suggestion by Florian Mertes.}
+% The conservation data can also be displayed in the
+% consensus as well as feature color scales and bar plots.
+% (b) Two more feature lines were added on the top and at the
+% bottom (|ttttop|, |tttop|, |bbbottom|, |bbbbottom|).
+% (c) The |startnumber| and |setends| commands have been fused;
+% either command can set both, a new start number as well as
+% end definitions of the sequence section to be displayed.
+% \bigskip
+%
+% \newpage
+%
% \textbf{v1.17 2007/06/19}
% \medskip
%
@@ -438,7 +478,7 @@
% |\featurenamescolor|, |\featurestylenamescolor|,
% Font styles in feature names can be set as usual, e.g.
% |\setsize{featurenames}{large}| or
-% |\featurestylenamesrm|, etc.
+% |\featurestylenamesrm|.
% \bigskip
%
%
@@ -593,6 +633,7 @@
% alignment\footnote{Inspired by Christoph Gille's {\tt STRAP}}.
% \bigskip
%
+%
% \textbf{v1.7 2004/01/05}
% \medskip
%
@@ -650,6 +691,7 @@
% breaks of the gaps after the sequences.
% \bigskip
%
+%
% \textbf{v1.4\&4a 2000/9/12 \& 2000/10/3}
% \medskip
%
@@ -774,7 +816,7 @@
% as \textsc{PostScript} and on-line viewable PDF.
% I also put a link from the \BioTeX{} (\TeXshade/\TeXtopo) homepage
% to the document collection
-% (|http://homepages.uni-tuebingen.de/beitz/biotex.html|).
+% (|http://pharmazie.uni-kiel.de/chem/Prof_Beitz/BioTeX|).
%
%
% \subsubsection{Memory shortness when using \TeX{}shade}
@@ -1052,12 +1094,53 @@
% \end{verbatim}}
%
% Probably you know
-% this kind of shading from the VMS/Unix and DOS public domain program
+% this kind of shading from the public domain program
% |BoxShade|
% by \textsc{Kay Hofmann} or from the Macintosh version
% |MacBoxShade| by \textsc{Michael D. Barron}. \TeXshade{}
% provides the same functionality---and goes truly beyond---for the
% \TeX{} community.
+%
+%
+% \subsubsection{T-Coffee shading}
+%
+% \label{TCoffee}
+%
+% \TeXshade{}'s capabilities of calculating alignment shadings are
+% limited. |T-Coffee| (|www.tcoffee.org|) is a sophisticated alignment/shading
+% software. You can apply shading from |T-Coffee| in \TeXshade{}
+% by loading the shading information file (|score_ascii|) generated by
+% |T-Coffee|.
+% \medskip
+%
+%
+% \begin{texshade}{AQPpro.MSF}
+% \shadingmode[AQP_TC.asc]{T-Coffee}
+% \setends{1}{30..63}
+% \hideconsensus
+% \feature{top}{1}{30..63}{color:conservation[T-Coffee]}{}
+% \showfeaturestylename{top}{feat-cons}
+% \showconsensus{bottom}
+% \end{texshade}
+%
+% Code:\medskip
+%
+% \vbox{%
+% \begin{verbatim}
+% \begin{texshade}{AQPpro.MSF}
+% \shadingmode[AQP_TC.asc]{T-Coffee}
+% \setends{1}{30..63}
+% \hideconsensus
+% \feature{top}{1}{30..63}{color:conservation[T-Coffee]}{}
+% \showfeaturestylename{top}{feat-cons}
+% \showconsensus{bottom}
+% \end{texshade}
+% \end{verbatim}}
+%
+%
+%
+%
+%
%
%
% \subsubsection{Diversity mode}
@@ -1952,7 +2035,7 @@
% modes or new color schemes (i.\,e.\ for a satisfying grayscale output)
% with other users. If you have created a
% parameter file, which you think is of interest for others, please
-% submit it to me\footnote{|eric.beitz@uni-tuebingen.de|} as an e-mail
+% submit it to me\footnote{|ebeitz@pharmazie.uni-kiel.de|} as an e-mail
% attachment together with a short
% description. I will take care of those files and post them---with
% a reference to the author---together with the next \TeXshade{}
@@ -2195,6 +2278,23 @@
% \end{verbatim}
%
%
+% \item |\shadingmode[|\meta{filename}|]{T-Coffee}|
+%
+% Enter a \meta{filename} to load the shading
+% information from a |T-Coffee| |score_ascii| file (|www.tcoffee.org|);
+% see example in \ref{TCoffee}. Make sure
+% that the alignment file specified in the |\texshade| command
+% and this shading file correspond to each other.
+%
+% If you do not enter a \meta{filename} here, a separate
+% command |\includeTCoffee{|\meta{filename}|}| must be used.
+%
+% |T-Coffee| shading can also be used in the consensus
+% p.\,\pageref{Lshowconsensus} and in the feature lines,
+% in particular color scales and bar plots p.\,\pageref{Lgraphs},
+% for the display of shading information.
+%
+%
% \item |\shadingmode[|\meta{seqref}|]{diverse}|
%
% \ref{diverse} depicts an example alignment. Choose the
@@ -2413,7 +2513,7 @@
%
% with
% \meta{scale} |Gray|, |BlueRed|, |RedBlue|, |GreenRed|, |RedGreen|,
-% |ColdHot| (recommended) or |HotCold| and \meta{position} |top|
+% |ColdHot| (recommended), |HotCold|, or |T-Coffee| \ref{TCoffee}, and \meta{position} |top|
% or |bottom|.
%
% The first color defines the foreground, i.e. the letters, the
@@ -2735,13 +2835,15 @@
% displayed, one
% may not want to have the residue numbering start out with number~1.
% The command
-% |\startnumber{|\meta{seqref}|}{|\meta{first residue number}|}|
+% |\startnumber[|\meta{start..stop}|]{|\meta{seqref}|}{|\meta{startnumber}|}|
% allows one to set the starting number of any sequence to any value
% incl.\ negative values but except `0' which is not usually used in
% sequence numbering (the transition from negative to positive
% values is like this: \ldots\ $-2$, $-1$, 1, 2 \ldots). If, however,
% the use of the number `0' is wanted as sometimes in sequence logos
% this can be turned on by |\allowzero| and off with |\disallowzero|.
+% The optional parameter can be used to truncate the sequence display
+% to a certain section (see also |\setends| below).
%
% \label{Lseqlength}
% \TeXshade{} needs to know the correct length of the sequences
@@ -2783,7 +2885,7 @@
% is done by
% \medskip
%
-% \quad|\setends{|\meta{seqref}|}{|\meta{startnumber}|..|\meta{stopnumber}|}|.
+% \quad|\setends[|\meta{startnumber}|]{|\meta{seqref}|}{|\meta{start..stop}|}|.
% \medskip
%
% Again, \meta{seqref} is the sequence number based on the
@@ -2791,28 +2893,44 @@
% the consensus as a measure for the sequence section the
% string `|consensus|' as \meta{seqref} is accepted. The
% specified sequence is truncated at
-% positions \meta{startnumber} and \meta{stopnumber}. All other
+% positions \meta{start} and \meta{stop}. All other
% sequences are cut accordingly. If the number of the first
% residue in the sequence is set to a new value with the
-% |\startnumber| command (s.\,a.) this is taken into account. Some examples:
+% |\startnumber| command (s.\,a.) this is taken into account. The
+% \meta{startnumber} can be set as an optional parameter directly
+% in the |\setends| command as well.
+% \medskip
+%
+% Some examples:
% \medskip
%
-% \quad a) |\setends{1}{20..100}|
+% \quad a) |\setends{1}{21..100}|
% \medskip
%
-% \quad b) |\startnumber{1}{15} \setends{1}{35..115}|
+% \quad b) |\startnumber{1}{101} \setends{1}{121..200}|
% \medskip
%
-% Both commands select the same section from the alignment but the
-% numbering for sequence 1 starts at position~20 in the first example and at
-% position~35 in the latter.
+% Both commands select the same sequence section from the alignment but
+% numbering for sequence 1 starts at position~21 in the first example and at
+% position~121 in the latter.
% \medskip
%
-% \quad c) |\setends{consensus}{20..100}|
+% \quad c) |\setends[101]{1}{121..200}| equals example b.
% \medskip
%
-% This may describe a completely different section of the multiple
-% sequence alignment.
+% \medskip
+%
+% \quad d) |\startnumber[121..200]{1}{101}| also equals example b.
+% \medskip
+%
+% \medskip
+%
+% \quad e) |\setends{consensus}{21..100}|
+% \medskip
+%
+% This may describe a very different section of the multiple
+% sequence alignment because the consensus counts every position
+% including gaps.
%
% \label{Lshowruler}\label{Lhideruler}
% \label{Lrulersteps}\label{Lrulercolor}
@@ -3147,7 +3265,7 @@
% With the optional parameter the default line thickness of the frame can
% be changed, example: |\frameblock{1}{10..20,50..70}{Red[2pt]}|
%
-% \subsubsection{Hiding blocks of the alignment (still experimental!)}
+% \subsubsection{Hiding blocks of the alignment (experimental!)}
%
% \label{Lhideblock}
% \textit{Be aware that this feature is still highly experimental. There are many instances
@@ -3208,20 +3326,21 @@
% this rather complex but mighty command are discussed in detail.
% The parameter \meta{position} tells \TeXshade{} where to display
% the feature label, i.\,e. on the top of the alignment (|top|),
-% or at the bottom (|bottom|). Further, there can be a feature line
-% ontop of the top feature line (|ttop|) or below the bottom
-% feature line (|bbottom|). Thus, up to four features
-% overlapping in four different lines may be displayed.
+% or at the bottom (|bottom|). Further, there can be three more feature lines
+% ontop of the top feature line (|ttop|, |tttop|, and |ttttop|) or below the bottom
+% feature line (|bbottom|, |bbbottom|, |bbbbottom|). Thus, up to eight features
+% overlapping in eight different lines may be displayed.
% Depending on the content of the feature lines the gaps between
% them might be not satisfactory.
% \label{Ltopspace}\label{Lttopspace}
+% \label{Ltttopspace}\label{Lttttopspace}
% \label{Lbottomspace}\label{Lbbottomspace}
-% Therefore, four separate commands can be employed to change the
-% space between |ttop| and |top|
-% (|\ttopspace{|\meta{length}|}|), between |top| and the alignment
-% (|\topspace{|\meta{length}|}|), between the alignment and
-% |bottom| (|\bottomspace{|\meta{length}|}|) and between |bottom|
-% and |bbottom| (|\bbottomspace{|\meta{length}|}|). Use positive
+% \label{Lbbbottomspace}\label{Lbbbbottomspace}
+% Therefore, eight separate commands can be employed to change the
+% space below |ttttop|, |tttop|, |ttop|, or |top|
+% (|\topspace{|\meta{length}|}| etc.), and above
+% |bottom|, |bbottom|, |bbbottom|, or |bbbbottom|
+% (|\bottomspace{|\meta{length}|}| etc.). Use positive
% values to further separate the lines, e.\,g.
% |\ttopspace{3mm}| or negative values to reduce the space, e.\,g.
% |\bottomspace{-0.1in}|.
@@ -3240,7 +3359,8 @@
% \textbf{Braces:}\\
% In order to display an over- or underbrace as
% a label use the parameter |{brace}|. Depending on the
-% \meta{position} (|ttop|, |top|, |bottom| or |bbottom|) the respective brace is
+% \meta{position} (|ttttop|, |tttop|, |ttop|, |top|, |bottom|,
+% |bbottom|, |bbbottom|, or |bbbbottom|) the respective brace is
% displayed. The standard color of braces is
% black. It can be changed by an optional parameter directly after
% the definition of the symbol, e.\,g. |{brace[Red]}|.
@@ -3491,7 +3611,11 @@
% color scales is a 5\% gray scale from very light gray to black (|Gray|).
% More colorful scales have been implemented, i.e. |BlueRed|, |RedBlue|, |GreenRed|,
% |RedGreen|, |ColdHot| and |HotCold|, the latter two being particularly
-% useful for ranges from negative to positive values.
+% useful for ranges from negative to positive values. Further, a scale called |T-Coffee|
+% is available if |T-Coffee| shading information has been imported as the
+% |\shadindmode| \ref{Lshadingmode}.
+%
+%
%
% The general format of this feature label definition for bar graphs is:
% \medskip
@@ -3511,6 +3635,9 @@
% \qquad |{bar:conservation}|
% \medskip
%
+% \qquad |{bar:conservation[T-Coffee]}|
+% \medskip
+%
% \qquad |{bar:hydrophobicity}|
% \medskip
%
@@ -3535,6 +3662,9 @@
% \qquad |{color:conservation[BlueRed]}|
% \medskip
%
+% \qquad |{color:conservation[T-Coffee]}|
+% \medskip
+%
% \qquad |{color:hydrophobicity[GreenRed]}|
% \medskip
%
@@ -3588,16 +3718,16 @@
% \label{Lshowfeaturename} \label{Lshowfeaturestylename}
% \label{Lhidefeaturename} \label{Lhidefeaturestylename}
% \label{Lhidefeaturenames} \label{Lhidefeaturestylenames}
-% \quad |\showfeaturename{|\meta{ttop/top/bottom/bbottom}|}{|\meta{name}|}|,
+% \quad |\showfeaturename{|\meta{ttttop...bbbbottom}|}{|\meta{name}|}|,
% \medskip
%
-% \quad |\showfeaturestylename{|\meta{ttop/top/bottom/bbottom}|}{|\meta{name}|}|
+% \quad |\showfeaturestylename{|\meta{ttttop...bbbbottom}|}{|\meta{name}|}|
% \medskip
%
-% \quad |\hidefeaturename{|\meta{ttop/top/bottom/bbottom}|}|
+% \quad |\hidefeaturename{|\meta{ttttop...bbbbottom}|}|
% \medskip
%
-% \quad |\hidefeaturestylename{|\meta{ttop/top/bottom/bbottom}|}|
+% \quad |\hidefeaturestylename{|\meta{ttttop...bbbbottom}|}|
% \medskip
%
% \quad |\hidefeaturenames|, and |\hidefeaturestylenames|.
@@ -3619,10 +3749,10 @@
% or individually with \label{Lfeaturenamecolor}
% \medskip
%
-% \quad |\featurenamecolor{|\meta{ttop/top/bottom/bbottom}|}{|\meta{color}|}| and \label{Lfeaturestylenamecolor}
+% \quad |\featurenamecolor{|\meta{ttttop...bbbbottom}|}{|\meta{color}|}| and \label{Lfeaturestylenamecolor}
% \medskip
%
-% \quad |\featurestylenamecolor{|\meta{ttop/top/bottom/bbottom}|}{|\meta{color}|}|
+% \quad |\featurestylenamecolor{|\meta{ttttop...bbbbottom}|}{|\meta{color}|}|
% \medskip
%
% See section \ref{colors} for how to select colors in \TeX{}shade.
@@ -3645,6 +3775,13 @@
% \quad|\feature{bottom}{1}{98..98}{fill:$\uparrow$}{second...}|
% \medskip
%
+% \emph{T-Coffee mode} (\ref{TCoffee}): |T-Coffee| color scale
+%
+% \quad|\feature{top}{1}{30..63}{color:conservation[T-Coffee]}{}|
+%
+% \quad|\showfeaturestylename{bottom}{cons}|
+% \medskip
+%
% \emph{diversity mode} (\ref{diverse}): frames, text only
%
% \quad|\feature{top}{1}{77..109}{}{AQP2 species variants}|
@@ -4530,6 +4667,7 @@
% \meta{mode} & \meta{option} &\\ \hline
% |identical| & |allmatchspecial/number| &\\
% |similar| & |allmatchspecial/number| &\\
+% |T-Coffee| & \meta{filename} &\\
% |diverse| & \meta{seqref} &\\
% |functional|& \meta{type} & |charge| \\
% & & |hydropathy| \\
@@ -4745,7 +4883,7 @@
% \quad|\showresidues|
% \hfill[\pageref{Lshowresidues}]
%
-% \quad|\startnumber{|\meta{seqref}|}{|\meta{first residue number}|}|
+% \quad|\startnumber[|\meta{start..stop}|]{|\meta{seqref}|}{|\meta{startnumber}|}|
% \hfill[\pageref{Lstartnumber}]
%
% \quad|\allowzero|
@@ -4757,7 +4895,7 @@
% \quad|\seqlength{|\meta{seqref}|}{|\meta{length}|}|
% \hfill[\pageref{Lseqlength}]
%
-% \quad|\setends{|\meta{seqref}|}{|\meta{startnumber}|..|\meta{stopnumber}|}|
+% \quad|\setends[|\meta{startnumber}|]{|\meta{seqref}|}{|\meta{start..stop}|}|
% \hfill[\pageref{Lsetends}]
%
% \quad|\showruler[|\meta{color}|]{|\meta{top/bottom}|}{|\meta{seqref}|}|
@@ -4995,16 +5133,16 @@
% \> = |{vertical}|
% \end{tabbing}
%
-% \quad |\showfeaturename{|\meta{ttop/top/bottom/bbottom}|}{|\meta{name}|}|
+% \quad |\showfeaturename{|\meta{ttttop...bbbbottom}|}{|\meta{name}|}|
% \hfill[\pageref{Lshowfeaturename}]
%
-% \quad |\showfeaturestylename{|\meta{ttop/\ldots/bbottom}|}{|\meta{name}|}|
+% \quad |\showfeaturestylename{|\meta{ttttop...bbbbottom}|}{|\meta{name}|}|
% \hfill[\pageref{Lshowfeaturestylename}]
%
-% \quad |\hidefeaturename{|\meta{ttop/top/bottom/bbottom}|}|
+% \quad |\hidefeaturename{|\meta{ttttop...bbbbottom}|}|
% \hfill[\pageref{Lhidefeaturename}]
%
-% \quad |\hidefeaturestylename{|\meta{ttop/top/bottom/bbottom}|}|
+% \quad |\hidefeaturestylename{|\meta{ttttop...bbbbottom}|}|
% \hfill[\pageref{Lhidefeaturestylename}]
%
% \quad |\hidefeaturenames|
@@ -5019,10 +5157,10 @@
% \quad |\featurestylenamescolor{|\meta{color}|}|
% \hfill[\pageref{Lfeaturestylenamescolor}]
%
-% \quad |\featurenamecolor{|\meta{ttop/top/bottom/bbottom}|}{|\meta{color}|}|
+% \quad |\featurenamecolor{|\meta{ttttop...bbbbottom}|}{|\meta{color}|}|
% \hfill[\pageref{Lfeaturenamecolor}]
%
-% \quad |\featurestylenamecolor{|\meta{ttop/\ldots/bbottom}|}{|\meta{color}|}|
+% \quad |\featurestylenamecolor{|\meta{ttttop...bbbbottom}|}{|\meta{color}|}|
% \hfill[\pageref{Lfeaturestylenamecolor}]
%
% \vspace{1.5\baselineskip}
@@ -5380,6 +5518,7 @@
\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
@@ -5387,6 +5526,8 @@
\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
@@ -5397,8 +5538,12 @@
\newif\ifregionalshadenow
\newif\iftopfeaturenow
\newif\ifttopfeaturenow
+\newif\iftttopfeaturenow
+\newif\ifttttopfeaturenow
\newif\ifbottomfeaturenow
\newif\ifbbottomfeaturenow
+\newif\ifbbbottomfeaturenow
+\newif\ifbbbbottomfeaturenow
\newif\ifframenow
\newif\iffix@
@@ -6097,6 +6242,17 @@
\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}
@@ -6188,6 +6344,16 @@
\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}
@@ -6279,6 +6445,16 @@
\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}
@@ -6371,6 +6547,16 @@
\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}
@@ -6686,6 +6872,16 @@
\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,@}
@@ -6737,10 +6933,18 @@
\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
@@ -6782,10 +6986,18 @@
\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}
@@ -7061,10 +7273,18 @@
\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}
@@ -7868,6 +8088,97 @@
\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}
@@ -9158,10 +9469,18 @@
\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@
@@ -9226,6 +9545,10 @@
\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@
@@ -9270,6 +9593,11 @@
\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}
@@ -9290,6 +9618,11 @@
\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@
@@ -9313,9 +9646,11 @@
\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}
@@ -9375,8 +9710,12 @@
\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}}
@@ -9400,6 +9739,7 @@
\fi
\fi}
\newcommand{\shadingmode}[2][-1]{%
+ \T@coffeefalse
\xdef\last@{#2}
\xdef\first@{identical}
\ifx\first@\last@
@@ -9445,6 +9785,12 @@
\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}
@@ -9463,7 +9809,7 @@
\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}
@@ -9480,8 +9826,8 @@
\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'>}
@@ -9491,14 +9837,14 @@
\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
@@ -9506,20 +9852,21 @@
\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@
@@ -9527,6 +9874,7 @@
\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@
@@ -10491,16 +10839,24 @@
\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}}
@@ -10611,6 +10967,9 @@
\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}}
@@ -11669,6 +12028,66 @@
\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
@@ -12089,6 +12508,18 @@
\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
}
@@ -12989,10 +13420,15 @@
\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
@@ -13009,9 +13445,13 @@
\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}
@@ -13075,6 +13515,14 @@
\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}
@@ -13083,6 +13531,14 @@
\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
@@ -13108,6 +13564,30 @@
\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}
@@ -13132,6 +13612,30 @@
\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{%
@@ -13151,6 +13655,14 @@
\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}
@@ -13159,6 +13671,14 @@
\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 -}
@@ -13167,6 +13687,14 @@
\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 -}
@@ -13175,6 +13703,14 @@
\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
@@ -13212,6 +13748,18 @@
\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
@@ -13224,6 +13772,18 @@
\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
@@ -13260,10 +13820,14 @@
\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
@@ -13279,13 +13843,16 @@
\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
@@ -13297,10 +13864,14 @@
\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}
@@ -13315,6 +13886,10 @@
\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}
@@ -13339,6 +13914,10 @@
\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}
@@ -13354,8 +13933,10 @@
\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
@@ -13422,6 +14003,28 @@
\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
@@ -13444,12 +14047,35 @@
\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
@@ -13548,6 +14174,28 @@
\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
@@ -13570,6 +14218,28 @@
\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}
@@ -13588,6 +14258,115 @@
\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
@@ -13682,6 +14461,7 @@
\newline\hbox{}\noindent
\fi
\fi
+ \fi
}
\def\put@name<#1>#2@{%
\ifnames@%
@@ -13729,6 +14509,13 @@
\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}%
@@ -13754,7 +14541,7 @@
\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@%
@@ -13791,20 +14578,48 @@
\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}%
@@ -13823,7 +14638,7 @@
\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@%
@@ -14102,9 +14917,19 @@
\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@%
@@ -14169,12 +14994,15 @@
\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}%
@@ -14204,7 +15032,13 @@
{\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%
@@ -14339,7 +15173,13 @@
\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@@ ,%
@@ -14568,12 +15408,46 @@
\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%
@@ -14583,14 +15457,14 @@
\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%
@@ -14600,12 +15474,12 @@
\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%
@@ -14615,14 +15489,14 @@
\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%
@@ -14632,14 +15506,31 @@
\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%
@@ -14649,12 +15540,29 @@
\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 @}%
@@ -14665,8 +15573,8 @@
\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{%
@@ -15298,10 +16206,32 @@
\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}%
@@ -15464,12 +16394,56 @@
\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
@@ -15491,6 +16465,10 @@
\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@
@@ -15573,15 +16551,23 @@
\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{%
@@ -15673,7 +16659,12 @@
\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
@@ -15717,7 +16708,12 @@
\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
@@ -15858,8 +16854,12 @@
\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}
@@ -15871,6 +16871,7 @@
\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}
@@ -15882,8 +16883,12 @@
\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}
@@ -15925,10 +16930,14 @@
\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}
@@ -15972,17 +16981,18 @@
\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
@@ -16192,23 +17202,29 @@
\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}
@@ -16218,23 +17234,36 @@
\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}
@@ -16283,6 +17312,7 @@
\xdef\divref@{0}
\xdef\all@thresh@ld{100} \all@shadefalse
\hidefeaturenames \hidefeaturestylenames
+\xdef\T@coffee@ccons{n} \xdef\T@coffee@bcons{n}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%% %%%%%
@@ -16824,7 +17854,7 @@ AQP5.PRO MK........................KEVCSLAFFKAVFAEFLATLIFVFFGLGSALKWP
61 120
AQP1.PRO YPLERNQTLVQDNVKVSLAFGLSIATLAQSVGHISGAHSNPAVTLGLLLSCQISILRAVM
AQP2.PRO ...SS....PPSVLQIAVAFGLGIGILVQALGHVSGAHINPAVTVACLVGCHVSFLRAAF
-AQP3.PRO LSRGTHGGF....LTINLAFGFAVTLAILVAGQVSGAHLNPAVTFAMCFLAREPWIKLPI
+AQP3.PRO LSRGTH....GGFLTINLAFGFAVTLAILVAGQVSGAHLNPAVTFAMCFLAREPWIKLPI
AQP4.PRO ...GSENPLPVDMVLISLCFGLSIATMVQCFGHISGGHINPAVTVAMVCTRKISIAKSVF
AQP5.PRO ...SA....LPTILQISIAFGLAIGTLAQALGPVSGGHINPAITLALLIGNQISLLRAVF
@@ -19070,6 +20100,70 @@ The best path:
%</AQPHMMext>
% \end{macrocode}
% \begin{macrocode}
+%<*TCoffee>
+T-COFFEE, Version_5.31(Fri Oct 26 17:01:36 2007)
+Cedric Notredame
+CPU TIME:1 sec.
+SCORE=54
+*
+ BAD AVG GOOD
+*
+AQP1.PRO : 55
+AQP2.PRO : 58
+AQP3.PRO : 46
+AQP4.PRO : 55
+AQP5.PRO : 58
+cons : 54
+
+AQP1.PRO 1 65------------------------3777666677777766666666556666666554 36
+AQP2.PRO 1 -2------------------------2776667777777777777667666666666654 35
+AQP3.PRO 1 5---------9644-----33322111------457777665555556555657555544 40
+AQP4.PRO 1 63DGAAARRW9644PPCSR33322113667667677777666666666666767666665 60
+AQP5.PRO 1 65------------------------4877667667777777776666666667666665 36
+cons 1 54--------9644-----33322113777667667777766666666666666666554 60
+
+
+AQP1.PRO 37 111221111223454555555555444444444554455555555544544445555444 96
+AQP2.PRO 36 ---33----323444444444444444454444455556666555555555455565555 88
+AQP3.PRO 41 111211----11444444444433333232333344455565555544444445555444 96
+AQP4.PRO 61 ---331111223554555555544444454455555666666666555555455555555 117
+AQP5.PRO 37 ---43----323555555555554444454455555555666555555555555565555 89
+cons 61 111331111323454545444444444444444455555665555555555455555555 120
+
+
+AQP1.PRO 97 5555555556555655555----------4444445555555555555555-----5555 141
+AQP2.PRO 89 6556666666666665555----------5555555566666666666666-----5556 133
+AQP3.PRO 97 4445555555555554443YYDAIWAFAG2322222333333344443454LDMVN4445 156
+AQP4.PRO 118 5556666666666665544----------4445545555555555665666-----6666 162
+AQP5.PRO 90 5555555556666665554----------4455555666666666666677-----6676 134
+cons 121 5555556666666655554----------4444444555555555555566-----5566 180
+
+
+AQP1.PRO 142 6677777777777766666666-5666656666666555666556677777778777766 200
+AQP2.PRO 134 5566777777777766666555-5565556666666555556556788888888888777 192
+AQP3.PRO 157 7666777777777777765444V3454455554444322222224577777777777665 216
+AQP4.PRO 163 7777777777777777776666-5555555555666555555555677777777777766 221
+AQP5.PRO 135 7777888788887777776666-5666666666666555555556677777777777776 193
+cons 181 7677777777777777666555-5565555565556544555555677777777777766 240
+
+
+AQP1.PRO 201 7766--666---------66666666665555666666555566544455555220111- 248
+AQP2.PRO 193 7766--666---------6666666665555555555555556664456666633-222- 239
+AQP3.PRO 217 5544LA2220EVFTTGQN223333434333334433332322------------------ 258
+AQP4.PRO 222 6555--555---------55655666656666655555555454-33345544100111- 268
+AQP5.PRO 194 6666--5440--------5555556655555555555544445664444555533-222T 242
+cons 241 6665--5550--------55555555555555555555444455544455555220221- 300
+
+
+AQP1.PRO 249 22222--2111111111----11000----------------------------3 269
+AQP2.PRO 240 33333--42222222223--3333333233322-------------------223 271
+AQP3.PRO 259 --------------------2111222122211122-111112221-------12 285
+AQP4.PRO 269 11111KG22111111123VE3222333233322122D111112221SSGEVL224 323
+AQP5.PRO 243 23333--33222223334--3333333---------------------------- 265
+cons 301 23322--32222222223--3222223233322122-111112221------223 355
+%</TCoffee>
+% \end{macrocode}
+% \begin{macrocode}
%<*Standard>
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%% %%%%%
diff --git a/Master/texmf-dist/source/latex/texshade/texshade.ins b/Master/texmf-dist/source/latex/texshade/texshade.ins
index 26560329661..7f548d9cdb8 100644
--- a/Master/texmf-dist/source/latex/texshade/texshade.ins
+++ b/Master/texmf-dist/source/latex/texshade/texshade.ins
@@ -1,7 +1,7 @@
%%
%% docstrip install file for texshade.sty
%%
-%% Copyright 1999-2007 Eric Beitz
+%% Copyright 1999-2008 Eric Beitz
%%
\def\batchfile{texshade.ins}
@@ -31,6 +31,7 @@ See the file texshade.txt
\file{AQP1.phd}{\from{texshade.dtx}{AQP1PHD}}
\file{AQP_HMM.sgl}{\from{texshade.dtx}{AQPHMMsgl}}
\file{AQP_HMM.ext}{\from{texshade.dtx}{AQPHMMext}}
+ \file{AQP_TC.asc}{\from{texshade.dtx}{TCoffee}}
\file{standard.cod}{\from{texshade.dtx}{Standard}}
\file{ciliate.cod}{\from{texshade.dtx}{Ciliate}}}
generated by cgit v1.2.3 (git 2.39.1) at 2024-11-20 16:20:13 +0000