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authorKarl Berry <karl@freefriends.org>2009-03-09 23:14:54 +0000
committerKarl Berry <karl@freefriends.org>2009-03-09 23:14:54 +0000
commit5a93e784e01b2dc5b07c6fe841e31e90eff72f4a (patch)
tree05285154adeba332bb2d3a93c7068052407a2833 /Master/texmf-dist
parente02a26695ee487b4e603f07117207e454665a0a4 (diff)
texshade 1.19 (9mar09)
git-svn-id: svn://tug.org/texlive/trunk@12351 c570f23f-e606-0410-a88d-b1316a301751
Diffstat (limited to 'Master/texmf-dist')
-rw-r--r--Master/texmf-dist/doc/latex/texshade/README9
-rw-r--r--Master/texmf-dist/doc/latex/texshade/texshade.pdfbin640261 -> 660034 bytes
-rw-r--r--Master/texmf-dist/source/latex/texshade/texshade.dtx2043
-rw-r--r--Master/texmf-dist/source/latex/texshade/texshade.ins4
-rw-r--r--Master/texmf-dist/tex/latex/texshade/texshade.def6
-rw-r--r--Master/texmf-dist/tex/latex/texshade/texshade.sty1483
6 files changed, 2533 insertions, 1012 deletions
diff --git a/Master/texmf-dist/doc/latex/texshade/README b/Master/texmf-dist/doc/latex/texshade/README
index bb80eed3bd1..a766b4725a2 100644
--- a/Master/texmf-dist/doc/latex/texshade/README
+++ b/Master/texmf-dist/doc/latex/texshade/README
@@ -1,4 +1,4 @@
- TeXshade v1.18
+ TeXshade v1.19
>>
>> A LaTeX package for setting nucleotide and peptide alignments.
>>
@@ -26,7 +26,7 @@
>> ding modes. TeXshade combines highest flexibility and the
>> habitual TeX output quality--with reasonable time expenditure.
>>
- Copyright (C) 1999 - 2008 Eric Beitz
+ Copyright (C) 1999 - 2009 Eric Beitz
@@ -51,9 +51,12 @@
texshade.def Standard definitions
AQPDNA.MSF Example nucleotide alignment file (MSF-format)
AQPpro.MSF Example protein alignment file (MSF-format)
+ AQP_TC.asc Example T-Coffee shading file
AQP2spec.ALN Example protein alignment file (ALN-format)
AQP1.top Example topology data file generated from PHD
AQP1.phd Example PHD secondary structure file
+ AQP1_HMM.sgl Example HMMTOP topology data (single line format)
+ AQP1_HMM.ext Example HMMTOP topology data (extended format)
Standard.cod Standard genetic code definitions
Ciliate.cod Ciliate macronuclear genetic code definitions
@@ -125,7 +128,7 @@
3 - CONTACT
E-Mail: ebeitz@pharmazie.uni-kiel.de
- WWW: http://www.pharmazie.uni-kiel.de/chem/Prof_Beitz/biotex.html
+ WWW: http://www.pharmazie.uni-kiel.de/chem/
(On-line documentation and updates)
Address: Eric Beitz, University of Kiel, Pharmaceutical Chemistry,
Gutenbergstrasse 76, D-24118 Kiel (Germany)
diff --git a/Master/texmf-dist/doc/latex/texshade/texshade.pdf b/Master/texmf-dist/doc/latex/texshade/texshade.pdf
index 1b47c480cdc..012391e2322 100644
--- a/Master/texmf-dist/doc/latex/texshade/texshade.pdf
+++ b/Master/texmf-dist/doc/latex/texshade/texshade.pdf
Binary files differ
diff --git a/Master/texmf-dist/source/latex/texshade/texshade.dtx b/Master/texmf-dist/source/latex/texshade/texshade.dtx
index 61e88ddf8d0..3fe76ed81cf 100644
--- a/Master/texmf-dist/source/latex/texshade/texshade.dtx
+++ b/Master/texmf-dist/source/latex/texshade/texshade.dtx
@@ -7,10 +7,10 @@
% first run the file `texshade.ins' through LaTeX. This produces
% the needed style file `texshade.sty' and the parameter file
% `texshade.def' as well as several example files. See the file
-% `texshade.txt' for further information!
+% `README' for further information!
%
%
-% Copyright (C) 1999-2008 Eric Beitz
+% Copyright (C) 1999-2009 Eric Beitz
% See the file texshade.txt
%
% \fi
@@ -308,12 +308,10 @@
%
%
% \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
+% Corrections: bug fixes (featurenames, ordering, numbering).
+% Introduction: T-Coffee shading in alignment, consensus and
+% feature color scales and bar graphs
+% `shadingmode[ASCII-file]{T-Coffee}'
% `includeTCoffee';
% two more feature lines on top and at bottom:
% `ttttop', `tttop', `bbbottom', and `bbbbottom';
@@ -321,6 +319,22 @@
% via optional parameters.
% }
%
+% \changes{1.19}{2009-03-09}{%
+% Corrections: horizontal scaling of logo characters with `charstretch';
+% further bug fixes.
+% Introduction: selection of residues depending on PDB file coordinates;
+% works with `feature', `shaderegion', `shadeblock',
+% `tintregion', `tintblock', `emphregion',
+% `emphblock', `frameblock';
+% 3D selection possible around a point, along a line, or
+% within a plane;
+% list of selected residues printable with `printPDBlist',
+% or viewable during the TeX run with `messagePDBlist';
+% show only selected residues in alignment with `setdomain',
+% `domaingaprule' sets thickness of a domain separator rule,
+% `domaingapcolors' sets fg/bg colors for the separator rule,
+% these commands replace the unstable `hideblock' command.
+% }
%
%
%
@@ -361,7 +375,7 @@
% for further information, updates and on-line documentation
% see my homepage at
% \texttt{www.pharmazie.uni-kiel.de/chem/Prof\_Beitz/biotex.html} }}
-% \date{v1.18; 2008/04/15\\}
+% \date{\small v1.19; 2009/03/09\\[2pt] {*** incredible 10 years since first release ***}}
% \maketitle
% \begin{abstract}
% Setting alignments of nucleotides and peptides for publication
@@ -440,6 +454,29 @@
%
% \subsection{Version History}
%
+% \textbf{v1.19 2009/03/09}
+% \medskip
+%
+% \emph{Correction:} logo characters are now horizontally
+% scalable using |\charstretch|. Minor bugs were fixed.
+%
+% \emph{Introduction:}
+% (a) Selection of residue positions was enhanced (\ref{Lshaderegion})
+% \TeXshade{} can
+% now select residues based on their 3D coordinates provided in a
+% PDB structure file. 3D selection can be due to a certain distance
+% around a point, along a line, or above and below a plane. It
+% works with |\feature|, |\shaderegion|, |\shadeblock|, |\tintregion|,
+% |\tintblock|, |\emphregion|, |\emphblock|, |\frameblock|.
+% (b) The list of selected residues is printable with |\printPDBlist| or
+% viewable during the \TeX{} run with |\messagePDBlist|.
+% (c) |\hideblock| and related commands were replaced by |\setdomain|
+% (\ref{Lsetdomain}).
+% This command will display only selected residues in the alignment.
+% Thickness and colors of a domain separator rule can be set using
+% |\domaingaprule| and |\domaingapcolors|.
+% \bigskip
+%
% \textbf{v1.18 2008/04/15}
% \medskip
%
@@ -458,8 +495,6 @@
% end definitions of the sequence section to be displayed.
% \bigskip
%
-% \newpage
-%
% \textbf{v1.17 2007/06/19}
% \medskip
%
@@ -482,7 +517,7 @@
% \bigskip
%
%
-% \textbf{v1.17 2007/06/19}
+% \textbf{v1.16 2007/02/18}
% \medskip
%
% \emph{Correction:} \TeXshade{} crashed when calculating conservation
@@ -547,6 +582,8 @@
% implemented, i.e. subfamily logos (p.\pageref{Lshowsubfamilylogo}) [14].
% \bigskip
%
+% \newpage
+%
% \textbf{v1.12 2005/09/20}
% \medskip
%
@@ -598,6 +635,8 @@
% bar graphs and color scales.
% \bigskip
%
+% \newpage
+%
% \textbf{v1.9 2005/02/08}
% \medskip
%
@@ -652,6 +691,8 @@
% A new feature label style |helix| has been introduced.
% \bigskip
%
+% \newpage
+%
% \textbf{v1.6 2002/03/26}
% \medskip
%
@@ -764,6 +805,8 @@
% `|\Alphacount|'. All commands are described in \ref{structure}.
% \bigskip
%
+% \newpage
+%
% \textbf{v1.1 1999/5/26}
% \medskip
%
@@ -1020,6 +1063,57 @@
% \end{verbatim}
% }
%
+% Quite uncommon for an alignment shading software is the possibility
+% to display selected residues only, e.\,g.\ to eliminate uninteresting
+% positions from the output:
+% \medskip
+%
+% \begin{texshade}{AQPpro.MSF}
+% \setdomain{1}{80..90,100..110,120..130}
+% \showruler{1}{top}
+% \hidenumbering
+% \hideconsensus
+% \end{texshade}
+%
+% Code:\medskip
+%
+% \vbox{%
+% \begin{verbatim}
+% \begin{texshade}{AQPpro.MSF}
+% \setdomain{1}{80..90,100..110,120..130}
+% \showruler{1}{top}
+% \hidenumbering
+% \hideconsensus
+% \end{texshade}
+% \end{verbatim}
+% }
+%
+% This goes even furher. You can have \TeXshade{} select positions
+% based on the 3D coordinates provided by a PDB file, e.\,g.\ show
+% all residues that are within an 8 \AA{} radius around the
+% $\alpha$-carbon of the residue at position 81:
+% \bigskip
+%
+% \begin{texshade}{AQPpro.MSF}
+% \setdomain{1}{75..86,103..103,148..148,151..153,155..156,193..195,218..219,222..222}
+% \showruler{1}{top} \rulersteps{1}
+% \hidenumbering
+% \hideconsensus
+% \end{texshade}
+%
+% Code:\medskip
+%
+% \vbox{%
+% \begin{verbatim}
+% \begin{texshade}{AQPpro.MSF}
+% \setdomain{1}{point[8]:1J4N.pdb,81[CA]}
+% \showruler{1}{top} \rulersteps{1}
+% \hidenumbering
+% \hideconsensus
+% \end{texshade}
+% \end{verbatim}
+% }
+%
% If you like, positions where conservation is very high (here $\ge$ 80\%) can
% be shaded in a special color and the consensus can be shown with
% or without shading according to the degree of conservation:
@@ -1117,7 +1211,6 @@
% \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}
@@ -1130,7 +1223,6 @@
% \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}
@@ -1157,7 +1249,6 @@
% \medskip
%
% \begin{texshade}{AQP2spec.ALN}
-% \seqtype{P}
% \shadingmode{diverse}
% \setends{1}{77..109} \residuesperline*{33}
% \featureslarge
@@ -1179,7 +1270,6 @@
% \vbox{%
% \begin{verbatim}
% \begin{texshade}{AQP2spec.ALN}
-% \seqtype{P}
% \shadingmode{diverse}
% \setends{1}{77..109}
% \featureslarge
@@ -2124,7 +2214,7 @@
% conserved residues, e.\,g.\ |\shadingmode[90]{identical}|.
% \label{Lallmatchspecial}|\allmatchspecial| can also be
% used as a command with or without an optional parameter for
-% setting the high conservation threshold. As both, option or command
+% setting the high conservation threshold. As both, option or command,
% |allmatchspecial| is only active in the \emph{identical} and
% \emph{similar} shading modes.
%
@@ -2871,6 +2961,58 @@
% residues long.
%
%
+% \label{Lshowruler}\label{Lhideruler}
+% \label{Lrulersteps}\label{Lrulercolor}
+% \label{Lrotateruler}\label{Lunrotateruler}
+% \label{Lnamerulerpos}
+% Another possibility to label sequence positions is to switch
+% on a ruler on the top or at the bottom of the sequence block
+% using \label{ruler}
+% |\showruler[|\meta{color}|]{|\meta{position}|}{|\meta{seqref}|}|.
+% The residue ruler of one sequence \meta{seqref} or the consensus
+% (declare `|consensus|' as \meta{seqref}) can be
+% displayed at \meta{position} |top| or |bottom|.
+% The ruler is hidden with |\hideruler|. The steps between two
+% numbers are set by |\rulersteps{|\meta{number}|}|. If the steps
+% are set to be very close ($< 4$) or when every position is numbered, the
+% numbering is automatically rotated by 90$^\circ$. Using |\rotateruler|
+% and |\unrotateruler| this can be done and undone manually.
+% In order to change the
+% ruler color use the optional parameter or the command
+% |\rulercolor{|\meta{color}|}|. Also, the label and its color at individual
+% ruler positions can be changed by the user to a string using
+% |\namerulerpos{|\meta{number}|}{|\meta{text}|[|\meta{color}|]}|
+% (see example on p.\ \pageref{ras}).
+%
+% \label{Lgapchar}\label{Lgaprule}
+% \label{Lgapcolors}\label{gapchar}
+% Further, the symbol which is displayed in sequence gaps is freely
+% selectable with
+% |\gapchar{|\meta{symbol}|}|. \meta{symbol} can be any character
+% or symbol. If math symbols are to be used math mode must be
+% activated by |$| characters, i.\,e. |\gapchar{{$\triangle$}}|.
+% Note the double curly braces in the last command. Everytime a
+% `complex' character is used, i.\,e. a character definition consisting
+% of more than one letter, it must be braced in order to be interpreted as one
+% character. One exception is |\gapchar{rule}|; with this
+% parameter lines are drawn in the sequence gaps with a certain
+% thickness defined by |\gaprule{|\meta{thickness}|}|, e.\,g.
+% |\gaprule{1.5pt}|. The colors of the gaps and gap symbols are set by
+% |\gapcolors{|\meta{symbol color}|}{|\meta{background color}|}|.
+%
+% There are some discussions whether or not to display gap symbols before
+% and after the actual sequence. Since v1.3a one can control the
+% appearance of those gap symbols by the commands
+% \label{Lshowleadinggaps} \label{Lhideleadinggaps}
+% |\showleadinggaps| and |\hideleadinggaps|. By default, leading
+% gaps are indicated by symbols despite my personal
+% thinking that it could suggest that
+% there are some not displayed residues upstream resp.\ downstream of the
+% gap.
+%
+%
+% \subsubsection{Displaying selected residues in the alignment}
+%
% \label{Lsetends}
% \TeXshade{} can display a section of the complete alignment
% without the need to edit the alignment input file or even
@@ -2932,55 +3074,64 @@
% sequence alignment because the consensus counts every position
% including gaps.
%
-% \label{Lshowruler}\label{Lhideruler}
-% \label{Lrulersteps}\label{Lrulercolor}
-% \label{Lrotateruler}\label{Lunrotateruler}
-% \label{Lnamerulerpos}
-% Another possibility to label sequence positions is to switch
-% on a ruler on the top or at the bottom of the sequence block
-% using \label{ruler}
-% |\showruler[|\meta{color}|]{|\meta{position}|}{|\meta{seqref}|}|.
-% The residue ruler of one sequence \meta{seqref} or the consensus
-% (declare `|consensus|' as \meta{seqref}) can be
-% displayed at \meta{position} |top| or |bottom|.
-% The ruler is hidden with |\hideruler|. The steps between two
-% numbers are set by |\rulersteps{|\meta{number}|}|. If the steps
-% are set to be very close ($< 4$) or when every position is numbered, the
-% numbering is automatically rotated by 90$^\circ$. Using |\rotateruler|
-% and |\unrotateruler| this can be done and undone manually.
-% In order to change the
-% ruler color use the optional parameter or the command
-% |\rulercolor{|\meta{color}|}|. Also, the label and its color at individual
-% ruler positions can be changed by the user to a string using
-% |\namerulerpos{|\meta{number}|}{|\meta{text}|[|\meta{color}|]}|
-% (see example on p.\ \pageref{ras}).
+% \label{Lsetdomain}
+% The output can be even further restricted to
+% individually selected residues, e.g.\ to eliminate uninteresting alignment stretches or
+% to condense the output, by:
+% \medskip
%
-% \label{Lgapchar}\label{Lgaprule}
-% \label{Lgapcolors}\label{gapchar}
-% Further, the symbol which is displayed in sequence gaps is freely
-% selectable with
-% |\gapchar{|\meta{symbol}|}|. \meta{symbol} can be any character
-% or symbol. If math symbols are to be used math mode must be
-% activated by |$| characters, i.\,e. |\gapchar{{$\triangle$}}|.
-% Note the double curly braces in the last command. Everytime a
-% `complex' character is used, i.\,e. a character definition consisting
-% of more than one letter, it must be braced in order to be interpreted as one
-% character. One exception is |\gapchar{rule}|; with this
-% parameter lines are drawn in the sequence gaps with a certain
-% thickness defined by |\gaprule{|\meta{thickness}|}|, e.\,g.
-% |\gaprule{1.5pt}|. The colors of the gaps and gap symbols are set by
-% |\gapcolors{|\meta{symbol color}|}{|\meta{background color}|}|.
+% \quad|\setdomain{|\meta{seqref}|}{|\meta{selection}|}|
+% \medskip
%
-% There are some discussions whether or not to display gap symbols before
-% and after the actual sequence. Since v1.3a one can control the
-% appearance of those gap symbols by the commands
-% \label{Lshowleadinggaps} \label{Lhideleadinggaps}
-% |\showleadinggaps| and |\hideleadinggaps|. By default, leading
-% gaps are indicated by symbols despite my personal
-% thinking that it could suggest that
-% there are some not displayed residues upstream resp.\ downstream of the
-% gap.
+% Here, \meta{seqref} denotes the reference sequence by its number or name.
+% This sequence is used to define the alignment positions \meta{selection}
+% to be shown.
+% \meta{selection} can have two different formats
+% depending on whether (a) the user wants to select the positions manually
+% or (b) \TeXshade{} is supposed to select the residues based on 3D
+% coordinates provided by a PDB file.
%
+% To select the residues manually, the user provides a position list of
+% the following format:
+% \medskip
+%
+% \quad|{|\meta{start1}..\meta{stop1}|,|\meta{start2}..\meta{stop2}|,|\ldots|,|\meta{start n}..\meta{stop n}|}|
+% \medskip
+%
+% For how to select positions by 3D coordinates
+% provided by a PDB file, see \ref{Lshaderegion}.
+% \medskip
+%
+% Examples (see also p.\,\pageref{ident}ff):
+%
+% \quad|\setdomain{1}{20..80}|
+%
+% \quad|\setdomain{consensus}{20..80,100..150,200..220}|
+%
+% \quad|\setdomain{AQP1}{point[6]:1FX8.pdb,173[side]}|
+%
+% \quad|\setdomain{3}{plane[0.5]:1JN4.pdb,66[CA],73[side],199[CA]}|
+% \medskip
+%
+%
+% It is helpful to show a ruler (probably single-stepped, see p.\,\pageref{Lshowruler}) to
+% label the residue positions.
+%
+% The resulting gaps between sequence stretches are marked by a vertical rule, which
+% can be changed in thickness by
+% \medskip
+%
+% \quad|\domaingaprule{|\meta{thickness}|}|, e.\,g.\
+% |\domaingaprule{1pt}|. \label{Ldomaingaprule}
+% \medskip
+%
+% Also, the colors can be set by
+% \medskip
+%
+% \quad|\domaingapcolors{|\meta{foreground}|}{|\meta{background}|}| \label{Ldomaingapcolors}
+% \medskip
+%
+% e.\,g.\ |\domaingapcolors{Blue}{Yellow}|.
%
%
% \subsubsection{Hiding, killing, separating and ordering}
@@ -3147,28 +3298,42 @@
%
% \subsection{Individual shading and labeling of sequence stretches}
%
-% Computer calculated alignment shading is informative---but
-% even more information can be visualized by manual labeling
+% Computer calculated conservation shading is informative---but
+% even more information can be visualized by additional labeling
% of positions and regions of interest with different colors,
% text styles or graphical marks and descriptive text. All this
% is provided by easy to handle \TeXshade{} commands.
%
%
-% \subsubsection{Manual shading of regions and blocks}
+% \subsubsection{Shading of regions and blocks}
% \label{shaderegion}
%
% \label{Lshaderegion}
% Besides the shading calculated by \TeXshade{} any region can be
-% shaded manually with a color specified by the user. This is very
+% additionally shaded with a color specified by the user. This is very
% useful to highlight secondary protein modification
-% sites such as phosphorylation or glycosylation sites or longer
-% motifs for example protein/protein interaction sites.
-% This is done by the use of the following command:
+% sites such as phosphorylation or glycosylation sites, or longer
+% motifs for example protein/protein interaction sites or protein domains.
+% This is done with the following command:
+% \medskip
+%
+% \quad|\shaderegion{|\meta{seqref}|}{|\meta{selection}|}{|\meta{res.col.}|}{|\meta{shad.col.}|}|
% \medskip
%
-% \quad|\shaderegion{|\meta{seqref}|}{|\meta{start1}..\meta{stop1}|,|\meta{start2}..\meta{stop2}|,|
+% Here, \meta{seqref} refers to the sequence by its name or number
+% within the alignment. The
+% foreground and background colors can be set with the last two
+% parameters.
+% \meta{selection} can have two different formats
+% depending on whether (a) the user wants to select the positions manually
+% or (b) \TeXshade{} is supposed to select the residues based on 3D
+% coordinates provided by a PDB file.
+%
+% To select the residues manually, the user provides a position list of
+% the following format:
+% \medskip
%
-% \hfill\ldots|,|\meta{start n}..\meta{stop n}|}{|\meta{res.col.}|}{|\meta{shad.col.}|}|
+% \quad|{|\meta{start1}..\meta{stop1}|,|\meta{start2}..\meta{stop2}|,|\ldots|,|\meta{start n}..\meta{stop n}|}|
% \medskip
%
% Example: in order to shade residue number 13 and the region
@@ -3181,22 +3346,80 @@
%
% If the consensus is to be shaded use |consensus| as
% \meta{seqref}.
+% \medskip
+%
+% In order to select positions based on the 3D structure a PDB
+% structure file is required. \TeXshade{} can select residues within
+% a given distance in \AA{} around a point, along a line, or above and
+% below a plane, which are defined by one to three residues. The points
+% can be further specified to be the $\alpha$-carbon atom, i.\,e.\ the
+% protein backbone, or the most distant atom of the sidechain. Accordingly,
+% \meta{selection} has one of the formats:
+% \medskip
+%
+% \quad|{point[|\meta{dist}|]:|\meta{file}|,|\meta{num}|[CA/side]}|
+% \medskip
+%
+% \quad|{line[|\meta{dist}|]:|\meta{file}|,|\meta{num1}|[CA/side],|\meta{num2}|[CA/side]}|
+% \medskip
+%
+% \vbox{%
+% \quad|{plane[|\meta{dist}|]:|\meta{file}|,|\meta{num1}|[CA/side],|\meta{num2}|[CA/side],|
+% \medskip
+%
+% \hfill\meta{num3}|[CA/side]}|
+% }
+% \medskip
+%
+%
+% Example: in order to select and shade as above all residues that are within an 8\ \AA{}
+% sphere around the $\alpha$-carbon of residue 81 and the data are
+% provided in the PDB file |1J4N.pdb|, type:
+% \medskip
+%
+% \quad|\shaderegion{1}{point[8]:1J4N.pdb,81[CA]}{Red}{Green}|
+% \medskip
+%
+% Example: two points denote a line, hence, give two residues to select
+% everything within 1\ \AA{} along the line between the $\alpha$-carbon of
+% residue 81 and the sidechain of residue 168 with:
+% \medskip
+%
+% \quad|\shaderegion{1}{line[1]:1J4N.pdb,81[CA],168[side]}|
+% \medskip
+%
+% \hfill|{Red}{Green}|
+% \medskip
%
+% Definition of a plane follows the same format but requires three points.
+% If the optional parameters |[\meta{dist}]| and |[CA/side]| are not given,
+% \TeXshade{} assumes |[1]| and |[side]|, respectively.
+%
+% In case one needs the position numbers of the selected residues for usage
+% in other applications, those can be either printed in the \TeX{} document with
+% |\printPDBlist{|\meta{selection}|}| or shown during the \TeX{} run with
+% |\messagePDBlist{|\meta{selection}|}|. The commands can be used outside of the
+% \TeXshade{} environment. \label{LprintPDBlist}\label{LmessagePDBlist}
+%
+% Both selection formats, i.\,e. a manually given list and the 3D selection,
+% can be used with |\shadeblock| (see below),
+% |\tintregion|, |\tintblock|, |\emphregion|, |\emphblock|,
+% |\frameblock| (all in \ref{Lframeblock}), and |\feature| (\ref{Lfeature}).
+%
+%
% \label{Lshadeblock}
-% In analogy to |\shaderegion| which is restricted to one single
-% sequence |\shadeblock| shades the corresponding region in all
+% In analogy to |\shaderegion| which is restricted to a single
+% sequence, |\shadeblock| shades the corresponding region in all
% other sequences as well
% except the consensus. If also the consensus is to be shaded
% define the region using |consensus| as \meta{seqref}.
% \medskip
%
-% \quad|\shadeblock{|\meta{seqref}|}{|\meta{start1}..\meta{stop1}|,|\meta{start2}..\meta{stop2}|,|
-%
-% \hfill\ldots|,|\meta{start n}..\meta{stop n}|}{|\meta{res.col.}|}{|\meta{shad.col.}|}|
+% \quad|\shadeblock{|\meta{seqref}|}{|\meta{selection}|}{|\meta{res.col.}|}{|\meta{shad.col.}|}|
% \medskip
%
%
-% \subsubsection{Emphasizing and tinting regions and blocks}
+% \subsubsection{Emphasizing, tinting, and framing}
%
% \label{Lemphregion}\label{Lemphblock}
% If it is prefered to keep the calculated shading colors
@@ -3205,19 +3428,17 @@
% such regions:
% \medskip
%
-% \quad|\emphregion{|\meta{seqref}|}{|\meta{start1}..\meta{stop1}|,|\meta{start2}..\meta{stop2}|,|
-%
-% \hfill\ldots|,|\meta{start n}..\meta{stop n}|}|
+% \quad|\emphregion{|\meta{seqref}|}{|\meta{selection}|}|
% \medskip
%
% and
% \medskip
%
-% \quad|\emphblock{|\meta{seqref}|}{|\meta{start1}..\meta{stop1}|,|\meta{start2}..\meta{stop2}|,|
-%
-% \hfill\ldots|,|\meta{start n}..\meta{stop n}|}|
+% \quad|\emphblock{|\meta{seqref}|}{|\meta{selection}|}|
% \medskip
%
+% For the format possibilities of the \meta{selection} parameter please see \ref{Lshaderegion}.
+%
% \label{Lemphdefault}
% Which style \TeXshade{} uses for emphasizing regions is defined by
% |\emphdefault{|\meta{style}|}|. Default setting is the
@@ -3233,17 +3454,13 @@
% \pageref{hydro}):
% \medskip
%
-% \quad|\tintregion{|\meta{seqref}|}{|\meta{start1}..\meta{stop1}|,|\meta{start2}..\meta{stop2}|,|
-%
-% \hfill\ldots|,|\meta{start n}..\meta{stop n}|}|
+% \quad|\tintregion{|\meta{seqref}|}{|\meta{selection}|}|
% \medskip
%
% and
% \medskip
%
-% \quad|\tintblock{|\meta{seqref}|}{|\meta{start1}..\meta{stop1}|,|\meta{start2}..\meta{stop2}|,|
-%
-% \hfill\ldots|,|\meta{start n}..\meta{stop n}|}|
+% \quad|\tintblock{|\meta{seqref}|}{|\meta{selection}|}|
% \medskip
%
% \label{Ltintdefault}
@@ -3257,56 +3474,15 @@
% command:\footnote{Thanks to Alan Robinson for inspiration.}
% \medskip\label{Lframeblock}
%
-% \quad|\frameblock{|\meta{seqref}|}{|\meta{start1}..\meta{stop1}|,|\meta{start2}..\meta{stop2}|,|
-%
-% \hfill\ldots|,|\meta{start n}..\meta{stop n}|}{|\meta{color}|[|\meta{length}|]}|
+% \quad|\frameblock{|\meta{seqref}|}{|\meta{selection}|}{|\meta{color}|[|\meta{length}|]}|
% \medskip
%
% 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 (experimental!)}
-%
-% \label{Lhideblock}
-% \textit{Be aware that this feature is still highly experimental. There are many instances
-% in which this command fails. Please be patient until everything is fixed.}
%
-% Complete blocks of the alignment incl. all sequences, consensus and labels
-% can be hidden, e.g.\ to eliminate uninteresting alignment stretches or
-% to condense the output, by:
-% \medskip
-%
-% \quad|\hideblock{|\meta{seqref}|}{|\meta{start1}..\meta{stop1}|,|\meta{start2}..\meta{stop2}|,|
-%
-% \hfill\ldots|,|\meta{start n}..\meta{stop n}|}{|\meta{label}|[|\meta{color}|]}{|\meta{text}|[|\meta{color}|]}|
-% \medskip
-%
-% Here, \meta{seqref} denotes the sequence by its number of name
-% which is used to define the alignment positions \meta{start1}..\meta{stop1}
-% etc.\ to be hidden. A symbol can be displayed as a
-% \meta{label} of the alignment deletion, i.e.\ |circ|, |triangle|, |square|,
-% or |none|. A color can be assigned to the label by the optional parameter
-% \meta{color}. Further, an explanatory text can be displayed above the symbol
-% \meta{text} with an optional \meta{color}. For how to change the appearance
-% of the font see p.\pageref{Lsetfont}.
-% \medskip
-%
-% Examples:
%
-% \quad|\hideblock{1}{20..80}{circ}{condensed![Red]}|
-%
-% \quad|\hideblock{1}{20..80}{triangle[Red]}{hidden block}|
-%
-% \quad|\hideblock{AQP1}{20..80}{none[Blue]}{$\Delta$20-80)}|
-%
-% \quad|\hideblock{consensus}{20..80,100..150,200..220}{none}{}|
-% \medskip
%
-% It may be advisable to show a ruler (probably single-stepped, see p.\pageref{Lshowruler}) to
-% further indicate the alignment deletion. Make sure that there are no
-% feature definitions (also frames, emphs, shades, tints) starting or
-% ending within the hidden block. This may cause messy sequence labels.
-%
% \subsubsection{Graphical labeling of sequence features}
%
% \label{feature}
@@ -3317,9 +3493,7 @@
% text. It needs five parameters:
% \medskip
%
-% \quad|\feature{|\meta{position}|}{|\meta{seqref}|}{|\meta{start1}..\meta{stop1}|,|
-%
-% \quad\quad\meta{start2}..\meta{stop2}|,|\ldots|,|\meta{start n}..\meta{stop n}|}{|\meta{labelstyle}|}{|\meta{text}|}|
+% \quad|\feature{|\meta{position}|}{|\meta{seqref}|}{|\meta{selection}|}{|\meta{labelstyle}|}{|\meta{text}|}|
% \medskip
%
% In the following paragraphs all possible parameter settings of
@@ -3346,7 +3520,7 @@
% |\bottomspace{-0.1in}|.
%
% The argument \meta{seqref} and the third
-% parameter containing the definitions of the specified regions
+% parameter containing the selection of the specified residues
% are identical to the ones described before in several commands, e.\,g.
% |\ruler| (\ref{ruler}) or |\shaderegion| (\ref{shaderegion}).
%
@@ -4895,9 +5069,6 @@
% \quad|\seqlength{|\meta{seqref}|}{|\meta{length}|}|
% \hfill[\pageref{Lseqlength}]
%
-% \quad|\setends[|\meta{startnumber}|]{|\meta{seqref}|}{|\meta{start..stop}|}|
-% \hfill[\pageref{Lsetends}]
-%
% \quad|\showruler[|\meta{color}|]{|\meta{top/bottom}|}{|\meta{seqref}|}|
% \hfill[\pageref{Lshowruler}]
%
@@ -4936,6 +5107,23 @@
%
% \vspace{1.5\baselineskip}
%
+% \textbf{Displaying selected residues in the alignment}
+% \medskip
+%
+% \quad|\setends[|\meta{startnumber}|]{|\meta{seqref}|}{|\meta{start..stop}|}|
+% \hfill[\pageref{Lsetends}]
+%
+% \quad|\setdomain{|\meta{seqref}|}{|\meta{selection}|}| (see |\shaderegion| p.\,\pageref{Lshaderegion})
+% \hfill[\pageref{Lsetdomain}]
+%
+% \quad|\domaingaprule{|\meta{thickness}|}|
+% \hfill[\pageref{Lsetdomain}]
+%
+% \quad|\domaingapcolors{|\meta{foreground}|}{|\meta{background}|}|
+% \hfill[\pageref{Lsetdomain}]
+%
+% \vspace{1.5\baselineskip}
+%
% \textbf{Hiding, killing, separating and ordering}
% \medskip
%
@@ -5018,62 +5206,69 @@
%
% \vspace{1.5\baselineskip}
%
+% \newpage
+%
%
% \textbf{Individual shading and labeling of sequence stretches}
% \medskip
%
-% \quad|\shaderegion{|\meta{seqref}|}{|\meta{start1}..\meta{stop1}|,|\meta{start2}..\meta{stop2}|,|
+% \quad|\shaderegion{|\meta{seqref}|}{|\meta{selection}|}{|\meta{res.col.}|}{|\meta{shad.col.}|}|
+% \hfill[\pageref{Lshaderegion}]
+%
+% \medskip
%
-% \hfill\ldots|,|\meta{start n}..\meta{stop n}|}{|\meta{res.col.}|}{|\meta{shad.col.}|}|
-% [\pageref{Lshaderegion}]
+% \quad |{|\meta{selection}|}| =
+% \medskip%
%
-% \newpage
+% \quad\quad|{|\meta{start1}..\meta{stop1}|,|\meta{start2}..\meta{stop2}|,|\ldots|,|\meta{start n}..\meta{stop n}|}|
+% \medskip
+%
+% \quad\quad|{point[|\meta{dist}|]:|\meta{file}|,|\meta{num}|[CA/side]}|
+% \medskip
+%
+% \quad\quad|{line[|\meta{dist}|]:|\meta{file}|,|\meta{num1}|[CA/side],|\meta{num2}|[CA/side]}|
+% \medskip
+%
+% \quad\quad|{plane[|\meta{dist}|]:|\meta{file}|,|\meta{num1}|[CA/side],|\meta{num2}|[CA/side],|
+% \medskip
%
-% \quad|\shadeblock{|\meta{seqref}|}{|\meta{start1}..\meta{stop1}|,|\meta{start2}..\meta{stop2}|,|
+% \hfill\meta{num3}|[CA/side]}|
+% \medskip
+%
%
-% \hfill\ldots|,|\meta{start n}..\meta{stop n}|}{|\meta{res.col.}|}{|\meta{shad.col.}|}|
-% [\pageref{Lshadeblock}]
+% \quad|\printPDBlist{|\meta{selection}|}| \quad|\messagePDBlist{|\meta{selection}|}|
+% \hfill[\pageref{LprintPDBlist}]
%
-% \quad|\emphregion{|\meta{seqref}|}{|\meta{start1}..\meta{stop1}|,|\meta{start2}..\meta{stop2}|,|
+% \quad|\shadeblock{|\meta{seqref}|}{|\meta{selection}|}{|\meta{res.col.}|}{|\meta{shad.col.}|}|
+% \hfill[\pageref{Lshadeblock}]
%
-% \hfill\ldots|,|\meta{start n}..\meta{stop n}|}|
-% [\pageref{Lemphregion}]
+% \quad|\shadeblock{|\meta{seqref}|}{|\meta{selection}|}{|\meta{res.col.}|}{|\meta{shad.col.}|}|
+% \hfill[\pageref{Lshadeblock}]
%
-% \quad|\emphblock{|\meta{seqref}|}{|\meta{start1}..\meta{stop1}|,|\meta{start2}..\meta{stop2}|,|
+% \quad|\emphregion{|\meta{seqref}|}{|\meta{selection}|}|
+% \hfill[\pageref{Lemphregion}]
%
-% \hfill\ldots|,|\meta{start n}..\meta{stop n}|}|
-% [\pageref{Lemphblock}]
+% \quad|\emphblock{|\meta{seqref}|}{|\meta{selection}|}|
+% \hfill[\pageref{Lemphblock}]
%
% \quad|\emphdefault{|\meta{style}|}|
% \hfill[\pageref{Lemphdefault}]
%
-% \quad|\tintregion{|\meta{seqref}|}{|\meta{start1}..\meta{stop1}|,|\meta{start2}..\meta{stop2}|,|
-%
-% \hfill\ldots|,|\meta{start n}..\meta{stop n}|}|
-% [\pageref{Ltintregion}]
+% \quad|\tintregion{|\meta{seqref}|}{|\meta{selection}|}|
+% \hfill[\pageref{Ltintregion}]
%
-% \quad|\tintblock{|\meta{seqref}|}{|\meta{start1}..\meta{stop1}|,|\meta{start2}..\meta{stop2}|,|
-%
-% \hfill\ldots|,|\meta{start n}..\meta{stop n}|}|
-% [\pageref{Ltintblock}]
+% \quad|\tintblock{|\meta{seqref}|}{|\meta{selection}|}|
+% \hfill[\pageref{Ltintblock}]
%
% \quad|\tintdefault{|\meta{effect}|}| \qquad\qquad|weak, normal, strong|
% \hfill[\pageref{Ltintdefault}]
%
-% \quad|\frameblock{|\meta{seqref}|}{|\meta{start1}..\meta{stop1}|,|\meta{start2}..\meta{stop2}|,|
+% \quad|\frameblock{|\meta{seqref}|}{|\meta{selection}|}{|\meta{color}|[|\meta{length}|]}|
+% \hfill[\pageref{Lframeblock}]
%
-% \hfill\ldots|,|\meta{start n}..\meta{stop n}|}{|\meta{color}|[|\meta{length}|]}|
-% [\pageref{Lframeblock}]
-%
-% \quad|\hideblock{|\meta{seqref}|}{|\meta{start1}..\meta{stop1}|,|\meta{start2}..\meta{stop2}|,|
+% \quad|\feature{|\meta{position}|}{|\meta{seqref}|}{|\meta{selection}|}|
%
-% \hfill\ldots|,|\meta{start n}..\meta{stop n}|}{|\meta{label}|[|\meta{color}|]}{|\meta{text}|[|\meta{color}|]}|
-% [\pageref{Lhideblock}]
-%
-% \quad|\feature{|\meta{position}|}{|\meta{seqref}|}{|\meta{start1}..\meta{stop1}|,|
-%
-% \hfill\meta{start2}..\meta{stop2}|,|\ldots|,|\meta{start n}..\meta{stop n}|}{|\meta{labelstyle}|}{|\meta{text}|}|
-% [\pageref{Lfeature}]
+% \hfill |{|\meta{labelstyle}|}{|\meta{text}|}| [\pageref{Lfeature}]
%
% \begin{tabbing}
% \quad\quad\quad|{|\meta{labelstyle}|}|\ \= = |{brace[|\meta{color}|]}|\\
@@ -5090,6 +5285,9 @@
% \hspace{5cm}\meta{properties/file/data}|[|\meta{scale}|]}|\\
% \hspace{5cm}\meta{properties}: |hydrophobicity|, |charge|,\\
% \hspace{7.4cm}|molweight|, |conservation|\\
+% \hspace{5cm}\meta{scale}: |Gray|, |BlueRed|, |RedBlue|,\\
+% \hspace{6.5cm}|GreenRed|, |RedGreen|, |ColdHot|,\\
+% \hspace{6.5cm}|HotCold|, |T-Coffee|\\
% \end{tabbing}
%
% \quad|\ttopspace{|\meta{length}|}|
@@ -5430,8 +5628,8 @@
% \begin{macrocode}
%<*texshade>
\NeedsTeXFormat{LaTeX2e}
-\ProvidesPackage{texshade}[2007/06/19 LaTeX TeXshade (v1.17)]
-\message{Package `texshade', Version 1.17 of 2007/06/19.}
+\ProvidesPackage{texshade}[2009/03/09 LaTeX TeXshade (v1.19)]
+\message{Package `texshade', Version 1.19 of 2009/03/09.}
\PassOptionsToPackage{dvips}{color}
\PassOptionsToPackage{dvips}{graphicx}
@@ -5554,8 +5752,10 @@
\def\n@me{Name:} \def\@msf{MSF:} \def\he@derend{//} \def\ampers@nd{&}
\def\comm@{,} \def\@loc{LOC} \def\@asg{ASG} \def\@t{@} \def\@HP{>HP:}
\def\gre@ter{>} \def\sm@ller{<} \def\N@{N} \def\equ@l{=} \def\H@{H}
-\def\gap@char{.} \def\yes{yes} \def\y@{y} \def\n@{n} \def\o@{o} \def\d@t{.}
+\def\gap@char{.} \def\dom@char{{\dom@rule}} \def\yes{yes} \def\y@{y} \def\n@{n} \def\o@{o} \def\d@t{.}
+\def\@TOM{ATOM} \def\C@lpha{CA} \def\@point@{point} \def\@line@{line} \def\@plane@{plane}
\def\gap@rule{\rule[0.3\box@height]{\box@width}{\gap@rulethick}}
+\def\dom@rule{\vrule depth\box@depth height\box@height width\domgap@rulethick}
\def\fgroup@num{0} \def\max@seqnumber{0} \def\@lign@count{0}
\def\resn@m@tch{upper} \def\ressimm@tch{upper}
\def\resm@tch{upper} \def\res@llm@tch{upper}
@@ -6120,6 +6320,8 @@
\expandafter\xdef\csname cons.Z\endcsname{0}
\expandafter\xdef\csname cons..\endcsname{0}
+\expandafter\xdef\csname cons==\endcsname{0}
+
\def\c@d@ns{%
\codon{A}{GCA,GCG,GCC,GCT,GCU,GCN}
\codon{B}{---}
@@ -6872,6 +7074,7 @@
\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\get@temp#1@{\xdef\temp@{#1}}
\def\TC@get#1#2@{\xdef\char@num{`#1}
\ifnum\char@num=45 \xdef\TC@first@{*}
\else
@@ -7016,6 +7219,7 @@
\ifnum\loopcount<\killseq@count \repeat
\ifnum\cons@num>0 \xdef\cons@num{\csname @rd\cons@num\endcsname} \fi
\ifnum\rule@num>0 \xdef\rule@num{\csname @rd\rule@num\endcsname} \fi
+ \ifnum\divref@>0 \xdef\divref@{\csname @rd\divref@\endcsname} \fi
\loopcount=0
\loop
\advance\loopcount by 1
@@ -7506,9 +7710,9 @@
\xdef\second@{rasmol}
\ifx\temp@\second@
\funcgroup{Asp, Glu}{DE}{Red}{White}{upper}{up}
- \funcgroup{Arg, Lys, His}{KR}{Blue}{White}{upper}{up}
- \funcgroup{Phe, Tyr, Trp}{FY}{MidnightBlue}{White}{upper}{up}
- \funcgroup{Ala, Gly}{G}{Gray}{White}{upper}{up}
+ \funcgroup{Arg, Lys, His}{KRH}{Blue}{White}{upper}{up}
+ \funcgroup{Phe, Tyr, Trp}{FYW}{MidnightBlue}{White}{upper}{up}
+ \funcgroup{Ala, Gly}{AG}{Gray}{White}{upper}{up}
\funcgroup{Cys, Met}{CM}{Yellow}{White}{upper}{up}
\funcgroup{Ser, Thr}{ST}{Orange}{White}{upper}{up}
\funcgroup{Asn, Gln}{NQ}{Cyan}{White}{upper}{up}
@@ -7574,14 +7778,6 @@
\xdef\tmpstack{\tmpstack\first@;\second@;\third@;\fourth@;} \sort@hidestack
\fi\fi
}
-\def\get@hideregions#1..#2,#3@{%
- \xdef\hide@true{y}
- \xdef\st@rt{#1} \xdef\st@p{#2} \xdef\list@{#3}
- \xdef\last@{\csname stack@hidereg\seq@\endcsname}
- \xdef\tmpstack{}
- \sort@hidestack
- \expandafter\xdef\csname stack@hidereg\seq@\endcsname{\tmpstack}
-}
\def\get@fromemphstack#1;#2;#3;#4@{%
\xdef\first@{#1} \xdef\second@{#2}
\xdef\third@{#3} \xdef\last@{#4@}
@@ -7614,6 +7810,40 @@
\sort@emphstack
\expandafter\xdef\csname stack@emphreg\seq@\endcsname{\tmpstack}
}
+\def\get@fromdomstack#1;#2;#3@{%
+ \xdef\first@{#1} \xdef\second@{#2}
+ \xdef\last@{#3@}
+}
+\def\sort@domstack{%
+ \expandafter\get@fromdomstack\last@
+ \ifx\first@\ampers@nd
+ \xdef\tmpstack{\tmpstack\st@rt;\st@p;&;&;@}
+ \else
+ \ifnum\st@rt<\second@
+ \xdef\tmpstack{\tmpstack\st@rt;\st@p;\first@;\second@;\last@}
+ \else
+ \xdef\tmpstack{\tmpstack\first@;\second@;} \sort@domstack
+ \fi\fi
+}
+\def\get@domainregions#1..#2,#3@{%
+ \xdef\st@rt{#1} \xdef\st@p{#2} \xdef\list@{#3}
+ \xdef\last@{\stack@dom}
+ \xdef\tmpstack{}
+ \sort@domstack
+ \xdef\stack@dom{\tmpstack}
+}
+\def\get@domain{%
+ \expandafter\get@fromdomstack\last@
+ \ifx\first@\ampers@nd
+ \else
+ \loopcount=\first@
+ \loop
+ \xdef\domain@num@list{\domain@num@list \the\loopcount,}
+ \advance\loopcount by 1
+ \ifnum\loopcount>\second@\else\repeat
+ \get@domain
+ \fi
+}
\def\getregion@fromtintstack#1{%
\xdef\temp@{#1}
\xdef\first@{\csname stack@tintreg\temp@\endcsname}
@@ -7785,6 +8015,132 @@
\fi%
\fi%
}
+
+\def\test@PDB#1:#2,#3,#4,#5,#6@{%
+ \xdef\last@{#1[,]&}\expandafter\opt@color\last@
+ \ifx\f@color\comm@
+ \xdef\PDB@distance{no}
+ \else
+ \xdef\f@color{\f@color .&&@}
+ \expandafter\coord@get\f@color
+ \temp@count=\c@@rd
+ \multiply\temp@count by \temp@count
+ \xdef\PDB@distance{\the\temp@count}
+ \fi
+ \xdef\PDB@hitpos{0}
+ \xdef\PDB@stack{}
+ \xdef\PDB@name{#2}
+ \xdef\PDB@type{point}
+ \ifx\fourth@\PDB@type
+ \xdef\last@{#3[,]&}\expandafter\opt@color\last@
+ \xdef\PDB@refnum@a{\fourth@}
+ \ifx\f@color\C@lpha
+ \xdef\PDB@back@side@a{CA}
+ \else
+ \xdef\PDB@back@side@a{side}
+ \fi
+ \xdef\PDB@refnum@b{0} \xdef\PDB@back@side@b{x}
+ \xdef\PDB@refnum@c{0} \xdef\PDB@back@side@c{x}
+ \ifx\PDB@distance\n@ \xdef\PDB@distance{3600}\fi
+ \load@PDB
+ \expandafter\get@item\PDB@stack \xdef\list@{\first@@}
+ \else
+ \xdef\PDB@type{line}
+ \ifx\fourth@\PDB@type
+ \xdef\last@{#3[,]&}\expandafter\opt@color\last@
+ \xdef\PDB@refnum{\fourth@}
+ \ifx\f@color\C@lpha
+ \xdef\PDB@back@side{CA}
+ \else
+ \xdef\PDB@back@side{side}
+ \fi
+ \xdef\last@{#4[,]&}\expandafter\opt@color\last@
+ \ifnum\PDB@refnum<\fourth@
+ \xdef\PDB@refnum@a{\PDB@refnum}
+ \xdef\PDB@refnum@b{\fourth@}
+ \xdef\PDB@back@side@a{\PDB@back@side}
+ \ifx\f@color\C@lpha
+ \xdef\PDB@back@side@b{CA}
+ \else
+ \xdef\PDB@back@side@b{side}
+ \fi
+ \else
+ \xdef\PDB@refnum@b{\PDB@refnum}
+ \xdef\PDB@refnum@a{\fourth@}
+ \xdef\PDB@back@side@b{\PDB@back@side}
+ \ifx\f@color\C@lpha
+ \xdef\PDB@back@side@a{CA}
+ \else
+ \xdef\PDB@back@side@a{side}
+ \fi
+ \fi
+ \xdef\PDB@refnum@c{0} \xdef\PDB@back@side@c{x}
+ \ifx\PDB@distance\n@ \xdef\PDB@distance{100}\fi
+ \load@PDB
+ \expandafter\get@item\PDB@stack \xdef\list@{\first@@}
+ \else
+ \xdef\PDB@type{plane}
+ \ifx\fourth@\PDB@type
+ \xdef\last@{#3[,]&}\expandafter\opt@color\last@
+ \xdef\PDB@refnum{\fourth@}
+ \ifx\f@color\C@lpha
+ \xdef\PDB@back@side{CA}
+ \else
+ \xdef\PDB@back@side{side}
+ \fi
+ \xdef\last@{#4[,]&}\expandafter\opt@color\last@
+ \ifnum\PDB@refnum<\fourth@
+ \xdef\PDB@refnum@a{\PDB@refnum}
+ \xdef\PDB@refnum@b{\fourth@}
+ \xdef\PDB@back@side@a{\PDB@back@side}
+ \ifx\f@color\C@lpha
+ \xdef\PDB@back@side@b{CA}
+ \else
+ \xdef\PDB@back@side@b{side}
+ \fi
+ \else
+ \xdef\PDB@refnum@b{\PDB@refnum}
+ \xdef\PDB@refnum@a{\fourth@}
+ \xdef\PDB@back@side@b{\PDB@back@side}
+ \ifx\f@color\C@lpha
+ \xdef\PDB@back@side@a{CA}
+ \else
+ \xdef\PDB@back@side@a{side}
+ \fi
+ \fi
+ \xdef\last@{#5[,]&}\expandafter\opt@color\last@
+ \xdef\PDB@refnum{\fourth@}
+ \ifx\f@color\C@lpha
+ \xdef\PDB@back@side{CA}
+ \else
+ \xdef\PDB@back@side{side}
+ \fi
+ \ifnum\PDB@refnum>\PDB@refnum@b
+ \xdef\PDB@refnum@c{\PDB@refnum}
+ \xdef\PDB@back@side@c{\PDB@back@side}
+ \else
+ \ifnum\PDB@refnum>\PDB@refnum@a
+ \xdef\PDB@refnum@c{\PDB@refnum@b}
+ \xdef\PDB@back@side@c{\PDB@back@side@b}
+ \xdef\PDB@refnum@b{\PDB@refnum}
+ \xdef\PDB@back@side@b{\PDB@back@side}
+ \else
+ \xdef\PDB@refnum@c{\PDB@refnum@b}
+ \xdef\PDB@back@side@c{\PDB@back@side@b}
+ \xdef\PDB@refnum@b{\PDB@refnum@a}
+ \xdef\PDB@back@side@b{\PDB@back@side@a}
+ \xdef\PDB@refnum@a{\PDB@refnum}
+ \xdef\PDB@back@side@a{\PDB@back@side}
+ \fi
+ \fi
+ \ifx\PDB@distance\n@ \xdef\PDB@distance{100}\fi
+ \load@PDB
+ \expandafter\get@item\PDB@stack \xdef\list@{\first@@}
+ \fi
+ \fi
+ \fi
+}
+
\def\test@fill#1:#2:#3&{%
\xdef\last@{#1[,][,]&}\expandafter\arrow@col@width\last@%
\xdef\second@@{\fourth@}%
@@ -7961,6 +8317,7 @@
\expandafter\xdef\csname \prfx grpZ\endcsname{-26}
\expandafter\xdef\csname \prfx grp-\endcsname{-999}
\expandafter\xdef\csname \prfx grp.\endcsname{-999}
+ \expandafter\xdef\csname \prfx grp=\endcsname{-999}
}
\def\inactivate@chars{%
\catcode`\#=12
@@ -7975,9 +8332,15 @@
\def\romancount{\@roman\loopcount}
\def\Romancount{\@Roman\loopcount}
\def\cut@name#1.#2@{\global\xdef\file@n@me{#1}}
+\def\coord@get#1.#2#3@{%
+ \xdef\temp@{#2}
+ \ifx\temp@\ampers@nd \xdef\temp@{0} \fi
+ \xdef\c@@rd{#1\temp@}
+}
\def\struc@get#1 #2 #3 #4 #5 #6 #7 #8 #9@{%
\xdef\first@{#1} \xdef\second@{#2} \xdef\third@{#3} \xdef\fourth@{#4}
- \xdef\fifth@{#5} \xdef\sixth@{#6} \xdef\seventh@{#7}\xdef\eighth@{#8}}
+ \xdef\fifth@{#5} \xdef\sixth@{#6} \xdef\seventh@{#7}\xdef\eighth@{#8}
+ \xdef\nineth@{#9}}
\def\get@PHD#1|#2|#3@{\xdef\PHD@line{\PHD@line #2}}
\def\write@PHDsec{%
\expandafter\get@sim\last@
@@ -8945,7 +9308,7 @@
\xdef\fourth@{#2,&,@}
\expandafter\get@triplet\fourth@
\fi}
-
+\def\get@dom@count#1,#2@{\res@count=#1 \xdef\temp@{#2 @}}
\def\get@name@number{%
\xdef\second@{n}
\loopcount=0
@@ -8961,7 +9324,323 @@
\xdef\first@{1}
\fi
}
+
+\def\calc@distance@point{%
+ \loopcount=\xref@coord@a \advance\loopcount by -\x@coord\relax
+ \multiply\loopcount by \loopcount \xdef\x@distance{\the\loopcount}
+ \loopcount=\yref@coord@a \advance\loopcount by -\y@coord\relax
+ \multiply\loopcount by \loopcount \xdef\y@distance{\the\loopcount}
+ \loopcount=\zref@coord@a \advance\loopcount by -\z@coord\relax
+ \multiply\loopcount by \loopcount \xdef\z@distance{\the\loopcount}
+ \advance\loopcount by \y@distance\relax
+ \advance\loopcount by \x@distance\relax
+ \ifnum\loopcount > \PDB@distance \else
+ \loopcount=\PDB@hitpos \advance\loopcount by 1
+ \ifnum\loopcount=\PDB@pos
+ \else
+ \xdef\PDB@stack{\PDB@stack\PDB@hitpos,\PDB@pos..}
+ \fi
+ \xdef\PDB@hitpos{\PDB@pos}
+ \fi
+}
+
+\def\calc@distance@line{%
+ \loopcount=\x@coord\relax \multiply\loopcount by \x@orient
+ \temp@count=\y@coord \relax \multiply\temp@count by \y@orient
+ \advance\loopcount by \temp@count
+ \temp@count=\z@coord \relax \multiply\temp@count by \z@orient
+ \advance\loopcount by \temp@count
+ \advance\loopcount by -\c@nst@
+ \xdef\z@hler{\the\loopcount}
+ \multiply\loopcount by \x@orient \divide\loopcount by \f@ct@r \advance\loopcount by \xref@coord@a
+ \advance\loopcount by -\x@coord
+ \multiply\loopcount by \loopcount \xdef\x@distance{\the\loopcount}
+ \loopcount=\z@hler
+ \multiply\loopcount by \y@orient \divide\loopcount by \f@ct@r \advance\loopcount by \yref@coord@a
+ \advance\loopcount by -\y@coord
+ \multiply\loopcount by \loopcount \xdef\y@distance{\the\loopcount}
+ \loopcount=\z@hler
+ \multiply\loopcount by \z@orient \divide\loopcount by \f@ct@r \advance\loopcount by \zref@coord@a
+ \advance\loopcount by -\z@coord
+ \multiply\loopcount by \loopcount \xdef\z@distance{\the\loopcount}
+ \advance\loopcount by \y@distance\relax
+ \advance\loopcount by \x@distance\relax
+ \ifnum\loopcount > \PDB@distance \else
+ \loopcount=\PDB@hitpos \advance\loopcount by 1
+ \ifnum\loopcount=\PDB@pos
+ \else
+ \xdef\PDB@stack{\PDB@stack\PDB@hitpos,\PDB@pos..}
+ \fi
+ \xdef\PDB@hitpos{\PDB@pos}
+ \fi
+}
+
+
+\def\intr@@t{%
+ \loopcount=\r@@t
+ \temp@count=1
+ \loop
+ \advance\loopcount by \temp@count
+ \divide\loopcount by 2
+ \temp@count=\r@@t
+ \divide\temp@count by \loopcount
+ \ifnum\loopcount>\temp@count\repeat
+}
+
+
+\def\calc@distance@plane{%
+ \loopcount=\x@coord\relax
+ \multiply\loopcount by \x@orient
+ \temp@count=\y@coord \relax
+ \multiply\temp@count by \y@orient
+ \advance\loopcount by \temp@count
+ \temp@count=\z@coord \relax
+ \multiply\temp@count by \z@orient
+ \advance\loopcount by \temp@count
+ \advance\loopcount by \c@nst@
+ \divide\loopcount by \f@ct@r
+ \multiply\loopcount by \loopcount
+ \ifnum\loopcount > \PDB@distance \else
+ \loopcount=\PDB@hitpos \advance\loopcount by 1
+ \ifnum\loopcount=\PDB@pos
+ \else
+ \xdef\PDB@stack{\PDB@stack\PDB@hitpos,\PDB@pos..}
+ \fi
+ \xdef\PDB@hitpos{\PDB@pos}
+ \fi
+}
+
+\def\load@PDB{%
+ \bgroup
+ \immediate\openin\structurefile = \PDB@name\relax
+ \ifeof\structurefile
+ \PackageError{TeXshade}
+ {File `\PDB@name' not found}
+ {\MessageBreak
+ The file you specified is missing or you have \MessageBreak
+ misspelled it. \MessageBreak\MessageBreak
+ No PDB domain labeling will be displayed. \MessageBreak
+ Type <return> to proceed. \MessageBreak
+ Type X <return> to quit. \MessageBreak
+}
+ \immediate\closein\structurefile\egroup
+ \else
+ \message{<reading PDB: \PDB@name>}
+ \xdef\first@{}
+ \loop
+ \read\structurefile to \readline
+ \xdef\test@{\expandafter\string\readline}
+ \ifx\test@\par@
+ \else
+ \xdef\structureline{\readline & & & & & & & & &@}
+ \expandafter\struc@get\structureline
+ \ifx\first@\@TOM
+ \ifx\PDB@back@side@a\C@lpha
+ \ifx\third@\C@lpha
+ \xdef\temp@@@{\fifth@ &&@}
+ \expandafter\check@letter\temp@@@
+ \ifnumber
+ \ifnum\fifth@=\PDB@refnum@a
+ \xdef\sixth@{\sixth@ &.&&@} \expandafter\coord@get\sixth@ \xdef\xref@coord@a{\c@@rd}
+ \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\yref@coord@a{\c@@rd}
+ \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\zref@coord@a{\c@@rd}
+ \fi
+ \else
+ \ifnum\sixth@=\PDB@refnum@a
+ \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\xref@coord@a{\c@@rd}
+ \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\yref@coord@a{\c@@rd}
+ \xdef\nineth@{\nineth@ &.&&@} \expandafter\coord@get\nineth@ \xdef\zref@coord@a{\c@@rd}
+ \fi
+ \fi
+ \fi
+ \else
+ \xdef\temp@@@{\fifth@ &&@}
+ \expandafter\check@letter\temp@@@
+ \ifnumber
+ \ifnum\fifth@=\PDB@refnum@a
+ \xdef\sixth@{\sixth@ &.&&@} \expandafter\coord@get\sixth@ \xdef\xref@coord@a{\c@@rd}
+ \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\yref@coord@a{\c@@rd}
+ \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\zref@coord@a{\c@@rd}
+ \fi
+ \else
+ \ifnum\sixth@=\PDB@refnum@a
+ \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\xref@coord@a{\c@@rd}
+ \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\yref@coord@a{\c@@rd}
+ \xdef\nineth@{\nineth@ &.&&@} \expandafter\coord@get\nineth@ \xdef\zref@coord@a{\c@@rd}
+ \fi
+ \fi
+ \fi
+ \ifx\PDB@back@side@b\C@lpha
+ \ifx\third@\C@lpha
+ \xdef\temp@@@{\fifth@ &&@}
+ \expandafter\check@letter\temp@@@
+ \ifnumber
+ \ifnum\fifth@=\PDB@refnum@b
+ \xdef\sixth@{\sixth@ &.&&@} \expandafter\coord@get\sixth@ \xdef\xref@coord@b{\c@@rd}
+ \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\yref@coord@b{\c@@rd}
+ \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\zref@coord@b{\c@@rd}
+ \fi
+ \else
+ \ifnum\sixth@=\PDB@refnum@b
+ \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\xref@coord@b{\c@@rd}
+ \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\yref@coord@b{\c@@rd}
+ \xdef\nineth@{\nineth@ &.&&@} \expandafter\coord@get\nineth@ \xdef\zref@coord@b{\c@@rd}
+ \fi
+ \fi
+ \fi
+ \else
+ \xdef\temp@@@{\fifth@ &&@}
+ \expandafter\check@letter\temp@@@
+ \ifnumber
+ \ifnum\fifth@=\PDB@refnum@b
+ \xdef\sixth@{\sixth@ &.&&@} \expandafter\coord@get\sixth@ \xdef\xref@coord@b{\c@@rd}
+ \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\yref@coord@b{\c@@rd}
+ \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\zref@coord@b{\c@@rd}
+ \fi
+ \else
+ \ifnum\sixth@=\PDB@refnum@b
+ \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\xref@coord@b{\c@@rd}
+ \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\yref@coord@b{\c@@rd}
+ \xdef\nineth@{\nineth@ &.&&@} \expandafter\coord@get\nineth@ \xdef\zref@coord@b{\c@@rd}
+ \fi
+ \fi
+ \fi
+ \ifx\PDB@back@side@c\C@lpha
+ \ifx\third@\C@lpha
+ \xdef\temp@@@{\fifth@ &&@}
+ \expandafter\check@letter\temp@@@
+ \ifnumber
+ \ifnum\fifth@=\PDB@refnum@c
+ \xdef\sixth@{\sixth@ &.&&@} \expandafter\coord@get\sixth@ \xdef\xref@coord@c{\c@@rd}
+ \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\yref@coord@c{\c@@rd}
+ \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\zref@coord@c{\c@@rd}
+ \fi
+ \else
+ \ifnum\sixth@=\PDB@refnum@c
+ \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\xref@coord@c{\c@@rd}
+ \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\yref@coord@c{\c@@rd}
+ \xdef\nineth@{\nineth@ &.&&@} \expandafter\coord@get\nineth@ \xdef\zref@coord@c{\c@@rd}
+ \fi
+ \fi
+ \fi
+ \else
+ \xdef\temp@@@{\fifth@ &&@}
+ \expandafter\check@letter\temp@@@
+ \ifnumber
+ \ifnum\fifth@=\PDB@refnum@c
+ \xdef\sixth@{\sixth@ &.&&@} \expandafter\coord@get\sixth@ \xdef\xref@coord@c{\c@@rd}
+ \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\yref@coord@c{\c@@rd}
+ \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\zref@coord@c{\c@@rd}
+ \fi
+ \else
+ \ifnum\sixth@=\PDB@refnum@c
+ \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\xref@coord@c{\c@@rd}
+ \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\yref@coord@c{\c@@rd}
+ \xdef\nineth@{\nineth@ &.&&@} \expandafter\coord@get\nineth@ \xdef\zref@coord@c{\c@@rd}
+ \fi
+ \fi
+ \fi
+ \fi
+ \fi
+ \ifeof\structurefile \else\repeat
+ \closein\structurefile
+ \ifx\PDB@type\@line@
+ \loopcount=\xref@coord@a \advance\loopcount by -\xref@coord@b \xdef\x@orient{\the\loopcount}
+ \loopcount=\yref@coord@a \advance\loopcount by -\yref@coord@b \xdef\y@orient{\the\loopcount}
+ \loopcount=\zref@coord@a \advance\loopcount by -\zref@coord@b \xdef\z@orient{\the\loopcount}
+ \loopcount=\xref@coord@a \multiply\loopcount by \x@orient
+ \temp@count=\yref@coord@a \multiply\temp@count by \y@orient
+ \advance\loopcount by \temp@count
+ \temp@count=\zref@coord@a \multiply\temp@count by \z@orient
+ \advance\loopcount by \temp@count
+ \xdef\c@nst@{\the\loopcount}
+ \loopcount=\x@orient \multiply\loopcount by \x@orient
+ \temp@count=\y@orient \multiply\temp@count by \y@orient
+ \advance\loopcount by \temp@count
+ \temp@count=\z@orient \multiply\temp@count by \z@orient
+ \advance\loopcount by \temp@count
+ \xdef\f@ct@r{\the\loopcount}
+ \fi
+ \ifx\PDB@type\@plane@
+ \loopcount=\xref@coord@a \advance\loopcount by -\xref@coord@b \xdef\x@orient@r{\the\loopcount}
+ \loopcount=\yref@coord@a \advance\loopcount by -\yref@coord@b \xdef\y@orient@r{\the\loopcount}
+ \loopcount=\zref@coord@a \advance\loopcount by -\zref@coord@b \xdef\z@orient@r{\the\loopcount}
+ \loopcount=\xref@coord@a \advance\loopcount by -\xref@coord@c \xdef\x@orient@s{\the\loopcount}
+ \loopcount=\yref@coord@a \advance\loopcount by -\yref@coord@c \xdef\y@orient@s{\the\loopcount}
+ \loopcount=\zref@coord@a \advance\loopcount by -\zref@coord@c \xdef\z@orient@s{\the\loopcount}
+ \loopcount=\y@orient@r \multiply\loopcount by \z@orient@s
+ \temp@count=\z@orient@r \multiply\temp@count by \y@orient@s
+ \advance\loopcount by -\temp@count \divide\loopcount by 100 \xdef\x@orient{\the\loopcount}
+ \loopcount=\z@orient@r \multiply\loopcount by \x@orient@s
+ \temp@count=\x@orient@r \multiply\temp@count by \z@orient@s
+ \advance\loopcount by -\temp@count \divide\loopcount by 100 \xdef\y@orient{\the\loopcount}
+ \loopcount=\x@orient@r \multiply\loopcount by \y@orient@s
+ \temp@count=\y@orient@r \multiply\temp@count by \x@orient@s
+ \advance\loopcount by -\temp@count \divide\loopcount by 100 \xdef\z@orient{\the\loopcount}
+ \loopcount=\x@orient \multiply\loopcount by \xref@coord@a
+ \temp@count=\y@orient \multiply\temp@count by \yref@coord@a
+ \advance\loopcount by \temp@count
+ \temp@count=\z@orient \multiply\temp@count by \zref@coord@a
+ \advance\loopcount by \temp@count
+ \multiply\loopcount by -1\relax
+ \xdef\c@nst@{\the\loopcount}
+ \loopcount=\x@orient \multiply\loopcount by \loopcount
+ \temp@count=\y@orient \multiply\temp@count by \temp@count
+ \advance\loopcount by \temp@count
+ \temp@count=\z@orient \multiply\temp@count by \temp@count
+ \advance\loopcount by \temp@count
+ \xdef\r@@t{\the\loopcount} \intr@@t
+ \xdef\f@ct@r{\the\loopcount}
+ \fi
+ \immediate\openin\structurefile = \PDB@name\relax
+ \xdef\first@{}
+ \loop
+ \read\structurefile to \readline
+ \xdef\test@{\expandafter\string\readline}
+ \ifx\test@\par@
+ \else
+ \xdef\structureline{\readline & & & & & & & & &@}
+ \expandafter\struc@get\structureline
+ \ifx\first@\@TOM
+ \xdef\temp@@@{\fifth@ &&@}
+ \expandafter\check@letter\temp@@@
+ \ifnumber
+ \xdef\PDB@pos{\fifth@}
+ \xdef\sixth@{\sixth@ &.&&@} \expandafter\coord@get\sixth@ \xdef\x@coord{\c@@rd}
+ \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\y@coord{\c@@rd}
+ \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\z@coord{\c@@rd}
+ \else
+ \xdef\PDB@pos{\sixth@}
+ \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\x@coord{\c@@rd}
+ \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\y@coord{\c@@rd}
+ \xdef\nineth@{\nineth@ &.&&@} \expandafter\coord@get\nineth@ \xdef\z@coord{\c@@rd}
+ \fi
+ \ifnum\PDB@hitpos=\PDB@pos
+ \else
+ \ifx\PDB@type\@point@
+ \calc@distance@point
+ \else
+ \ifx\PDB@type\@line@
+ \calc@distance@line
+ \else
+ \ifx\PDB@type\@plane@
+ \calc@distance@plane
+ \fi
+ \fi
+ \fi
+ \fi
+ \fi
+ \fi
+ \ifeof\structurefile \xdef\PDB@stack{\PDB@stack\PDB@hitpos,&@}
+ \else\repeat
+ \closein\structurefile
+
+ \fi
+ \egroup
+ }
+
+
%%%%% Definition of user commands
@@ -9051,6 +9730,34 @@
\separationline{\the\loopcount}
\ifnum\loopcount<\seq@count\repeat
\fi}
+\def\printPDBlist#1{%
+ \xdef\list@{}
+ \xdef\temp@{#1,,,:,,,,@} \expandafter\test@PDB\temp@
+ \xdef\first@{\list@ &}
+ \ifx\first@\ampers@nd
+ \else
+ \xdef\first@{\list@ @}
+ \loop
+ \expandafter\get@item\first@
+ \fourth@
+ \ifx\first@@\ampers@nd\else{,\ }\repeat
+ \fi
+}
+\def\messagePDBlist#1{%
+ \xdef\list@{}
+ \xdef\temp@{#1,,,:,,,,@} \expandafter\test@PDB\temp@
+ \xdef\first@{\list@ &}
+ \ifx\first@\ampers@nd
+ \else
+ \message{(#1:}
+ \xdef\first@{\list@ @}%
+ \loop%
+ \expandafter\get@item\first@%
+ \message{\fourth@}%
+ \ifx\first@@\ampers@nd\else\repeat%
+ \message{)}
+ \fi
+}
\def\shaderegion#1#2#3#4{%
\regionalshadetrue
\xdef\seq@{#1}
@@ -9068,6 +9775,7 @@
\expandafter\xdef\csname fgseqregion\the\loopcount\endcsname{#3}
\expandafter\xdef\csname bgseqregion\the\loopcount\endcsname{#4}
\xdef\list@{#2,&}
+ \xdef\temp@{#2,,,:,,,,@} \expandafter\test@PDB\temp@
\loop
\xdef\list@{\list@ @}
\expandafter\get@regions\list@
@@ -9091,6 +9799,7 @@
\else
\ifx\@ll\yes \xdef\@ll{y}\else \xdef\@ll{n}\fi
\xdef\list@{#2,&}
+ \xdef\temp@{#2,,,:,,,,@} \expandafter\test@PDB\temp@
\loop
\xdef\list@{\list@ @}
\expandafter\get@tintregions\list@
@@ -9131,6 +9840,7 @@
\else
\ifx\@ll\yes \xdef\@ll{y}\else \xdef\@ll{n}\fi
\xdef\list@{#2,&}
+ \xdef\temp@{#2,,,:,,,,@} \expandafter\test@PDB\temp@
\loop
\xdef\list@{\list@ @}
\expandafter\get@emphregions\list@
@@ -9155,29 +9865,13 @@
\else
\xdef\@ll{#3}
\xdef\list@{#2,&}
+ \xdef\temp@{#2,,,:,,,,@} \expandafter\test@PDB\temp@
\loop
\xdef\list@{\list@ @}
\expandafter\get@frameregions\list@
\ifx\list@\ampers@nd\else\repeat
\fi
}
-\def\hideblock#1#2#3#4{%
- \xdef\seq@{#1}
- \xdef\temp@{consensus} \ifx\seq@\temp@ \xdef\seq@{0} \fi
- \xdef\first@{\seq@ @} \expandafter\check@letter\first@
- \xdef\first@{\seq@}
- \ifletter \get@name@number \xdef\seq@{\first@} \fi
- \ifnum\seq@>\seq@count
- \message{<Ignored seq `\seq@' in \noexpand\hideblock>}
- \else
- \xdef\@ll{#3} \xdef\text@{#4}
- \xdef\list@{#2,&}
- \loop
- \xdef\list@{\list@ @}
- \expandafter\get@hideregions\list@
- \ifx\list@\ampers@nd\else\repeat
- \fi
-}
\def\bargraphstretch#1{\def\b@r@stretch{#1}}
\def\colorscalestretch#1{\def\sc@le@stretch{#1}}
\def\rm@@measure#1#2@{%
@@ -9539,7 +10233,7 @@
\ifx\second@@\last@
\xdef\list@{#3,&}
\xdef\style@{#4}
- \xdef\f@text@{#5}
+ \def\f@text@{#5}
\do@bargraph
\xdef\temp@{bottom}
\ifx\bottop@\temp@ \xdef\bottom@stretch{y}\fi
@@ -9554,11 +10248,14 @@
\ifx\second@@\last@
\xdef\list@{#3,&}
\xdef\style@{#4}
- \xdef\f@text@{#5}
+ \def\f@text@{#5}
\do@colorgraph
\else
- \xdef\f@text@{#5}
+ \xdef\f@@color{\f@color}
\xdef\list@{#3,&}
+ \xdef\temp@{#3,,,:,,,,@} \expandafter\test@PDB\temp@
+ \def\f@text@{#5}
+ \xdef\f@color{\f@@color}
\xdef\temp@{#4&}
\ifx\temp@\ampers@nd
\xdef\style@{&}
@@ -9636,7 +10333,9 @@
\fi
\fi
\fi
+ \loopcount=0
\loop
+ \advance\loopcount by 1\relax
\xdef\list@{\list@ @}
\expandafter\get@fregions\list@
\ifx\list@\ampers@nd\else\repeat
@@ -9694,7 +10393,23 @@
\def\decide@{\ifx\l@@k * \let\next\@rplfix \else \let\next\@rplvar \fi \next}
\futurelet\l@@k\decide@}
\def\numberingwidth#1{\def\num@width{#1}}
-\def\charstretch#1{\def\char@stretch{#1}}
+\def\charstretch#1{%
+ \def\char@stretch{#1}
+ \xdef\temp@{\char@stretch .00@} \expandafter\coord@get\temp@ \loopcount=\c@@rd
+ \multiply \loopcount by 7
+ \divide \loopcount by 10
+ \ifnum\loopcount<10
+ \xdef\temp@{0\the\loopcount @}
+ \else
+ \xdef\temp@{\the\loopcount @}
+ \fi
+ \expandafter\decimal@B\temp@
+ \ifnum\loopcount>99
+ \xdef\char@stretch@W{#1}
+ \else
+ \xdef\char@stretch@W{\temp@}
+ \fi
+}
\def\linestretch#1{\def\line@stretch{#1}}
\def\logostretch#1{%
\def\logo@stretch{#1}
@@ -9826,6 +10541,7 @@
\ifx\first@\second@\def\gap@char{o}
\else\def\gap@char{#1}\fi}
\def\gaprule#1{\def\gap@rulethick{#1}}
+\def\domaingaprule#1{\def\domgap@rulethick{#1}}
\newcommand{\setends}[3][&]{%
\xdef\start@seq{#2}
\xdef\temp@{consensus}
@@ -10298,9 +11014,6 @@
\xdef\temp@{legend}
\ifx\first@\temp@ \xdef\legend@family{\third@}
\else
- \xdef\temp@{hideblock}
- \ifx\first@\temp@ \xdef\hideblock@family{\third@}
- \else
\xdef\temp@{labels}
\ifx\first@\temp@ \xdef\label@family{\third@}
\else
@@ -10318,9 +11031,8 @@
\xdef\residues@family{\third@}
\xdef\legend@family{\third@}
\xdef\label@family{\third@}
- \xdef\hideblock@family{\third@}
\xdef\ruler@family{\second@}
- \fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi
+ \fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi
\fi
}
\def\setseries#1#2{%
@@ -10363,9 +11075,6 @@
\xdef\temp@{legend}
\ifx\first@\temp@ \xdef\legend@series{\third@}
\else
- \xdef\temp@{hideblock}
- \ifx\first@\temp@ \xdef\hideblock@series{\third@}
- \else
\xdef\temp@{labels}
\ifx\first@\temp@ \xdef\label@series{\third@}
\else
@@ -10379,9 +11088,8 @@
\xdef\namestext@series{\third@}
\xdef\residues@series{\third@}
\xdef\legend@series{\third@}
- \xdef\hideblock@series{\third@}
\xdef\label@series{\third@}
- \fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi
+ \fi\fi\fi\fi\fi\fi\fi\fi\fi\fi
\fi
}
\def\setshape#1#2{%
@@ -10432,9 +11140,6 @@
\xdef\temp@{legend}
\ifx\first@\temp@ \xdef\legend@shape{\third@}
\else
- \xdef\temp@{hideblock}
- \ifx\first@\temp@ \xdef\hideblock@shape{\third@}
- \else
\xdef\temp@{labels}
\ifx\first@\temp@ \xdef\label@shape{\third@}
\else
@@ -10448,9 +11153,8 @@
\xdef\namestext@shape{\third@}
\xdef\residues@shape{\third@}
\xdef\legend@shape{\third@}
- \xdef\hideblock@shape{\third@}
\xdef\label@shape{\third@}
- \fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi
+ \fi\fi\fi\fi\fi\fi\fi\fi\fi\fi
\fi
}
\def\setsize#1#2{%
@@ -10486,20 +11190,6 @@
\ifx\first@\temp@
\def\legend@size{\csname #2\endcsname}
\else
- \xdef\temp@{hideblock}
- \ifx\first@\temp@
- \xdef\temp@@{#2}
- \xdef\temp@{huge}
- \ifx\temp@\temp@@
- \def\hideblock@size{\csname LARGE\endcsname}
- \else
- \xdef\temp@{Huge}
- \ifx\temp@\temp@@
- \def\hideblock@size{\csname LARGE\endcsname}
- \else
- \def\hideblock@size{\csname #2\endcsname}
- \fi\fi
- \else
\xdef\temp@{labels}
\ifx\first@\temp@
\def\label@size{\csname #2\endcsname}
@@ -10518,11 +11208,10 @@
\def\numbertext@size{\csname #2\endcsname}
\def\namestext@size{\csname #2\endcsname}
\def\legend@size{\csname #2\endcsname}
- \def\hideblock@size{\csname #2\endcsname}
\def\label@size{\csname #2\endcsname}
\def\residues@size{\csname #2\endcsname}
\xdef\res@size{#2}
- \fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi
+ \fi\fi\fi\fi\fi\fi\fi\fi\fi\fi
\xdef\temp@{Huge}
\ifx\temp@\res@size
\def\bottomruler@size{\csname Large\endcsname}
@@ -10706,25 +11395,6 @@
\def\legendLARGE {\setsize{legend}{LARGE}}
\def\legendhuge {\setsize{legend}{huge}}
\def\legendHuge {\setsize{legend}{Huge}}
-\def\hideblockrm{\setfamily{hideblock}{rm}}
-\def\hideblocksf{\setfamily{hideblock}{sf}}
-\def\hideblocktt{\setfamily{hideblock}{tt}}
-\def\hideblockmd{\setseries{hideblock}{md}}
-\def\hideblockbf{\setseries{hideblock}{bf}}
-\def\hideblockup{\setshape {hideblock}{up}}
-\def\hideblockit{\setshape {hideblock}{it}}
-\def\hideblocksl{\setshape {hideblock}{sl}}
-\def\hideblocksc{\setshape {hideblock}{sc}}
-\def\hideblocktiny {\setsize{hideblock}{tiny}}
-\def\hideblockscriptsize {\setsize{hideblock}{scriptsize}}
-\def\hideblockfootnotesize{\setsize{hideblock}{footnotesize}}
-\def\hideblocksmall {\setsize{hideblock}{small}}
-\def\hideblocknormalsize {\setsize{hideblock}{normalsize}}
-\def\hideblocklarge {\setsize{hideblock}{large}}
-\def\hideblockLarge {\setsize{hideblock}{Large}}
-\def\hideblockLARGE {\setsize{hideblock}{LARGE}}
-\def\hideblockhuge {\setsize{hideblock}{LARGE}}
-\def\hideblockHuge {\setsize{hideblock}{LARGE}}
\def\rulerrm{\setfamily{ruler}{rm}}
\def\rulersf{\setfamily{ruler}{sf}}
\def\rulertt{\setfamily{ruler}{tt}}
@@ -10817,6 +11487,12 @@
\expandafter\def\csname fg@textcolor*\endcsname{#1}\fi
\ifx\second@\last@\else\def\gap@bg{#2}
\expandafter\def\csname fg@color*\endcsname{#2}\fi}
+\def\domaingapcolors#1#2 {\xdef\first@{#1&}\xdef\second@{#2&}
+ \xdef\last@{\ampers@nd}
+ \ifx\first@\last@\else\def\domgap@fg{#1}
+ \expandafter\def\csname fg@textcolor!\endcsname{#1}\fi
+ \ifx\second@\last@\else\def\domgap@bg{#2}
+ \expandafter\def\csname fg@color!\endcsname{#2}\fi}
\def\shadebox#1{%
\xdef\first@{White}%
\xdef\third@{#1}%
@@ -11289,6 +11965,24 @@
\fi
}
+\def\setdomain#1#2{%
+ \xdef\first@{#1}
+ \xdef\temp@{consensus}
+ \ifx\first@\temp@ \xdef\domain@seq{0}
+ \else
+ \xdef\first@{#1 @} \expandafter\check@letter\first@
+ \xdef\first@{#1} \ifletter \get@name@number \fi
+ \xdef\domain@seq{\csname @rd\first@\endcsname}%
+ \fi
+ \xdef\list@{#2,&}
+ \xdef\temp@{#2,,,:,,,,@} \expandafter\test@PDB\temp@
+ \loop
+ \xdef\list@{\list@ @}
+ \expandafter\get@domainregions\list@
+ \ifx\list@\ampers@nd\else\repeat
+ \xdef\dom@in{y}
+}
+
%%%%% Calculate consensus
\def\check@sim{%
@@ -11354,7 +12048,7 @@
\fi
\else
\newresfalse
- \expandafter\xdef\csname res\the\loopcount\endcsname{\d@t}
+% \expandafter\xdef\csname res\the\loopcount\endcsname{\d@t} %%%%% or \equ@l for domains!!!
\fi
\ifnewres
@@ -11448,13 +12142,29 @@
\expandafter\xdef\csname seq\the\loopcount\endcsname{%
\csname seq\the\loopcount\endcsname3\gap@char}
\else
+ \expandafter\ifx\csname res\the\loopcount\endcsname\equ@l
+ \expandafter\xdef\csname seq\the\loopcount\endcsname{%
+ \csname seq\the\loopcount\endcsname!\dom@char} \xdef\g@p{y}
+ \else
\expandafter\xdef\csname seq\the\loopcount\endcsname{%
\csname seq\the\loopcount\endcsname%
3\csname res\the\loopcount\endcsname}
\fi
+ \fi
\else
\xdef\first@{\csname res\the\loopcount\endcsname}
- \ifx\first@\d@t
+ \ifx\first@\equ@l
+ \def\first@{\dom@char} \def\third@{9}
+ \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\third@\first@} \xdef\g@p{y}
+ \else
+ \ifx\first@\d@t
\expandafter\ifnum\csname res@count\the\loopcount\endcsname%
<\csname seq@start\the\loopcount\endcsname
\ifsh@wg@ps
@@ -11474,27 +12184,28 @@
\fi
\fi
\fi
- \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\third@\first@}
- \else
- \ifnum\divref@=\loopcount\else
- \xdef\low@up{lower} \ifx\resn@m@tch\low@up \make@lower \else
- \xdef\low@up{upper} \ifx\resn@m@tch\low@up
- \else \xdef\first@{\resn@m@tch} \fi\fi\fi
- \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
- \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
+ \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}
+ \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\endcsname3\first@}
+ \expandafter\xdef\csname seq\the\loopcount\endcsname{%
+ \csname seq\the\loopcount\endcsname\third@\first@}
+ \else
+ \ifnum\divref@=\loopcount\else
+ \xdef\low@up{lower} \ifx\resn@m@tch\low@up \make@lower \else
+ \xdef\low@up{upper} \ifx\resn@m@tch\low@up
+ \else \xdef\first@{\resn@m@tch} \fi\fi\fi
+ \expandafter\ifx\csname 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\endcsname3\first@}
+ \fi
\fi
\fi
\ifnum\loopcount<\seq@count \repeat
@@ -11507,9 +12218,13 @@
\expandafter\ifx\csname emph@seq0\endcsname\y@
\expandafter\xdef\csname emph@seq0\endcsname{n}
\xdef\first@{,\first@}\fi
- \xdef\consensus{\consensus 4\first@}
- \expandafter\ifx\csname res\cons@num\endcsname\d@t
+ \ifx\g@p\y@
+ \xdef\consensus{\consensus 8{}}
+ \else
+ \xdef\consensus{\consensus 4\first@}
+ \expandafter\ifx\csname res\cons@num\endcsname\d@t
\else\xdef\constopo{\constopo 0}\fi
+ \fi
\else
\ifnum\cons@num>0
\xdef\tmp@{\csname res\cons@num\endcsname}
@@ -11525,6 +12240,7 @@
\expandafter\ifx\csname hide@seq\the\loopcount\endcsname\first@
\xdef\first@{\csname res\the\loopcount\endcsname}
\ifx\first@\d@t\def\first@{\gap@char}\fi
+ \ifx\first@\equ@l\def\first@{\dom@char} \xdef\g@p{y} \fi
\expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
\expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
\xdef\first@{=\first@}\fi
@@ -11532,8 +12248,7 @@
\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%
- 3\first@}
+ \csname seq\the\loopcount\endcsname3\first@}
\else
\xdef\first@{\csname res\the\loopcount\endcsname}
\xdef\last@{\csname res\the\loopcount\endcsname}
@@ -11544,6 +12259,9 @@
\xdef\low@up{upper} \ifx\ressimm@tch\low@up
\else \xdef\first@{\ressimm@tch} \fi\fi\fi
\else
+ \ifx\first@\equ@l
+ \def\first@{\dom@char} \def\third@{9} \xdef\g@p{y}
+ \else
\ifx\first@\d@t
\expandafter\ifnum\csname res@count\the\loopcount\endcsname%
<\csname seq@start\the\loopcount\endcsname
@@ -11571,6 +12289,7 @@
\xdef\low@up{upper} \ifx\resn@m@tch\low@up
\else \xdef\first@{\resn@m@tch} \fi\fi\fi
\fi
+ \fi
\fi
\expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
\expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
@@ -11592,8 +12311,12 @@
\expandafter\ifx\csname emph@seq0\endcsname\y@
\expandafter\xdef\csname emph@seq0\endcsname{n}
\xdef\first@{,\first@}\fi
- \xdef\consensus{\consensus5\first@}
- \xdef\constopo{\constopo 1}
+ \ifx\g@p\y@
+ \xdef\consensus{\consensus 8{}}
+ \else
+ \xdef\consensus{\consensus5\first@}
+ \xdef\constopo{\constopo 1}
+ \fi
\fi
\else
\iffuncmode
@@ -11601,6 +12324,17 @@
\loop
\advance\loopcount by 1
\xdef\first@{\csname res\the\loopcount\endcsname}
+ \ifx\first@\equ@l
+ \def\first@{\dom@char} \def\third@{!} \xdef\g@p{y}
+ \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\third@\first@}
+ \else
\ifx\first@\d@t
\expandafter\ifnum\csname res@count\the\loopcount\endcsname%
<\csname seq@start\the\loopcount\endcsname
@@ -11642,6 +12376,7 @@
\expandafter\xdef\csname seq\the\loopcount\endcsname{%
\csname seq\the\loopcount\endcsname0\first@}
\fi
+ \fi
\ifnum\loopcount<\seq@count \repeat
\else
\loopcount=0
@@ -11651,6 +12386,7 @@
\expandafter\ifx\csname hide@seq\the\loopcount\endcsname\first@
\xdef\first@{\csname res\the\loopcount\endcsname}
\ifx\first@\d@t\def\first@{\gap@char}\fi
+ \ifx\first@\equ@l\def\first@{\dom@char} \xdef\g@p{y} \fi
\expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
\expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
\xdef\first@{=\first@}\fi
@@ -11662,6 +12398,17 @@
3\first@}
\else
\xdef\first@{\csname res\the\loopcount\endcsname}
+ \ifx\first@\equ@l
+ \def\first@{\dom@char} \def\third@{9} \xdef\g@p{y}
+ \expandafter\ifx\csname 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\third@\first@}
+ \else
\ifx\first@\d@t
\expandafter\ifnum\csname res@count\the\loopcount\endcsname%
<\csname seq@start\the\loopcount\endcsname
@@ -11704,6 +12451,7 @@
\expandafter\xdef\csname seq\the\loopcount\endcsname{%
\csname seq\the\loopcount\endcsname3\first@}
\fi
+ \fi
\fi
\ifnum\loopcount<\seq@count \repeat
\xdef\low@up{lower} \ifx\n@m@tch\low@up \xdef\first@{{ }} \else
@@ -11715,8 +12463,12 @@
\expandafter\ifx\csname emph@seq0\endcsname\y@
\expandafter\xdef\csname emph@seq0\endcsname{n}
\xdef\first@{,\first@}\fi
- \xdef\consensus{\consensus 4\first@}
- \xdef\constopo{\constopo 0}
+ \ifx\g@p\y@
+ \xdef\consensus{\consensus 8{}}
+ \else
+ \xdef\consensus{\consensus 4\first@}
+ \xdef\constopo{\constopo 0}
+ \fi
\fi\fi}
\def\c@nserved{%
@@ -11728,6 +12480,7 @@
\expandafter\ifx\csname hide@seq\the\loopcount\endcsname\first@
\xdef\first@{\csname res\the\loopcount\endcsname}
\ifx\first@\d@t\def\first@{\gap@char}\fi
+ \ifx\first@\equ@l\def\first@{\dom@char} \xdef\g@p{y} \fi
\expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
\expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
\xdef\first@{=\first@}\fi
@@ -11766,6 +12519,7 @@
\xdef\low@up{upper} \ifx\resn@m@tch\low@up
\else \xdef\first@{\resn@m@tch} \fi\fi\fi
\fi
+ \ifx\first@\equ@l \def\first@{\dom@char} \def\third@{9} \xdef\g@p{y} \fi
\ifx\first@\d@t
\expandafter\ifnum\csname res@count\the\loopcount\endcsname%
<\csname seq@start\the\loopcount\endcsname
@@ -11807,9 +12561,13 @@
\expandafter\ifx\csname emph@seq0\endcsname\y@
\expandafter\xdef\csname emph@seq0\endcsname{n}
\xdef\first@{,\first@}\fi
- \xdef\consensus{\consensus 5\first@}
- \xdef\constopo{\constopo 2}}
-
+ \ifx\g@p\y@
+ \xdef\consensus{\consensus 8{}}
+ \else
+ \xdef\consensus{\consensus 5\first@}
+ \xdef\constopo{\constopo 2}
+ \fi}
+
\def\allm@tch{%
\xdef\tmp@{\csname res\cons@seq\endcsname}
\loopcount=0
@@ -11819,6 +12577,7 @@
\expandafter\ifx\csname hide@seq\the\loopcount\endcsname\first@
\xdef\first@{\csname res\the\loopcount\endcsname}
\ifx\first@\d@t\def\first@{\gap@char}\fi
+ \ifx\first@\equ@l\def\first@{\dom@char} \xdef\g@p{y} \fi
\expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
\expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
\xdef\first@{=\first@}\fi
@@ -11862,6 +12621,7 @@
\xdef\low@up{upper} \ifx\resn@m@tch\low@up
\else \xdef\first@{\resn@m@tch} \fi\fi\fi
\fi
+ \ifx\first@\equ@l \def\first@{\dom@char} \def\third@{9} \xdef\g@p{y} \fi
\ifx\first@\d@t
\expandafter\ifnum\csname res@count\the\loopcount\endcsname%
<\csname seq@start\the\loopcount\endcsname
@@ -11903,8 +12663,12 @@
\expandafter\ifx\csname emph@seq0\endcsname\y@
\expandafter\xdef\csname emph@seq0\endcsname{n}
\xdef\first@{,\first@}\fi
- \xdef\consensus{\consensus 6\first@}
- \xdef\constopo{\constopo 3}}
+ \ifx\g@p\y@
+ \xdef\consensus{\consensus 8{}}
+ \else
+ \xdef\consensus{\consensus 6\first@}
+ \xdef\constopo{\constopo 3}
+ \fi}
\def\functi@nal{%
\ifnum\cons@num>0
@@ -11930,6 +12694,9 @@
0\first@}
\else
\xdef\first@{\csname res\the\loopcount\endcsname}
+ \ifx\first@\equ@l
+ \def\first@{\dom@char} \def\third@{!} \xdef\g@p{y}
+ \else
\ifx\first@\d@t
\expandafter\ifnum\csname res@count\the\loopcount\endcsname%
<\csname seq@start\the\loopcount\endcsname
@@ -11961,6 +12728,7 @@
\xdef\low@up{upper} \ifx\resn@m@tch\low@up
\else \xdef\first@{\resn@m@tch} \fi\fi
\fi
+ \fi
\fi
\expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
\expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
@@ -11980,6 +12748,7 @@
\xdef\first@{\csname res\the\loopcount\endcsname}
\xdef\second@{\csname funcgrp\first@\endcsname}
\ifnum\second@<0 \xdef\second@{0} \fi
+ \ifx\first@\equ@l \def\first@{\dom@char} \def\second@{!} \xdef\g@p{y} \fi
\ifx\first@\d@t
\expandafter\ifnum\csname res@count\the\loopcount\endcsname%
<\csname seq@start\the\loopcount\endcsname
@@ -12030,19 +12799,11 @@
\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@\equ@l \def\first@{\dom@char} \def\second@{!} \xdef\g@p{y} \fi
\ifx\first@\d@t
\expandafter\ifnum\csname res@count\the\loopcount\endcsname%
<\csname seq@start\the\loopcount\endcsname
@@ -12086,7 +12847,22 @@
\csname seq\the\loopcount\endcsname%
\second@\first@}
\fi
- \ifnum\loopcount<\seq@count \repeat}
+ \ifnum\loopcount<\seq@count \repeat
+ \xdef\first@{\csname res0\endcsname}
+ \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}
+ \ifx\g@p\y@
+ \xdef\consensus{\consensus 8{}}
+ \else
+ \xdef\consensus{\consensus\second@\n@m@tch}
+ \xdef\constopo{\constopo\second@}
+ \fi
+ }
\def\getregion@fromstack@first{%
\expandafter\getregion@fromstack{\the\loopcount}
@@ -12129,7 +12905,6 @@
\fi
\fi\fi
\ifnum\loopcount<\seq@count \repeat
- \ifx\hide@now\n@
\loopcount=0
\expandafter\ifx\csname shade@style\the\loopcount\endcsname\y@
\else
@@ -12149,7 +12924,6 @@
&\csname shade@style\the\loopcount\endcsname)}
\fi
\ifnum\loopcount<\seq@count \repeat
- \fi
}
\def\getregion@fromemphstack@first{%
@@ -12512,13 +13286,13 @@
\xdef\cons@val{\csname TC@num0\endcsname}
\if\cons@val *
\xdef\cons@val{99}
- \fi \message{(b(\cons@val)b)}
+ \fi
\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
\fi
}
@@ -13417,11 +14191,25 @@
% \advance\pos@count by 1
}
+\def\add@to@rule@tens{%
+ \advance\innerloopcount by \ruler@step\relax
+ \ifnum\innerloopcount=0
+ \ifx\allow@zero\n@ \innerloopcount=\ruler@step \fi
+ \fi
+ \expandafter\ifnum\csname res@count\rule@num\endcsname>\innerloopcount \add@to@rule@tens
+ \else
+ \xdef\rule@tens{\the\innerloopcount}
+ \fi
+}
+
+
\def\c@nsensus{%
\ifnum\pos@count>\res@perline
\else
\loopcount=0
- \global\advance\cons@count by 1\relax
+ \ifx\g@p\n@
+ \global\advance\cons@count by 1\relax
+ \fi
\ifnum\cons@count=0\relax
\ifx\allow@zero\n@ \global\advance\cons@count by 1 \fi
\fi
@@ -13430,21 +14218,6 @@
\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
- \else
- \expandafter\ifnum\csname hidestart0\endcsname>\cons@count
- \else
- \expandafter\ifnum\csname hidestop0\endcsname<\cons@count
- \else
- \xdef\hide@now{y} \xdef\eighth@{0}
- \fi
- \expandafter\ifnum\csname hidestop0\endcsname=\cons@count
- \getregion@fromhidestack{0}
- \fi
- \fi
- \fi
- \fi
\loop
\advance\loopcount by 1
\ifT@coffee
@@ -13452,53 +14225,42 @@
\expandafter\TC@get\TC@line
\xdef\TC@first@{\csname TC@num\the\loopcount\endcsname}
\fi
- \xdef\seq@line{\csname sequence\the\loopcount\endcsname}
+ \xdef\seq@line{\csname sequence\the\loopcount\endcsname}
\expandafter\residue@get\seq@line
\xdef\first@{\csname res\the\loopcount\endcsname}
\innerloopcount=\csname res@num\first@\endcsname
\advance\innerloopcount by 1
\expandafter\xdef\csname res@num\first@\endcsname{\the\innerloopcount}
\expandafter\check@char\first@
+ \ifx\dom@in\y@ %%%%%%%%%%%*****
+ \xdef\temp@{\csname dom@num\the\loopcount\endcsname}
+ \expandafter\get@dom@count\temp@
+ \expandafter\xdef\csname dom@num\the\loopcount\endcsname{\temp@}
+ \fi %%%%%%%%%%%*****
\ifletter
- \res@count=\csname res@count\the\loopcount\endcsname
- \advance\res@count by 1
- \ifnum\res@count=0\relax
- \ifx\allow@zero\n@ \advance\res@count by 1 \fi
- \fi
- \expandafter\xdef\csname res@count\the\loopcount\endcsname{\the\res@count}
- \ifnum\loopcount=\exp@rt@num \xdef\sixth@{\the\res@count}\xdef\seventh@{y}\fi
- \ifx\hide@true\y@
- \expandafter\ifx\csname hidestart\the\loopcount\endcsname\ampers@nd
- \else
- \expandafter\ifnum\csname hidestart\the\loopcount\endcsname>\res@count
+ \ifx\dom@in\y@
\else
- \expandafter\ifnum\csname hidestop\the\loopcount\endcsname<\res@count
- \else
- \xdef\hide@now{y}\xdef\eighth@{\the\loopcount}
- \fi
- \expandafter\ifnum\csname hidestop\the\loopcount\endcsname=\res@count
- \xdef\first@@{\first@}
- \expandafter\getregion@fromhidestack{\the\loopcount}
- \xdef\first@{\first@@}
- \fi
- \fi
+ \res@count=\csname res@count\the\loopcount\endcsname
+ \advance\res@count by 1
+ \ifnum\res@count=0\relax
+ \ifx\allow@zero\n@ \advance\res@count by 1 \fi
\fi
\fi
+ \expandafter\xdef\csname res@count\the\loopcount\endcsname{\the\res@count}
+ \ifnum\loopcount=\exp@rt@num \xdef\sixth@{\the\res@count}\xdef\seventh@{y}\fi
\ifnum\loopcount=\rule@num\relax
+ \expandafter\ifnum\csname res@count\rule@num\endcsname>\rule@tens
+ \innerloopcount=\rule@tens \add@to@rule@tens
+ \fi
\expandafter\ifnum\csname res@count\rule@num\endcsname=\rule@tens
\expandafter\ifx\csname alt@ruler\rule@tens\endcsname\relax
\xdef\temp@{\rule@tens}
\else
\xdef\temp@{\csname alt@ruler\rule@tens\endcsname}
\fi
- \ifx\hide@now\n@ \xdef\ruler@{\ruler@ !<\temp@>} \fi
- \innerloopcount=\rule@tens \advance\innerloopcount by \ruler@step\relax
- \ifnum\innerloopcount=0
- \ifx\allow@zero\n@ \innerloopcount=\ruler@step \fi
- \fi
- \xdef\rule@tens{\the\innerloopcount}
+ \xdef\ruler@{\ruler@ !<\temp@>}
\else
- \ifx\hide@now\n@ \xdef\ruler@{\ruler@ -} \fi
+ \xdef\ruler@{\ruler@ -}
\fi
\xdef\temp@{\csname res@count\rule@num\endcsname}
\expandafter\ifx\csname alt@ruler\temp@\endcsname\relax
@@ -13506,7 +14268,6 @@
\expandafter\xdef\csname alt@ruler\temp@\endcsname{\temp@}
\fi
\fi
- \ifx\hide@now\n@
\ifx\collect@valtop\yes
\ifnum\v@lseqtop=\loopcount
\xdef\v@ltop{\v@ltop,\csname \ffourth@top\first@\endcsname}
@@ -13539,14 +14300,11 @@
\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
\xdef\last@restop{\last@@restop}
\xdef\last@@restop{\first@}
- \ifx\hide@now\n@
- \xdef\tr@nslatetop{\tr@nslatetop\first@}
- \fi
+ \xdef\tr@nslatetop{\tr@nslatetop\first@}
\innerloopcount=\triple@counttop
\advance\innerloopcount by 1
\ifnum\innerloopcount>3 \innerloopcount=1 \fi
@@ -13556,9 +14314,7 @@
\ifnum\tr@nsseqttop=\loopcount
\xdef\last@resttop{\last@@resttop}
\xdef\last@@resttop{\first@}
- \ifx\hide@now\n@
- \xdef\tr@nslatettop{\tr@nslatettop\first@}
- \fi
+ \xdef\tr@nslatettop{\tr@nslatettop\first@}
\innerloopcount=\triple@countttop
\advance\innerloopcount by 1
\ifnum\innerloopcount>3 \innerloopcount=1 \fi
@@ -13567,10 +14323,8 @@
\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
+ \last@@restttop{\first@}
+ \xdef\tr@nslatetttop{\tr@nslatetttop\first@}
\innerloopcount=\triple@counttttop
\advance\innerloopcount by 1
\ifnum\innerloopcount>3 \innerloopcount=1 \fi
@@ -13580,9 +14334,7 @@
\ifnum\tr@nsseqttttop=\loopcount
\xdef\last@resttttop{\last@@resttttop}
\xdef\last@@resttttop{\first@}
- \ifx\hide@now\n@
- \xdef\tr@nslatettttop{\tr@nslatettttop\first@}
- \fi
+ \xdef\tr@nslatettttop{\tr@nslatettttop\first@}
\innerloopcount=\triple@countttttop
\advance\innerloopcount by 1
\ifnum\innerloopcount>3 \innerloopcount=1 \fi
@@ -13592,9 +14344,7 @@
\ifnum\tr@nsseqbottom=\loopcount
\xdef\last@resbottom{\last@@resbottom}
\xdef\last@@resbottom{\first@}
- \ifx\hide@now\n@
- \xdef\tr@nslatebottom{\tr@nslatebottom\first@}
- \fi
+ \xdef\tr@nslatebottom{\tr@nslatebottom\first@}
\innerloopcount=\triple@countbottom
\advance\innerloopcount by 1
\ifnum\innerloopcount>3 \innerloopcount=1 \fi
@@ -13604,9 +14354,7 @@
\ifnum\tr@nsseqbbottom=\loopcount
\xdef\last@resbbottom{\last@@resbbottom}
\xdef\last@@resbbottom{\first@}
- \ifx\hide@now\n@
- \xdef\tr@nslatebbottom{\tr@nslatebbottom\first@}
- \fi
+ \xdef\tr@nslatebbottom{\tr@nslatebbottom\first@}
\innerloopcount=\triple@countbbottom
\advance\innerloopcount by 1
\ifnum\innerloopcount>3 \innerloopcount=1 \fi
@@ -13616,9 +14364,7 @@
\ifnum\tr@nsseqbbbottom=\loopcount
\xdef\last@resbbbottom{\last@@resbbbottom}
\xdef\last@@resbbbottom{\first@}
- \ifx\hide@now\n@
- \xdef\tr@nslatebbbottom{\tr@nslatebbbottom\first@}
- \fi
+ \xdef\tr@nslatebbbottom{\tr@nslatebbbottom\first@}
\innerloopcount=\triple@countbbbottom
\advance\innerloopcount by 1
\ifnum\innerloopcount>3 \innerloopcount=1 \fi
@@ -13628,9 +14374,7 @@
\ifnum\tr@nsseqbbbbottom=\loopcount
\xdef\last@resbbbbottom{\last@@resbbbbottom}
\xdef\last@@resbbbbottom{\first@}
- \ifx\hide@now\n@
- \xdef\tr@nslatebbbbottom{\tr@nslatebbbbottom\first@}
- \fi
+ \xdef\tr@nslatebbbbottom{\tr@nslatebbbbottom\first@}
\innerloopcount=\triple@countbbbbottom
\advance\innerloopcount by 1
\ifnum\innerloopcount>3 \innerloopcount=1 \fi
@@ -13645,8 +14389,7 @@
\expandafter\xdef\csname ch@rge\the\loopcount\endcsname{%
\the\innerloopcount}
\else
- \ifnum\loopcount=\rule@num \ifx\hide@now\n@ \xdef\ruler@{\ruler@ -} \fi\fi
- \ifx\hide@now\n@
+ \ifnum\loopcount=\rule@num \xdef\ruler@{\ruler@ -} \fi
\ifx\collect@valtop\yes
\ifnum\v@lseqtop=\loopcount
\xdef\v@ltop{\v@ltop,N}
@@ -13711,31 +14454,8 @@
\ifnum\tr@nsseqbbbbottom=\loopcount
\xdef\tr@nslatebbbbottom{\tr@nslatebbbbottom -}
\fi\fi
- \fi
\fi
\ifnum\loopcount<\seq@count \repeat
- \ifnum\rule@num=0
- \ifnum\cons@count=\rule@tens
- \expandafter\ifx\csname alt@ruler\rule@tens\endcsname\relax
- \xdef\temp@{\rule@tens}
- \else
- \xdef\temp@{\csname alt@ruler\rule@tens\endcsname}
- \fi
- \ifx\hide@now\n@ \xdef\ruler@{\ruler@ !<\temp@>} \fi
- \innerloopcount=\rule@tens \advance\innerloopcount by \ruler@step\relax
- \ifnum\innerloopcount=0
- \ifx\allow@zero\n@ \innerloopcount=\ruler@step \fi
- \fi
- \xdef\rule@tens{\the\innerloopcount}
- \else
- \ifx\hide@now\n@ \xdef\ruler@{\ruler@ -} \fi
- \fi
- \expandafter\ifx\csname alt@ruler\the\cons@count\endcsname\relax
- \else
- \expandafter\xdef\csname alt@ruler\the\cons@count\endcsname{\the\cons@count}
- \fi
- \fi
- \ifx\hide@now\n@
\ifx\collect@cons@graphtop\yes
\outerloopcount=1\relax
\temp@count=0\relax
@@ -13809,13 +14529,8 @@
\immediate\write\exp@rtfile{\string color col\the\outerloopcount, resi \sixth@}
\fi
\fi
- \fi
-%%%%%%%%%%%%%
- \ifx\hide@now\y@
- \regionalshadenowtrue \regionaltintnowtrue
- \regionalemphnowtrue \framenowtrue
- \fi
+ \xdef\g@p{n}
\ifregionalshadenow \calc@regshade \fi
\ifregionaltintnow \calc@regtint \fi
\ifregionalemphnow \calc@regemph \fi
@@ -13828,17 +14543,6 @@
\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
- \else
- \loopcount=\pos@count
- \advance\loopcount by -\bar@pos
- \xdef\bar@pos{\the\pos@count}
- \xdef\stylehidebar{\stylehidebar\the\loopcount;\csname hidestyle\eighth@\endcsname;\csname hidetext\eighth@\endcsname;}
- \fi
- \else
-%%%%%%%%%%%%%
\advance\pos@count by 1
\ifshow@logo \calc@logo \fi
\ifall@fshade \all@funcshade
@@ -13854,10 +14558,31 @@
\ifcase\match@case \unc@nserved \or \c@nserved \or \allm@tch \else \functi@nal \fi
\fi
\fi
-%%%%%%%%
- \fi
- \xdef\hide@now{n}
-%%%%%%%%
+ \ifnum\rule@num=0
+ \ifx\g@p\y@
+ \xdef\ruler@{\ruler@ -}
+ \else
+ \ifnum\cons@count=\rule@tens
+ \expandafter\ifx\csname alt@ruler\rule@tens\endcsname\relax
+ \xdef\temp@{\rule@tens}
+ \else
+ \xdef\temp@{\csname alt@ruler\rule@tens\endcsname}
+ \fi
+ \xdef\ruler@{\ruler@ !<\temp@>}
+ \innerloopcount=\rule@tens \advance\innerloopcount by \ruler@step\relax
+ \ifnum\innerloopcount=0
+ \ifx\allow@zero\n@ \innerloopcount=\ruler@step \fi
+ \fi
+ \xdef\rule@tens{\the\innerloopcount}
+ \else
+ \xdef\ruler@{\ruler@ -}
+ \fi
+ \expandafter\ifx\csname alt@ruler\the\cons@count\endcsname\relax
+ \else
+ \expandafter\xdef\csname alt@ruler\the\cons@count\endcsname{\the\cons@count}
+ \fi
+ \fi
+ \fi
\expandafter\ifnum\csname res@count\start@seq\endcsname<\end@num\relax
\c@nsensus
\else
@@ -13900,6 +14625,11 @@
\ifnum\res@count=0
\ifx\allow@zero\n@ \advance\res@count by 1 \fi
\fi
+ \ifx\dom@in\y@
+ \xdef\temp@{\csname dom@num\the\loopcount\endcsname}
+ \expandafter\get@dom@count\temp@
+ \expandafter\xdef\csname dom@num\the\loopcount\endcsname{\temp@}
+ \fi %%%%%%%%%%%*****
\expandafter\xdef\csname res@count\the\loopcount\endcsname{\the\res@count}
\ifnum\rule@num=\loopcount
\temp@count=\csname res@count\the\loopcount\endcsname
@@ -13929,10 +14659,6 @@
\csname sequence\the\loopcount\endcsname @}
\ifnum\loopcount<\seq@count \repeat
\end@count=0 \count@first \end@count=0 \xdef\start@number{0}
- \ifx\hide@now\n@
- \regionalshadenowfalse \regionalemphnowfalse \regionaltintnowfalse
- \framenowfalse
- \fi
\topfeaturenowfalse \bottomfeaturenowfalse
\ttopfeaturenowfalse \bbottomfeaturenowfalse
\tttopfeaturenowfalse \bbbottomfeaturenowfalse
@@ -14072,7 +14798,7 @@
\loop
\advance\loopcount by 1
\ifnumbers@left
- \innerloopcount=\csname seq@len\the\loopcount\endcsname\relax
+ \innerloopcount=\csname seq@len\the\loopcount\endcsname\relax
\expandafter\ifnum\csname res@count\the\loopcount\endcsname=%
\innerloopcount
\res@count=\innerloopcount
@@ -14083,6 +14809,11 @@
\ifx\allow@zero\n@ \advance\res@count by 1 \fi
\fi
\fi
+ \ifx\dom@in\y@
+ \xdef\temp@{\csname dom@num\the\loopcount\endcsname}
+ \expandafter\get@dom@count\temp@
+ \expandafter\xdef\csname dom@num\the\loopcount\endcsname{\the\res@count,\temp@}
+ \fi %%%%%%%%%%*****
\expandafter\xdef\csname res@count\the\loopcount\endcsname{\the\res@count}
\ifnames@right
\expandafter\xdef\csname seq\the\loopcount\endcsname{%
@@ -14092,15 +14823,18 @@
<\csname newseqname\the\loopcount\endcsname>
\csname res@count\the\loopcount\endcsname)}
\fi
- \expandafter\ifnum\csname res@count\the\loopcount\endcsname=%
- \innerloopcount
+ \ifx\dom@in\y@
\else
- \res@count=\csname res@count\the\loopcount\endcsname
- \advance\res@count by -1
- \ifnum\res@count=0
- \ifx\allow@zero\n@ \advance\res@count by -1 \fi
+ \expandafter\ifnum\csname res@count\the\loopcount\endcsname=%
+ \innerloopcount
+ \else
+ \res@count=\csname res@count\the\loopcount\endcsname
+ \advance\res@count by -1
+ \ifnum\res@count=0
+ \ifx\allow@zero\n@ \advance\res@count by -1 \fi
+ \fi
+ \expandafter\xdef\csname res@count\the\loopcount\endcsname{\the\res@count}
\fi
- \expandafter\xdef\csname res@count\the\loopcount\endcsname{\the\res@count}
\fi
\else
\ifnames@right
@@ -14110,8 +14844,16 @@
<\csname newseqname\the\loopcount\endcsname>}
\fi
\fi
- \innerloopcount=\csname res@count\the\loopcount\endcsname
- \advance\innerloopcount by \res@perline \advance\innerloopcount by 1
+ \ifx\dom@in\y@
+ \xdef\temp@{\csname dom@num@break\the\loopcount\endcsname}
+ \expandafter\get@dom@count\temp@
+ \expandafter\xdef\csname dom@num@break\the\loopcount\endcsname{\temp@}
+ \innerloopcount=\res@count
+ \else
+ \innerloopcount=\csname res@count\the\loopcount\endcsname
+ \advance\innerloopcount by \res@perline
+ \fi %%%%%%%%%%%%%*****
+ \advance\innerloopcount by 1
\ifregionalshade
\expandafter\ifx\csname start\the\loopcount\endcsname\ampers@nd
\else
@@ -14515,6 +15257,7 @@
\def\res@@style{\csname func@style#1\endcsname}%
\if\last@ *\def\last@{0}\fi
\if\last@ /\def\last@{10}\fi
+ \if\last@ !\def\last@{11}\fi
\else%
\iffuncmode%
\xdef\boxc@l@r{\csname fg@color#1\endcsname}%
@@ -14522,8 +15265,9 @@
\def\res@@style{\csname func@style#1\endcsname}%
\if\last@ *\def\last@{0}\fi
\if\last@ /\def\last@{10}\fi
+ \if\last@ !\def\last@{11}\fi
\else%
- \ifcase#1\xdef\boxc@l@r{\Allmatch}\xdef\textc@l@r{\TextAllmatch}%
+ \ifcase\last@\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}%
\def\res@@style{\id@style}%
@@ -14539,7 +15283,9 @@
\def\res@@style{\csname relax\endcsname}%
\or\xdef\boxc@l@r{\gap@bg}\xdef\textc@l@r{\gap@fg}%
\def\res@@style{\csname relax\endcsname}%
- \else\xdef\boxc@l@r{White}\xdef\textc@l@r{White}%
+ \or\xdef\boxc@l@r{White}\xdef\textc@l@r{White}%
+ \def\res@@style{\csname relax\endcsname}%
+ \else\xdef\boxc@l@r{\domgap@bg}\xdef\textc@l@r{\domgap@fg}%
\def\res@@style{\csname relax\endcsname}%
\fi\fi\fi\fi%
\ifx\second@\comm@%
@@ -14581,6 +15327,9 @@
\if\last@ *%
\xdef\boxc@l@r{\gap@bg}\xdef\textc@l@r{\gap@bg}%
\else%
+ \if\last@ !%
+ \xdef\boxc@l@r{\domgap@bg}\xdef\textc@l@r{\domgap@bg}%
+ \else%
\if\last@ /%
\xdef\boxc@l@r{White}\xdef\textc@l@r{White}%
\else%
@@ -14605,18 +15354,22 @@
\else
\xdef\textc@l@r{\c@nsc@l}%
\fi%
- \fi\fi\fi%
+ \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}%
+ \if\last@ !%
+ \xdef\boxc@l@r{\domgap@bg}\xdef\textc@l@r{\domgap@bg}%
\else%
- \xdef\boxc@l@r{White}\xdef\textc@l@r{TC\last@}%
- \def\res@@style{\csname relax\endcsname}%
+ \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%
\fi%
\else%
@@ -14636,7 +15389,9 @@
\def\res@@style{\csname relax\endcsname}%
\or\xdef\boxc@l@r{\gap@bg}\xdef\textc@l@r{\gap@fg}%
\def\res@@style{\csname relax\endcsname}%
- \else\xdef\boxc@l@r{White}\xdef\textc@l@r{White}%
+ \or\xdef\boxc@l@r{White}\xdef\textc@l@r{White}%
+ \def\res@@style{\csname relax\endcsname}%
+ \else\xdef\boxc@l@r{\domgap@bg}\xdef\textc@l@r{\domgap@fg}%
\def\res@@style{\csname relax\endcsname}%
\fi\fi\fi\fi%
\xdef\first@{#3@}%
@@ -15650,124 +16405,6 @@
\fi%
\fi%
}
-\def\next@hidebar#1;#2;#3;#4@{%
- \xdef\first@{#1}%
- \ifx\first@\ampers@nd%
- \else%
- \fontfamily{\hideblock@family}\fontseries{\hideblock@series}%
- \fontshape{\hideblock@shape}%
- \selectfont%
- \newline\hbox{}%
- \ifnames@right\else\ifnames@\hbox to \name@width{\hss}\fi\fi%
- \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi%
- \hbox to -\box@width{\hss}%
- \kern-0.1\box@width%
- \xdef\last@{#3[,]&}\expandafter\opt@color\last@%
- \ifx\f@color\comm@\xdef\f@color{Black}\fi%
- \textcolor{\f@color}{%
- \hbox to \first@\box@width{}%
- \hbox to 0pt{\hss\strut\hideblock@size{\,\fourth@}\hss}}%
- \xdef\last@{#2[,]&}\expandafter\opt@color\last@%
- \ifx\f@color\comm@\xdef\f@color{Black}\fi%
- \vspace{-0.23\box@height}%
- \xdef\temp@{triangle}%
- \ifx\fourth@\temp@%
- \else
- \xdef\temp@{square}%
- \ifx\fourth@\temp@%
- \else
- \xdef\temp@{none}%
- \ifx\fourth@\temp@%
- \else
- \vspace{-0.06\box@height}%
- \fi\fi\fi%
- \newline\hbox{}%
- \ifnames@right\else\ifnames@\hbox to \name@width{\hss}\fi\fi%
- \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi%
- \hbox to -\box@width{\hss}%
- \hbox to \first@\box@width{}%
- \kern-0.1\box@width%
- \textcolor{\f@color}{%
- \raisebox{0.47\box@height}{\rule{0.2\box@width}{\temp@@length}}%
- \xdef\first@{triangle}%
- \ifx\fourth@\first@%
- \kern-0.582\box@width%
- \raisebox{\temp@@length}{\hbox to \box@width{\hss$\bigtriangledown$\hss}}%
- \kern-0.418\box@width%
- \else
- \xdef\first@{square}%
- \ifx\fourth@\first@%
- \kern-0.6\box@width%
- \raisebox{-0.12\box@height}{%
- \raisebox{\temp@@length}{\hbox to \box@width{\hss$\square$\hss}}}%
- \raisebox{-0.19\box@height}{%
- \raisebox{\temp@@length}{\hbox to \box@width{\hss\strut}}}%
- \kern-1.4\box@width%
- \else
- \xdef\first@{none}%
- \ifx\fourth@\first@%
- \kern-0.6\box@width%
- \raisebox{-0.19\box@height}{%
- \raisebox{\temp@@length}{\hbox to \box@width{\hss\strut}}}%
- \kern-0.4\box@width%
- \else
- \kern-0.6\box@width%
- \raisebox{\temp@@length}{\hbox to \box@width{\hss$\bigodot$\hss}}%
- \kern-0.4\box@width%
- \fi%
- \fi%
- \fi%
- \kern-0.58\box@width%
- \raisebox{\temp@@length}{\hbox to \box@width{\hss$\bullet$\hss}}%
- \xdef\first@{#4@}}%
- \fi
-}
-\def\put@@hidebar{%
- \if\first@ @%
- \else
- \hbox to -\box@width{\hss}%
- \expandafter\next@hidebar\first@%
- \put@@hidebar%
- \fi%
-}
-\def\put@hidebar{%
- \ifx\hide@seqs\n@%
- \ifshow@cons\ifnum\cons@top=1 \vspace{-\baselineskip}\fi\fi%
- \temp@count=\seq@count%
- \advance\temp@count by 1%
- \ifx\hide@seqs\y@
- \advance\temp@count by -1 %
- \else%
- \loopcount=1%
- \xdef\first@{true}%
- \loop%
- \expandafter\ifx\csname hide@seq\the\loopcount\endcsname\first@%
- \advance\temp@count by -1\fi%
- \advance\loopcount by 1%
- \ifnum\loopcount>\seq@count\else\repeat%
- \fi
- \ifnum\temp@count>0%
- \setlength\temp@@length{\box@height}%
- \advance\temp@@length by \box@depth%
- \setlength\arrow@height{0.5\temp@@length}%
- \setlength\temp@@length{\temp@count\temp@@length}%
- \advance\temp@@length by \arrow@height%
- \advance\temp@@length by -0.75\box@height%%%%%%%
- \setlength\arrow@width{\sep@space}%
- \setlength\arrow@width{\seq@gap@num\arrow@width}%
- \advance\temp@@length by \arrow@width%
- \vspace{\arrow@height}%
- \vspace{-\temp@@length}%
- \vspace{-2.56\baselineskip}%
- \xdef\first@{\stylehidebar @}%
- \put@@hidebar%
- \vspace{-\arrow@height}%
- \vspace{-0.47\box@height}%
- \ifshow@cons\ifnum\cons@top=1 \vspace{\baselineskip}\fi\fi%
- \newline\hbox{}%
- \fi%
- \fi%
-}
\def\decimal@A#1#2@{%
\def\decimal@AB##1##2@{\xdef\temp@{##1.##2}}%
\xdef\temp@@{#1}%
@@ -15899,14 +16536,15 @@
\expandafter\decimal@E\fourth@%
\fi\fi\fi\fi%
\xdef\fourth@{\fl@g\temp@}%
- \if\first@ W%
+ \if\first@ W%
\hbox to \box@width{\hss%
- \raisebox{\temp@@length}{\raisebox{\fourth@\logo@height}{\scalebox{0.8}[\third@]%
+ \raisebox{\temp@@length}{\raisebox{\fourth@\logo@height}{\scalebox{\char@stretch@W}[\third@]%
{\hbox to \box@width{\textcolor{\tint@\csname logo@col\first@\endcsname}{\hss\residues@size{W}\hss}}}}}\hss}%
\kern-\box@width%
\else%
- \raisebox{\temp@@length}{\raisebox{\fourth@\logo@height}{\scalebox{1}[\third@]%
- {\hbox to \box@width{\textcolor{\tint@\csname logo@col\first@\endcsname}{\hss\residues@size{\first@}\hss}}}}}%
+ \hbox to \box@width{\hss%
+ \raisebox{\temp@@length}{\raisebox{\fourth@\logo@height}{\scalebox{\char@stretch}[\third@]%
+ {\hbox to \box@width{\textcolor{\tint@\csname logo@col\first@\endcsname}{\hss\residues@size{\first@}\hss}}}}}\hss}%
\kern-\box@width%
\fi%
\advance\temp@count by \second@%
@@ -16205,7 +16843,7 @@
\def\set@lines{%
\pos@count=1
- \xdef\frame@pos{1}\xdef\bar@pos{0}\xdef\hidebar@on{0}%
+ \xdef\frame@pos{1}\xdef\bar@pos{0}%
\xdef\featurepostop{1} \xdef\featureposbottom{1}%
\xdef\featureposttop{1} \xdef\featureposbbottom{1}%
\xdef\featurepostttop{1} \xdef\featureposbbbottom{1}%
@@ -16327,9 +16965,6 @@
\ifnum\frame@on=0 \xdef\frame@{0}\fi%
\put@frame%
\fi%
- \ifnum\hidebar@on=1 %
- \put@hidebar%
- \fi%
\ifshow@logo\ifnum\logo@top=1 %
\xdef\last@{\stack@sequencelogo @}%
\ifx\logo@name@user\ampers@nd\xdef\logo@name{logo}\else\xdef\logo@name{\logo@name@user}\fi
@@ -16435,7 +17070,7 @@
\fi
\fi
\xdef\consensus{} \xdef\ruler@{}
- \xdef\styleframe{} \xdef\stylehidebar{}
+ \xdef\styleframe{}
\xdef\textfeaturetop{} \xdef\textfeaturebottom{}
\xdef\textfeaturettop{} \xdef\textfeaturebbottom{}
\xdef\textfeaturetttop{} \xdef\textfeaturebbbottom{}
@@ -16559,7 +17194,7 @@
\xdef\textfeaturebbottom{} \xdef\featureonbbottom{0}
\xdef\textfeaturebbbottom{} \xdef\featureonbbbottom{0}
\xdef\textfeaturebbbbottom{} \xdef\featureonbbbbottom{0}
- \xdef\styleframe{} \xdef\stylehidebar{}
+ \xdef\styleframe{}
\xdef\stylefeaturetop{}
\xdef\stylefeaturettop{}
\xdef\stylefeaturetttop{}
@@ -16570,6 +17205,134 @@
\xdef\stylefeaturebbbbottom{}}
\def\guess@protein{\seqtype{P}\message{<Seqtype guess: protein>}}
\def\guess@DNA{\seqtype{N}\message{<Seqtype guess: nucleotide>}}
+\def\domain@count{%
+ \loopcount=0
+ \ifT@coffee
+ \xdef\seq@line{\csname T@cof\the\loopcount\endcsname}
+ \expandafter\res@get\seq@line
+ \expandafter\xdef\csname TC@num\the\loopcount\endcsname{\first@}
+ \expandafter\xdef\csname T@cof\the\loopcount\endcsname{\seq@line}
+ \fi
+ \loop
+ \advance\loopcount by 1
+ \xdef\seq@line{\csname seq\the\loopcount\endcsname}
+ \expandafter\res@get\seq@line
+ \expandafter\xdef\csname res\the\loopcount\endcsname{\first@}
+ \expandafter\xdef\csname seq\the\loopcount\endcsname{\seq@line}
+ \ifT@coffee
+ \xdef\seq@line{\csname T@cof\the\loopcount\endcsname}
+ \expandafter\res@get\seq@line
+ \expandafter\xdef\csname TC@num\the\loopcount\endcsname{\first@}
+ \expandafter\xdef\csname T@cof\the\loopcount\endcsname{\seq@line}
+ \fi
+ \ifnum\loopcount<\seq@count\repeat
+ \ifx\first@\ampers@nd
+ \else
+ \ifnum\next@domain@num>-99999\relax
+ \ifnum\domain@seq=0
+ \temp@count=\csname dom@count0\endcsname
+ \advance\temp@count by 1
+ \expandafter\xdef\csname dom@count0\endcsname{\the\temp@count}
+ \fi
+ \loopcount=0
+ \loop
+ \advance\loopcount by 1
+ \xdef\first@{\csname res\the\loopcount\endcsname}
+ \expandafter\check@char\first@
+ \ifletter
+ \temp@count=\csname dom@count\the\loopcount\endcsname
+ \advance\temp@count by 1
+ \expandafter\xdef\csname dom@count\the\loopcount\endcsname{\the\temp@count}
+ \if\seq@type A \relax
+ \temp@count=\char@num
+ \ifnum\temp@count>96 \advance\temp@count by -32 \fi
+ \ifnum\temp@count=69 \guess@protein
+ \else
+ \ifnum\temp@count=70 \guess@protein
+ \else
+ \ifnum\temp@count=73 \guess@protein
+ \else
+ \ifnum\temp@count=76 \guess@protein
+ \else
+ \ifnum\temp@count=80 \guess@protein
+ \else
+ \ifnum\temp@count=81 \guess@protein
+ \fi\fi\fi\fi\fi\fi
+ \fi
+ \fi
+ \ifnum\loopcount<\seq@count\repeat
+ \expandafter\ifnum\csname dom@count\domain@seq\endcsname=\next@domain@num
+ \advance\total@count by 1
+ \advance\outerloopcount by 1 \ifnum\outerloopcount=\res@perline \outerloopcount=0 \fi
+ \loopcount=0
+ \ifx\g@p\y@
+ \ifT@coffee
+ \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{%
+ \csname T@coffee\the\loopcount\endcsname \csname TC@num\the\loopcount\endcsname}
+ \fi
+ \fi
+ \ifT@coffee
+ \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{%
+ \csname T@coffee\the\loopcount\endcsname \csname TC@num\the\loopcount\endcsname}
+ \fi
+ \loop
+ \advance\loopcount by 1
+ \ifx\g@p\y@
+ \ifT@coffee
+ \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{%
+ \csname T@coffee\the\loopcount\endcsname \csname TC@num\the\loopcount\endcsname}
+ \fi
+ \expandafter\xdef\csname sequence\the\loopcount\endcsname{%
+ \csname sequence\the\loopcount\endcsname\equ@l}
+ \expandafter\xdef\csname dom@num\the\loopcount\endcsname{%
+ \csname dom@num\the\loopcount\endcsname \csname dom@count\the\loopcount\endcsname,}
+ \ifnum\outerloopcount=0
+ \expandafter\xdef\csname dom@num@break\the\loopcount\endcsname{%
+ \csname dom@num@break\the\loopcount\endcsname \csname dom@count\the\loopcount\endcsname,}
+ \fi
+ \fi
+ \ifT@coffee
+ \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{%
+ \csname T@coffee\the\loopcount\endcsname \csname TC@num\the\loopcount\endcsname}
+ \fi
+ \expandafter\xdef\csname sequence\the\loopcount\endcsname{%
+ \csname sequence\the\loopcount\endcsname \csname res\the\loopcount\endcsname}
+ \expandafter\xdef\csname dom@num\the\loopcount\endcsname{%
+ \csname dom@num\the\loopcount\endcsname \csname dom@count\the\loopcount\endcsname,}
+ \ifnum\outerloopcount=0
+ \expandafter\xdef\csname dom@num@break\the\loopcount\endcsname{%
+ \csname dom@num@break\the\loopcount\endcsname \csname dom@count\the\loopcount\endcsname,}
+ \fi
+ \ifnum\loopcount<\seq@count\repeat
+ \expandafter\get@item\domain@num@list
+ \xdef\domain@num@list{\first@}
+ \ifx\fourth@\ampers@nd \xdef\next@domain@num{-99999}
+ \else
+ \loopcount=\next@domain@num
+ \advance\loopcount by 1
+ \ifnum\loopcount=\fourth@
+ \xdef\g@p{n}
+ \else
+ \xdef\g@p{y}
+ \advance\total@count by 1
+ \advance\outerloopcount by 1
+ \ifnum\outerloopcount=\res@perline
+ \outerloopcount=0
+ \loopcount=0
+ \loop
+ \advance\loopcount by 1
+ \expandafter\xdef\csname dom@num@break\the\loopcount\endcsname{%
+ \csname dom@num@break\the\loopcount\endcsname \csname dom@count\the\loopcount\endcsname,}
+ \ifnum\loopcount<\seq@count\repeat
+ \fi
+ \fi
+ \xdef\next@domain@num{\fourth@} \xdef\end@num{\fourth@}
+ \fi
+ \fi
+ \domain@count
+ \fi
+ \fi
+}
\def\residue@count{%
\expandafter\res@get\seq@line
\if\first@\ampers@nd
@@ -16648,6 +17411,55 @@
\fi
\fi
\ifeof\alignfile
+ \ifx\dom@in\y@
+ \loopcount=0
+ \ifT@coffee
+ \xdef\temp@{\csname T@coffee\the\loopcount\endcsname}
+ \expandafter\get@temp\temp@
+ \expandafter\xdef\csname T@cof\the\loopcount\endcsname{\temp@ &@}
+ \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{}
+ \fi
+ \expandafter\xdef\csname dom@count\the\loopcount\endcsname{0}
+ \loop
+ \advance\loopcount by 1
+ \ifT@coffee
+ \xdef\temp@{\csname T@coffee\the\loopcount\endcsname}
+ \expandafter\get@temp\temp@
+ \expandafter\xdef\csname T@cof\the\loopcount\endcsname{\temp@ &@}
+ \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{}
+ \fi
+ \expandafter\xdef\csname seq\the\loopcount\endcsname{\csname sequence\the\loopcount\endcsname &@}
+ \expandafter\xdef\csname sequence\the\loopcount\endcsname{}
+ \expandafter\xdef\csname dom@num\the\loopcount\endcsname{}
+ \expandafter\xdef\csname dom@num@break\the\loopcount\endcsname{}
+ \expandafter\xdef\csname dom@count\the\loopcount\endcsname{0}
+ \ifnum\loopcount<\seq@count\repeat
+ \xdef\domain@num@list{}
+ \xdef\last@{\stack@dom}
+ \get@domain
+ \xdef\domain@num@list{\domain@num@list &,@}
+ \expandafter\get@item\domain@num@list
+ \xdef\next@domain@num{\fourth@} \xdef\domain@num@list{\first@}
+ \domain@count
+ \loopcount=0
+ \ifT@coffee
+ \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{\csname T@coffee\the\loopcount\endcsname @}
+ \fi
+ \loop
+ \advance\loopcount by 1
+ \ifT@coffee
+ \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{\csname T@coffee\the\loopcount\endcsname @}
+ \fi
+ \expandafter\xdef\csname dom@num\the\loopcount\endcsname{\csname dom@num\the\loopcount\endcsname @}
+ \expandafter\xdef\csname dom@num@break\the\loopcount\endcsname{%
+ \csname dom@num@break\the\loopcount\endcsname \csname dom@count\the\loopcount\endcsname,@}
+ \ifnum\loopcount<\seq@count\repeat
+ \if\seq@type A \guess@DNA \fi
+ \advance\seq@pointer by \total@count\relax
+ \xdef\total@pos{\the\total@count}
+
+ \else
+
\ifnum\start@seq=0
\xdef\seq@line{\csname sequence1\endcsname &@}
\else
@@ -16665,9 +17477,10 @@
\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
+ \fi
+ \ifshow@sublogo \prep@sublogo \fi
+ \ifshow@logo \prep@logo \fi
+ \ifnum\seq@pointer>\res@perline \block@output \fi
\else \read@loop
\fi}
\def\read@fasta{%
@@ -16697,6 +17510,55 @@
\fi
\fi
\ifeof\alignfile
+ \ifx\dom@in\y@
+ \loopcount=0
+ \ifT@coffee
+ \xdef\temp@{\csname T@coffee\the\loopcount\endcsname}
+ \expandafter\get@temp\temp@
+ \expandafter\xdef\csname T@cof\the\loopcount\endcsname{\temp@ &@}
+ \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{}
+ \fi
+ \expandafter\xdef\csname dom@count\the\loopcount\endcsname{0}
+ \loop
+ \advance\loopcount by 1
+ \ifT@coffee
+ \xdef\temp@{\csname T@coffee\the\loopcount\endcsname}
+ \expandafter\get@temp\temp@
+ \expandafter\xdef\csname T@cof\the\loopcount\endcsname{\temp@ &@}
+ \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{}
+ \fi
+ \expandafter\xdef\csname seq\the\loopcount\endcsname{\csname sequence\the\loopcount\endcsname &@}
+ \expandafter\xdef\csname sequence\the\loopcount\endcsname{}
+ \expandafter\xdef\csname dom@num\the\loopcount\endcsname{}
+ \expandafter\xdef\csname dom@num@break\the\loopcount\endcsname{}
+ \expandafter\xdef\csname dom@count\the\loopcount\endcsname{0}
+ \ifnum\loopcount<\seq@count\repeat
+ \xdef\domain@num@list{}
+ \xdef\last@{\stack@dom}
+ \get@domain
+ \xdef\domain@num@list{\domain@num@list &,@}
+ \expandafter\get@item\domain@num@list
+ \xdef\next@domain@num{\fourth@} \xdef\domain@num@list{\first@}
+ \domain@count
+ \loopcount=0
+ \ifT@coffee
+ \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{\csname T@coffee\the\loopcount\endcsname @}
+ \fi
+ \loop
+ \advance\loopcount by 1
+ \ifT@coffee
+ \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{\csname T@coffee\the\loopcount\endcsname @}
+ \fi
+ \expandafter\xdef\csname dom@num\the\loopcount\endcsname{\csname dom@num\the\loopcount\endcsname @}
+ \expandafter\xdef\csname dom@num@break\the\loopcount\endcsname{%
+ \csname dom@num@break\the\loopcount\endcsname \csname dom@count\the\loopcount\endcsname,@}
+ \ifnum\loopcount<\seq@count\repeat
+ \if\seq@type A \guess@DNA \fi
+ \advance\seq@pointer by \total@count\relax
+ \xdef\total@pos{\the\total@count}
+
+ \else
+
\ifnum\start@seq=0
\xdef\seq@line{\csname sequence1\endcsname &@}
\else
@@ -16714,9 +17576,10 @@
\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
+ \fi
+ \ifshow@sublogo \prep@sublogo \fi
+ \ifshow@logo \prep@logo \fi
+ \ifnum\seq@pointer>\res@perline \block@output \fi
\else
\read@fasta
\fi}
@@ -16847,6 +17710,7 @@
\fi
\set@savedseqlength
\loopcount=0 \xdef\seq@order{}
+ \expandafter\xdef\csname stack@dom\endcsname{&;&;&;&;@}
\expandafter\xdef\csname stack@reg\the\loopcount\endcsname{&;&;&;&;@}
\expandafter\xdef\csname stack@tintreg\the\loopcount\endcsname{&;&;&;@}
\expandafter\xdef\csname stack@hidereg\the\loopcount\endcsname{&;&;&;&;@}
@@ -17280,6 +18144,7 @@
\xdef\res@numW{0} \xdef\res@numX{0}
\xdef\res@numY{0} \xdef\res@numZ{0}
\expandafter\xdef\csname res@num\d@t\endcsname{0}
+\expandafter\xdef\csname res@num\equ@l\endcsname{0}
\xdef\res@corrA{0} \xdef\res@corrB{0}
\xdef\res@corrC{0} \xdef\res@corrD{0}
\xdef\res@corrE{0} \xdef\res@corrF{0}
@@ -17294,6 +18159,7 @@
\xdef\res@corrW{0} \xdef\res@corrX{0}
\xdef\res@corrY{0} \xdef\res@corrZ{0}
\expandafter\xdef\csname res@corr\d@t\endcsname{0}
+\expandafter\xdef\csname res@corr\equ@l\endcsname{0}
\xdef\corr@max{0} \xdef\do@freq@correction{n}
\xdef\res@total{0}
\xdef\stack@sequencelogo{} \xdef\bit@total{0}
@@ -17307,12 +18173,11 @@
\expandafter\xdef\csname group@num1\endcsname{0}
\expandafter\xdef\csname group@num2\endcsname{0}
\xdef\exp@rt@num{0} \xdef\exp@rt{n}
-\xdef\hide@true{n} \xdef\hide@now{n}
-\xdef\hide@label{circ}
\xdef\divref@{0}
\xdef\all@thresh@ld{100} \all@shadefalse
\hidefeaturenames \hidefeaturestylenames
\xdef\T@coffee@ccons{n} \xdef\T@coffee@bcons{n}
+\xdef\dom@in{no}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%% %%%%%
@@ -17345,6 +18210,8 @@
\gapchar{.} % . is printed in sequence gaps
\gaprule{0.3pt} % If a rule is printed in gaps use 0.3 pt
\gapcolors{Black}{White} % Gap symbols appear `Black on White'
+\domaingaprule{1pt} % If a rule is set between domains use 1 pt
+\domaingapcolors{Red}{White} % Domain separation line appears `Red on White'
\numberingcolor{Black} % Numbering color is `Black'
\shownumbering{right} % Show sequence numbering on the left
\namescolor{Black} % Names' color is `Black'
@@ -17406,10 +18273,6 @@
\setseries{featurestyles}{md} % Use normal series for feature styles
\setshape {featurestyles}{up} % Use upright shape for feature styles
\setsize {featurestyles}{normalsize}% Use normal size for feature styles
-\setfamily{hideblock}{rm} % Use roman family for hidden block labels
-\setseries{hideblock}{md} % Use normal series for hidden block labels
-\setshape {hideblock}{it} % Use italics shape for hidden block labels
-\setsize {hideblock}{normalsize} % Use normal size for hidden block labels
\setfamily{legend}{tt} % Use typewriter family for legend texts
\setseries{legend}{md} % Use normal series for legend texts
\setshape {legend}{up} % Use upright shape for legend texts
@@ -17546,6 +18409,8 @@
\gapchar{.} % . is printed in sequence gaps
\gaprule{0.3pt} % If a rule is printed in gaps use 0.3 pt
\gapcolors{Black}{White} % Gap symbols appear `Black on White'
+\domaingaprule{1pt} % If a rule is set between domains use 1 pt
+\domaingapcolors{Red}{White} % Domain separation line appears `Red on White'
\numberingcolor{Black} % Numbering color is `Black'
\shownumbering{right} % Show sequence numbering on the left
\namescolor{Black} % Names' color is `Black'
@@ -17603,10 +18468,6 @@
\setseries{features}{md} % Use normal series for feature texts
\setshape {features}{it} % Use italics shape for feature texts
\setsize {features}{normalsize} % Use normal size for feature texts
-\setfamily{hideblock}{rm} % Use roman family for hidden block labels
-\setseries{hideblock}{md} % Use normal series for hidden block labels
-\setshape {hideblock}{it} % Use italics shape for hidden block labels
-\setsize {hideblock}{normalsize} % Use normal size for hidden block labels
\setfamily{legend}{tt} % Use typewriter family for legend texts
\setseries{legend}{md} % Use normal series for legend texts
\setshape {legend}{up} % Use upright shape for legend texts
diff --git a/Master/texmf-dist/source/latex/texshade/texshade.ins b/Master/texmf-dist/source/latex/texshade/texshade.ins
index 7f548d9cdb8..51f043c8d20 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 1999-2008 Eric Beitz
+%% Copyright 1999-2009 Eric Beitz
%%
\def\batchfile{texshade.ins}
@@ -14,7 +14,7 @@
LaTeX package for typesetting nucleotide and peptide alignments
-Copyright (C) 1999-2007 Eric Beitz
+Copyright (C) 1999-2009 Eric Beitz
See the file texshade.txt
\endpreamble
diff --git a/Master/texmf-dist/tex/latex/texshade/texshade.def b/Master/texmf-dist/tex/latex/texshade/texshade.def
index 2de06346a09..a69d64f5d23 100644
--- a/Master/texmf-dist/tex/latex/texshade/texshade.def
+++ b/Master/texmf-dist/tex/latex/texshade/texshade.def
@@ -32,6 +32,8 @@
\gapchar{.} % . is printed in sequence gaps
\gaprule{0.3pt} % If a rule is printed in gaps use 0.3 pt
\gapcolors{Black}{White} % Gap symbols appear `Black on White'
+\domaingaprule{1pt} % If a rule is set between domains use 1 pt
+\domaingapcolors{Red}{White} % Domain separation line appears `Red on White'
\numberingcolor{Black} % Numbering color is `Black'
\shownumbering{right} % Show sequence numbering on the left
\namescolor{Black} % Names' color is `Black'
@@ -89,10 +91,6 @@
\setseries{features}{md} % Use normal series for feature texts
\setshape {features}{it} % Use italics shape for feature texts
\setsize {features}{normalsize} % Use normal size for feature texts
-\setfamily{hideblock}{rm} % Use roman family for hidden block labels
-\setseries{hideblock}{md} % Use normal series for hidden block labels
-\setshape {hideblock}{it} % Use italics shape for hidden block labels
-\setsize {hideblock}{normalsize} % Use normal size for hidden block labels
\setfamily{legend}{tt} % Use typewriter family for legend texts
\setseries{legend}{md} % Use normal series for legend texts
\setshape {legend}{up} % Use upright shape for legend texts
diff --git a/Master/texmf-dist/tex/latex/texshade/texshade.sty b/Master/texmf-dist/tex/latex/texshade/texshade.sty
index a3cd5b24ade..96221a75e00 100644
--- a/Master/texmf-dist/tex/latex/texshade/texshade.sty
+++ b/Master/texmf-dist/tex/latex/texshade/texshade.sty
@@ -8,13 +8,13 @@
%%
%% LaTeX package for typesetting nucleotide and peptide alignments
%%
-%% Copyright (C) 1999-2007 Eric Beitz
+%% Copyright (C) 1999-2009 Eric Beitz
%% See the file texshade.txt
%%
\NeedsTeXFormat{LaTeX2e}
-\ProvidesPackage{texshade}[2007/06/19 LaTeX TeXshade (v1.17)]
-\message{Package `texshade', Version 1.17 of 2007/06/19.}
+\ProvidesPackage{texshade}[2009/03/09 LaTeX TeXshade (v1.19)]
+\message{Package `texshade', Version 1.19 of 2009/03/09.}
\PassOptionsToPackage{dvips}{color}
\PassOptionsToPackage{dvips}{graphicx}
@@ -137,8 +137,10 @@
\def\n@me{Name:} \def\@msf{MSF:} \def\he@derend{//} \def\ampers@nd{&}
\def\comm@{,} \def\@loc{LOC} \def\@asg{ASG} \def\@t{@} \def\@HP{>HP:}
\def\gre@ter{>} \def\sm@ller{<} \def\N@{N} \def\equ@l{=} \def\H@{H}
-\def\gap@char{.} \def\yes{yes} \def\y@{y} \def\n@{n} \def\o@{o} \def\d@t{.}
+\def\gap@char{.} \def\dom@char{{\dom@rule}} \def\yes{yes} \def\y@{y} \def\n@{n} \def\o@{o} \def\d@t{.}
+\def\@TOM{ATOM} \def\C@lpha{CA} \def\@point@{point} \def\@line@{line} \def\@plane@{plane}
\def\gap@rule{\rule[0.3\box@height]{\box@width}{\gap@rulethick}}
+\def\dom@rule{\vrule depth\box@depth height\box@height width\domgap@rulethick}
\def\fgroup@num{0} \def\max@seqnumber{0} \def\@lign@count{0}
\def\resn@m@tch{upper} \def\ressimm@tch{upper}
\def\resm@tch{upper} \def\res@llm@tch{upper}
@@ -701,6 +703,8 @@
\expandafter\xdef\csname cons.Z\endcsname{0}
\expandafter\xdef\csname cons..\endcsname{0}
+\expandafter\xdef\csname cons==\endcsname{0}
+
\def\c@d@ns{%
\codon{A}{GCA,GCG,GCC,GCT,GCU,GCN}
\codon{B}{---}
@@ -1452,6 +1456,7 @@
\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\get@temp#1@{\xdef\temp@{#1}}
\def\TC@get#1#2@{\xdef\char@num{`#1}
\ifnum\char@num=45 \xdef\TC@first@{*}
\else
@@ -1596,6 +1601,7 @@
\ifnum\loopcount<\killseq@count \repeat
\ifnum\cons@num>0 \xdef\cons@num{\csname @rd\cons@num\endcsname} \fi
\ifnum\rule@num>0 \xdef\rule@num{\csname @rd\rule@num\endcsname} \fi
+ \ifnum\divref@>0 \xdef\divref@{\csname @rd\divref@\endcsname} \fi
\loopcount=0
\loop
\advance\loopcount by 1
@@ -2086,9 +2092,9 @@
\xdef\second@{rasmol}
\ifx\temp@\second@
\funcgroup{Asp, Glu}{DE}{Red}{White}{upper}{up}
- \funcgroup{Arg, Lys, His}{KR}{Blue}{White}{upper}{up}
- \funcgroup{Phe, Tyr, Trp}{FY}{MidnightBlue}{White}{upper}{up}
- \funcgroup{Ala, Gly}{G}{Gray}{White}{upper}{up}
+ \funcgroup{Arg, Lys, His}{KRH}{Blue}{White}{upper}{up}
+ \funcgroup{Phe, Tyr, Trp}{FYW}{MidnightBlue}{White}{upper}{up}
+ \funcgroup{Ala, Gly}{AG}{Gray}{White}{upper}{up}
\funcgroup{Cys, Met}{CM}{Yellow}{White}{upper}{up}
\funcgroup{Ser, Thr}{ST}{Orange}{White}{upper}{up}
\funcgroup{Asn, Gln}{NQ}{Cyan}{White}{upper}{up}
@@ -2154,14 +2160,6 @@
\xdef\tmpstack{\tmpstack\first@;\second@;\third@;\fourth@;} \sort@hidestack
\fi\fi
}
-\def\get@hideregions#1..#2,#3@{%
- \xdef\hide@true{y}
- \xdef\st@rt{#1} \xdef\st@p{#2} \xdef\list@{#3}
- \xdef\last@{\csname stack@hidereg\seq@\endcsname}
- \xdef\tmpstack{}
- \sort@hidestack
- \expandafter\xdef\csname stack@hidereg\seq@\endcsname{\tmpstack}
-}
\def\get@fromemphstack#1;#2;#3;#4@{%
\xdef\first@{#1} \xdef\second@{#2}
\xdef\third@{#3} \xdef\last@{#4@}
@@ -2194,6 +2192,40 @@
\sort@emphstack
\expandafter\xdef\csname stack@emphreg\seq@\endcsname{\tmpstack}
}
+\def\get@fromdomstack#1;#2;#3@{%
+ \xdef\first@{#1} \xdef\second@{#2}
+ \xdef\last@{#3@}
+}
+\def\sort@domstack{%
+ \expandafter\get@fromdomstack\last@
+ \ifx\first@\ampers@nd
+ \xdef\tmpstack{\tmpstack\st@rt;\st@p;&;&;@}
+ \else
+ \ifnum\st@rt<\second@
+ \xdef\tmpstack{\tmpstack\st@rt;\st@p;\first@;\second@;\last@}
+ \else
+ \xdef\tmpstack{\tmpstack\first@;\second@;} \sort@domstack
+ \fi\fi
+}
+\def\get@domainregions#1..#2,#3@{%
+ \xdef\st@rt{#1} \xdef\st@p{#2} \xdef\list@{#3}
+ \xdef\last@{\stack@dom}
+ \xdef\tmpstack{}
+ \sort@domstack
+ \xdef\stack@dom{\tmpstack}
+}
+\def\get@domain{%
+ \expandafter\get@fromdomstack\last@
+ \ifx\first@\ampers@nd
+ \else
+ \loopcount=\first@
+ \loop
+ \xdef\domain@num@list{\domain@num@list \the\loopcount,}
+ \advance\loopcount by 1
+ \ifnum\loopcount>\second@\else\repeat
+ \get@domain
+ \fi
+}
\def\getregion@fromtintstack#1{%
\xdef\temp@{#1}
\xdef\first@{\csname stack@tintreg\temp@\endcsname}
@@ -2365,6 +2397,132 @@
\fi%
\fi%
}
+
+\def\test@PDB#1:#2,#3,#4,#5,#6@{%
+ \xdef\last@{#1[,]&}\expandafter\opt@color\last@
+ \ifx\f@color\comm@
+ \xdef\PDB@distance{no}
+ \else
+ \xdef\f@color{\f@color .&&@}
+ \expandafter\coord@get\f@color
+ \temp@count=\c@@rd
+ \multiply\temp@count by \temp@count
+ \xdef\PDB@distance{\the\temp@count}
+ \fi
+ \xdef\PDB@hitpos{0}
+ \xdef\PDB@stack{}
+ \xdef\PDB@name{#2}
+ \xdef\PDB@type{point}
+ \ifx\fourth@\PDB@type
+ \xdef\last@{#3[,]&}\expandafter\opt@color\last@
+ \xdef\PDB@refnum@a{\fourth@}
+ \ifx\f@color\C@lpha
+ \xdef\PDB@back@side@a{CA}
+ \else
+ \xdef\PDB@back@side@a{side}
+ \fi
+ \xdef\PDB@refnum@b{0} \xdef\PDB@back@side@b{x}
+ \xdef\PDB@refnum@c{0} \xdef\PDB@back@side@c{x}
+ \ifx\PDB@distance\n@ \xdef\PDB@distance{3600}\fi
+ \load@PDB
+ \expandafter\get@item\PDB@stack \xdef\list@{\first@@}
+ \else
+ \xdef\PDB@type{line}
+ \ifx\fourth@\PDB@type
+ \xdef\last@{#3[,]&}\expandafter\opt@color\last@
+ \xdef\PDB@refnum{\fourth@}
+ \ifx\f@color\C@lpha
+ \xdef\PDB@back@side{CA}
+ \else
+ \xdef\PDB@back@side{side}
+ \fi
+ \xdef\last@{#4[,]&}\expandafter\opt@color\last@
+ \ifnum\PDB@refnum<\fourth@
+ \xdef\PDB@refnum@a{\PDB@refnum}
+ \xdef\PDB@refnum@b{\fourth@}
+ \xdef\PDB@back@side@a{\PDB@back@side}
+ \ifx\f@color\C@lpha
+ \xdef\PDB@back@side@b{CA}
+ \else
+ \xdef\PDB@back@side@b{side}
+ \fi
+ \else
+ \xdef\PDB@refnum@b{\PDB@refnum}
+ \xdef\PDB@refnum@a{\fourth@}
+ \xdef\PDB@back@side@b{\PDB@back@side}
+ \ifx\f@color\C@lpha
+ \xdef\PDB@back@side@a{CA}
+ \else
+ \xdef\PDB@back@side@a{side}
+ \fi
+ \fi
+ \xdef\PDB@refnum@c{0} \xdef\PDB@back@side@c{x}
+ \ifx\PDB@distance\n@ \xdef\PDB@distance{100}\fi
+ \load@PDB
+ \expandafter\get@item\PDB@stack \xdef\list@{\first@@}
+ \else
+ \xdef\PDB@type{plane}
+ \ifx\fourth@\PDB@type
+ \xdef\last@{#3[,]&}\expandafter\opt@color\last@
+ \xdef\PDB@refnum{\fourth@}
+ \ifx\f@color\C@lpha
+ \xdef\PDB@back@side{CA}
+ \else
+ \xdef\PDB@back@side{side}
+ \fi
+ \xdef\last@{#4[,]&}\expandafter\opt@color\last@
+ \ifnum\PDB@refnum<\fourth@
+ \xdef\PDB@refnum@a{\PDB@refnum}
+ \xdef\PDB@refnum@b{\fourth@}
+ \xdef\PDB@back@side@a{\PDB@back@side}
+ \ifx\f@color\C@lpha
+ \xdef\PDB@back@side@b{CA}
+ \else
+ \xdef\PDB@back@side@b{side}
+ \fi
+ \else
+ \xdef\PDB@refnum@b{\PDB@refnum}
+ \xdef\PDB@refnum@a{\fourth@}
+ \xdef\PDB@back@side@b{\PDB@back@side}
+ \ifx\f@color\C@lpha
+ \xdef\PDB@back@side@a{CA}
+ \else
+ \xdef\PDB@back@side@a{side}
+ \fi
+ \fi
+ \xdef\last@{#5[,]&}\expandafter\opt@color\last@
+ \xdef\PDB@refnum{\fourth@}
+ \ifx\f@color\C@lpha
+ \xdef\PDB@back@side{CA}
+ \else
+ \xdef\PDB@back@side{side}
+ \fi
+ \ifnum\PDB@refnum>\PDB@refnum@b
+ \xdef\PDB@refnum@c{\PDB@refnum}
+ \xdef\PDB@back@side@c{\PDB@back@side}
+ \else
+ \ifnum\PDB@refnum>\PDB@refnum@a
+ \xdef\PDB@refnum@c{\PDB@refnum@b}
+ \xdef\PDB@back@side@c{\PDB@back@side@b}
+ \xdef\PDB@refnum@b{\PDB@refnum}
+ \xdef\PDB@back@side@b{\PDB@back@side}
+ \else
+ \xdef\PDB@refnum@c{\PDB@refnum@b}
+ \xdef\PDB@back@side@c{\PDB@back@side@b}
+ \xdef\PDB@refnum@b{\PDB@refnum@a}
+ \xdef\PDB@back@side@b{\PDB@back@side@a}
+ \xdef\PDB@refnum@a{\PDB@refnum}
+ \xdef\PDB@back@side@a{\PDB@back@side}
+ \fi
+ \fi
+ \ifx\PDB@distance\n@ \xdef\PDB@distance{100}\fi
+ \load@PDB
+ \expandafter\get@item\PDB@stack \xdef\list@{\first@@}
+ \fi
+ \fi
+ \fi
+}
+
\def\test@fill#1:#2:#3&{%
\xdef\last@{#1[,][,]&}\expandafter\arrow@col@width\last@%
\xdef\second@@{\fourth@}%
@@ -2541,6 +2699,7 @@
\expandafter\xdef\csname \prfx grpZ\endcsname{-26}
\expandafter\xdef\csname \prfx grp-\endcsname{-999}
\expandafter\xdef\csname \prfx grp.\endcsname{-999}
+ \expandafter\xdef\csname \prfx grp=\endcsname{-999}
}
\def\inactivate@chars{%
\catcode`\#=12
@@ -2555,9 +2714,15 @@
\def\romancount{\@roman\loopcount}
\def\Romancount{\@Roman\loopcount}
\def\cut@name#1.#2@{\global\xdef\file@n@me{#1}}
+\def\coord@get#1.#2#3@{%
+ \xdef\temp@{#2}
+ \ifx\temp@\ampers@nd \xdef\temp@{0} \fi
+ \xdef\c@@rd{#1\temp@}
+}
\def\struc@get#1 #2 #3 #4 #5 #6 #7 #8 #9@{%
\xdef\first@{#1} \xdef\second@{#2} \xdef\third@{#3} \xdef\fourth@{#4}
- \xdef\fifth@{#5} \xdef\sixth@{#6} \xdef\seventh@{#7}\xdef\eighth@{#8}}
+ \xdef\fifth@{#5} \xdef\sixth@{#6} \xdef\seventh@{#7}\xdef\eighth@{#8}
+ \xdef\nineth@{#9}}
\def\get@PHD#1|#2|#3@{\xdef\PHD@line{\PHD@line #2}}
\def\write@PHDsec{%
\expandafter\get@sim\last@
@@ -3525,7 +3690,7 @@
\xdef\fourth@{#2,&,@}
\expandafter\get@triplet\fourth@
\fi}
-
+\def\get@dom@count#1,#2@{\res@count=#1 \xdef\temp@{#2 @}}
\def\get@name@number{%
\xdef\second@{n}
\loopcount=0
@@ -3542,6 +3707,318 @@
\fi
}
+\def\calc@distance@point{%
+ \loopcount=\xref@coord@a \advance\loopcount by -\x@coord\relax
+ \multiply\loopcount by \loopcount \xdef\x@distance{\the\loopcount}
+ \loopcount=\yref@coord@a \advance\loopcount by -\y@coord\relax
+ \multiply\loopcount by \loopcount \xdef\y@distance{\the\loopcount}
+ \loopcount=\zref@coord@a \advance\loopcount by -\z@coord\relax
+ \multiply\loopcount by \loopcount \xdef\z@distance{\the\loopcount}
+ \advance\loopcount by \y@distance\relax
+ \advance\loopcount by \x@distance\relax
+ \ifnum\loopcount > \PDB@distance \else
+ \loopcount=\PDB@hitpos \advance\loopcount by 1
+ \ifnum\loopcount=\PDB@pos
+ \else
+ \xdef\PDB@stack{\PDB@stack\PDB@hitpos,\PDB@pos..}
+ \fi
+ \xdef\PDB@hitpos{\PDB@pos}
+ \fi
+}
+
+\def\calc@distance@line{%
+ \loopcount=\x@coord\relax \multiply\loopcount by \x@orient
+ \temp@count=\y@coord \relax \multiply\temp@count by \y@orient
+ \advance\loopcount by \temp@count
+ \temp@count=\z@coord \relax \multiply\temp@count by \z@orient
+ \advance\loopcount by \temp@count
+ \advance\loopcount by -\c@nst@
+ \xdef\z@hler{\the\loopcount}
+ \multiply\loopcount by \x@orient \divide\loopcount by \f@ct@r \advance\loopcount by \xref@coord@a
+ \advance\loopcount by -\x@coord
+ \multiply\loopcount by \loopcount \xdef\x@distance{\the\loopcount}
+ \loopcount=\z@hler
+ \multiply\loopcount by \y@orient \divide\loopcount by \f@ct@r \advance\loopcount by \yref@coord@a
+ \advance\loopcount by -\y@coord
+ \multiply\loopcount by \loopcount \xdef\y@distance{\the\loopcount}
+ \loopcount=\z@hler
+ \multiply\loopcount by \z@orient \divide\loopcount by \f@ct@r \advance\loopcount by \zref@coord@a
+ \advance\loopcount by -\z@coord
+ \multiply\loopcount by \loopcount \xdef\z@distance{\the\loopcount}
+ \advance\loopcount by \y@distance\relax
+ \advance\loopcount by \x@distance\relax
+ \ifnum\loopcount > \PDB@distance \else
+ \loopcount=\PDB@hitpos \advance\loopcount by 1
+ \ifnum\loopcount=\PDB@pos
+ \else
+ \xdef\PDB@stack{\PDB@stack\PDB@hitpos,\PDB@pos..}
+ \fi
+ \xdef\PDB@hitpos{\PDB@pos}
+ \fi
+}
+
+\def\intr@@t{%
+ \loopcount=\r@@t
+ \temp@count=1
+ \loop
+ \advance\loopcount by \temp@count
+ \divide\loopcount by 2
+ \temp@count=\r@@t
+ \divide\temp@count by \loopcount
+ \ifnum\loopcount>\temp@count\repeat
+}
+
+\def\calc@distance@plane{%
+ \loopcount=\x@coord\relax
+ \multiply\loopcount by \x@orient
+ \temp@count=\y@coord \relax
+ \multiply\temp@count by \y@orient
+ \advance\loopcount by \temp@count
+ \temp@count=\z@coord \relax
+ \multiply\temp@count by \z@orient
+ \advance\loopcount by \temp@count
+ \advance\loopcount by \c@nst@
+ \divide\loopcount by \f@ct@r
+ \multiply\loopcount by \loopcount
+ \ifnum\loopcount > \PDB@distance \else
+ \loopcount=\PDB@hitpos \advance\loopcount by 1
+ \ifnum\loopcount=\PDB@pos
+ \else
+ \xdef\PDB@stack{\PDB@stack\PDB@hitpos,\PDB@pos..}
+ \fi
+ \xdef\PDB@hitpos{\PDB@pos}
+ \fi
+}
+
+\def\load@PDB{%
+ \bgroup
+ \immediate\openin\structurefile = \PDB@name\relax
+ \ifeof\structurefile
+ \PackageError{TeXshade}
+ {File `\PDB@name' not found}
+ {\MessageBreak
+ The file you specified is missing or you have \MessageBreak
+ misspelled it. \MessageBreak\MessageBreak
+ No PDB domain labeling will be displayed. \MessageBreak
+ Type <return> to proceed. \MessageBreak
+ Type X <return> to quit. \MessageBreak
+}
+ \immediate\closein\structurefile\egroup
+ \else
+ \message{<reading PDB: \PDB@name>}
+ \xdef\first@{}
+ \loop
+ \read\structurefile to \readline
+ \xdef\test@{\expandafter\string\readline}
+ \ifx\test@\par@
+ \else
+ \xdef\structureline{\readline & & & & & & & & &@}
+ \expandafter\struc@get\structureline
+ \ifx\first@\@TOM
+ \ifx\PDB@back@side@a\C@lpha
+ \ifx\third@\C@lpha
+ \xdef\temp@@@{\fifth@ &&@}
+ \expandafter\check@letter\temp@@@
+ \ifnumber
+ \ifnum\fifth@=\PDB@refnum@a
+ \xdef\sixth@{\sixth@ &.&&@} \expandafter\coord@get\sixth@ \xdef\xref@coord@a{\c@@rd}
+ \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\yref@coord@a{\c@@rd}
+ \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\zref@coord@a{\c@@rd}
+ \fi
+ \else
+ \ifnum\sixth@=\PDB@refnum@a
+ \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\xref@coord@a{\c@@rd}
+ \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\yref@coord@a{\c@@rd}
+ \xdef\nineth@{\nineth@ &.&&@} \expandafter\coord@get\nineth@ \xdef\zref@coord@a{\c@@rd}
+ \fi
+ \fi
+ \fi
+ \else
+ \xdef\temp@@@{\fifth@ &&@}
+ \expandafter\check@letter\temp@@@
+ \ifnumber
+ \ifnum\fifth@=\PDB@refnum@a
+ \xdef\sixth@{\sixth@ &.&&@} \expandafter\coord@get\sixth@ \xdef\xref@coord@a{\c@@rd}
+ \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\yref@coord@a{\c@@rd}
+ \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\zref@coord@a{\c@@rd}
+ \fi
+ \else
+ \ifnum\sixth@=\PDB@refnum@a
+ \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\xref@coord@a{\c@@rd}
+ \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\yref@coord@a{\c@@rd}
+ \xdef\nineth@{\nineth@ &.&&@} \expandafter\coord@get\nineth@ \xdef\zref@coord@a{\c@@rd}
+ \fi
+ \fi
+ \fi
+ \ifx\PDB@back@side@b\C@lpha
+ \ifx\third@\C@lpha
+ \xdef\temp@@@{\fifth@ &&@}
+ \expandafter\check@letter\temp@@@
+ \ifnumber
+ \ifnum\fifth@=\PDB@refnum@b
+ \xdef\sixth@{\sixth@ &.&&@} \expandafter\coord@get\sixth@ \xdef\xref@coord@b{\c@@rd}
+ \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\yref@coord@b{\c@@rd}
+ \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\zref@coord@b{\c@@rd}
+ \fi
+ \else
+ \ifnum\sixth@=\PDB@refnum@b
+ \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\xref@coord@b{\c@@rd}
+ \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\yref@coord@b{\c@@rd}
+ \xdef\nineth@{\nineth@ &.&&@} \expandafter\coord@get\nineth@ \xdef\zref@coord@b{\c@@rd}
+ \fi
+ \fi
+ \fi
+ \else
+ \xdef\temp@@@{\fifth@ &&@}
+ \expandafter\check@letter\temp@@@
+ \ifnumber
+ \ifnum\fifth@=\PDB@refnum@b
+ \xdef\sixth@{\sixth@ &.&&@} \expandafter\coord@get\sixth@ \xdef\xref@coord@b{\c@@rd}
+ \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\yref@coord@b{\c@@rd}
+ \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\zref@coord@b{\c@@rd}
+ \fi
+ \else
+ \ifnum\sixth@=\PDB@refnum@b
+ \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\xref@coord@b{\c@@rd}
+ \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\yref@coord@b{\c@@rd}
+ \xdef\nineth@{\nineth@ &.&&@} \expandafter\coord@get\nineth@ \xdef\zref@coord@b{\c@@rd}
+ \fi
+ \fi
+ \fi
+ \ifx\PDB@back@side@c\C@lpha
+ \ifx\third@\C@lpha
+ \xdef\temp@@@{\fifth@ &&@}
+ \expandafter\check@letter\temp@@@
+ \ifnumber
+ \ifnum\fifth@=\PDB@refnum@c
+ \xdef\sixth@{\sixth@ &.&&@} \expandafter\coord@get\sixth@ \xdef\xref@coord@c{\c@@rd}
+ \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\yref@coord@c{\c@@rd}
+ \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\zref@coord@c{\c@@rd}
+ \fi
+ \else
+ \ifnum\sixth@=\PDB@refnum@c
+ \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\xref@coord@c{\c@@rd}
+ \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\yref@coord@c{\c@@rd}
+ \xdef\nineth@{\nineth@ &.&&@} \expandafter\coord@get\nineth@ \xdef\zref@coord@c{\c@@rd}
+ \fi
+ \fi
+ \fi
+ \else
+ \xdef\temp@@@{\fifth@ &&@}
+ \expandafter\check@letter\temp@@@
+ \ifnumber
+ \ifnum\fifth@=\PDB@refnum@c
+ \xdef\sixth@{\sixth@ &.&&@} \expandafter\coord@get\sixth@ \xdef\xref@coord@c{\c@@rd}
+ \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\yref@coord@c{\c@@rd}
+ \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\zref@coord@c{\c@@rd}
+ \fi
+ \else
+ \ifnum\sixth@=\PDB@refnum@c
+ \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\xref@coord@c{\c@@rd}
+ \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\yref@coord@c{\c@@rd}
+ \xdef\nineth@{\nineth@ &.&&@} \expandafter\coord@get\nineth@ \xdef\zref@coord@c{\c@@rd}
+ \fi
+ \fi
+ \fi
+ \fi
+ \fi
+ \ifeof\structurefile \else\repeat
+ \closein\structurefile
+ \ifx\PDB@type\@line@
+ \loopcount=\xref@coord@a \advance\loopcount by -\xref@coord@b \xdef\x@orient{\the\loopcount}
+ \loopcount=\yref@coord@a \advance\loopcount by -\yref@coord@b \xdef\y@orient{\the\loopcount}
+ \loopcount=\zref@coord@a \advance\loopcount by -\zref@coord@b \xdef\z@orient{\the\loopcount}
+ \loopcount=\xref@coord@a \multiply\loopcount by \x@orient
+ \temp@count=\yref@coord@a \multiply\temp@count by \y@orient
+ \advance\loopcount by \temp@count
+ \temp@count=\zref@coord@a \multiply\temp@count by \z@orient
+ \advance\loopcount by \temp@count
+ \xdef\c@nst@{\the\loopcount}
+ \loopcount=\x@orient \multiply\loopcount by \x@orient
+ \temp@count=\y@orient \multiply\temp@count by \y@orient
+ \advance\loopcount by \temp@count
+ \temp@count=\z@orient \multiply\temp@count by \z@orient
+ \advance\loopcount by \temp@count
+ \xdef\f@ct@r{\the\loopcount}
+ \fi
+ \ifx\PDB@type\@plane@
+ \loopcount=\xref@coord@a \advance\loopcount by -\xref@coord@b \xdef\x@orient@r{\the\loopcount}
+ \loopcount=\yref@coord@a \advance\loopcount by -\yref@coord@b \xdef\y@orient@r{\the\loopcount}
+ \loopcount=\zref@coord@a \advance\loopcount by -\zref@coord@b \xdef\z@orient@r{\the\loopcount}
+ \loopcount=\xref@coord@a \advance\loopcount by -\xref@coord@c \xdef\x@orient@s{\the\loopcount}
+ \loopcount=\yref@coord@a \advance\loopcount by -\yref@coord@c \xdef\y@orient@s{\the\loopcount}
+ \loopcount=\zref@coord@a \advance\loopcount by -\zref@coord@c \xdef\z@orient@s{\the\loopcount}
+ \loopcount=\y@orient@r \multiply\loopcount by \z@orient@s
+ \temp@count=\z@orient@r \multiply\temp@count by \y@orient@s
+ \advance\loopcount by -\temp@count \divide\loopcount by 100 \xdef\x@orient{\the\loopcount}
+ \loopcount=\z@orient@r \multiply\loopcount by \x@orient@s
+ \temp@count=\x@orient@r \multiply\temp@count by \z@orient@s
+ \advance\loopcount by -\temp@count \divide\loopcount by 100 \xdef\y@orient{\the\loopcount}
+ \loopcount=\x@orient@r \multiply\loopcount by \y@orient@s
+ \temp@count=\y@orient@r \multiply\temp@count by \x@orient@s
+ \advance\loopcount by -\temp@count \divide\loopcount by 100 \xdef\z@orient{\the\loopcount}
+ \loopcount=\x@orient \multiply\loopcount by \xref@coord@a
+ \temp@count=\y@orient \multiply\temp@count by \yref@coord@a
+ \advance\loopcount by \temp@count
+ \temp@count=\z@orient \multiply\temp@count by \zref@coord@a
+ \advance\loopcount by \temp@count
+ \multiply\loopcount by -1\relax
+ \xdef\c@nst@{\the\loopcount}
+ \loopcount=\x@orient \multiply\loopcount by \loopcount
+ \temp@count=\y@orient \multiply\temp@count by \temp@count
+ \advance\loopcount by \temp@count
+ \temp@count=\z@orient \multiply\temp@count by \temp@count
+ \advance\loopcount by \temp@count
+ \xdef\r@@t{\the\loopcount} \intr@@t
+ \xdef\f@ct@r{\the\loopcount}
+ \fi
+ \immediate\openin\structurefile = \PDB@name\relax
+ \xdef\first@{}
+ \loop
+ \read\structurefile to \readline
+ \xdef\test@{\expandafter\string\readline}
+ \ifx\test@\par@
+ \else
+ \xdef\structureline{\readline & & & & & & & & &@}
+ \expandafter\struc@get\structureline
+ \ifx\first@\@TOM
+ \xdef\temp@@@{\fifth@ &&@}
+ \expandafter\check@letter\temp@@@
+ \ifnumber
+ \xdef\PDB@pos{\fifth@}
+ \xdef\sixth@{\sixth@ &.&&@} \expandafter\coord@get\sixth@ \xdef\x@coord{\c@@rd}
+ \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\y@coord{\c@@rd}
+ \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\z@coord{\c@@rd}
+ \else
+ \xdef\PDB@pos{\sixth@}
+ \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\x@coord{\c@@rd}
+ \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\y@coord{\c@@rd}
+ \xdef\nineth@{\nineth@ &.&&@} \expandafter\coord@get\nineth@ \xdef\z@coord{\c@@rd}
+ \fi
+ \ifnum\PDB@hitpos=\PDB@pos
+ \else
+ \ifx\PDB@type\@point@
+ \calc@distance@point
+ \else
+ \ifx\PDB@type\@line@
+ \calc@distance@line
+ \else
+ \ifx\PDB@type\@plane@
+ \calc@distance@plane
+ \fi
+ \fi
+ \fi
+ \fi
+ \fi
+ \fi
+ \ifeof\structurefile \xdef\PDB@stack{\PDB@stack\PDB@hitpos,&@}
+ \else\repeat
+ \closein\structurefile
+
+ \fi
+ \egroup
+ }
+
%%%%% Definition of user commands
\def\clearfuncgroups{\xdef\prfx{func} \clear@groups \xdef\fgroup@num{0}}
@@ -3630,6 +4107,34 @@
\separationline{\the\loopcount}
\ifnum\loopcount<\seq@count\repeat
\fi}
+\def\printPDBlist#1{%
+ \xdef\list@{}
+ \xdef\temp@{#1,,,:,,,,@} \expandafter\test@PDB\temp@
+ \xdef\first@{\list@ &}
+ \ifx\first@\ampers@nd
+ \else
+ \xdef\first@{\list@ @}
+ \loop
+ \expandafter\get@item\first@
+ \fourth@
+ \ifx\first@@\ampers@nd\else{,\ }\repeat
+ \fi
+}
+\def\messagePDBlist#1{%
+ \xdef\list@{}
+ \xdef\temp@{#1,,,:,,,,@} \expandafter\test@PDB\temp@
+ \xdef\first@{\list@ &}
+ \ifx\first@\ampers@nd
+ \else
+ \message{(#1:}
+ \xdef\first@{\list@ @}%
+ \loop%
+ \expandafter\get@item\first@%
+ \message{\fourth@}%
+ \ifx\first@@\ampers@nd\else\repeat%
+ \message{)}
+ \fi
+}
\def\shaderegion#1#2#3#4{%
\regionalshadetrue
\xdef\seq@{#1}
@@ -3647,6 +4152,7 @@
\expandafter\xdef\csname fgseqregion\the\loopcount\endcsname{#3}
\expandafter\xdef\csname bgseqregion\the\loopcount\endcsname{#4}
\xdef\list@{#2,&}
+ \xdef\temp@{#2,,,:,,,,@} \expandafter\test@PDB\temp@
\loop
\xdef\list@{\list@ @}
\expandafter\get@regions\list@
@@ -3670,6 +4176,7 @@
\else
\ifx\@ll\yes \xdef\@ll{y}\else \xdef\@ll{n}\fi
\xdef\list@{#2,&}
+ \xdef\temp@{#2,,,:,,,,@} \expandafter\test@PDB\temp@
\loop
\xdef\list@{\list@ @}
\expandafter\get@tintregions\list@
@@ -3710,6 +4217,7 @@
\else
\ifx\@ll\yes \xdef\@ll{y}\else \xdef\@ll{n}\fi
\xdef\list@{#2,&}
+ \xdef\temp@{#2,,,:,,,,@} \expandafter\test@PDB\temp@
\loop
\xdef\list@{\list@ @}
\expandafter\get@emphregions\list@
@@ -3734,29 +4242,13 @@
\else
\xdef\@ll{#3}
\xdef\list@{#2,&}
+ \xdef\temp@{#2,,,:,,,,@} \expandafter\test@PDB\temp@
\loop
\xdef\list@{\list@ @}
\expandafter\get@frameregions\list@
\ifx\list@\ampers@nd\else\repeat
\fi
}
-\def\hideblock#1#2#3#4{%
- \xdef\seq@{#1}
- \xdef\temp@{consensus} \ifx\seq@\temp@ \xdef\seq@{0} \fi
- \xdef\first@{\seq@ @} \expandafter\check@letter\first@
- \xdef\first@{\seq@}
- \ifletter \get@name@number \xdef\seq@{\first@} \fi
- \ifnum\seq@>\seq@count
- \message{<Ignored seq `\seq@' in \noexpand\hideblock>}
- \else
- \xdef\@ll{#3} \xdef\text@{#4}
- \xdef\list@{#2,&}
- \loop
- \xdef\list@{\list@ @}
- \expandafter\get@hideregions\list@
- \ifx\list@\ampers@nd\else\repeat
- \fi
-}
\def\bargraphstretch#1{\def\b@r@stretch{#1}}
\def\colorscalestretch#1{\def\sc@le@stretch{#1}}
\def\rm@@measure#1#2@{%
@@ -4118,7 +4610,7 @@
\ifx\second@@\last@
\xdef\list@{#3,&}
\xdef\style@{#4}
- \xdef\f@text@{#5}
+ \def\f@text@{#5}
\do@bargraph
\xdef\temp@{bottom}
\ifx\bottop@\temp@ \xdef\bottom@stretch{y}\fi
@@ -4133,11 +4625,14 @@
\ifx\second@@\last@
\xdef\list@{#3,&}
\xdef\style@{#4}
- \xdef\f@text@{#5}
+ \def\f@text@{#5}
\do@colorgraph
\else
- \xdef\f@text@{#5}
+ \xdef\f@@color{\f@color}
\xdef\list@{#3,&}
+ \xdef\temp@{#3,,,:,,,,@} \expandafter\test@PDB\temp@
+ \def\f@text@{#5}
+ \xdef\f@color{\f@@color}
\xdef\temp@{#4&}
\ifx\temp@\ampers@nd
\xdef\style@{&}
@@ -4215,7 +4710,9 @@
\fi
\fi
\fi
+ \loopcount=0
\loop
+ \advance\loopcount by 1\relax
\xdef\list@{\list@ @}
\expandafter\get@fregions\list@
\ifx\list@\ampers@nd\else\repeat
@@ -4273,7 +4770,23 @@
\def\decide@{\ifx\l@@k * \let\next\@rplfix \else \let\next\@rplvar \fi \next}
\futurelet\l@@k\decide@}
\def\numberingwidth#1{\def\num@width{#1}}
-\def\charstretch#1{\def\char@stretch{#1}}
+\def\charstretch#1{%
+ \def\char@stretch{#1}
+ \xdef\temp@{\char@stretch .00@} \expandafter\coord@get\temp@ \loopcount=\c@@rd
+ \multiply \loopcount by 7
+ \divide \loopcount by 10
+ \ifnum\loopcount<10
+ \xdef\temp@{0\the\loopcount @}
+ \else
+ \xdef\temp@{\the\loopcount @}
+ \fi
+ \expandafter\decimal@B\temp@
+ \ifnum\loopcount>99
+ \xdef\char@stretch@W{#1}
+ \else
+ \xdef\char@stretch@W{\temp@}
+ \fi
+}
\def\linestretch#1{\def\line@stretch{#1}}
\def\logostretch#1{%
\def\logo@stretch{#1}
@@ -4405,6 +4918,7 @@
\ifx\first@\second@\def\gap@char{o}
\else\def\gap@char{#1}\fi}
\def\gaprule#1{\def\gap@rulethick{#1}}
+\def\domaingaprule#1{\def\domgap@rulethick{#1}}
\newcommand{\setends}[3][&]{%
\xdef\start@seq{#2}
\xdef\temp@{consensus}
@@ -4877,9 +5391,6 @@
\xdef\temp@{legend}
\ifx\first@\temp@ \xdef\legend@family{\third@}
\else
- \xdef\temp@{hideblock}
- \ifx\first@\temp@ \xdef\hideblock@family{\third@}
- \else
\xdef\temp@{labels}
\ifx\first@\temp@ \xdef\label@family{\third@}
\else
@@ -4897,9 +5408,8 @@
\xdef\residues@family{\third@}
\xdef\legend@family{\third@}
\xdef\label@family{\third@}
- \xdef\hideblock@family{\third@}
\xdef\ruler@family{\second@}
- \fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi
+ \fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi
\fi
}
\def\setseries#1#2{%
@@ -4942,9 +5452,6 @@
\xdef\temp@{legend}
\ifx\first@\temp@ \xdef\legend@series{\third@}
\else
- \xdef\temp@{hideblock}
- \ifx\first@\temp@ \xdef\hideblock@series{\third@}
- \else
\xdef\temp@{labels}
\ifx\first@\temp@ \xdef\label@series{\third@}
\else
@@ -4958,9 +5465,8 @@
\xdef\namestext@series{\third@}
\xdef\residues@series{\third@}
\xdef\legend@series{\third@}
- \xdef\hideblock@series{\third@}
\xdef\label@series{\third@}
- \fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi
+ \fi\fi\fi\fi\fi\fi\fi\fi\fi\fi
\fi
}
\def\setshape#1#2{%
@@ -5011,9 +5517,6 @@
\xdef\temp@{legend}
\ifx\first@\temp@ \xdef\legend@shape{\third@}
\else
- \xdef\temp@{hideblock}
- \ifx\first@\temp@ \xdef\hideblock@shape{\third@}
- \else
\xdef\temp@{labels}
\ifx\first@\temp@ \xdef\label@shape{\third@}
\else
@@ -5027,9 +5530,8 @@
\xdef\namestext@shape{\third@}
\xdef\residues@shape{\third@}
\xdef\legend@shape{\third@}
- \xdef\hideblock@shape{\third@}
\xdef\label@shape{\third@}
- \fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi
+ \fi\fi\fi\fi\fi\fi\fi\fi\fi\fi
\fi
}
\def\setsize#1#2{%
@@ -5065,20 +5567,6 @@
\ifx\first@\temp@
\def\legend@size{\csname #2\endcsname}
\else
- \xdef\temp@{hideblock}
- \ifx\first@\temp@
- \xdef\temp@@{#2}
- \xdef\temp@{huge}
- \ifx\temp@\temp@@
- \def\hideblock@size{\csname LARGE\endcsname}
- \else
- \xdef\temp@{Huge}
- \ifx\temp@\temp@@
- \def\hideblock@size{\csname LARGE\endcsname}
- \else
- \def\hideblock@size{\csname #2\endcsname}
- \fi\fi
- \else
\xdef\temp@{labels}
\ifx\first@\temp@
\def\label@size{\csname #2\endcsname}
@@ -5097,11 +5585,10 @@
\def\numbertext@size{\csname #2\endcsname}
\def\namestext@size{\csname #2\endcsname}
\def\legend@size{\csname #2\endcsname}
- \def\hideblock@size{\csname #2\endcsname}
\def\label@size{\csname #2\endcsname}
\def\residues@size{\csname #2\endcsname}
\xdef\res@size{#2}
- \fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi
+ \fi\fi\fi\fi\fi\fi\fi\fi\fi\fi
\xdef\temp@{Huge}
\ifx\temp@\res@size
\def\bottomruler@size{\csname Large\endcsname}
@@ -5285,25 +5772,6 @@
\def\legendLARGE {\setsize{legend}{LARGE}}
\def\legendhuge {\setsize{legend}{huge}}
\def\legendHuge {\setsize{legend}{Huge}}
-\def\hideblockrm{\setfamily{hideblock}{rm}}
-\def\hideblocksf{\setfamily{hideblock}{sf}}
-\def\hideblocktt{\setfamily{hideblock}{tt}}
-\def\hideblockmd{\setseries{hideblock}{md}}
-\def\hideblockbf{\setseries{hideblock}{bf}}
-\def\hideblockup{\setshape {hideblock}{up}}
-\def\hideblockit{\setshape {hideblock}{it}}
-\def\hideblocksl{\setshape {hideblock}{sl}}
-\def\hideblocksc{\setshape {hideblock}{sc}}
-\def\hideblocktiny {\setsize{hideblock}{tiny}}
-\def\hideblockscriptsize {\setsize{hideblock}{scriptsize}}
-\def\hideblockfootnotesize{\setsize{hideblock}{footnotesize}}
-\def\hideblocksmall {\setsize{hideblock}{small}}
-\def\hideblocknormalsize {\setsize{hideblock}{normalsize}}
-\def\hideblocklarge {\setsize{hideblock}{large}}
-\def\hideblockLarge {\setsize{hideblock}{Large}}
-\def\hideblockLARGE {\setsize{hideblock}{LARGE}}
-\def\hideblockhuge {\setsize{hideblock}{LARGE}}
-\def\hideblockHuge {\setsize{hideblock}{LARGE}}
\def\rulerrm{\setfamily{ruler}{rm}}
\def\rulersf{\setfamily{ruler}{sf}}
\def\rulertt{\setfamily{ruler}{tt}}
@@ -5396,6 +5864,12 @@
\expandafter\def\csname fg@textcolor*\endcsname{#1}\fi
\ifx\second@\last@\else\def\gap@bg{#2}
\expandafter\def\csname fg@color*\endcsname{#2}\fi}
+\def\domaingapcolors#1#2 {\xdef\first@{#1&}\xdef\second@{#2&}
+ \xdef\last@{\ampers@nd}
+ \ifx\first@\last@\else\def\domgap@fg{#1}
+ \expandafter\def\csname fg@textcolor!\endcsname{#1}\fi
+ \ifx\second@\last@\else\def\domgap@bg{#2}
+ \expandafter\def\csname fg@color!\endcsname{#2}\fi}
\def\shadebox#1{%
\xdef\first@{White}%
\xdef\third@{#1}%
@@ -5868,6 +6342,24 @@
\fi
}
+\def\setdomain#1#2{%
+ \xdef\first@{#1}
+ \xdef\temp@{consensus}
+ \ifx\first@\temp@ \xdef\domain@seq{0}
+ \else
+ \xdef\first@{#1 @} \expandafter\check@letter\first@
+ \xdef\first@{#1} \ifletter \get@name@number \fi
+ \xdef\domain@seq{\csname @rd\first@\endcsname}%
+ \fi
+ \xdef\list@{#2,&}
+ \xdef\temp@{#2,,,:,,,,@} \expandafter\test@PDB\temp@
+ \loop
+ \xdef\list@{\list@ @}
+ \expandafter\get@domainregions\list@
+ \ifx\list@\ampers@nd\else\repeat
+ \xdef\dom@in{y}
+}
+
%%%%% Calculate consensus
\def\check@sim{%
@@ -5933,7 +6425,6 @@
\fi
\else
\newresfalse
- \expandafter\xdef\csname res\the\loopcount\endcsname{\d@t}
\fi
\ifnewres
@@ -6027,13 +6518,29 @@
\expandafter\xdef\csname seq\the\loopcount\endcsname{%
\csname seq\the\loopcount\endcsname3\gap@char}
\else
+ \expandafter\ifx\csname res\the\loopcount\endcsname\equ@l
+ \expandafter\xdef\csname seq\the\loopcount\endcsname{%
+ \csname seq\the\loopcount\endcsname!\dom@char} \xdef\g@p{y}
+ \else
\expandafter\xdef\csname seq\the\loopcount\endcsname{%
\csname seq\the\loopcount\endcsname%
3\csname res\the\loopcount\endcsname}
\fi
+ \fi
\else
\xdef\first@{\csname res\the\loopcount\endcsname}
- \ifx\first@\d@t
+ \ifx\first@\equ@l
+ \def\first@{\dom@char} \def\third@{9}
+ \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\third@\first@} \xdef\g@p{y}
+ \else
+ \ifx\first@\d@t
\expandafter\ifnum\csname res@count\the\loopcount\endcsname%
<\csname seq@start\the\loopcount\endcsname
\ifsh@wg@ps
@@ -6053,27 +6560,28 @@
\fi
\fi
\fi
- \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\third@\first@}
- \else
- \ifnum\divref@=\loopcount\else
- \xdef\low@up{lower} \ifx\resn@m@tch\low@up \make@lower \else
- \xdef\low@up{upper} \ifx\resn@m@tch\low@up
- \else \xdef\first@{\resn@m@tch} \fi\fi\fi
- \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
- \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
+ \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}
+ \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\endcsname3\first@}
+ \expandafter\xdef\csname seq\the\loopcount\endcsname{%
+ \csname seq\the\loopcount\endcsname\third@\first@}
+ \else
+ \ifnum\divref@=\loopcount\else
+ \xdef\low@up{lower} \ifx\resn@m@tch\low@up \make@lower \else
+ \xdef\low@up{upper} \ifx\resn@m@tch\low@up
+ \else \xdef\first@{\resn@m@tch} \fi\fi\fi
+ \expandafter\ifx\csname 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\endcsname3\first@}
+ \fi
\fi
\fi
\ifnum\loopcount<\seq@count \repeat
@@ -6086,9 +6594,13 @@
\expandafter\ifx\csname emph@seq0\endcsname\y@
\expandafter\xdef\csname emph@seq0\endcsname{n}
\xdef\first@{,\first@}\fi
- \xdef\consensus{\consensus 4\first@}
- \expandafter\ifx\csname res\cons@num\endcsname\d@t
+ \ifx\g@p\y@
+ \xdef\consensus{\consensus 8{}}
+ \else
+ \xdef\consensus{\consensus 4\first@}
+ \expandafter\ifx\csname res\cons@num\endcsname\d@t
\else\xdef\constopo{\constopo 0}\fi
+ \fi
\else
\ifnum\cons@num>0
\xdef\tmp@{\csname res\cons@num\endcsname}
@@ -6104,6 +6616,7 @@
\expandafter\ifx\csname hide@seq\the\loopcount\endcsname\first@
\xdef\first@{\csname res\the\loopcount\endcsname}
\ifx\first@\d@t\def\first@{\gap@char}\fi
+ \ifx\first@\equ@l\def\first@{\dom@char} \xdef\g@p{y} \fi
\expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
\expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
\xdef\first@{=\first@}\fi
@@ -6111,8 +6624,7 @@
\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%
- 3\first@}
+ \csname seq\the\loopcount\endcsname3\first@}
\else
\xdef\first@{\csname res\the\loopcount\endcsname}
\xdef\last@{\csname res\the\loopcount\endcsname}
@@ -6123,6 +6635,9 @@
\xdef\low@up{upper} \ifx\ressimm@tch\low@up
\else \xdef\first@{\ressimm@tch} \fi\fi\fi
\else
+ \ifx\first@\equ@l
+ \def\first@{\dom@char} \def\third@{9} \xdef\g@p{y}
+ \else
\ifx\first@\d@t
\expandafter\ifnum\csname res@count\the\loopcount\endcsname%
<\csname seq@start\the\loopcount\endcsname
@@ -6150,6 +6665,7 @@
\xdef\low@up{upper} \ifx\resn@m@tch\low@up
\else \xdef\first@{\resn@m@tch} \fi\fi\fi
\fi
+ \fi
\fi
\expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
\expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
@@ -6171,8 +6687,12 @@
\expandafter\ifx\csname emph@seq0\endcsname\y@
\expandafter\xdef\csname emph@seq0\endcsname{n}
\xdef\first@{,\first@}\fi
- \xdef\consensus{\consensus5\first@}
- \xdef\constopo{\constopo 1}
+ \ifx\g@p\y@
+ \xdef\consensus{\consensus 8{}}
+ \else
+ \xdef\consensus{\consensus5\first@}
+ \xdef\constopo{\constopo 1}
+ \fi
\fi
\else
\iffuncmode
@@ -6180,6 +6700,17 @@
\loop
\advance\loopcount by 1
\xdef\first@{\csname res\the\loopcount\endcsname}
+ \ifx\first@\equ@l
+ \def\first@{\dom@char} \def\third@{!} \xdef\g@p{y}
+ \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\third@\first@}
+ \else
\ifx\first@\d@t
\expandafter\ifnum\csname res@count\the\loopcount\endcsname%
<\csname seq@start\the\loopcount\endcsname
@@ -6221,6 +6752,7 @@
\expandafter\xdef\csname seq\the\loopcount\endcsname{%
\csname seq\the\loopcount\endcsname0\first@}
\fi
+ \fi
\ifnum\loopcount<\seq@count \repeat
\else
\loopcount=0
@@ -6230,6 +6762,7 @@
\expandafter\ifx\csname hide@seq\the\loopcount\endcsname\first@
\xdef\first@{\csname res\the\loopcount\endcsname}
\ifx\first@\d@t\def\first@{\gap@char}\fi
+ \ifx\first@\equ@l\def\first@{\dom@char} \xdef\g@p{y} \fi
\expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
\expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
\xdef\first@{=\first@}\fi
@@ -6241,6 +6774,17 @@
3\first@}
\else
\xdef\first@{\csname res\the\loopcount\endcsname}
+ \ifx\first@\equ@l
+ \def\first@{\dom@char} \def\third@{9} \xdef\g@p{y}
+ \expandafter\ifx\csname 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\third@\first@}
+ \else
\ifx\first@\d@t
\expandafter\ifnum\csname res@count\the\loopcount\endcsname%
<\csname seq@start\the\loopcount\endcsname
@@ -6283,6 +6827,7 @@
\expandafter\xdef\csname seq\the\loopcount\endcsname{%
\csname seq\the\loopcount\endcsname3\first@}
\fi
+ \fi
\fi
\ifnum\loopcount<\seq@count \repeat
\xdef\low@up{lower} \ifx\n@m@tch\low@up \xdef\first@{{ }} \else
@@ -6294,8 +6839,12 @@
\expandafter\ifx\csname emph@seq0\endcsname\y@
\expandafter\xdef\csname emph@seq0\endcsname{n}
\xdef\first@{,\first@}\fi
- \xdef\consensus{\consensus 4\first@}
- \xdef\constopo{\constopo 0}
+ \ifx\g@p\y@
+ \xdef\consensus{\consensus 8{}}
+ \else
+ \xdef\consensus{\consensus 4\first@}
+ \xdef\constopo{\constopo 0}
+ \fi
\fi\fi}
\def\c@nserved{%
@@ -6307,6 +6856,7 @@
\expandafter\ifx\csname hide@seq\the\loopcount\endcsname\first@
\xdef\first@{\csname res\the\loopcount\endcsname}
\ifx\first@\d@t\def\first@{\gap@char}\fi
+ \ifx\first@\equ@l\def\first@{\dom@char} \xdef\g@p{y} \fi
\expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
\expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
\xdef\first@{=\first@}\fi
@@ -6345,6 +6895,7 @@
\xdef\low@up{upper} \ifx\resn@m@tch\low@up
\else \xdef\first@{\resn@m@tch} \fi\fi\fi
\fi
+ \ifx\first@\equ@l \def\first@{\dom@char} \def\third@{9} \xdef\g@p{y} \fi
\ifx\first@\d@t
\expandafter\ifnum\csname res@count\the\loopcount\endcsname%
<\csname seq@start\the\loopcount\endcsname
@@ -6386,8 +6937,12 @@
\expandafter\ifx\csname emph@seq0\endcsname\y@
\expandafter\xdef\csname emph@seq0\endcsname{n}
\xdef\first@{,\first@}\fi
- \xdef\consensus{\consensus 5\first@}
- \xdef\constopo{\constopo 2}}
+ \ifx\g@p\y@
+ \xdef\consensus{\consensus 8{}}
+ \else
+ \xdef\consensus{\consensus 5\first@}
+ \xdef\constopo{\constopo 2}
+ \fi}
\def\allm@tch{%
\xdef\tmp@{\csname res\cons@seq\endcsname}
@@ -6398,6 +6953,7 @@
\expandafter\ifx\csname hide@seq\the\loopcount\endcsname\first@
\xdef\first@{\csname res\the\loopcount\endcsname}
\ifx\first@\d@t\def\first@{\gap@char}\fi
+ \ifx\first@\equ@l\def\first@{\dom@char} \xdef\g@p{y} \fi
\expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
\expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
\xdef\first@{=\first@}\fi
@@ -6441,6 +6997,7 @@
\xdef\low@up{upper} \ifx\resn@m@tch\low@up
\else \xdef\first@{\resn@m@tch} \fi\fi\fi
\fi
+ \ifx\first@\equ@l \def\first@{\dom@char} \def\third@{9} \xdef\g@p{y} \fi
\ifx\first@\d@t
\expandafter\ifnum\csname res@count\the\loopcount\endcsname%
<\csname seq@start\the\loopcount\endcsname
@@ -6482,8 +7039,12 @@
\expandafter\ifx\csname emph@seq0\endcsname\y@
\expandafter\xdef\csname emph@seq0\endcsname{n}
\xdef\first@{,\first@}\fi
- \xdef\consensus{\consensus 6\first@}
- \xdef\constopo{\constopo 3}}
+ \ifx\g@p\y@
+ \xdef\consensus{\consensus 8{}}
+ \else
+ \xdef\consensus{\consensus 6\first@}
+ \xdef\constopo{\constopo 3}
+ \fi}
\def\functi@nal{%
\ifnum\cons@num>0
@@ -6509,6 +7070,9 @@
0\first@}
\else
\xdef\first@{\csname res\the\loopcount\endcsname}
+ \ifx\first@\equ@l
+ \def\first@{\dom@char} \def\third@{!} \xdef\g@p{y}
+ \else
\ifx\first@\d@t
\expandafter\ifnum\csname res@count\the\loopcount\endcsname%
<\csname seq@start\the\loopcount\endcsname
@@ -6540,6 +7104,7 @@
\xdef\low@up{upper} \ifx\resn@m@tch\low@up
\else \xdef\first@{\resn@m@tch} \fi\fi
\fi
+ \fi
\fi
\expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
\expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
@@ -6559,6 +7124,7 @@
\xdef\first@{\csname res\the\loopcount\endcsname}
\xdef\second@{\csname funcgrp\first@\endcsname}
\ifnum\second@<0 \xdef\second@{0} \fi
+ \ifx\first@\equ@l \def\first@{\dom@char} \def\second@{!} \xdef\g@p{y} \fi
\ifx\first@\d@t
\expandafter\ifnum\csname res@count\the\loopcount\endcsname%
<\csname seq@start\the\loopcount\endcsname
@@ -6609,19 +7175,11 @@
\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@\equ@l \def\first@{\dom@char} \def\second@{!} \xdef\g@p{y} \fi
\ifx\first@\d@t
\expandafter\ifnum\csname res@count\the\loopcount\endcsname%
<\csname seq@start\the\loopcount\endcsname
@@ -6665,7 +7223,22 @@
\csname seq\the\loopcount\endcsname%
\second@\first@}
\fi
- \ifnum\loopcount<\seq@count \repeat}
+ \ifnum\loopcount<\seq@count \repeat
+ \xdef\first@{\csname res0\endcsname}
+ \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}
+ \ifx\g@p\y@
+ \xdef\consensus{\consensus 8{}}
+ \else
+ \xdef\consensus{\consensus\second@\n@m@tch}
+ \xdef\constopo{\constopo\second@}
+ \fi
+ }
\def\getregion@fromstack@first{%
\expandafter\getregion@fromstack{\the\loopcount}
@@ -6708,7 +7281,6 @@
\fi
\fi\fi
\ifnum\loopcount<\seq@count \repeat
- \ifx\hide@now\n@
\loopcount=0
\expandafter\ifx\csname shade@style\the\loopcount\endcsname\y@
\else
@@ -6728,7 +7300,6 @@
&\csname shade@style\the\loopcount\endcsname)}
\fi
\ifnum\loopcount<\seq@count \repeat
- \fi
}
\def\getregion@fromemphstack@first{%
@@ -7089,13 +7660,13 @@
\xdef\cons@val{\csname TC@num0\endcsname}
\if\cons@val *
\xdef\cons@val{99}
- \fi \message{(b(\cons@val)b)}
+ \fi
\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
\fi
}
@@ -7990,11 +8561,24 @@
\ifnum\loopcount<\seq@count \repeat
}
+\def\add@to@rule@tens{%
+ \advance\innerloopcount by \ruler@step\relax
+ \ifnum\innerloopcount=0
+ \ifx\allow@zero\n@ \innerloopcount=\ruler@step \fi
+ \fi
+ \expandafter\ifnum\csname res@count\rule@num\endcsname>\innerloopcount \add@to@rule@tens
+ \else
+ \xdef\rule@tens{\the\innerloopcount}
+ \fi
+}
+
\def\c@nsensus{%
\ifnum\pos@count>\res@perline
\else
\loopcount=0
- \global\advance\cons@count by 1\relax
+ \ifx\g@p\n@
+ \global\advance\cons@count by 1\relax
+ \fi
\ifnum\cons@count=0\relax
\ifx\allow@zero\n@ \global\advance\cons@count by 1 \fi
\fi
@@ -8003,21 +8587,6 @@
\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
- \else
- \expandafter\ifnum\csname hidestart0\endcsname>\cons@count
- \else
- \expandafter\ifnum\csname hidestop0\endcsname<\cons@count
- \else
- \xdef\hide@now{y} \xdef\eighth@{0}
- \fi
- \expandafter\ifnum\csname hidestop0\endcsname=\cons@count
- \getregion@fromhidestack{0}
- \fi
- \fi
- \fi
- \fi
\loop
\advance\loopcount by 1
\ifT@coffee
@@ -8032,46 +8601,35 @@
\advance\innerloopcount by 1
\expandafter\xdef\csname res@num\first@\endcsname{\the\innerloopcount}
\expandafter\check@char\first@
+ \ifx\dom@in\y@ %%%%%%%%%%%*****
+ \xdef\temp@{\csname dom@num\the\loopcount\endcsname}
+ \expandafter\get@dom@count\temp@
+ \expandafter\xdef\csname dom@num\the\loopcount\endcsname{\temp@}
+ \fi %%%%%%%%%%%*****
\ifletter
- \res@count=\csname res@count\the\loopcount\endcsname
- \advance\res@count by 1
- \ifnum\res@count=0\relax
- \ifx\allow@zero\n@ \advance\res@count by 1 \fi
- \fi
- \expandafter\xdef\csname res@count\the\loopcount\endcsname{\the\res@count}
- \ifnum\loopcount=\exp@rt@num \xdef\sixth@{\the\res@count}\xdef\seventh@{y}\fi
- \ifx\hide@true\y@
- \expandafter\ifx\csname hidestart\the\loopcount\endcsname\ampers@nd
- \else
- \expandafter\ifnum\csname hidestart\the\loopcount\endcsname>\res@count
+ \ifx\dom@in\y@
\else
- \expandafter\ifnum\csname hidestop\the\loopcount\endcsname<\res@count
- \else
- \xdef\hide@now{y}\xdef\eighth@{\the\loopcount}
- \fi
- \expandafter\ifnum\csname hidestop\the\loopcount\endcsname=\res@count
- \xdef\first@@{\first@}
- \expandafter\getregion@fromhidestack{\the\loopcount}
- \xdef\first@{\first@@}
- \fi
- \fi
+ \res@count=\csname res@count\the\loopcount\endcsname
+ \advance\res@count by 1
+ \ifnum\res@count=0\relax
+ \ifx\allow@zero\n@ \advance\res@count by 1 \fi
\fi
\fi
+ \expandafter\xdef\csname res@count\the\loopcount\endcsname{\the\res@count}
+ \ifnum\loopcount=\exp@rt@num \xdef\sixth@{\the\res@count}\xdef\seventh@{y}\fi
\ifnum\loopcount=\rule@num\relax
+ \expandafter\ifnum\csname res@count\rule@num\endcsname>\rule@tens
+ \innerloopcount=\rule@tens \add@to@rule@tens
+ \fi
\expandafter\ifnum\csname res@count\rule@num\endcsname=\rule@tens
\expandafter\ifx\csname alt@ruler\rule@tens\endcsname\relax
\xdef\temp@{\rule@tens}
\else
\xdef\temp@{\csname alt@ruler\rule@tens\endcsname}
\fi
- \ifx\hide@now\n@ \xdef\ruler@{\ruler@ !<\temp@>} \fi
- \innerloopcount=\rule@tens \advance\innerloopcount by \ruler@step\relax
- \ifnum\innerloopcount=0
- \ifx\allow@zero\n@ \innerloopcount=\ruler@step \fi
- \fi
- \xdef\rule@tens{\the\innerloopcount}
+ \xdef\ruler@{\ruler@ !<\temp@>}
\else
- \ifx\hide@now\n@ \xdef\ruler@{\ruler@ -} \fi
+ \xdef\ruler@{\ruler@ -}
\fi
\xdef\temp@{\csname res@count\rule@num\endcsname}
\expandafter\ifx\csname alt@ruler\temp@\endcsname\relax
@@ -8079,7 +8637,6 @@
\expandafter\xdef\csname alt@ruler\temp@\endcsname{\temp@}
\fi
\fi
- \ifx\hide@now\n@
\ifx\collect@valtop\yes
\ifnum\v@lseqtop=\loopcount
\xdef\v@ltop{\v@ltop,\csname \ffourth@top\first@\endcsname}
@@ -8112,14 +8669,11 @@
\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
\xdef\last@restop{\last@@restop}
\xdef\last@@restop{\first@}
- \ifx\hide@now\n@
- \xdef\tr@nslatetop{\tr@nslatetop\first@}
- \fi
+ \xdef\tr@nslatetop{\tr@nslatetop\first@}
\innerloopcount=\triple@counttop
\advance\innerloopcount by 1
\ifnum\innerloopcount>3 \innerloopcount=1 \fi
@@ -8129,9 +8683,7 @@
\ifnum\tr@nsseqttop=\loopcount
\xdef\last@resttop{\last@@resttop}
\xdef\last@@resttop{\first@}
- \ifx\hide@now\n@
- \xdef\tr@nslatettop{\tr@nslatettop\first@}
- \fi
+ \xdef\tr@nslatettop{\tr@nslatettop\first@}
\innerloopcount=\triple@countttop
\advance\innerloopcount by 1
\ifnum\innerloopcount>3 \innerloopcount=1 \fi
@@ -8140,10 +8692,8 @@
\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
+ \last@@restttop{\first@}
+ \xdef\tr@nslatetttop{\tr@nslatetttop\first@}
\innerloopcount=\triple@counttttop
\advance\innerloopcount by 1
\ifnum\innerloopcount>3 \innerloopcount=1 \fi
@@ -8153,9 +8703,7 @@
\ifnum\tr@nsseqttttop=\loopcount
\xdef\last@resttttop{\last@@resttttop}
\xdef\last@@resttttop{\first@}
- \ifx\hide@now\n@
- \xdef\tr@nslatettttop{\tr@nslatettttop\first@}
- \fi
+ \xdef\tr@nslatettttop{\tr@nslatettttop\first@}
\innerloopcount=\triple@countttttop
\advance\innerloopcount by 1
\ifnum\innerloopcount>3 \innerloopcount=1 \fi
@@ -8165,9 +8713,7 @@
\ifnum\tr@nsseqbottom=\loopcount
\xdef\last@resbottom{\last@@resbottom}
\xdef\last@@resbottom{\first@}
- \ifx\hide@now\n@
- \xdef\tr@nslatebottom{\tr@nslatebottom\first@}
- \fi
+ \xdef\tr@nslatebottom{\tr@nslatebottom\first@}
\innerloopcount=\triple@countbottom
\advance\innerloopcount by 1
\ifnum\innerloopcount>3 \innerloopcount=1 \fi
@@ -8177,9 +8723,7 @@
\ifnum\tr@nsseqbbottom=\loopcount
\xdef\last@resbbottom{\last@@resbbottom}
\xdef\last@@resbbottom{\first@}
- \ifx\hide@now\n@
- \xdef\tr@nslatebbottom{\tr@nslatebbottom\first@}
- \fi
+ \xdef\tr@nslatebbottom{\tr@nslatebbottom\first@}
\innerloopcount=\triple@countbbottom
\advance\innerloopcount by 1
\ifnum\innerloopcount>3 \innerloopcount=1 \fi
@@ -8189,9 +8733,7 @@
\ifnum\tr@nsseqbbbottom=\loopcount
\xdef\last@resbbbottom{\last@@resbbbottom}
\xdef\last@@resbbbottom{\first@}
- \ifx\hide@now\n@
- \xdef\tr@nslatebbbottom{\tr@nslatebbbottom\first@}
- \fi
+ \xdef\tr@nslatebbbottom{\tr@nslatebbbottom\first@}
\innerloopcount=\triple@countbbbottom
\advance\innerloopcount by 1
\ifnum\innerloopcount>3 \innerloopcount=1 \fi
@@ -8201,9 +8743,7 @@
\ifnum\tr@nsseqbbbbottom=\loopcount
\xdef\last@resbbbbottom{\last@@resbbbbottom}
\xdef\last@@resbbbbottom{\first@}
- \ifx\hide@now\n@
- \xdef\tr@nslatebbbbottom{\tr@nslatebbbbottom\first@}
- \fi
+ \xdef\tr@nslatebbbbottom{\tr@nslatebbbbottom\first@}
\innerloopcount=\triple@countbbbbottom
\advance\innerloopcount by 1
\ifnum\innerloopcount>3 \innerloopcount=1 \fi
@@ -8218,8 +8758,7 @@
\expandafter\xdef\csname ch@rge\the\loopcount\endcsname{%
\the\innerloopcount}
\else
- \ifnum\loopcount=\rule@num \ifx\hide@now\n@ \xdef\ruler@{\ruler@ -} \fi\fi
- \ifx\hide@now\n@
+ \ifnum\loopcount=\rule@num \xdef\ruler@{\ruler@ -} \fi
\ifx\collect@valtop\yes
\ifnum\v@lseqtop=\loopcount
\xdef\v@ltop{\v@ltop,N}
@@ -8284,31 +8823,8 @@
\ifnum\tr@nsseqbbbbottom=\loopcount
\xdef\tr@nslatebbbbottom{\tr@nslatebbbbottom -}
\fi\fi
- \fi
\fi
\ifnum\loopcount<\seq@count \repeat
- \ifnum\rule@num=0
- \ifnum\cons@count=\rule@tens
- \expandafter\ifx\csname alt@ruler\rule@tens\endcsname\relax
- \xdef\temp@{\rule@tens}
- \else
- \xdef\temp@{\csname alt@ruler\rule@tens\endcsname}
- \fi
- \ifx\hide@now\n@ \xdef\ruler@{\ruler@ !<\temp@>} \fi
- \innerloopcount=\rule@tens \advance\innerloopcount by \ruler@step\relax
- \ifnum\innerloopcount=0
- \ifx\allow@zero\n@ \innerloopcount=\ruler@step \fi
- \fi
- \xdef\rule@tens{\the\innerloopcount}
- \else
- \ifx\hide@now\n@ \xdef\ruler@{\ruler@ -} \fi
- \fi
- \expandafter\ifx\csname alt@ruler\the\cons@count\endcsname\relax
- \else
- \expandafter\xdef\csname alt@ruler\the\cons@count\endcsname{\the\cons@count}
- \fi
- \fi
- \ifx\hide@now\n@
\ifx\collect@cons@graphtop\yes
\outerloopcount=1\relax
\temp@count=0\relax
@@ -8382,13 +8898,8 @@
\immediate\write\exp@rtfile{\string color col\the\outerloopcount, resi \sixth@}
\fi
\fi
- \fi
-%%%%%%%%%%%%%
- \ifx\hide@now\y@
- \regionalshadenowtrue \regionaltintnowtrue
- \regionalemphnowtrue \framenowtrue
- \fi
+ \xdef\g@p{n}
\ifregionalshadenow \calc@regshade \fi
\ifregionaltintnow \calc@regtint \fi
\ifregionalemphnow \calc@regemph \fi
@@ -8401,17 +8912,6 @@
\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
- \else
- \loopcount=\pos@count
- \advance\loopcount by -\bar@pos
- \xdef\bar@pos{\the\pos@count}
- \xdef\stylehidebar{\stylehidebar\the\loopcount;\csname hidestyle\eighth@\endcsname;\csname hidetext\eighth@\endcsname;}
- \fi
- \else
-%%%%%%%%%%%%%
\advance\pos@count by 1
\ifshow@logo \calc@logo \fi
\ifall@fshade \all@funcshade
@@ -8427,10 +8927,31 @@
\ifcase\match@case \unc@nserved \or \c@nserved \or \allm@tch \else \functi@nal \fi
\fi
\fi
-%%%%%%%%
- \fi
- \xdef\hide@now{n}
-%%%%%%%%
+ \ifnum\rule@num=0
+ \ifx\g@p\y@
+ \xdef\ruler@{\ruler@ -}
+ \else
+ \ifnum\cons@count=\rule@tens
+ \expandafter\ifx\csname alt@ruler\rule@tens\endcsname\relax
+ \xdef\temp@{\rule@tens}
+ \else
+ \xdef\temp@{\csname alt@ruler\rule@tens\endcsname}
+ \fi
+ \xdef\ruler@{\ruler@ !<\temp@>}
+ \innerloopcount=\rule@tens \advance\innerloopcount by \ruler@step\relax
+ \ifnum\innerloopcount=0
+ \ifx\allow@zero\n@ \innerloopcount=\ruler@step \fi
+ \fi
+ \xdef\rule@tens{\the\innerloopcount}
+ \else
+ \xdef\ruler@{\ruler@ -}
+ \fi
+ \expandafter\ifx\csname alt@ruler\the\cons@count\endcsname\relax
+ \else
+ \expandafter\xdef\csname alt@ruler\the\cons@count\endcsname{\the\cons@count}
+ \fi
+ \fi
+ \fi
\expandafter\ifnum\csname res@count\start@seq\endcsname<\end@num\relax
\c@nsensus
\else
@@ -8473,6 +8994,11 @@
\ifnum\res@count=0
\ifx\allow@zero\n@ \advance\res@count by 1 \fi
\fi
+ \ifx\dom@in\y@
+ \xdef\temp@{\csname dom@num\the\loopcount\endcsname}
+ \expandafter\get@dom@count\temp@
+ \expandafter\xdef\csname dom@num\the\loopcount\endcsname{\temp@}
+ \fi %%%%%%%%%%%*****
\expandafter\xdef\csname res@count\the\loopcount\endcsname{\the\res@count}
\ifnum\rule@num=\loopcount
\temp@count=\csname res@count\the\loopcount\endcsname
@@ -8502,10 +9028,6 @@
\csname sequence\the\loopcount\endcsname @}
\ifnum\loopcount<\seq@count \repeat
\end@count=0 \count@first \end@count=0 \xdef\start@number{0}
- \ifx\hide@now\n@
- \regionalshadenowfalse \regionalemphnowfalse \regionaltintnowfalse
- \framenowfalse
- \fi
\topfeaturenowfalse \bottomfeaturenowfalse
\ttopfeaturenowfalse \bbottomfeaturenowfalse
\tttopfeaturenowfalse \bbbottomfeaturenowfalse
@@ -8656,6 +9178,11 @@
\ifx\allow@zero\n@ \advance\res@count by 1 \fi
\fi
\fi
+ \ifx\dom@in\y@
+ \xdef\temp@{\csname dom@num\the\loopcount\endcsname}
+ \expandafter\get@dom@count\temp@
+ \expandafter\xdef\csname dom@num\the\loopcount\endcsname{\the\res@count,\temp@}
+ \fi %%%%%%%%%%*****
\expandafter\xdef\csname res@count\the\loopcount\endcsname{\the\res@count}
\ifnames@right
\expandafter\xdef\csname seq\the\loopcount\endcsname{%
@@ -8665,15 +9192,18 @@
<\csname newseqname\the\loopcount\endcsname>
\csname res@count\the\loopcount\endcsname)}
\fi
- \expandafter\ifnum\csname res@count\the\loopcount\endcsname=%
- \innerloopcount
+ \ifx\dom@in\y@
\else
- \res@count=\csname res@count\the\loopcount\endcsname
- \advance\res@count by -1
- \ifnum\res@count=0
- \ifx\allow@zero\n@ \advance\res@count by -1 \fi
+ \expandafter\ifnum\csname res@count\the\loopcount\endcsname=%
+ \innerloopcount
+ \else
+ \res@count=\csname res@count\the\loopcount\endcsname
+ \advance\res@count by -1
+ \ifnum\res@count=0
+ \ifx\allow@zero\n@ \advance\res@count by -1 \fi
+ \fi
+ \expandafter\xdef\csname res@count\the\loopcount\endcsname{\the\res@count}
\fi
- \expandafter\xdef\csname res@count\the\loopcount\endcsname{\the\res@count}
\fi
\else
\ifnames@right
@@ -8683,8 +9213,16 @@
<\csname newseqname\the\loopcount\endcsname>}
\fi
\fi
- \innerloopcount=\csname res@count\the\loopcount\endcsname
- \advance\innerloopcount by \res@perline \advance\innerloopcount by 1
+ \ifx\dom@in\y@
+ \xdef\temp@{\csname dom@num@break\the\loopcount\endcsname}
+ \expandafter\get@dom@count\temp@
+ \expandafter\xdef\csname dom@num@break\the\loopcount\endcsname{\temp@}
+ \innerloopcount=\res@count
+ \else
+ \innerloopcount=\csname res@count\the\loopcount\endcsname
+ \advance\innerloopcount by \res@perline
+ \fi %%%%%%%%%%%%%*****
+ \advance\innerloopcount by 1
\ifregionalshade
\expandafter\ifx\csname start\the\loopcount\endcsname\ampers@nd
\else
@@ -9088,6 +9626,7 @@
\def\res@@style{\csname func@style#1\endcsname}%
\if\last@ *\def\last@{0}\fi
\if\last@ /\def\last@{10}\fi
+ \if\last@ !\def\last@{11}\fi
\else%
\iffuncmode%
\xdef\boxc@l@r{\csname fg@color#1\endcsname}%
@@ -9095,8 +9634,9 @@
\def\res@@style{\csname func@style#1\endcsname}%
\if\last@ *\def\last@{0}\fi
\if\last@ /\def\last@{10}\fi
+ \if\last@ !\def\last@{11}\fi
\else%
- \ifcase#1\xdef\boxc@l@r{\Allmatch}\xdef\textc@l@r{\TextAllmatch}%
+ \ifcase\last@\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}%
\def\res@@style{\id@style}%
@@ -9112,7 +9652,9 @@
\def\res@@style{\csname relax\endcsname}%
\or\xdef\boxc@l@r{\gap@bg}\xdef\textc@l@r{\gap@fg}%
\def\res@@style{\csname relax\endcsname}%
- \else\xdef\boxc@l@r{White}\xdef\textc@l@r{White}%
+ \or\xdef\boxc@l@r{White}\xdef\textc@l@r{White}%
+ \def\res@@style{\csname relax\endcsname}%
+ \else\xdef\boxc@l@r{\domgap@bg}\xdef\textc@l@r{\domgap@fg}%
\def\res@@style{\csname relax\endcsname}%
\fi\fi\fi\fi%
\ifx\second@\comm@%
@@ -9154,6 +9696,9 @@
\if\last@ *%
\xdef\boxc@l@r{\gap@bg}\xdef\textc@l@r{\gap@bg}%
\else%
+ \if\last@ !%
+ \xdef\boxc@l@r{\domgap@bg}\xdef\textc@l@r{\domgap@bg}%
+ \else%
\if\last@ /%
\xdef\boxc@l@r{White}\xdef\textc@l@r{White}%
\else%
@@ -9178,18 +9723,22 @@
\else
\xdef\textc@l@r{\c@nsc@l}%
\fi%
- \fi\fi\fi%
+ \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}%
+ \if\last@ !%
+ \xdef\boxc@l@r{\domgap@bg}\xdef\textc@l@r{\domgap@bg}%
\else%
- \xdef\boxc@l@r{White}\xdef\textc@l@r{TC\last@}%
- \def\res@@style{\csname relax\endcsname}%
+ \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%
\fi%
\else%
@@ -9209,7 +9758,9 @@
\def\res@@style{\csname relax\endcsname}%
\or\xdef\boxc@l@r{\gap@bg}\xdef\textc@l@r{\gap@fg}%
\def\res@@style{\csname relax\endcsname}%
- \else\xdef\boxc@l@r{White}\xdef\textc@l@r{White}%
+ \or\xdef\boxc@l@r{White}\xdef\textc@l@r{White}%
+ \def\res@@style{\csname relax\endcsname}%
+ \else\xdef\boxc@l@r{\domgap@bg}\xdef\textc@l@r{\domgap@fg}%
\def\res@@style{\csname relax\endcsname}%
\fi\fi\fi\fi%
\xdef\first@{#3@}%
@@ -10223,124 +10774,6 @@
\fi%
\fi%
}
-\def\next@hidebar#1;#2;#3;#4@{%
- \xdef\first@{#1}%
- \ifx\first@\ampers@nd%
- \else%
- \fontfamily{\hideblock@family}\fontseries{\hideblock@series}%
- \fontshape{\hideblock@shape}%
- \selectfont%
- \newline\hbox{}%
- \ifnames@right\else\ifnames@\hbox to \name@width{\hss}\fi\fi%
- \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi%
- \hbox to -\box@width{\hss}%
- \kern-0.1\box@width%
- \xdef\last@{#3[,]&}\expandafter\opt@color\last@%
- \ifx\f@color\comm@\xdef\f@color{Black}\fi%
- \textcolor{\f@color}{%
- \hbox to \first@\box@width{}%
- \hbox to 0pt{\hss\strut\hideblock@size{\,\fourth@}\hss}}%
- \xdef\last@{#2[,]&}\expandafter\opt@color\last@%
- \ifx\f@color\comm@\xdef\f@color{Black}\fi%
- \vspace{-0.23\box@height}%
- \xdef\temp@{triangle}%
- \ifx\fourth@\temp@%
- \else
- \xdef\temp@{square}%
- \ifx\fourth@\temp@%
- \else
- \xdef\temp@{none}%
- \ifx\fourth@\temp@%
- \else
- \vspace{-0.06\box@height}%
- \fi\fi\fi%
- \newline\hbox{}%
- \ifnames@right\else\ifnames@\hbox to \name@width{\hss}\fi\fi%
- \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi%
- \hbox to -\box@width{\hss}%
- \hbox to \first@\box@width{}%
- \kern-0.1\box@width%
- \textcolor{\f@color}{%
- \raisebox{0.47\box@height}{\rule{0.2\box@width}{\temp@@length}}%
- \xdef\first@{triangle}%
- \ifx\fourth@\first@%
- \kern-0.582\box@width%
- \raisebox{\temp@@length}{\hbox to \box@width{\hss$\bigtriangledown$\hss}}%
- \kern-0.418\box@width%
- \else
- \xdef\first@{square}%
- \ifx\fourth@\first@%
- \kern-0.6\box@width%
- \raisebox{-0.12\box@height}{%
- \raisebox{\temp@@length}{\hbox to \box@width{\hss$\square$\hss}}}%
- \raisebox{-0.19\box@height}{%
- \raisebox{\temp@@length}{\hbox to \box@width{\hss\strut}}}%
- \kern-1.4\box@width%
- \else
- \xdef\first@{none}%
- \ifx\fourth@\first@%
- \kern-0.6\box@width%
- \raisebox{-0.19\box@height}{%
- \raisebox{\temp@@length}{\hbox to \box@width{\hss\strut}}}%
- \kern-0.4\box@width%
- \else
- \kern-0.6\box@width%
- \raisebox{\temp@@length}{\hbox to \box@width{\hss$\bigodot$\hss}}%
- \kern-0.4\box@width%
- \fi%
- \fi%
- \fi%
- \kern-0.58\box@width%
- \raisebox{\temp@@length}{\hbox to \box@width{\hss$\bullet$\hss}}%
- \xdef\first@{#4@}}%
- \fi
-}
-\def\put@@hidebar{%
- \if\first@ @%
- \else
- \hbox to -\box@width{\hss}%
- \expandafter\next@hidebar\first@%
- \put@@hidebar%
- \fi%
-}
-\def\put@hidebar{%
- \ifx\hide@seqs\n@%
- \ifshow@cons\ifnum\cons@top=1 \vspace{-\baselineskip}\fi\fi%
- \temp@count=\seq@count%
- \advance\temp@count by 1%
- \ifx\hide@seqs\y@
- \advance\temp@count by -1 %
- \else%
- \loopcount=1%
- \xdef\first@{true}%
- \loop%
- \expandafter\ifx\csname hide@seq\the\loopcount\endcsname\first@%
- \advance\temp@count by -1\fi%
- \advance\loopcount by 1%
- \ifnum\loopcount>\seq@count\else\repeat%
- \fi
- \ifnum\temp@count>0%
- \setlength\temp@@length{\box@height}%
- \advance\temp@@length by \box@depth%
- \setlength\arrow@height{0.5\temp@@length}%
- \setlength\temp@@length{\temp@count\temp@@length}%
- \advance\temp@@length by \arrow@height%
- \advance\temp@@length by -0.75\box@height%%%%%%%
- \setlength\arrow@width{\sep@space}%
- \setlength\arrow@width{\seq@gap@num\arrow@width}%
- \advance\temp@@length by \arrow@width%
- \vspace{\arrow@height}%
- \vspace{-\temp@@length}%
- \vspace{-2.56\baselineskip}%
- \xdef\first@{\stylehidebar @}%
- \put@@hidebar%
- \vspace{-\arrow@height}%
- \vspace{-0.47\box@height}%
- \ifshow@cons\ifnum\cons@top=1 \vspace{\baselineskip}\fi\fi%
- \newline\hbox{}%
- \fi%
- \fi%
-}
\def\decimal@A#1#2@{%
\def\decimal@AB##1##2@{\xdef\temp@{##1.##2}}%
\xdef\temp@@{#1}%
@@ -10474,12 +10907,13 @@
\xdef\fourth@{\fl@g\temp@}%
\if\first@ W%
\hbox to \box@width{\hss%
- \raisebox{\temp@@length}{\raisebox{\fourth@\logo@height}{\scalebox{0.8}[\third@]%
+ \raisebox{\temp@@length}{\raisebox{\fourth@\logo@height}{\scalebox{\char@stretch@W}[\third@]%
{\hbox to \box@width{\textcolor{\tint@\csname logo@col\first@\endcsname}{\hss\residues@size{W}\hss}}}}}\hss}%
\kern-\box@width%
\else%
- \raisebox{\temp@@length}{\raisebox{\fourth@\logo@height}{\scalebox{1}[\third@]%
- {\hbox to \box@width{\textcolor{\tint@\csname logo@col\first@\endcsname}{\hss\residues@size{\first@}\hss}}}}}%
+ \hbox to \box@width{\hss%
+ \raisebox{\temp@@length}{\raisebox{\fourth@\logo@height}{\scalebox{\char@stretch}[\third@]%
+ {\hbox to \box@width{\textcolor{\tint@\csname logo@col\first@\endcsname}{\hss\residues@size{\first@}\hss}}}}}\hss}%
\kern-\box@width%
\fi%
\advance\temp@count by \second@%
@@ -10778,7 +11212,7 @@
\def\set@lines{%
\pos@count=1
- \xdef\frame@pos{1}\xdef\bar@pos{0}\xdef\hidebar@on{0}%
+ \xdef\frame@pos{1}\xdef\bar@pos{0}%
\xdef\featurepostop{1} \xdef\featureposbottom{1}%
\xdef\featureposttop{1} \xdef\featureposbbottom{1}%
\xdef\featurepostttop{1} \xdef\featureposbbbottom{1}%
@@ -10900,9 +11334,6 @@
\ifnum\frame@on=0 \xdef\frame@{0}\fi%
\put@frame%
\fi%
- \ifnum\hidebar@on=1 %
- \put@hidebar%
- \fi%
\ifshow@logo\ifnum\logo@top=1 %
\xdef\last@{\stack@sequencelogo @}%
\ifx\logo@name@user\ampers@nd\xdef\logo@name{logo}\else\xdef\logo@name{\logo@name@user}\fi
@@ -11008,7 +11439,7 @@
\fi
\fi
\xdef\consensus{} \xdef\ruler@{}
- \xdef\styleframe{} \xdef\stylehidebar{}
+ \xdef\styleframe{}
\xdef\textfeaturetop{} \xdef\textfeaturebottom{}
\xdef\textfeaturettop{} \xdef\textfeaturebbottom{}
\xdef\textfeaturetttop{} \xdef\textfeaturebbbottom{}
@@ -11132,7 +11563,7 @@
\xdef\textfeaturebbottom{} \xdef\featureonbbottom{0}
\xdef\textfeaturebbbottom{} \xdef\featureonbbbottom{0}
\xdef\textfeaturebbbbottom{} \xdef\featureonbbbbottom{0}
- \xdef\styleframe{} \xdef\stylehidebar{}
+ \xdef\styleframe{}
\xdef\stylefeaturetop{}
\xdef\stylefeaturettop{}
\xdef\stylefeaturetttop{}
@@ -11143,6 +11574,134 @@
\xdef\stylefeaturebbbbottom{}}
\def\guess@protein{\seqtype{P}\message{<Seqtype guess: protein>}}
\def\guess@DNA{\seqtype{N}\message{<Seqtype guess: nucleotide>}}
+\def\domain@count{%
+ \loopcount=0
+ \ifT@coffee
+ \xdef\seq@line{\csname T@cof\the\loopcount\endcsname}
+ \expandafter\res@get\seq@line
+ \expandafter\xdef\csname TC@num\the\loopcount\endcsname{\first@}
+ \expandafter\xdef\csname T@cof\the\loopcount\endcsname{\seq@line}
+ \fi
+ \loop
+ \advance\loopcount by 1
+ \xdef\seq@line{\csname seq\the\loopcount\endcsname}
+ \expandafter\res@get\seq@line
+ \expandafter\xdef\csname res\the\loopcount\endcsname{\first@}
+ \expandafter\xdef\csname seq\the\loopcount\endcsname{\seq@line}
+ \ifT@coffee
+ \xdef\seq@line{\csname T@cof\the\loopcount\endcsname}
+ \expandafter\res@get\seq@line
+ \expandafter\xdef\csname TC@num\the\loopcount\endcsname{\first@}
+ \expandafter\xdef\csname T@cof\the\loopcount\endcsname{\seq@line}
+ \fi
+ \ifnum\loopcount<\seq@count\repeat
+ \ifx\first@\ampers@nd
+ \else
+ \ifnum\next@domain@num>-99999\relax
+ \ifnum\domain@seq=0
+ \temp@count=\csname dom@count0\endcsname
+ \advance\temp@count by 1
+ \expandafter\xdef\csname dom@count0\endcsname{\the\temp@count}
+ \fi
+ \loopcount=0
+ \loop
+ \advance\loopcount by 1
+ \xdef\first@{\csname res\the\loopcount\endcsname}
+ \expandafter\check@char\first@
+ \ifletter
+ \temp@count=\csname dom@count\the\loopcount\endcsname
+ \advance\temp@count by 1
+ \expandafter\xdef\csname dom@count\the\loopcount\endcsname{\the\temp@count}
+ \if\seq@type A \relax
+ \temp@count=\char@num
+ \ifnum\temp@count>96 \advance\temp@count by -32 \fi
+ \ifnum\temp@count=69 \guess@protein
+ \else
+ \ifnum\temp@count=70 \guess@protein
+ \else
+ \ifnum\temp@count=73 \guess@protein
+ \else
+ \ifnum\temp@count=76 \guess@protein
+ \else
+ \ifnum\temp@count=80 \guess@protein
+ \else
+ \ifnum\temp@count=81 \guess@protein
+ \fi\fi\fi\fi\fi\fi
+ \fi
+ \fi
+ \ifnum\loopcount<\seq@count\repeat
+ \expandafter\ifnum\csname dom@count\domain@seq\endcsname=\next@domain@num
+ \advance\total@count by 1
+ \advance\outerloopcount by 1 \ifnum\outerloopcount=\res@perline \outerloopcount=0 \fi
+ \loopcount=0
+ \ifx\g@p\y@
+ \ifT@coffee
+ \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{%
+ \csname T@coffee\the\loopcount\endcsname \csname TC@num\the\loopcount\endcsname}
+ \fi
+ \fi
+ \ifT@coffee
+ \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{%
+ \csname T@coffee\the\loopcount\endcsname \csname TC@num\the\loopcount\endcsname}
+ \fi
+ \loop
+ \advance\loopcount by 1
+ \ifx\g@p\y@
+ \ifT@coffee
+ \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{%
+ \csname T@coffee\the\loopcount\endcsname \csname TC@num\the\loopcount\endcsname}
+ \fi
+ \expandafter\xdef\csname sequence\the\loopcount\endcsname{%
+ \csname sequence\the\loopcount\endcsname\equ@l}
+ \expandafter\xdef\csname dom@num\the\loopcount\endcsname{%
+ \csname dom@num\the\loopcount\endcsname \csname dom@count\the\loopcount\endcsname,}
+ \ifnum\outerloopcount=0
+ \expandafter\xdef\csname dom@num@break\the\loopcount\endcsname{%
+ \csname dom@num@break\the\loopcount\endcsname \csname dom@count\the\loopcount\endcsname,}
+ \fi
+ \fi
+ \ifT@coffee
+ \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{%
+ \csname T@coffee\the\loopcount\endcsname \csname TC@num\the\loopcount\endcsname}
+ \fi
+ \expandafter\xdef\csname sequence\the\loopcount\endcsname{%
+ \csname sequence\the\loopcount\endcsname \csname res\the\loopcount\endcsname}
+ \expandafter\xdef\csname dom@num\the\loopcount\endcsname{%
+ \csname dom@num\the\loopcount\endcsname \csname dom@count\the\loopcount\endcsname,}
+ \ifnum\outerloopcount=0
+ \expandafter\xdef\csname dom@num@break\the\loopcount\endcsname{%
+ \csname dom@num@break\the\loopcount\endcsname \csname dom@count\the\loopcount\endcsname,}
+ \fi
+ \ifnum\loopcount<\seq@count\repeat
+ \expandafter\get@item\domain@num@list
+ \xdef\domain@num@list{\first@}
+ \ifx\fourth@\ampers@nd \xdef\next@domain@num{-99999}
+ \else
+ \loopcount=\next@domain@num
+ \advance\loopcount by 1
+ \ifnum\loopcount=\fourth@
+ \xdef\g@p{n}
+ \else
+ \xdef\g@p{y}
+ \advance\total@count by 1
+ \advance\outerloopcount by 1
+ \ifnum\outerloopcount=\res@perline
+ \outerloopcount=0
+ \loopcount=0
+ \loop
+ \advance\loopcount by 1
+ \expandafter\xdef\csname dom@num@break\the\loopcount\endcsname{%
+ \csname dom@num@break\the\loopcount\endcsname \csname dom@count\the\loopcount\endcsname,}
+ \ifnum\loopcount<\seq@count\repeat
+ \fi
+ \fi
+ \xdef\next@domain@num{\fourth@} \xdef\end@num{\fourth@}
+ \fi
+ \fi
+ \domain@count
+ \fi
+ \fi
+}
\def\residue@count{%
\expandafter\res@get\seq@line
\if\first@\ampers@nd
@@ -11221,6 +11780,55 @@
\fi
\fi
\ifeof\alignfile
+ \ifx\dom@in\y@
+ \loopcount=0
+ \ifT@coffee
+ \xdef\temp@{\csname T@coffee\the\loopcount\endcsname}
+ \expandafter\get@temp\temp@
+ \expandafter\xdef\csname T@cof\the\loopcount\endcsname{\temp@ &@}
+ \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{}
+ \fi
+ \expandafter\xdef\csname dom@count\the\loopcount\endcsname{0}
+ \loop
+ \advance\loopcount by 1
+ \ifT@coffee
+ \xdef\temp@{\csname T@coffee\the\loopcount\endcsname}
+ \expandafter\get@temp\temp@
+ \expandafter\xdef\csname T@cof\the\loopcount\endcsname{\temp@ &@}
+ \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{}
+ \fi
+ \expandafter\xdef\csname seq\the\loopcount\endcsname{\csname sequence\the\loopcount\endcsname &@}
+ \expandafter\xdef\csname sequence\the\loopcount\endcsname{}
+ \expandafter\xdef\csname dom@num\the\loopcount\endcsname{}
+ \expandafter\xdef\csname dom@num@break\the\loopcount\endcsname{}
+ \expandafter\xdef\csname dom@count\the\loopcount\endcsname{0}
+ \ifnum\loopcount<\seq@count\repeat
+ \xdef\domain@num@list{}
+ \xdef\last@{\stack@dom}
+ \get@domain
+ \xdef\domain@num@list{\domain@num@list &,@}
+ \expandafter\get@item\domain@num@list
+ \xdef\next@domain@num{\fourth@} \xdef\domain@num@list{\first@}
+ \domain@count
+ \loopcount=0
+ \ifT@coffee
+ \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{\csname T@coffee\the\loopcount\endcsname @}
+ \fi
+ \loop
+ \advance\loopcount by 1
+ \ifT@coffee
+ \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{\csname T@coffee\the\loopcount\endcsname @}
+ \fi
+ \expandafter\xdef\csname dom@num\the\loopcount\endcsname{\csname dom@num\the\loopcount\endcsname @}
+ \expandafter\xdef\csname dom@num@break\the\loopcount\endcsname{%
+ \csname dom@num@break\the\loopcount\endcsname \csname dom@count\the\loopcount\endcsname,@}
+ \ifnum\loopcount<\seq@count\repeat
+ \if\seq@type A \guess@DNA \fi
+ \advance\seq@pointer by \total@count\relax
+ \xdef\total@pos{\the\total@count}
+
+ \else
+
\ifnum\start@seq=0
\xdef\seq@line{\csname sequence1\endcsname &@}
\else
@@ -11238,9 +11846,10 @@
\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
+ \fi
+ \ifshow@sublogo \prep@sublogo \fi
+ \ifshow@logo \prep@logo \fi
+ \ifnum\seq@pointer>\res@perline \block@output \fi
\else \read@loop
\fi}
\def\read@fasta{%
@@ -11270,6 +11879,55 @@
\fi
\fi
\ifeof\alignfile
+ \ifx\dom@in\y@
+ \loopcount=0
+ \ifT@coffee
+ \xdef\temp@{\csname T@coffee\the\loopcount\endcsname}
+ \expandafter\get@temp\temp@
+ \expandafter\xdef\csname T@cof\the\loopcount\endcsname{\temp@ &@}
+ \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{}
+ \fi
+ \expandafter\xdef\csname dom@count\the\loopcount\endcsname{0}
+ \loop
+ \advance\loopcount by 1
+ \ifT@coffee
+ \xdef\temp@{\csname T@coffee\the\loopcount\endcsname}
+ \expandafter\get@temp\temp@
+ \expandafter\xdef\csname T@cof\the\loopcount\endcsname{\temp@ &@}
+ \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{}
+ \fi
+ \expandafter\xdef\csname seq\the\loopcount\endcsname{\csname sequence\the\loopcount\endcsname &@}
+ \expandafter\xdef\csname sequence\the\loopcount\endcsname{}
+ \expandafter\xdef\csname dom@num\the\loopcount\endcsname{}
+ \expandafter\xdef\csname dom@num@break\the\loopcount\endcsname{}
+ \expandafter\xdef\csname dom@count\the\loopcount\endcsname{0}
+ \ifnum\loopcount<\seq@count\repeat
+ \xdef\domain@num@list{}
+ \xdef\last@{\stack@dom}
+ \get@domain
+ \xdef\domain@num@list{\domain@num@list &,@}
+ \expandafter\get@item\domain@num@list
+ \xdef\next@domain@num{\fourth@} \xdef\domain@num@list{\first@}
+ \domain@count
+ \loopcount=0
+ \ifT@coffee
+ \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{\csname T@coffee\the\loopcount\endcsname @}
+ \fi
+ \loop
+ \advance\loopcount by 1
+ \ifT@coffee
+ \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{\csname T@coffee\the\loopcount\endcsname @}
+ \fi
+ \expandafter\xdef\csname dom@num\the\loopcount\endcsname{\csname dom@num\the\loopcount\endcsname @}
+ \expandafter\xdef\csname dom@num@break\the\loopcount\endcsname{%
+ \csname dom@num@break\the\loopcount\endcsname \csname dom@count\the\loopcount\endcsname,@}
+ \ifnum\loopcount<\seq@count\repeat
+ \if\seq@type A \guess@DNA \fi
+ \advance\seq@pointer by \total@count\relax
+ \xdef\total@pos{\the\total@count}
+
+ \else
+
\ifnum\start@seq=0
\xdef\seq@line{\csname sequence1\endcsname &@}
\else
@@ -11287,9 +11945,10 @@
\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
+ \fi
+ \ifshow@sublogo \prep@sublogo \fi
+ \ifshow@logo \prep@logo \fi
+ \ifnum\seq@pointer>\res@perline \block@output \fi
\else
\read@fasta
\fi}
@@ -11419,6 +12078,7 @@
\fi
\set@savedseqlength
\loopcount=0 \xdef\seq@order{}
+ \expandafter\xdef\csname stack@dom\endcsname{&;&;&;&;@}
\expandafter\xdef\csname stack@reg\the\loopcount\endcsname{&;&;&;&;@}
\expandafter\xdef\csname stack@tintreg\the\loopcount\endcsname{&;&;&;@}
\expandafter\xdef\csname stack@hidereg\the\loopcount\endcsname{&;&;&;&;@}
@@ -11852,6 +12512,7 @@
\xdef\res@numW{0} \xdef\res@numX{0}
\xdef\res@numY{0} \xdef\res@numZ{0}
\expandafter\xdef\csname res@num\d@t\endcsname{0}
+\expandafter\xdef\csname res@num\equ@l\endcsname{0}
\xdef\res@corrA{0} \xdef\res@corrB{0}
\xdef\res@corrC{0} \xdef\res@corrD{0}
\xdef\res@corrE{0} \xdef\res@corrF{0}
@@ -11866,6 +12527,7 @@
\xdef\res@corrW{0} \xdef\res@corrX{0}
\xdef\res@corrY{0} \xdef\res@corrZ{0}
\expandafter\xdef\csname res@corr\d@t\endcsname{0}
+\expandafter\xdef\csname res@corr\equ@l\endcsname{0}
\xdef\corr@max{0} \xdef\do@freq@correction{n}
\xdef\res@total{0}
\xdef\stack@sequencelogo{} \xdef\bit@total{0}
@@ -11879,12 +12541,11 @@
\expandafter\xdef\csname group@num1\endcsname{0}
\expandafter\xdef\csname group@num2\endcsname{0}
\xdef\exp@rt@num{0} \xdef\exp@rt{n}
-\xdef\hide@true{n} \xdef\hide@now{n}
-\xdef\hide@label{circ}
\xdef\divref@{0}
\xdef\all@thresh@ld{100} \all@shadefalse
\hidefeaturenames \hidefeaturestylenames
\xdef\T@coffee@ccons{n} \xdef\T@coffee@bcons{n}
+\xdef\dom@in{no}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%% %%%%%
@@ -11917,6 +12578,8 @@
\gapchar{.} % . is printed in sequence gaps
\gaprule{0.3pt} % If a rule is printed in gaps use 0.3 pt
\gapcolors{Black}{White} % Gap symbols appear `Black on White'
+\domaingaprule{1pt} % If a rule is set between domains use 1 pt
+\domaingapcolors{Red}{White} % Domain separation line appears `Red on White'
\numberingcolor{Black} % Numbering color is `Black'
\shownumbering{right} % Show sequence numbering on the left
\namescolor{Black} % Names' color is `Black'
@@ -11978,10 +12641,6 @@
\setseries{featurestyles}{md} % Use normal series for feature styles
\setshape {featurestyles}{up} % Use upright shape for feature styles
\setsize {featurestyles}{normalsize}% Use normal size for feature styles
-\setfamily{hideblock}{rm} % Use roman family for hidden block labels
-\setseries{hideblock}{md} % Use normal series for hidden block labels
-\setshape {hideblock}{it} % Use italics shape for hidden block labels
-\setsize {hideblock}{normalsize} % Use normal size for hidden block labels
\setfamily{legend}{tt} % Use typewriter family for legend texts
\setseries{legend}{md} % Use normal series for legend texts
\setshape {legend}{up} % Use upright shape for legend texts