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-rw-r--r--Master/texmf-dist/doc/latex/texshade/README6
-rw-r--r--Master/texmf-dist/doc/latex/texshade/texshade.pdfbin617054 -> 628139 bytes
-rw-r--r--Master/texmf-dist/doc/latex/texshade/tsfaq.pdfbin72967 -> 77546 bytes
-rw-r--r--Master/texmf-dist/doc/latex/texshade/tsfaq.tex8
-rw-r--r--Master/texmf-dist/source/latex/texshade/texshade.dtx607
-rw-r--r--Master/texmf-dist/tex/latex/texshade/texshade.def10
-rw-r--r--Master/texmf-dist/tex/latex/texshade/texshade.sty352
7 files changed, 876 insertions, 107 deletions
diff --git a/Master/texmf-dist/doc/latex/texshade/README b/Master/texmf-dist/doc/latex/texshade/README
index 10db0a70f20..7f5f24c0a1c 100644
--- a/Master/texmf-dist/doc/latex/texshade/README
+++ b/Master/texmf-dist/doc/latex/texshade/README
@@ -1,4 +1,4 @@
- TeXshade v1.16
+ TeXshade v1.17
>>
>> A LaTeX package for setting nucleotide and peptide alignments.
>>
@@ -88,7 +88,7 @@
good test for this. (If you encounter problems texing the doc, you
should tex and read section A of the FAQ-list (see d below) or
download an on-line version [PDF-, DVI-, or PostScript format] at
- http://www.pharmazie.uni-kiel.de/chem/Prof_Beitz/biotex.html)
+ http://homepages.uni-tuebingen.de/beitz/)
The resulting file "texshade.dvi" can be viewed and printed using a
DVI-viewer which is able to display embedded PostScript. Another
@@ -125,7 +125,7 @@
3 - CONTACT
E-Mail: ebeitz@pharmazie.uni-kiel.de
- WWW: www.pharmazie.uni-kiel.de/chem/Prof_Beitz/biotech.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 8962949f95a..377a84ff478 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/doc/latex/texshade/tsfaq.pdf b/Master/texmf-dist/doc/latex/texshade/tsfaq.pdf
index b427f881113..53b9b895288 100644
--- a/Master/texmf-dist/doc/latex/texshade/tsfaq.pdf
+++ b/Master/texmf-dist/doc/latex/texshade/tsfaq.pdf
Binary files differ
diff --git a/Master/texmf-dist/doc/latex/texshade/tsfaq.tex b/Master/texmf-dist/doc/latex/texshade/tsfaq.tex
index 94d6b73193d..0ab7a0ec378 100644
--- a/Master/texmf-dist/doc/latex/texshade/tsfaq.tex
+++ b/Master/texmf-dist/doc/latex/texshade/tsfaq.tex
@@ -5,24 +5,24 @@
\noindent
-Eric Beitz \hfill February 2007
+Eric Beitz \hfill March 2005
\section*{\TeX{}shade: frequently asked questions }
\bigskip
This is the sixth update of the FAQ list for \TeX{}shade. Feel free to
contact me if you have problems, questions or suggestions about the
-package. I will post them and provide hints in
+package. I will post them and provide hopefully helpful hints in
future issues of this list.
\bigskip
\noindent
-\qquad email: \texttt{ebeitz@pharmazie.uni-kiel.de}
+\qquad email: \texttt{eric.beitz@uni-tuebingen.de}
\smallskip
\noindent
\TeX{}shade:
-\verb|www.pharmazie.uni-kiel.de/chem/Prof_Beitz/biotex.html|
+\texttt{http://homepages.uni-tuebingen.de/beitz/tse.html}
\subsection*{A. Increasing \TeX{}'s memory settings}
diff --git a/Master/texmf-dist/source/latex/texshade/texshade.dtx b/Master/texmf-dist/source/latex/texshade/texshade.dtx
index 8bbff957b77..67f26d001a0 100644
--- a/Master/texmf-dist/source/latex/texshade/texshade.dtx
+++ b/Master/texmf-dist/source/latex/texshade/texshade.dtx
@@ -283,6 +283,28 @@
% `www.pharmazie.uni-kiel.de/chem/' - click on `Beitz'
% }
%
+% \changes{1.17}{2007-06-19}{%
+% Introduction: `allmatchspecial' now accepts an optional threshold
+% percentage allowing one to set two levels off
+% conservation;
+% the same effect can be achieved by using a
+% number as an optional parameter in
+% `shadingmode',
+% or by setting an additional parameter in
+% `threshold';
+% names can be displayed left or right of feature
+% lines using:
+% `showfeaturename', `showfeaturestylename';
+% `hidefeaturename', `hidefeaturestylename';
+% `hidefeaturenames', `hidefeaturestylenames';
+% the color of such names can be changed with
+% `featurenamescolor'
+% `featurestylenamescolor'
+% font styles can be set as usual, e.g.
+% `setsize{featurenames}{large}' or
+% `featurestylenamesrm' etc.
+% }
+%
%
% \CharacterTable
% {Upper-case \A\B\C\D\E\F\G\H\I\J\K\L\M\N\O\P\Q\R\S\T\U\V\W\X\Y\Z
@@ -321,7 +343,7 @@
% for further information, updates and on-line documentation
% see my homepage at
% \texttt{www.pharmazie.uni-kiel.de/chem/} -- click on `Beitz'}}
-% \date{v1.16; 2007/02/18\\}
+% \date{v1.17; 2007/06/19\\}
% \maketitle
% \begin{abstract}
% Setting alignments of nucleotides and peptides for publication
@@ -398,7 +420,29 @@
%
% \subsection{Version History}
%
-% \textbf{v1.16 2007/02/18}
+% \textbf{v1.17 2007/06/19}
+% \medskip
+%
+% \emph{Introduction:}\footnote{Asked for by Marat Kazanov.}
+% (a) A second threshold percentage was introduced in order to label
+% two levels of conservation in `identical' and `similar' mode. This is
+% achieved by setting an optional parameter in |\threshold| or in
+% |\allmatchspecial|, or by using a number as an optional parameter in
+% |\shadingmode|. (b) The feature lines can be additionally labeled with
+% a name left or right of the feature. This is handled using
+% |\showfeaturename|, |\showfeaturestylename|,
+% |\hidefeaturename|, |\hidefeaturestylename|,
+% |\hidefeaturenames|, |\hidefeaturestylenames|.
+% The color of such names can be changed with
+% |\featurenamecolor|, |\featurestylenamecolor|,
+% |\featurenamescolor|, |\featurestylenamescolor|,
+% Font styles in feature names can be set as usual, e.g.
+% |\setsize{featurenames}{large}| or
+% |\featurestylenamesrm|, etc.
+% \bigskip
+%
+%
+% \textbf{v1.17 2007/06/19}
% \medskip
%
% \emph{Correction:} \TeXshade{} crashed when calculating conservation
@@ -916,7 +960,7 @@
% This basic type of shading is provided by almost any alignment
% program. All identical residues at a position are shaded if the
% number of matching residues is higher than a given threshold
-% percentage.\medskip
+% (default is 50\%).\medskip
%
% \begin{texshade}{AQPpro.MSF}
% \setends{1}{80..112}
@@ -934,16 +978,17 @@
% \end{verbatim}
% }
%
-% If you like, positions where all residues are identical can be
-% shaded in a special color and the consensus can be shown with
+% 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:
% \medskip\label{shadecons}
%
% \begin{texshade}{AQPpro.MSF}
-% \allmatchspecial
+% \threshold[80]{50}
% \setends{1}{80..112}
% \showconsensus[ColdHot]{bottom}
% \defconsensus{.}{lower}{upper}
+% \showlegend
% \end{texshade}
%
% Code:\medskip
@@ -951,10 +996,11 @@
% \vbox{%
% \begin{verbatim}
% \begin{texshade}{AQPpro.MSF}
-% \allmatchspecial
+% \threshold[80]{50}
% \setends{1}{80..112}
% \showconsensus[ColdHot]{bottom}
% \defconsensus{.}{lower}{upper}
+% \showlegend
% \end{texshade}
% \end{verbatim}}
%
@@ -983,7 +1029,8 @@
% \medskip
%
% \begin{texshade}{AQPpro.MSF}
-% \shadingmode[allmatchspecial]{similar}
+% \shadingmode{similar}
+% \threshold[80]{50}
% \setends{1}{80..112}
% \hideconsensus
% \feature{top}{1}{93..93}{fill:$\downarrow$}{first case (see text)}
@@ -995,7 +1042,8 @@
% \vbox{%
% \begin{verbatim}
% \begin{texshade}{AQPpro.MSF}
-% \shadingmode[allmatchspecial]{similar}
+% \shadingmode{similar}
+% \threshold[80]{50}
% \setends{1}{80..112}
% \hideconsensus
% \feature{top}{1}{93..93}{fill:$\downarrow$}{first case (see text)}
@@ -1189,8 +1237,7 @@
% \end{texshade}
% \end{verbatim}}
%
-% With |\shadeallresidues| \label{Lshadeallresidues} the
-% threshold is ignored and
+% With |\shadeallresidues| the threshold is ignored and
% all residues are shaded due to their group assignment.
% This is \emph{not} identical to a threshold of 0\%
% where only the majority group would be shaded. See the
@@ -1328,11 +1375,18 @@
% \begin{texshade}{AQPpro.MSF}
% \setends{1}{138..170}
% \feature{ttop}{1}{138..170}{bar:conservation}{}
+% \showfeaturestylename{ttop}{conserv.}
% \ttopspace{-\baselineskip}
% \feature{top}{1}{138..170}{color:charge}{}
+% \showfeaturestylename{top}{charge}
% \feature{bottom}{1}{138..170}{color:molweight[ColdHot]}{}
+% \showfeaturestylename{bottom}{weight}
% \bbottomspace{-\baselineskip}
% \feature{bbottom}{1}{138..170}{bar:hydrophobicity[Red,Gray10]}{}
+% \showfeaturestylename{bbottom}{hydrophob.}
+% \featurestylenamescolor{Red}
+% \featurestylenamesrm
+% \featurestylenamesit
% \hideconsensus
% \end{texshade}
%
@@ -1343,11 +1397,18 @@
% \begin{texshade}{AQPpro.MSF}
% \setends{1}{138..170}
% \feature{ttop}{1}{138..170}{bar:conservation}{}
+% \showfeaturestylename{ttop}{conserv.}
% \ttopspace{-\baselineskip}
% \feature{top}{1}{138..170}{color:charge}{}
+% \showfeaturestylename{top}{charge}
% \feature{bottom}{1}{138..170}{color:molweight[ColdHot]}{}
+% \showfeaturestylename{bottom}{weight}
% \bbottomspace{-\baselineskip}
% \feature{bbottom}{1}{138..170}{bar:hydrophobicity[Red,Gray10]}{}
+% \showfeaturestylename{bbottom}{hydrophob.}
+% \featurestylenamescolor{Red}
+% \featurestylenamesrm
+% \featurestylenamesit
% \hideconsensus
% \end{texshade}
% \end{verbatim}}
@@ -1420,6 +1481,9 @@
% aquaporin isoforms are most conserved.
% \medskip
%
+% A fingerprint of charge distribution on different aquaporins is shown.
+% below. Sequence gaps can be left blank (example above) or drawn as lines
+% between the sequence blocks.
%
% \begin{texshade}{AQPpro.MSF}
% \shadingmode[charge]{functional}
@@ -1556,7 +1620,7 @@
% from the remaining four aquaporins of this alignment (upside-down).
% The output can be directly compared to the sequence logo above,
% which displays the same section of the alignment.
-% Note, that five sequence are far too few to obtain meaningful
+% Note, that five sequences are far too few to obtain meaningful
% results with this method. This is just to illustrate the
% approach.
% \medskip
@@ -1968,13 +2032,16 @@
%
% \begin{enumerate}
%
-% \item |\shadingmode[|\meta{allmatchspecial}|]{identical}|
+% \item |\shadingmode[|\meta{allmatchspecial/number}|]{identical}|
%
% There is not much to explain here (see \ref{ident}). Use the
% option |allmatchspecial| to shade positions with a special color
-% where all residues are identical.
+% where all residues are identical. Or use a percentage number
+% (0--100) as an option to set an additional threshold for highly
+% conserved residues, e.\,g.\ |\shadingmode[90]{identical}|.
% \label{Lallmatchspecial}|\allmatchspecial| can also be
-% used as a command. As both, option or command
+% used as a command with or without an optional parameter for
+% setting the high conservation threshold. As both, option or command
% |allmatchspecial| is only active in the \emph{identical} and
% \emph{similar} shading modes.
%
@@ -1985,7 +2052,7 @@
% (used in the example, \ref{ident}), `reds', `greens',
% `grays' and `black'. Default is |\shadingcolors{blues}|. Further, the colors
% for the non matching, the
-% conserved and all matching residues can be set individually
+% conserved and all matching (or highly conserved) residues can be set individually
% plus the letter case (lower or upper) or any character
% can be chosen: \label{Lnomatchresidues}
% \label{Lconservedresidues}
@@ -2041,7 +2108,7 @@
% \bigskip
%
%
-% \item |\shadingmode[|\meta{allmatchspecial}|]{similar}|
+% \item |\shadingmode[|\meta{allmatchspecial/number}|]{similar}|
%
% \label{Lsimilarresidues}
% See \ref{similar} for an example output and an explanation
@@ -2072,7 +2139,7 @@
%
% What happens if there is no consensus residue? How does
% \TeXshade{} decide if a group of similars is greater than
-% the threshold? Therefore groups are pre-defined:
+% the threshold? For this groups are pre-defined:
%
% \quad |\pepgroups{FYW,ILVM,RK,DE,GA,ST,NQ}| This command allows
% one to set up to nine groups of similars, separated by commas.
@@ -2152,11 +2219,12 @@
% curly braces around the dot-symbol!).
%
% \item |\shadingmode[|\meta{type}|]{functional}|\label{funcdef}
-% There are six different functional shading modes available for
+% There are seven different functional shading modes available for
% peptide sequences; nucleotide sequences can not be shaded due
-% to functional aspects. Four of \TeXshade's functional modes
+% to functional aspects. Five of \TeXshade's functional modes
% correspond to the four `alphabets' employed by \textsc{Karlin}
-% and \textsc{Ghandour} for peptide alignments [2]. Additional
+% and \textsc{Ghandour} for peptide alignments [2] or by the
+% rasmol software. Additional
% `alphabets' to the standard 20-letter array of amino acids
% can highlight peptide similarities which were otherwise not visible.
% For the `alphabet' definitions see below:
@@ -2238,6 +2306,10 @@
% as described for example in |\nomatchresidues|.
% \end{enumerate}
%
+% With |\shadeallresidues| \label{Lshadeallresidues} the
+% threshold is ignored and
+% all residues are shaded due to their group assignment.
+%
% \subsection{Creating new functional shading modes}
%
% The grouping of amino acids due to other properties can make sense as
@@ -2308,6 +2380,10 @@
% mode. Any percentage between 0 and 100 is allowed and can be
% set with
% |\threshold{|\meta{percentage}|}|, e.\,g.\ |\threshold{50}|.
+%
+% Additionally, an optional parameter can be set, e.\,g.\,
+% |\threshold[90]{50}|, to label residues that are highly conserved
+% in a special color (see example on page \pageref{ident}).
%
% \label{Lconstosingleseq}
% Another possibility is to set one sequence of the alignment
@@ -2386,8 +2462,9 @@
% \item |{}| (empty braces) for blank space
% \end{itemize}
%
-% \item \meta{symbol3} = all match symbol (if all residues match and
-% \hfill |\allmatchspecial| is active)
+% \item \meta{symbol3} = highly conserved symbol (if
+%
+% \hfill|\allmatchspecial| is active)
%
% \begin{itemize}
% \item see \meta{symbol2}
@@ -2398,7 +2475,7 @@
% Example: |\defconsensus{{}}{*}{upper}| does not show non matching
% residues in the consensus line, marks conserved residues
% with `|*|', and displays the uppercase letter of the consensus
-% residue at positions where all residues match.
+% residue at positions with high conservation.
%
%
% \label{Lconsensuscolors}
@@ -2426,10 +2503,11 @@
%
% \meta{shad.col.2} = conserved background color
%
-% \item \meta{res.col.3} = all match residue color (if all residues match and
-% \hfill |\allmatchspecial| is active)
+% \item \meta{res.col.3} = highly conserved residue color (if
+%
+% \hfill|\allmatchspecial| is active)
%
-% \meta{shad.col.3} = all match background color
+% \meta{shad.col.3} = highly conserved background color
%
% \end{enumerate}
%
@@ -2441,8 +2519,8 @@
% \medskip
%
% Non matching symbol colors are not changed,
-% conserved residues are displayed blue on white and where all residues
-% match red symbols on green ground are displayed in the
+% conserved residues are displayed blue on white and highly conserved residues
+% appear as red symbols on a green background in the
% consensus line.
%
% \subsection{Display of logos}
@@ -3502,6 +3580,56 @@
% (|featurestyles|) or the in descriptive text line (|features|)
% see section \ref{Lsetsize}, page \pageref{Lsetsize}.
%
+% Another set of commands can be used to set a name for a feature
+% line, which is printed together with the sequence names at the
+% left or right side of the alignment, i.\,e.\
+% \medskip
+%
+% \label{Lshowfeaturename} \label{Lshowfeaturestylename}
+% \label{Lhidefeaturename} \label{Lhidefeaturestylename}
+% \label{Lhidefeaturenames} \label{Lhidefeaturestylenames}
+% \quad |\showfeaturename{|\meta{ttop/top/bottom/bbottom}|}{|\meta{name}|}|,
+% \medskip
+%
+% \quad |\showfeaturestylename{|\meta{ttop/top/bottom/bbottom}|}{|\meta{name}|}|
+% \medskip
+%
+% \quad |\hidefeaturename{|\meta{ttop/top/bottom/bbottom}|}|
+% \medskip
+%
+% \quad |\hidefeaturestylename{|\meta{ttop/top/bottom/bbottom}|}|
+% \medskip
+%
+% \quad |\hidefeaturenames|, and |\hidefeaturestylenames|.
+% \medskip
+%
+% Using |\showfeaturename| will print the name in the same line as
+% the descriptive text of the feature whereas | \showfeaturestylename|
+% will put the name in the same line as the feature symbols.
+%
+% The color of such names can be generally changed with \label{Lfeaturenamescolor}
+% \medskip
+%
+% \quad |\featurenamescolor{|\meta{color}|}| and \label{Lfeaturestylenamescolor}
+% \medskip
+%
+% \quad |\featurestylenamescolor{|\meta{color}|}|
+% \medskip
+%
+% or individually with \label{Lfeaturenamecolor}
+% \medskip
+%
+% \quad |\featurenamecolor{|\meta{ttop/top/bottom/bbottom}|}{|\meta{color}|}| and \label{Lfeaturestylenamecolor}
+% \medskip
+%
+% \quad |\featurestylenamecolor{|\meta{ttop/top/bottom/bbottom}|}{|\meta{color}|}|
+% \medskip
+%
+% See section \ref{colors} for how to select colors in \TeX{}shade.
+%
+% Font styles can be set as usual, e.\,g.\ |\setsize{featurenames}{large}| or
+% |\featurestylenamesrm| etc. (see section \ref{Lsetfamily}).
+%
%
% Examples for the appearance of features are given in the
% overview section (\ref{over}), see:
@@ -3788,8 +3916,8 @@
%
% \item |conserved| = the color used for conserved residues
%
-% \item |allmatch| = the color used for the case that all residues
-% match (if |\allmatchspecial| is active)
+% \item |allmatch| = the color used for highly conserved residues
+% (if |\allmatchspecial| is active)
%
% \end{itemize}
%
@@ -3941,7 +4069,10 @@
% Corresponding sets are provided for the
% numbering (|\numberingrm| etc.),
% featurestyles (|featurestylesrm| etc.), names (|\namesrm| etc.),
-% residues (|\residuesrm| etc.), hideblock labels (|hideblockrm| etc.), and
+% featurenames (|\featurenamesrm| etc.),
+% featurestylenames (|\featurestylenames| etc.),
+% residues (|\residuesrm| etc.),
+% hideblock labels (|hideblockrm| etc.), and
% legend texts (|legendrm| etc.).
%
%
@@ -4397,8 +4528,8 @@
% \begin{center}
% \begin{tabular}{lll}
% \meta{mode} & \meta{option} &\\ \hline
-% |identical| & |allmatchspecial| &\\
-% |similar| & |allmatchspecial| &\\
+% |identical| & |allmatchspecial/number| &\\
+% |similar| & |allmatchspecial/number| &\\
% |diverse| & \meta{seqref} &\\
% |functional|& \meta{type} & |charge| \\
% & & |hydropathy| \\
@@ -4411,6 +4542,9 @@
% \end{center}
% \medskip
%
+% \quad|\allmatchspecial[|\meta{percentage}|]|
+% \hfill[\pageref{Lallmatchspecial}]
+%
% \quad|\shadeallresidues|
% \hfill[\pageref{Lshadeallresidues}]
%
@@ -4469,7 +4603,7 @@
% \textbf{Appearance of the consensus line}
% \medskip
%
-% \quad|\threshold{|\meta{percentage}|}|
+% \quad|\threshold[|\meta{percentage}|]{|\meta{percentage}|}|
% \hfill[\pageref{Lthreshold}]
%
% \quad|\constosingleseq{|\meta{seqref}|}|
@@ -4861,6 +4995,36 @@
% \> = |{vertical}|
% \end{tabbing}
%
+% \quad |\showfeaturename{|\meta{ttop/top/bottom/bbottom}|}{|\meta{name}|}|
+% \hfill[\pageref{Lshowfeaturename}]
+%
+% \quad |\showfeaturestylename{|\meta{ttop/\ldots/bbottom}|}{|\meta{name}|}|
+% \hfill[\pageref{Lshowfeaturestylename}]
+%
+% \quad |\hidefeaturename{|\meta{ttop/top/bottom/bbottom}|}|
+% \hfill[\pageref{Lhidefeaturename}]
+%
+% \quad |\hidefeaturestylename{|\meta{ttop/top/bottom/bbottom}|}|
+% \hfill[\pageref{Lhidefeaturestylename}]
+%
+% \quad |\hidefeaturenames|
+% \hfill[\pageref{Lhidefeaturenames}]
+%
+% \quad|\hidefeaturestylenames|
+% \hfill[\pageref{Lhidefeaturestylenames}]
+%
+% \quad |\featurenamescolor{|\meta{color}|}|
+% \hfill[\pageref{Lfeaturenamescolor}]
+%
+% \quad |\featurestylenamescolor{|\meta{color}|}|
+% \hfill[\pageref{Lfeaturestylenamescolor}]
+%
+% \quad |\featurenamecolor{|\meta{ttop/top/bottom/bbottom}|}{|\meta{color}|}|
+% \hfill[\pageref{Lfeaturenamecolor}]
+%
+% \quad |\featurestylenamecolor{|\meta{ttop/\ldots/bbottom}|}{|\meta{color}|}|
+% \hfill[\pageref{Lfeaturestylenamecolor}]
+%
% \vspace{1.5\baselineskip}
%
%
@@ -4938,7 +5102,6 @@
%
% \vspace{1.5\baselineskip}
%
-% \newpage
%
% \textbf{Displaying and building legends}
% \medskip
@@ -5019,7 +5182,10 @@
% Corresponding sets are provided for the
% numbering (|\numberingrm| etc.),
% featurestyles (|featurestylesrm| etc.), names (|\namesrm| etc.),
-% residues (|\residuesrm| etc.) and
+% featurenames (|\featurenamesrm| etc.),
+% featurestylenames (|\featurestylenames| etc.),
+% residues (|\residuesrm| etc.),
+% hideblock labels (|hideblockrm| etc.), and
% legend texts (|legendrm| etc.).
% \bigskip
%
@@ -5105,11 +5271,11 @@
% \begin{macrocode}
%<*driver>
\documentclass[12pt,a4paper]{ltxdoc}
-\usepackage{texshade}
+\usepackage[dvips]{texshade}
\openin\structurefile = hyperref.sty
\ifeof\structurefile
\else
- \usepackage[colorlinks]{hyperref}
+ \usepackage[dvips,colorlinks]{hyperref}
\fi
\closein\structurefile
\DisableCrossrefs
@@ -5126,8 +5292,8 @@
% \begin{macrocode}
%<*texshade>
\NeedsTeXFormat{LaTeX2e}
-\ProvidesPackage{texshade}[2007/02/18 LaTeX TeXshade (v1.16)]
-\message{Package `texshade', Version 1.16 of 2007/02/18.}
+\ProvidesPackage{texshade}[2007/06/19 LaTeX TeXshade (v1.17)]
+\message{Package `texshade', Version 1.17 of 2007/06/19.}
\PassOptionsToPackage{dvips}{color}
\PassOptionsToPackage{dvips}{graphicx}
@@ -9144,6 +9310,12 @@
\fi\fi\fi
\fi
}
+\def\showfeaturename#1#2{\expandafter\xdef\csname featuretextn@me#1\endcsname{#2}}
+\def\showfeaturestylename#1#2{\expandafter\xdef\csname featurestylesn@me#1\endcsname{#2}}
+\def\hidefeaturename#1{\expandafter\xdef\csname featuretextn@me#1\endcsname{}}
+\def\hidefeaturenames{\xdef\featuretextn@mettop{}\xdef\featuretextn@metop{}\xdef\featuretextn@mebottom{}\xdef\featuretextn@mebbottom{}}
+\def\hidefeaturestylename#1{\expandafter\xdef\csname featurestylesn@me#1\endcsname{}}
+\def\hidefeaturestylenames{\xdef\featurestylesn@mettop{}\xdef\featurestylesn@metop{}\xdef\featurestylesn@mebottom{}\xdef\featurestylesn@mebbottom{}}
\def\seqtype#1{\xdef\seq@type{#1}
\if\seq@type P \xdef\prefix@{pep}
\else \if\seq@type p \xdef\seq@type{P} \xdef\prefix@{pep}
@@ -9153,7 +9325,21 @@
\xdef\first@{#1} \ifletter \get@name@number \fi
\expandafter\xdef\csname newseqname\first@\endcsname{#2}
}
-\def\threshold#1{\xdef\thresh@ld{#1}}
+\newcommand\threshold[2][n]{%
+ \xdef\first@{#1}
+ \ifx\first@\n@
+ \xdef\thresh@ld{#2}
+ \else
+ \all@shadetrue
+ \ifnum\first@>#2
+ \xdef\thresh@ld{#2}
+ \xdef\all@thresh@ld{#1}
+ \else
+ \xdef\thresh@ld{#1}
+ \xdef\all@thresh@ld{#2}
+ \fi
+ \fi
+}
\def\constosingleseq#1{%
\xdef\first@{#1 @} \expandafter\check@letter\first@
\xdef\first@{#1} \ifletter \get@name@number \fi
@@ -9213,20 +9399,45 @@
\xdef\seq@gap@num{\the\loopcount}
\fi
\fi}
-\newcommand{\shadingmode}[2][1]{%
+\newcommand{\shadingmode}[2][-1]{%
\xdef\last@{#2}
\xdef\first@{identical}
- \all@shadefalse
\ifx\first@\last@
\simmodefalse \funcmodefalse
- \xdef\last@{#1} \xdef\second@{allmatchspecial}
- \ifx\second@\last@ \all@shadetrue \fi
+ \xdef\second@{#1 @} \expandafter\check@letter\second@
+ \ifnumber \all@shadetrue
+ \ifnum#1<0 \all@shadefalse
+ \else
+ \ifnum#1>100 \xdef\all@thresh@ld{100}
+ \else
+ \xdef\all@thresh@ld{#1}
+ \fi\fi
+ \else
+ \xdef\last@{#1}
+ \xdef\first@{allmatchspecial}
+ \ifx\last@\first@
+ \xdef\all@thresh@ld{100} \all@shadetrue
+ \fi
+ \fi
\else
\xdef\first@{similar}
\ifx\first@\last@
\simmodetrue \funcmodefalse
- \xdef\last@{#1} \xdef\second@{allmatchspecial}
- \ifx\second@\last@ \all@shadetrue \fi
+ \xdef\second@{#1 @} \expandafter\check@letter\second@
+ \ifnumber \all@shadetrue
+ \ifnum#1<0 \all@shadefalse
+ \else
+ \ifnum#1>100 \xdef\all@thresh@ld{100}
+ \else
+ \xdef\all@thresh@ld{#1}
+ \fi\fi
+ \else
+ \xdef\last@{#1}
+ \xdef\first@{allmatchspecial}
+ \ifx\last@\first@
+ \xdef\all@thresh@ld{100} \all@shadetrue
+ \fi
+ \fi
\else
\xdef\first@{functional}
\ifx\first@\last@
@@ -9253,7 +9464,16 @@
\message{<Unknown shading mode - using `similar'>}
\simmodetrue \funcmodefalse
\fi\fi\fi\fi}
-\def\allmatchspecial{\all@shadetrue}
+\newcommand\allmatchspecial[1][100]{%
+ \ifnum#1<0
+ \xdef\all@thresh@ld{0}
+ \else
+ \ifnum#1>100
+ \xdef\all@thresh@ld{100}
+ \else
+ \xdef\all@thresh@ld{#1}
+ \fi\fi
+ \all@shadetrue}
\def\allmatchspecialoff{\all@shadefalse}
\def\gapchar#1{%
\xdef\first@{rule}\xdef\second@{#1}
@@ -9706,6 +9926,12 @@
\else
\xdef\third@{\second@}
\fi\fi\fi
+ \xdef\temp@{featurenames}
+ \ifx\first@\temp@ \xdef\ftext@family{\third@}
+ \else
+ \xdef\temp@{featurestylenames}
+ \ifx\first@\temp@ \xdef\fstyles@family{\third@}
+ \else
\xdef\temp@{features}
\ifx\first@\temp@ \xdef\featuretext@family{\third@}
\else
@@ -9735,6 +9961,8 @@
\else
\xdef\temp@{all}
\ifx\first@\temp@
+ \xdef\ftext@family{\third@}
+ \xdef\fstyles@family{\third@}
\xdef\featuretext@family{\third@}
\xdef\featurestyles@family{\third@}
\xdef\numbertext@family{\third@}
@@ -9744,7 +9972,7 @@
\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
}
\def\setseries#1#2{%
@@ -9763,6 +9991,12 @@
\else
\xdef\third@{\second@}
\fi\fi
+ \xdef\temp@{featurenames}
+ \ifx\first@\temp@ \xdef\ftext@series{\third@}
+ \else
+ \xdef\temp@{featurestylenames}
+ \ifx\first@\temp@ \xdef\fstyles@series{\third@}
+ \else
\xdef\temp@{features}
\ifx\first@\temp@ \xdef\featuretext@series{\third@}
\else
@@ -9789,6 +10023,8 @@
\else
\xdef\temp@{all}
\ifx\first@\temp@
+ \xdef\ftext@series{\third@}
+ \xdef\fstyles@series{\third@}
\xdef\featuretext@series{\third@}
\xdef\featurestyles@series{\third@}
\xdef\numbertext@series{\third@}
@@ -9797,7 +10033,7 @@
\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
}
\def\setshape#1#2{%
@@ -9824,6 +10060,12 @@
\else
\xdef\third@{\second@}
\fi\fi\fi\fi
+ \xdef\temp@{featurenames}
+ \ifx\first@\temp@ \xdef\ftext@shape{\third@}
+ \else
+ \xdef\temp@{featurestylenames}
+ \ifx\first@\temp@ \xdef\fstyles@shape{\third@}
+ \else
\xdef\temp@{features}
\ifx\first@\temp@ \xdef\featuretext@shape{\third@}
\else
@@ -9850,6 +10092,8 @@
\else
\xdef\temp@{all}
\ifx\first@\temp@
+ \xdef\ftext@shape{\third@}
+ \xdef\fstyles@shape{\third@}
\xdef\featuretext@shape{\third@}
\xdef\featurestyles@shape{\third@}
\xdef\numbertext@shape{\third@}
@@ -9858,7 +10102,7 @@
\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
}
\def\setsize#1#2{%
@@ -9874,6 +10118,14 @@
\ifx\first@\temp@
\def\featurestyles@size{\csname #2\endcsname}
\else
+ \xdef\temp@{featurenames}
+ \ifx\first@\temp@
+ \def\ftext@size{\csname #2\endcsname}
+ \else
+ \xdef\temp@{featurestylenames}
+ \ifx\first@\temp@
+ \def\fstyles@size{\csname #2\endcsname}
+ \else
\xdef\temp@{numbering}
\ifx\first@\temp@
\def\numbertext@size{\csname #2\endcsname}
@@ -9913,6 +10165,8 @@
\ifx\first@\temp@
\def\featuretext@size{\csname #2\endcsname}
\def\featurestyles@size{\csname #2\endcsname}
+ \def\ftext@size{\csname #2\endcsname}
+ \def\fstyles@size{\csname #2\endcsname}
\def\numbertext@size{\csname #2\endcsname}
\def\namestext@size{\csname #2\endcsname}
\def\legend@size{\csname #2\endcsname}
@@ -9920,7 +10174,7 @@
\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
\xdef\temp@{Huge}
\ifx\temp@\res@size
\def\bottomruler@size{\csname Large\endcsname}
@@ -9952,6 +10206,44 @@
\def\setfont#1#2#3#4#5{%
\setfamily{#1}{#2}\setseries{#1}{#3}
\setshape{#1}{#4}\setsize{#1}{#5}}
+\def\featurenamesrm{\setfamily{featurenames}{rm}}
+\def\featurenamessf{\setfamily{featurenames}{sf}}
+\def\featurenamestt{\setfamily{featurenames}{tt}}
+\def\featurenamesmd{\setseries{featurenames}{md}}
+\def\featurenamesbf{\setseries{featurenames}{bf}}
+\def\featurenamesup{\setshape {featurenames}{up}}
+\def\featurenamesit{\setshape {featurenames}{it}}
+\def\featurenamessl{\setshape {featurenames}{sl}}
+\def\featurenamessc{\setshape {featurenames}{sc}}
+\def\featurenamestiny {\setsize{featurenames}{tiny}}
+\def\featurenamesscriptsize {\setsize{featurenames}{scriptsize}}
+\def\featurenamesfootnotesize{\setsize{featurenames}{footnotesize}}
+\def\featurenamessmall {\setsize{featurenames}{small}}
+\def\featurenamesnormalsize {\setsize{featurenames}{normalsize}}
+\def\featurenameslarge {\setsize{featurenames}{large}}
+\def\featurenamesLarge {\setsize{featurenames}{Large}}
+\def\featurenamesLARGE {\setsize{featurenames}{LARGE}}
+\def\featurenameshuge {\setsize{featurenames}{huge}}
+\def\featurenamesHuge {\setsize{featurenames}{Huge}}
+\def\featurestylenamesrm{\setfamily{featurestylenames}{rm}}
+\def\featurestylenamessf{\setfamily{featurestylenames}{sf}}
+\def\featurestylenamestt{\setfamily{featurestylenames}{tt}}
+\def\featurestylenamesmd{\setseries{featurestylenames}{md}}
+\def\featurestylenamesbf{\setseries{featurestylenames}{bf}}
+\def\featurestylenamesup{\setshape {featurestylenames}{up}}
+\def\featurestylenamesit{\setshape {featurestylenames}{it}}
+\def\featurestylenamessl{\setshape {featurestylenames}{sl}}
+\def\featurestylenamessc{\setshape {featurestylenames}{sc}}
+\def\featurestylenamestiny {\setsize{featurestylenames}{tiny}}
+\def\featurestylenamesscriptsize {\setsize{featurestylenames}{scriptsize}}
+\def\featurestylenamesfootnotesize{\setsize{featurestylenames}{footnotesize}}
+\def\featurestylenamessmall {\setsize{featurestylenames}{small}}
+\def\featurestylenamesnormalsize {\setsize{featurestylenames}{normalsize}}
+\def\featurestylenameslarge {\setsize{featurestylenames}{large}}
+\def\featurestylenamesLarge {\setsize{featurestylenames}{Large}}
+\def\featurestylenamesLARGE {\setsize{featurestylenames}{LARGE}}
+\def\featurestylenameshuge {\setsize{featurestylenames}{huge}}
+\def\featurestylenamesHuge {\setsize{featurestylenames}{Huge}}
\def\featuresrm{\setfamily{features}{rm}}
\def\featuressf{\setfamily{features}{sf}}
\def\featurestt{\setfamily{features}{tt}}
@@ -10198,14 +10490,36 @@
\else
\ifx\third@\first@\white@box\else\textcolor{\third@}{\box@rule}\fi
\fi\fi\fi\fi}
+\def\featurenamescolor#1{%
+ \expandafter\xdef\csname ftext@fg@ttop\endcsname{#1}
+ \expandafter\xdef\csname ftext@fg@top\endcsname{#1}
+ \expandafter\xdef\csname ftext@fg@bottom\endcsname{#1}
+ \expandafter\xdef\csname ftext@fg@bbottom\endcsname{#1}
+}
+\def\featurestylenamescolor#1{%
+ \expandafter\xdef\csname fstyles@fg@ttop\endcsname{#1}
+ \expandafter\xdef\csname fstyles@fg@top\endcsname{#1}
+ \expandafter\xdef\csname fstyles@fg@bottom\endcsname{#1}
+ \expandafter\xdef\csname fstyles@fg@bbottom\endcsname{#1}
+}
+\def\featurenamecolor#1#2{\expandafter\xdef\csname ftext@fg@#1\endcsname{#2}}
+\def\featurestylenamecolor#1#2{\expandafter\xdef\csname fstyles@fg@#1\endcsname{#2}}
\def\namescolor#1{\xdef\names@fg{#1}}
\def\namecolor#1#2{%
\xdef\first@{consensus} \xdef\second@{#1}
\ifx\first@\second@
\expandafter\xdef\csname name@col0\endcsname{#2}
\else
+ \xdef\first@{featurenames} \xdef\second@{#1}
+ \ifx\first@\second@
+ \xdef\ftext@fg{#2}
+ \else
+ \xdef\first@{featurestylenames} \xdef\second@{#1}
+ \ifx\first@\second@
+ \xdef\fstyles@fg{#2}
+ \else
\xdef\first@{#1,&,@} \xdef\third@{#2} \namecolor@
- \fi
+ \fi\fi\fi
}
\def\numberingcolor#1{\xdef\numbering@fg{#1}}
\def\numbercolor#1#2{%
@@ -10703,7 +11017,11 @@
\else
\expandafter\ifnum\csname pos\the\loopcount\endcsname>\m@x
\xdef\m@x{\csname pos\the\loopcount\endcsname}
- \xdef\cons@seq{\the\loopcount} \xdef\match@case{1}
+ \expandafter\ifnum\csname pos\the\loopcount\endcsname<\all@thresh@ld
+ \xdef\cons@seq{\the\loopcount} \xdef\match@case{1}
+ \else
+ \xdef\cons@seq{\the\loopcount} \xdef\match@case{2}
+ \fi
\else
\expandafter\ifnum\csname pos\the\loopcount\endcsname=\m@x
\xdef\match@case{0}
@@ -11134,13 +11452,14 @@
\xdef\constopo{\constopo 2}}
\def\allm@tch{%
- \ifall@shade \xdef\third@{0} \else \xdef\third@{1} \fi
+ \xdef\tmp@{\csname res\cons@seq\endcsname}
\loopcount=0
\loop
\advance\loopcount by 1
\xdef\first@{noshade}
\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
\expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
\expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
\xdef\first@{=\first@}\fi
@@ -11151,11 +11470,60 @@
\csname seq\the\loopcount\endcsname%
3\first@}
\else
+ \xdef\second@{\csname res\the\loopcount\endcsname}
+ \ifx\tmp@\second@
+ \ifall@shade \xdef\third@{0} \else \xdef\third@{1} \fi
+ \else
+ \xdef\third@{3}
+ \ifsimmode
+ \xdef\last@{\csname \prefix@ sim\tmp@\endcsname &@}
+ \expandafter\get@count\last@
+ \innerloopcount=0 \getsim@char
+ \fi
+ \fi
\xdef\first@{\csname res\the\loopcount\endcsname}
+ \ifcase\third@
\ifnum\divref@=\loopcount\else
\xdef\low@up{lower} \ifx\res@llm@tch\low@up \make@lower \else
\xdef\low@up{upper} \ifx\res@llm@tch\low@up
\else \xdef\first@{\res@llm@tch} \fi\fi\fi
+ \or
+ \ifnum\divref@=\loopcount\else
+ \xdef\low@up{lower} \ifx\res@llm@tch\low@up \make@lower \else
+ \xdef\low@up{upper} \ifx\res@llm@tch\low@up
+ \else \xdef\first@{\res@llm@tch} \fi\fi\fi
+ \or
+ \ifnum\divref@=\loopcount\else
+ \xdef\low@up{lower} \ifx\ressimm@tch\low@up \make@lower \else
+ \xdef\low@up{upper} \ifx\ressimm@tch\low@up
+ \else \xdef\first@{\ressimm@tch} \fi\fi\fi
+ \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
+ \fi
+ \ifx\first@\d@t
+ \expandafter\ifnum\csname res@count\the\loopcount\endcsname%
+ <\csname seq@start\the\loopcount\endcsname
+ \ifsh@wg@ps
+ \def\first@{\gap@char}\def\third@{7}
+ \else
+ \def\first@{{}} \def\third@{8}
+ \fi
+ \else
+ \expandafter\ifnum\csname res@count\the\loopcount\endcsname%
+ <\csname seq@len\the\loopcount\endcsname
+ \def\third@{7}\def\first@{\gap@char}
+ \else
+ \ifsh@wg@ps
+ \def\first@{\gap@char}\def\third@{7}
+ \else
+ \def\first@{{}} \def\third@{8}
+ \fi
+ \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
@@ -11163,7 +11531,7 @@
\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\third@\first@}
+ \csname seq\the\loopcount\endcsname\third@\first@}
\fi
\ifnum\loopcount<\seq@count \repeat
\xdef\first@{\csname res\cons@seq\endcsname}
@@ -13238,7 +13606,7 @@
\def\temp@{x}\fi%
\ifhidechar\xdef\temp@{}\fi%
\kern-\box@width\textcolor{\third@}{\hbox to \box@width{%
- \res@@style{\hss\temp@\hss}}}%
+ \legend@size{\res@@style{\hss\temp@\hss}}}}%
\kern2ex\textcolor{\legend@fg}{%
\legend@size{\csname fgroup@name\the\loopcount\endcsname}}
\newline\hbox{}%
@@ -13254,7 +13622,7 @@
\def\temp@{X}\xdef\low@up{lower}\ifx\resn@m@tch\low@up\def\temp@{x}\fi%
\ifhidechar\xdef\temp@{}\fi%
\kern-\box@width\textcolor{\TextNomatch}{\hbox to \box@width{%
- \res@@style{\hss\temp@\hss}}}%
+ \legend@size{\res@@style{\hss\temp@\hss}}}}%
\textcolor{\legend@fg}{%
\ifgerm@n\kern2ex\legend@size{nicht konserviert}%
\else\ifsp@nish\kern2ex\legend@size{no conservado}%
@@ -13269,7 +13637,7 @@
\def\temp@{X}\xdef\low@up{lower}\ifx\ressimm@tch\low@up\def\temp@{x}\fi%
\ifhidechar\xdef\temp@{}\fi%
\kern-\box@width\textcolor{\TextSimilar}{\hbox to \box@width{%
- \res@@style{\hss\temp@\hss}}}%
+ \legend@size{\res@@style{\hss\temp@\hss}}}}%
\textcolor{\legend@fg}{%
\ifgerm@n\kern2ex\legend@size{\"ahnlich}%
\else\ifsp@nish\kern2ex\legend@size{similar}%
@@ -13284,11 +13652,11 @@
\def\temp@{X}\xdef\low@up{lower}\ifx\resm@tch\low@up\def\temp@{x}\fi%
\ifhidechar\xdef\temp@{}\fi%
\kern-\box@width\textcolor{\TextIdentical}{\hbox to \box@width{%
- \res@@style{\hss\temp@\hss}}}%
+ \legend@size{\res@@style{\hss\temp@\hss}}}}%
\textcolor{\legend@fg}{%
- \ifgerm@n\kern2ex\legend@size{konserviert}%
- \else\ifsp@nish\kern2ex\legend@size{conservado}%
- \else\kern2ex\legend@size{conserved}\fi\fi}
+ \ifgerm@n\kern2ex\legend@size{$\ge$\,\thresh@ld\% konserviert}%
+ \else\ifsp@nish\kern2ex\legend@size{$\ge$\,\thresh@ld\% conservado}%
+ \else\kern2ex\legend@size{$\ge$\,\thresh@ld\% conserved}\fi\fi}
\newline\hbox{}\noindent%
\ifall@shade%
\ifnames@\ifnames@right\else\hbox to \name@width{\hss}\fi\fi
@@ -13299,11 +13667,18 @@
\def\temp@{X}\xdef\low@up{lower}\ifx\res@llm@tch\low@up\def\temp@{x}\fi%
\ifhidechar\xdef\temp@{}\fi%
\kern-\box@width\textcolor{\TextAllmatch}{\hbox to \box@width{%
- \res@@style{\hss\temp@\hss}}}%
+ \legend@size{\res@@style{\hss\temp@\hss}}}}%
+ \ifnum\all@thresh@ld=100
\textcolor{\legend@fg}{%
\ifgerm@n\kern2ex\legend@size{alle identisch}%
\else\ifsp@nish\kern2ex\legend@size{todos id\'enticos}%
\else\kern2ex\legend@size{all match}\fi\fi}
+ \else
+ \textcolor{\legend@fg}{%
+ \ifgerm@n\kern2ex\legend@size{$\ge$\,\all@thresh@ld\% konserviert}%
+ \else\ifsp@nish\kern2ex\legend@size{$\ge$\,\all@thresh@ld\% conservado}%
+ \else\kern2ex\legend@size{$\ge$\,\all@thresh@ld\% conserved}\fi\fi}
+ \fi
\newline\hbox{}\noindent
\fi
\fi
@@ -14096,7 +14471,6 @@
}
\def\next@featuretext&#1;#2;#3@{%
\xdef\first@{#3@}%
-% \xdef\last@{#2::&}\expandafter\test@fill\last@%
\xdef\last@{fill:#2:&}\expandafter\test@fill\last@%
\ifx\f@color\comm@\xdef\f@color{Black}\fi%
\fontfamily{\featuretext@family}%
@@ -14166,6 +14540,7 @@
\textcolor{\f@color}{%
\hbox to #1\box@width{\hss\featuretext@size{\strut\fourth@}\hss}}%
\fi%
+ \advance\loopcount by -#1%
}
\def\put@featuretext{%
\if\first@ @%
@@ -14181,6 +14556,7 @@
\hbox to \second@\box@width%
{\hss\expandafter\putfeature@style{\first@}\hss}\fi%
\xdef\first@{#3@}%
+ \advance\loopcount by -\second@%
}
\def\put@featurestyle{%
\if\first@ @%
@@ -14192,35 +14568,104 @@
\def\put@feature{%
\vspace{-\baselineskip}%
\newline\hbox{}%
- \ifnames@right\else\ifnames@\hbox to \name@width{\hss}\fi\fi%
- \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi%
\xdef\temp@{ttop}%
\ifx\temp@\bottop@%
+ \ifnames@right\else\ifnames@%
+ \fontfamily{\ftext@family}\fontseries{\ftext@series}\fontshape{\ftext@shape}%
+ \selectfont%
+ \textcolor{\csname ftext@fg@\bottop@\endcsname}{\hbox to \name@width{\csname featuretextn@me\bottop@\endcsname\hss}}\fi\fi%
+ \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi%
\xdef\first@{\csname textfeature\bottop@\endcsname @}%
+ \loopcount=\res@perline%
\put@featuretext%
+ \ifnumbers@right\ifnumbers@\hbox to \number@width{\hss}\fi\fi%
+ \ifnames@right\ifnames@%
+ \fontfamily{\ftext@family}\fontseries{\ftext@series}\fontshape{\ftext@shape}%
+ \selectfont%
+ \kern1em\hbox to \loopcount\box@width{\hss}%
+ \textcolor{\csname ftext@fg@\bottop@\endcsname}{\hbox to \name@width{\csname featuretextn@me\bottop@\endcsname\hss}}\fi\fi%
\else%
\xdef\temp@{top}%
\ifx\temp@\bottop@%
+ \ifnames@right\else\ifnames@%
+ \fontfamily{\ftext@family}\fontseries{\ftext@series}\fontshape{\ftext@shape}%
+ \selectfont%
+ \textcolor{\csname ftext@fg@\bottop@\endcsname}{\hbox to \name@width{\csname featuretextn@me\bottop@\endcsname\hss}}\fi\fi%
+ \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi%
\xdef\first@{\csname textfeature\bottop@\endcsname @}%
+ \loopcount=\res@perline%
\put@featuretext%
+ \ifnumbers@right\ifnumbers@\hbox to \number@width{\hss}\fi\fi%
+ \ifnames@right\ifnames@%
+ \fontfamily{\ftext@family}\fontseries{\ftext@series}\fontshape{\ftext@shape}%
+ \selectfont%
+ \kern1em\hbox to \loopcount\box@width{\hss}%
+ \textcolor{\csname ftext@fg@\bottop@\endcsname}{\hbox to \name@width{\csname featuretextn@me\bottop@\endcsname\hss}}\fi\fi%
\else
+ \ifnames@right\else\ifnames@%
+ \fontfamily{\fstyles@family}\fontseries{\fstyles@series}\fontshape{\fstyles@shape}%
+ \selectfont%
+ \textcolor{\csname fstyles@fg@\bottop@\endcsname}{\hbox to \name@width{\csname featurestylesn@me\bottop@\endcsname\hss}}\fi\fi%
+ \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi%
\xdef\first@{\csname stylefeature\bottop@\endcsname @}%
+ \loopcount=\res@perline%
\put@featurestyle%
+ \ifnumbers@right\ifnumbers@\hbox to \number@width{\hss}\fi\fi%
+ \ifnames@right\ifnames@%
+ \fontfamily{\fstyles@family}\fontseries{\fstyles@series}\fontshape{\fstyles@shape}%
+ \selectfont%
+ \kern1em\hbox to \loopcount\box@width{\hss}%
+ \textcolor{\csname fstyles@fg@\bottop@\endcsname}{\hbox to \name@width{\csname featurestylesn@me\bottop@\endcsname\hss}}\fi\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%
\ifx\temp@\bottop@%
+ \ifnames@right\else\ifnames@%
+ \fontfamily{\fstyles@family}\fontseries{\fstyles@series}\fontshape{\fstyles@shape}%
+ \selectfont%
+ \textcolor{\csname fstyles@fg@\bottop@\endcsname}{\hbox to \name@width{\csname featurestylesn@me\bottop@\endcsname\hss}}\fi\fi%
+ \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi%
\xdef\first@{\csname stylefeature\bottop@\endcsname @}%
+ \loopcount=\res@perline%
\put@featurestyle%
+ \ifnumbers@right\ifnumbers@\hbox to \number@width{\hss}\fi\fi%
+ \ifnames@right\ifnames@%
+ \fontfamily{\fstyles@family}\fontseries{\fstyles@series}\fontshape{\fstyles@shape}%
+ \selectfont%
+ \kern1em\hbox to \loopcount\box@width{\hss}%
+ \textcolor{\csname fstyles@fg@\bottop@\endcsname}{\hbox to \name@width{\csname featurestylesn@me\bottop@\endcsname\hss}}\fi\fi%
\else%
\xdef\temp@{ttop}%
\ifx\temp@\bottop@%
+ \ifnames@right\else\ifnames@%
+ \fontfamily{\fstyles@family}\fontseries{\fstyles@series}\fontshape{\fstyles@shape}%
+ \selectfont%
+ \textcolor{\csname fstyles@fg@\bottop@\endcsname}{\hbox to \name@width{\csname featurestylesn@me\bottop@\endcsname\hss}}\fi\fi%
+ \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi%
\xdef\first@{\csname stylefeature\bottop@\endcsname @}%
+ \loopcount=\res@perline%
\put@featurestyle%
+ \ifnumbers@right\ifnumbers@\hbox to \number@width{\hss}\fi\fi%
+ \ifnames@right\ifnames@%
+ \fontfamily{\fstyles@family}\fontseries{\fstyles@series}\fontshape{\fstyles@shape}%
+ \selectfont%
+ \kern1em\hbox to \loopcount\box@width{\hss}%
+ \textcolor{\csname fstyles@fg@\bottop@\endcsname}{\hbox to \name@width{\csname featurestylesn@me\bottop@\endcsname\hss}}\fi\fi%
\else
+ \ifnames@right\else\ifnames@%
+ \fontfamily{\ftext@family}\fontseries{\ftext@series}\fontshape{\ftext@shape}%
+ \selectfont%
+ \textcolor{\csname ftext@fg@\bottop@\endcsname}{\hbox to \name@width{\csname featuretextn@me\bottop@\endcsname\hss}}\fi\fi%
+ \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi%
\xdef\first@{\csname textfeature\bottop@\endcsname @}%
+ \xdef\first@{\csname textfeature\bottop@\endcsname @}%
+ \loopcount=\res@perline%
\put@featuretext%
+ \ifnumbers@right\ifnumbers@\hbox to \number@width{\hss}\fi\fi%
+ \ifnames@right\ifnames@%
+ \fontfamily{\ftext@family}\fontseries{\ftext@series}\fontshape{\ftext@shape}%
+ \selectfont%
+ \kern1em\hbox to \loopcount\box@width{\hss}%
+ \textcolor{\csname ftext@fg@\bottop@\endcsname}{\hbox to \name@width{\csname featuretextn@me\bottop@\endcsname\hss}}\fi\fi%
\fi\fi%
\newline\hbox{}%
}
@@ -15836,6 +16281,8 @@
\xdef\hide@true{n} \xdef\hide@now{n}
\xdef\hide@label{circ}
\xdef\divref@{0}
+\xdef\all@thresh@ld{100} \all@shadefalse
+\hidefeaturenames \hidefeaturestylenames
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%% %%%%%
@@ -15871,6 +16318,8 @@
\numberingcolor{Black} % Numbering color is `Black'
\shownumbering{right} % Show sequence numbering on the left
\namescolor{Black} % Names' color is `Black'
+\featurenamescolor{Black} % Feature names' color is `Black'
+\featurestylenamescolor{Black} % Feature names' color is `Black'
\shownames{left} % Show sequence names on the right
\consensuscolors{Black}{White} % All consensus symbols/letters
{Black}{White} % appear `Black on White'
@@ -15911,6 +16360,14 @@
\setseries{names}{md} % Use normal series for names
\setshape {names}{up} % Use upright shape for names
\setsize {names}{normalsize} % Use normal size for names
+\setfamily{featurenames}{tt} % Use typewriter family for feature names
+\setseries{featurenames}{md} % Use normal series for feature names
+\setshape {featurenames}{up} % Use upright shape for feature names
+\setsize {featurenames}{normalsize}% Use normal size for feature names
+\setfamily{featurestylenames}{tt} % Use typewriter family for feature style names
+\setseries{featurestylenames}{md} % Use normal series for feature style names
+\setshape {featurestylenames}{up} % Use upright shape for feature style names
+\setsize {featurestylenames}{normalsize}% Use normal size for feature style names
\setfamily{features}{rm} % Use roman family for feature texts
\setseries{features}{md} % Use normal series for feature texts
\setshape {features}{it} % Use italics shape for feature texts
@@ -16062,6 +16519,8 @@
\numberingcolor{Black} % Numbering color is `Black'
\shownumbering{right} % Show sequence numbering on the left
\namescolor{Black} % Names' color is `Black'
+\featurenamescolor{Black} % Feature names' color is `Black'
+\featurestylenamescolor{Black} % Feature names' color is `Black'
\shownames{left} % Show sequence names on the right
\consensuscolors{Black}{White} % All consensus symbols/letters
{Black}{White} % appear `Black on White'
@@ -16102,6 +16561,14 @@
\setseries{names}{md} % Use normal series for names
\setshape {names}{up} % Use upright shape for names
\setsize {names}{normalsize} % Use normal size for names
+\setfamily{featurenames}{tt} % Use typewriter family for feature names
+\setseries{featurenames}{md} % Use normal series for feature names
+\setshape {featurenames}{up} % Use upright shape for feature names
+\setsize {featurenames}{normalsize}% Use normal size for feature names
+\setfamily{featurestylenames}{tt} % Use typewriter family for feature style names
+\setseries{featurestylenames}{md} % Use normal series for feature style names
+\setshape {featurestylenames}{up} % Use upright shape for feature style names
+\setsize {featurestylenames}{normalsize}% Use normal size for feature style names
\setfamily{features}{rm} % Use roman family for feature texts
\setseries{features}{md} % Use normal series for feature texts
\setshape {features}{it} % Use italics shape for feature texts
diff --git a/Master/texmf-dist/tex/latex/texshade/texshade.def b/Master/texmf-dist/tex/latex/texshade/texshade.def
index b9c55582a77..2de06346a09 100644
--- a/Master/texmf-dist/tex/latex/texshade/texshade.def
+++ b/Master/texmf-dist/tex/latex/texshade/texshade.def
@@ -35,6 +35,8 @@
\numberingcolor{Black} % Numbering color is `Black'
\shownumbering{right} % Show sequence numbering on the left
\namescolor{Black} % Names' color is `Black'
+\featurenamescolor{Black} % Feature names' color is `Black'
+\featurestylenamescolor{Black} % Feature names' color is `Black'
\shownames{left} % Show sequence names on the right
\consensuscolors{Black}{White} % All consensus symbols/letters
{Black}{White} % appear `Black on White'
@@ -75,6 +77,14 @@
\setseries{names}{md} % Use normal series for names
\setshape {names}{up} % Use upright shape for names
\setsize {names}{normalsize} % Use normal size for names
+\setfamily{featurenames}{tt} % Use typewriter family for feature names
+\setseries{featurenames}{md} % Use normal series for feature names
+\setshape {featurenames}{up} % Use upright shape for feature names
+\setsize {featurenames}{normalsize}% Use normal size for feature names
+\setfamily{featurestylenames}{tt} % Use typewriter family for feature style names
+\setseries{featurestylenames}{md} % Use normal series for feature style names
+\setshape {featurestylenames}{up} % Use upright shape for feature style names
+\setsize {featurestylenames}{normalsize}% Use normal size for feature style names
\setfamily{features}{rm} % Use roman family for feature texts
\setseries{features}{md} % Use normal series for feature texts
\setshape {features}{it} % Use italics shape for feature texts
diff --git a/Master/texmf-dist/tex/latex/texshade/texshade.sty b/Master/texmf-dist/tex/latex/texshade/texshade.sty
index 792807ef473..77a390d1fc3 100644
--- a/Master/texmf-dist/tex/latex/texshade/texshade.sty
+++ b/Master/texmf-dist/tex/latex/texshade/texshade.sty
@@ -13,8 +13,8 @@
%%
\NeedsTeXFormat{LaTeX2e}
-\ProvidesPackage{texshade}[2007/02/18 LaTeX TeXshade (v1.16)]
-\message{Package `texshade', Version 1.16 of 2007/02/18.}
+\ProvidesPackage{texshade}[2007/06/19 LaTeX TeXshade (v1.17)]
+\message{Package `texshade', Version 1.17 of 2007/06/19.}
\PassOptionsToPackage{dvips}{color}
\PassOptionsToPackage{dvips}{graphicx}
@@ -4027,6 +4027,12 @@
\fi\fi\fi
\fi
}
+\def\showfeaturename#1#2{\expandafter\xdef\csname featuretextn@me#1\endcsname{#2}}
+\def\showfeaturestylename#1#2{\expandafter\xdef\csname featurestylesn@me#1\endcsname{#2}}
+\def\hidefeaturename#1{\expandafter\xdef\csname featuretextn@me#1\endcsname{}}
+\def\hidefeaturenames{\xdef\featuretextn@mettop{}\xdef\featuretextn@metop{}\xdef\featuretextn@mebottom{}\xdef\featuretextn@mebbottom{}}
+\def\hidefeaturestylename#1{\expandafter\xdef\csname featurestylesn@me#1\endcsname{}}
+\def\hidefeaturestylenames{\xdef\featurestylesn@mettop{}\xdef\featurestylesn@metop{}\xdef\featurestylesn@mebottom{}\xdef\featurestylesn@mebbottom{}}
\def\seqtype#1{\xdef\seq@type{#1}
\if\seq@type P \xdef\prefix@{pep}
\else \if\seq@type p \xdef\seq@type{P} \xdef\prefix@{pep}
@@ -4036,7 +4042,21 @@
\xdef\first@{#1} \ifletter \get@name@number \fi
\expandafter\xdef\csname newseqname\first@\endcsname{#2}
}
-\def\threshold#1{\xdef\thresh@ld{#1}}
+\newcommand\threshold[2][n]{%
+ \xdef\first@{#1}
+ \ifx\first@\n@
+ \xdef\thresh@ld{#2}
+ \else
+ \all@shadetrue
+ \ifnum\first@>#2
+ \xdef\thresh@ld{#2}
+ \xdef\all@thresh@ld{#1}
+ \else
+ \xdef\thresh@ld{#1}
+ \xdef\all@thresh@ld{#2}
+ \fi
+ \fi
+}
\def\constosingleseq#1{%
\xdef\first@{#1 @} \expandafter\check@letter\first@
\xdef\first@{#1} \ifletter \get@name@number \fi
@@ -4096,20 +4116,45 @@
\xdef\seq@gap@num{\the\loopcount}
\fi
\fi}
-\newcommand{\shadingmode}[2][1]{%
+\newcommand{\shadingmode}[2][-1]{%
\xdef\last@{#2}
\xdef\first@{identical}
- \all@shadefalse
\ifx\first@\last@
\simmodefalse \funcmodefalse
- \xdef\last@{#1} \xdef\second@{allmatchspecial}
- \ifx\second@\last@ \all@shadetrue \fi
+ \xdef\second@{#1 @} \expandafter\check@letter\second@
+ \ifnumber \all@shadetrue
+ \ifnum#1<0 \all@shadefalse
+ \else
+ \ifnum#1>100 \xdef\all@thresh@ld{100}
+ \else
+ \xdef\all@thresh@ld{#1}
+ \fi\fi
+ \else
+ \xdef\last@{#1}
+ \xdef\first@{allmatchspecial}
+ \ifx\last@\first@
+ \xdef\all@thresh@ld{100} \all@shadetrue
+ \fi
+ \fi
\else
\xdef\first@{similar}
\ifx\first@\last@
\simmodetrue \funcmodefalse
- \xdef\last@{#1} \xdef\second@{allmatchspecial}
- \ifx\second@\last@ \all@shadetrue \fi
+ \xdef\second@{#1 @} \expandafter\check@letter\second@
+ \ifnumber \all@shadetrue
+ \ifnum#1<0 \all@shadefalse
+ \else
+ \ifnum#1>100 \xdef\all@thresh@ld{100}
+ \else
+ \xdef\all@thresh@ld{#1}
+ \fi\fi
+ \else
+ \xdef\last@{#1}
+ \xdef\first@{allmatchspecial}
+ \ifx\last@\first@
+ \xdef\all@thresh@ld{100} \all@shadetrue
+ \fi
+ \fi
\else
\xdef\first@{functional}
\ifx\first@\last@
@@ -4136,7 +4181,16 @@
\message{<Unknown shading mode - using `similar'>}
\simmodetrue \funcmodefalse
\fi\fi\fi\fi}
-\def\allmatchspecial{\all@shadetrue}
+\newcommand\allmatchspecial[1][100]{%
+ \ifnum#1<0
+ \xdef\all@thresh@ld{0}
+ \else
+ \ifnum#1>100
+ \xdef\all@thresh@ld{100}
+ \else
+ \xdef\all@thresh@ld{#1}
+ \fi\fi
+ \all@shadetrue}
\def\allmatchspecialoff{\all@shadefalse}
\def\gapchar#1{%
\xdef\first@{rule}\xdef\second@{#1}
@@ -4589,6 +4643,12 @@
\else
\xdef\third@{\second@}
\fi\fi\fi
+ \xdef\temp@{featurenames}
+ \ifx\first@\temp@ \xdef\ftext@family{\third@}
+ \else
+ \xdef\temp@{featurestylenames}
+ \ifx\first@\temp@ \xdef\fstyles@family{\third@}
+ \else
\xdef\temp@{features}
\ifx\first@\temp@ \xdef\featuretext@family{\third@}
\else
@@ -4618,6 +4678,8 @@
\else
\xdef\temp@{all}
\ifx\first@\temp@
+ \xdef\ftext@family{\third@}
+ \xdef\fstyles@family{\third@}
\xdef\featuretext@family{\third@}
\xdef\featurestyles@family{\third@}
\xdef\numbertext@family{\third@}
@@ -4627,7 +4689,7 @@
\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
}
\def\setseries#1#2{%
@@ -4646,6 +4708,12 @@
\else
\xdef\third@{\second@}
\fi\fi
+ \xdef\temp@{featurenames}
+ \ifx\first@\temp@ \xdef\ftext@series{\third@}
+ \else
+ \xdef\temp@{featurestylenames}
+ \ifx\first@\temp@ \xdef\fstyles@series{\third@}
+ \else
\xdef\temp@{features}
\ifx\first@\temp@ \xdef\featuretext@series{\third@}
\else
@@ -4672,6 +4740,8 @@
\else
\xdef\temp@{all}
\ifx\first@\temp@
+ \xdef\ftext@series{\third@}
+ \xdef\fstyles@series{\third@}
\xdef\featuretext@series{\third@}
\xdef\featurestyles@series{\third@}
\xdef\numbertext@series{\third@}
@@ -4680,7 +4750,7 @@
\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
}
\def\setshape#1#2{%
@@ -4707,6 +4777,12 @@
\else
\xdef\third@{\second@}
\fi\fi\fi\fi
+ \xdef\temp@{featurenames}
+ \ifx\first@\temp@ \xdef\ftext@shape{\third@}
+ \else
+ \xdef\temp@{featurestylenames}
+ \ifx\first@\temp@ \xdef\fstyles@shape{\third@}
+ \else
\xdef\temp@{features}
\ifx\first@\temp@ \xdef\featuretext@shape{\third@}
\else
@@ -4733,6 +4809,8 @@
\else
\xdef\temp@{all}
\ifx\first@\temp@
+ \xdef\ftext@shape{\third@}
+ \xdef\fstyles@shape{\third@}
\xdef\featuretext@shape{\third@}
\xdef\featurestyles@shape{\third@}
\xdef\numbertext@shape{\third@}
@@ -4741,7 +4819,7 @@
\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
}
\def\setsize#1#2{%
@@ -4757,6 +4835,14 @@
\ifx\first@\temp@
\def\featurestyles@size{\csname #2\endcsname}
\else
+ \xdef\temp@{featurenames}
+ \ifx\first@\temp@
+ \def\ftext@size{\csname #2\endcsname}
+ \else
+ \xdef\temp@{featurestylenames}
+ \ifx\first@\temp@
+ \def\fstyles@size{\csname #2\endcsname}
+ \else
\xdef\temp@{numbering}
\ifx\first@\temp@
\def\numbertext@size{\csname #2\endcsname}
@@ -4796,6 +4882,8 @@
\ifx\first@\temp@
\def\featuretext@size{\csname #2\endcsname}
\def\featurestyles@size{\csname #2\endcsname}
+ \def\ftext@size{\csname #2\endcsname}
+ \def\fstyles@size{\csname #2\endcsname}
\def\numbertext@size{\csname #2\endcsname}
\def\namestext@size{\csname #2\endcsname}
\def\legend@size{\csname #2\endcsname}
@@ -4803,7 +4891,7 @@
\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
\xdef\temp@{Huge}
\ifx\temp@\res@size
\def\bottomruler@size{\csname Large\endcsname}
@@ -4835,6 +4923,44 @@
\def\setfont#1#2#3#4#5{%
\setfamily{#1}{#2}\setseries{#1}{#3}
\setshape{#1}{#4}\setsize{#1}{#5}}
+\def\featurenamesrm{\setfamily{featurenames}{rm}}
+\def\featurenamessf{\setfamily{featurenames}{sf}}
+\def\featurenamestt{\setfamily{featurenames}{tt}}
+\def\featurenamesmd{\setseries{featurenames}{md}}
+\def\featurenamesbf{\setseries{featurenames}{bf}}
+\def\featurenamesup{\setshape {featurenames}{up}}
+\def\featurenamesit{\setshape {featurenames}{it}}
+\def\featurenamessl{\setshape {featurenames}{sl}}
+\def\featurenamessc{\setshape {featurenames}{sc}}
+\def\featurenamestiny {\setsize{featurenames}{tiny}}
+\def\featurenamesscriptsize {\setsize{featurenames}{scriptsize}}
+\def\featurenamesfootnotesize{\setsize{featurenames}{footnotesize}}
+\def\featurenamessmall {\setsize{featurenames}{small}}
+\def\featurenamesnormalsize {\setsize{featurenames}{normalsize}}
+\def\featurenameslarge {\setsize{featurenames}{large}}
+\def\featurenamesLarge {\setsize{featurenames}{Large}}
+\def\featurenamesLARGE {\setsize{featurenames}{LARGE}}
+\def\featurenameshuge {\setsize{featurenames}{huge}}
+\def\featurenamesHuge {\setsize{featurenames}{Huge}}
+\def\featurestylenamesrm{\setfamily{featurestylenames}{rm}}
+\def\featurestylenamessf{\setfamily{featurestylenames}{sf}}
+\def\featurestylenamestt{\setfamily{featurestylenames}{tt}}
+\def\featurestylenamesmd{\setseries{featurestylenames}{md}}
+\def\featurestylenamesbf{\setseries{featurestylenames}{bf}}
+\def\featurestylenamesup{\setshape {featurestylenames}{up}}
+\def\featurestylenamesit{\setshape {featurestylenames}{it}}
+\def\featurestylenamessl{\setshape {featurestylenames}{sl}}
+\def\featurestylenamessc{\setshape {featurestylenames}{sc}}
+\def\featurestylenamestiny {\setsize{featurestylenames}{tiny}}
+\def\featurestylenamesscriptsize {\setsize{featurestylenames}{scriptsize}}
+\def\featurestylenamesfootnotesize{\setsize{featurestylenames}{footnotesize}}
+\def\featurestylenamessmall {\setsize{featurestylenames}{small}}
+\def\featurestylenamesnormalsize {\setsize{featurestylenames}{normalsize}}
+\def\featurestylenameslarge {\setsize{featurestylenames}{large}}
+\def\featurestylenamesLarge {\setsize{featurestylenames}{Large}}
+\def\featurestylenamesLARGE {\setsize{featurestylenames}{LARGE}}
+\def\featurestylenameshuge {\setsize{featurestylenames}{huge}}
+\def\featurestylenamesHuge {\setsize{featurestylenames}{Huge}}
\def\featuresrm{\setfamily{features}{rm}}
\def\featuressf{\setfamily{features}{sf}}
\def\featurestt{\setfamily{features}{tt}}
@@ -5081,14 +5207,36 @@
\else
\ifx\third@\first@\white@box\else\textcolor{\third@}{\box@rule}\fi
\fi\fi\fi\fi}
+\def\featurenamescolor#1{%
+ \expandafter\xdef\csname ftext@fg@ttop\endcsname{#1}
+ \expandafter\xdef\csname ftext@fg@top\endcsname{#1}
+ \expandafter\xdef\csname ftext@fg@bottom\endcsname{#1}
+ \expandafter\xdef\csname ftext@fg@bbottom\endcsname{#1}
+}
+\def\featurestylenamescolor#1{%
+ \expandafter\xdef\csname fstyles@fg@ttop\endcsname{#1}
+ \expandafter\xdef\csname fstyles@fg@top\endcsname{#1}
+ \expandafter\xdef\csname fstyles@fg@bottom\endcsname{#1}
+ \expandafter\xdef\csname fstyles@fg@bbottom\endcsname{#1}
+}
+\def\featurenamecolor#1#2{\expandafter\xdef\csname ftext@fg@#1\endcsname{#2}}
+\def\featurestylenamecolor#1#2{\expandafter\xdef\csname fstyles@fg@#1\endcsname{#2}}
\def\namescolor#1{\xdef\names@fg{#1}}
\def\namecolor#1#2{%
\xdef\first@{consensus} \xdef\second@{#1}
\ifx\first@\second@
\expandafter\xdef\csname name@col0\endcsname{#2}
\else
+ \xdef\first@{featurenames} \xdef\second@{#1}
+ \ifx\first@\second@
+ \xdef\ftext@fg{#2}
+ \else
+ \xdef\first@{featurestylenames} \xdef\second@{#1}
+ \ifx\first@\second@
+ \xdef\fstyles@fg{#2}
+ \else
\xdef\first@{#1,&,@} \xdef\third@{#2} \namecolor@
- \fi
+ \fi\fi\fi
}
\def\numberingcolor#1{\xdef\numbering@fg{#1}}
\def\numbercolor#1#2{%
@@ -5586,7 +5734,11 @@
\else
\expandafter\ifnum\csname pos\the\loopcount\endcsname>\m@x
\xdef\m@x{\csname pos\the\loopcount\endcsname}
- \xdef\cons@seq{\the\loopcount} \xdef\match@case{1}
+ \expandafter\ifnum\csname pos\the\loopcount\endcsname<\all@thresh@ld
+ \xdef\cons@seq{\the\loopcount} \xdef\match@case{1}
+ \else
+ \xdef\cons@seq{\the\loopcount} \xdef\match@case{2}
+ \fi
\else
\expandafter\ifnum\csname pos\the\loopcount\endcsname=\m@x
\xdef\match@case{0}
@@ -6017,13 +6169,14 @@
\xdef\constopo{\constopo 2}}
\def\allm@tch{%
- \ifall@shade \xdef\third@{0} \else \xdef\third@{1} \fi
+ \xdef\tmp@{\csname res\cons@seq\endcsname}
\loopcount=0
\loop
\advance\loopcount by 1
\xdef\first@{noshade}
\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
\expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
\expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
\xdef\first@{=\first@}\fi
@@ -6034,11 +6187,60 @@
\csname seq\the\loopcount\endcsname%
3\first@}
\else
+ \xdef\second@{\csname res\the\loopcount\endcsname}
+ \ifx\tmp@\second@
+ \ifall@shade \xdef\third@{0} \else \xdef\third@{1} \fi
+ \else
+ \xdef\third@{3}
+ \ifsimmode
+ \xdef\last@{\csname \prefix@ sim\tmp@\endcsname &@}
+ \expandafter\get@count\last@
+ \innerloopcount=0 \getsim@char
+ \fi
+ \fi
\xdef\first@{\csname res\the\loopcount\endcsname}
+ \ifcase\third@
+ \ifnum\divref@=\loopcount\else
+ \xdef\low@up{lower} \ifx\res@llm@tch\low@up \make@lower \else
+ \xdef\low@up{upper} \ifx\res@llm@tch\low@up
+ \else \xdef\first@{\res@llm@tch} \fi\fi\fi
+ \or
\ifnum\divref@=\loopcount\else
\xdef\low@up{lower} \ifx\res@llm@tch\low@up \make@lower \else
\xdef\low@up{upper} \ifx\res@llm@tch\low@up
\else \xdef\first@{\res@llm@tch} \fi\fi\fi
+ \or
+ \ifnum\divref@=\loopcount\else
+ \xdef\low@up{lower} \ifx\ressimm@tch\low@up \make@lower \else
+ \xdef\low@up{upper} \ifx\ressimm@tch\low@up
+ \else \xdef\first@{\ressimm@tch} \fi\fi\fi
+ \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
+ \fi
+ \ifx\first@\d@t
+ \expandafter\ifnum\csname res@count\the\loopcount\endcsname%
+ <\csname seq@start\the\loopcount\endcsname
+ \ifsh@wg@ps
+ \def\first@{\gap@char}\def\third@{7}
+ \else
+ \def\first@{{}} \def\third@{8}
+ \fi
+ \else
+ \expandafter\ifnum\csname res@count\the\loopcount\endcsname%
+ <\csname seq@len\the\loopcount\endcsname
+ \def\third@{7}\def\first@{\gap@char}
+ \else
+ \ifsh@wg@ps
+ \def\first@{\gap@char}\def\third@{7}
+ \else
+ \def\first@{{}} \def\third@{8}
+ \fi
+ \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
@@ -6046,7 +6248,7 @@
\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\third@\first@}
+ \csname seq\the\loopcount\endcsname\third@\first@}
\fi
\ifnum\loopcount<\seq@count \repeat
\xdef\first@{\csname res\cons@seq\endcsname}
@@ -8115,7 +8317,7 @@
\def\temp@{x}\fi%
\ifhidechar\xdef\temp@{}\fi%
\kern-\box@width\textcolor{\third@}{\hbox to \box@width{%
- \res@@style{\hss\temp@\hss}}}%
+ \legend@size{\res@@style{\hss\temp@\hss}}}}%
\kern2ex\textcolor{\legend@fg}{%
\legend@size{\csname fgroup@name\the\loopcount\endcsname}}
\newline\hbox{}%
@@ -8131,7 +8333,7 @@
\def\temp@{X}\xdef\low@up{lower}\ifx\resn@m@tch\low@up\def\temp@{x}\fi%
\ifhidechar\xdef\temp@{}\fi%
\kern-\box@width\textcolor{\TextNomatch}{\hbox to \box@width{%
- \res@@style{\hss\temp@\hss}}}%
+ \legend@size{\res@@style{\hss\temp@\hss}}}}%
\textcolor{\legend@fg}{%
\ifgerm@n\kern2ex\legend@size{nicht konserviert}%
\else\ifsp@nish\kern2ex\legend@size{no conservado}%
@@ -8146,7 +8348,7 @@
\def\temp@{X}\xdef\low@up{lower}\ifx\ressimm@tch\low@up\def\temp@{x}\fi%
\ifhidechar\xdef\temp@{}\fi%
\kern-\box@width\textcolor{\TextSimilar}{\hbox to \box@width{%
- \res@@style{\hss\temp@\hss}}}%
+ \legend@size{\res@@style{\hss\temp@\hss}}}}%
\textcolor{\legend@fg}{%
\ifgerm@n\kern2ex\legend@size{\"ahnlich}%
\else\ifsp@nish\kern2ex\legend@size{similar}%
@@ -8161,11 +8363,11 @@
\def\temp@{X}\xdef\low@up{lower}\ifx\resm@tch\low@up\def\temp@{x}\fi%
\ifhidechar\xdef\temp@{}\fi%
\kern-\box@width\textcolor{\TextIdentical}{\hbox to \box@width{%
- \res@@style{\hss\temp@\hss}}}%
+ \legend@size{\res@@style{\hss\temp@\hss}}}}%
\textcolor{\legend@fg}{%
- \ifgerm@n\kern2ex\legend@size{konserviert}%
- \else\ifsp@nish\kern2ex\legend@size{conservado}%
- \else\kern2ex\legend@size{conserved}\fi\fi}
+ \ifgerm@n\kern2ex\legend@size{$\ge$\,\thresh@ld\% konserviert}%
+ \else\ifsp@nish\kern2ex\legend@size{$\ge$\,\thresh@ld\% conservado}%
+ \else\kern2ex\legend@size{$\ge$\,\thresh@ld\% conserved}\fi\fi}
\newline\hbox{}\noindent%
\ifall@shade%
\ifnames@\ifnames@right\else\hbox to \name@width{\hss}\fi\fi
@@ -8176,11 +8378,18 @@
\def\temp@{X}\xdef\low@up{lower}\ifx\res@llm@tch\low@up\def\temp@{x}\fi%
\ifhidechar\xdef\temp@{}\fi%
\kern-\box@width\textcolor{\TextAllmatch}{\hbox to \box@width{%
- \res@@style{\hss\temp@\hss}}}%
+ \legend@size{\res@@style{\hss\temp@\hss}}}}%
+ \ifnum\all@thresh@ld=100
\textcolor{\legend@fg}{%
\ifgerm@n\kern2ex\legend@size{alle identisch}%
\else\ifsp@nish\kern2ex\legend@size{todos id\'enticos}%
\else\kern2ex\legend@size{all match}\fi\fi}
+ \else
+ \textcolor{\legend@fg}{%
+ \ifgerm@n\kern2ex\legend@size{$\ge$\,\all@thresh@ld\% konserviert}%
+ \else\ifsp@nish\kern2ex\legend@size{$\ge$\,\all@thresh@ld\% conservado}%
+ \else\kern2ex\legend@size{$\ge$\,\all@thresh@ld\% conserved}\fi\fi}
+ \fi
\newline\hbox{}\noindent
\fi
\fi
@@ -9042,6 +9251,7 @@
\textcolor{\f@color}{%
\hbox to #1\box@width{\hss\featuretext@size{\strut\fourth@}\hss}}%
\fi%
+ \advance\loopcount by -#1%
}
\def\put@featuretext{%
\if\first@ @%
@@ -9057,6 +9267,7 @@
\hbox to \second@\box@width%
{\hss\expandafter\putfeature@style{\first@}\hss}\fi%
\xdef\first@{#3@}%
+ \advance\loopcount by -\second@%
}
\def\put@featurestyle{%
\if\first@ @%
@@ -9068,35 +9279,104 @@
\def\put@feature{%
\vspace{-\baselineskip}%
\newline\hbox{}%
- \ifnames@right\else\ifnames@\hbox to \name@width{\hss}\fi\fi%
- \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi%
\xdef\temp@{ttop}%
\ifx\temp@\bottop@%
+ \ifnames@right\else\ifnames@%
+ \fontfamily{\ftext@family}\fontseries{\ftext@series}\fontshape{\ftext@shape}%
+ \selectfont%
+ \textcolor{\csname ftext@fg@\bottop@\endcsname}{\hbox to \name@width{\csname featuretextn@me\bottop@\endcsname\hss}}\fi\fi%
+ \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi%
\xdef\first@{\csname textfeature\bottop@\endcsname @}%
+ \loopcount=\res@perline%
\put@featuretext%
+ \ifnumbers@right\ifnumbers@\hbox to \number@width{\hss}\fi\fi%
+ \ifnames@right\ifnames@%
+ \fontfamily{\ftext@family}\fontseries{\ftext@series}\fontshape{\ftext@shape}%
+ \selectfont%
+ \kern1em\hbox to \loopcount\box@width{\hss}%
+ \textcolor{\csname ftext@fg@\bottop@\endcsname}{\hbox to \name@width{\csname featuretextn@me\bottop@\endcsname\hss}}\fi\fi%
\else%
\xdef\temp@{top}%
\ifx\temp@\bottop@%
+ \ifnames@right\else\ifnames@%
+ \fontfamily{\ftext@family}\fontseries{\ftext@series}\fontshape{\ftext@shape}%
+ \selectfont%
+ \textcolor{\csname ftext@fg@\bottop@\endcsname}{\hbox to \name@width{\csname featuretextn@me\bottop@\endcsname\hss}}\fi\fi%
+ \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi%
\xdef\first@{\csname textfeature\bottop@\endcsname @}%
+ \loopcount=\res@perline%
\put@featuretext%
+ \ifnumbers@right\ifnumbers@\hbox to \number@width{\hss}\fi\fi%
+ \ifnames@right\ifnames@%
+ \fontfamily{\ftext@family}\fontseries{\ftext@series}\fontshape{\ftext@shape}%
+ \selectfont%
+ \kern1em\hbox to \loopcount\box@width{\hss}%
+ \textcolor{\csname ftext@fg@\bottop@\endcsname}{\hbox to \name@width{\csname featuretextn@me\bottop@\endcsname\hss}}\fi\fi%
\else
+ \ifnames@right\else\ifnames@%
+ \fontfamily{\fstyles@family}\fontseries{\fstyles@series}\fontshape{\fstyles@shape}%
+ \selectfont%
+ \textcolor{\csname fstyles@fg@\bottop@\endcsname}{\hbox to \name@width{\csname featurestylesn@me\bottop@\endcsname\hss}}\fi\fi%
+ \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi%
\xdef\first@{\csname stylefeature\bottop@\endcsname @}%
+ \loopcount=\res@perline%
\put@featurestyle%
+ \ifnumbers@right\ifnumbers@\hbox to \number@width{\hss}\fi\fi%
+ \ifnames@right\ifnames@%
+ \fontfamily{\fstyles@family}\fontseries{\fstyles@series}\fontshape{\fstyles@shape}%
+ \selectfont%
+ \kern1em\hbox to \loopcount\box@width{\hss}%
+ \textcolor{\csname fstyles@fg@\bottop@\endcsname}{\hbox to \name@width{\csname featurestylesn@me\bottop@\endcsname\hss}}\fi\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%
\ifx\temp@\bottop@%
+ \ifnames@right\else\ifnames@%
+ \fontfamily{\fstyles@family}\fontseries{\fstyles@series}\fontshape{\fstyles@shape}%
+ \selectfont%
+ \textcolor{\csname fstyles@fg@\bottop@\endcsname}{\hbox to \name@width{\csname featurestylesn@me\bottop@\endcsname\hss}}\fi\fi%
+ \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi%
\xdef\first@{\csname stylefeature\bottop@\endcsname @}%
+ \loopcount=\res@perline%
\put@featurestyle%
+ \ifnumbers@right\ifnumbers@\hbox to \number@width{\hss}\fi\fi%
+ \ifnames@right\ifnames@%
+ \fontfamily{\fstyles@family}\fontseries{\fstyles@series}\fontshape{\fstyles@shape}%
+ \selectfont%
+ \kern1em\hbox to \loopcount\box@width{\hss}%
+ \textcolor{\csname fstyles@fg@\bottop@\endcsname}{\hbox to \name@width{\csname featurestylesn@me\bottop@\endcsname\hss}}\fi\fi%
\else%
\xdef\temp@{ttop}%
\ifx\temp@\bottop@%
+ \ifnames@right\else\ifnames@%
+ \fontfamily{\fstyles@family}\fontseries{\fstyles@series}\fontshape{\fstyles@shape}%
+ \selectfont%
+ \textcolor{\csname fstyles@fg@\bottop@\endcsname}{\hbox to \name@width{\csname featurestylesn@me\bottop@\endcsname\hss}}\fi\fi%
+ \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi%
\xdef\first@{\csname stylefeature\bottop@\endcsname @}%
+ \loopcount=\res@perline%
\put@featurestyle%
+ \ifnumbers@right\ifnumbers@\hbox to \number@width{\hss}\fi\fi%
+ \ifnames@right\ifnames@%
+ \fontfamily{\fstyles@family}\fontseries{\fstyles@series}\fontshape{\fstyles@shape}%
+ \selectfont%
+ \kern1em\hbox to \loopcount\box@width{\hss}%
+ \textcolor{\csname fstyles@fg@\bottop@\endcsname}{\hbox to \name@width{\csname featurestylesn@me\bottop@\endcsname\hss}}\fi\fi%
\else
+ \ifnames@right\else\ifnames@%
+ \fontfamily{\ftext@family}\fontseries{\ftext@series}\fontshape{\ftext@shape}%
+ \selectfont%
+ \textcolor{\csname ftext@fg@\bottop@\endcsname}{\hbox to \name@width{\csname featuretextn@me\bottop@\endcsname\hss}}\fi\fi%
+ \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi%
+ \xdef\first@{\csname textfeature\bottop@\endcsname @}%
\xdef\first@{\csname textfeature\bottop@\endcsname @}%
+ \loopcount=\res@perline%
\put@featuretext%
+ \ifnumbers@right\ifnumbers@\hbox to \number@width{\hss}\fi\fi%
+ \ifnames@right\ifnames@%
+ \fontfamily{\ftext@family}\fontseries{\ftext@series}\fontshape{\ftext@shape}%
+ \selectfont%
+ \kern1em\hbox to \loopcount\box@width{\hss}%
+ \textcolor{\csname ftext@fg@\bottop@\endcsname}{\hbox to \name@width{\csname featuretextn@me\bottop@\endcsname\hss}}\fi\fi%
\fi\fi%
\newline\hbox{}%
}
@@ -10711,6 +10991,8 @@
\xdef\hide@true{n} \xdef\hide@now{n}
\xdef\hide@label{circ}
\xdef\divref@{0}
+\xdef\all@thresh@ld{100} \all@shadefalse
+\hidefeaturenames \hidefeaturestylenames
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%% %%%%%
@@ -10746,6 +11028,8 @@
\numberingcolor{Black} % Numbering color is `Black'
\shownumbering{right} % Show sequence numbering on the left
\namescolor{Black} % Names' color is `Black'
+\featurenamescolor{Black} % Feature names' color is `Black'
+\featurestylenamescolor{Black} % Feature names' color is `Black'
\shownames{left} % Show sequence names on the right
\consensuscolors{Black}{White} % All consensus symbols/letters
{Black}{White} % appear `Black on White'
@@ -10786,6 +11070,14 @@
\setseries{names}{md} % Use normal series for names
\setshape {names}{up} % Use upright shape for names
\setsize {names}{normalsize} % Use normal size for names
+\setfamily{featurenames}{tt} % Use typewriter family for feature names
+\setseries{featurenames}{md} % Use normal series for feature names
+\setshape {featurenames}{up} % Use upright shape for feature names
+\setsize {featurenames}{normalsize}% Use normal size for feature names
+\setfamily{featurestylenames}{tt} % Use typewriter family for feature style names
+\setseries{featurestylenames}{md} % Use normal series for feature style names
+\setshape {featurestylenames}{up} % Use upright shape for feature style names
+\setsize {featurestylenames}{normalsize}% Use normal size for feature style names
\setfamily{features}{rm} % Use roman family for feature texts
\setseries{features}{md} % Use normal series for feature texts
\setshape {features}{it} % Use italics shape for feature texts
generated by cgit v1.2.3 (git 2.39.1) at 2024-11-06 02:29:48 +0000