texshade update

git-svn-id: svn://tug.org/texlive/trunk@4493 c570f23f-e606-0410-a88d-b1316a301751

1 files changed, 537 insertions, 70 deletions

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