texshade (6feb18)

git-svn-id: svn://tug.org/texlive/trunk@46559 c570f23f-e606-0410-a88d-b1316a301751

4 files changed, 491 insertions, 138 deletions

diff --git a/Master/texmf-dist/doc/latex/texshade/README b/Master/texmf-dist/doc/latex/texshade/README
index 38bdbf86c1c..71e52fa0c26 100644
--- a/Master/texmf-dist/doc/latex/texshade/README
+++ b/Master/texmf-dist/doc/latex/texshade/README
@@ -1,6 +1,7 @@
-    TeXshade v1.24
+    TeXshade v1.25
     >>
-    >> A LaTeX package for setting nucleotide and peptide alignments.
+    >> A LaTeX package for setting nucleotide and peptide alignments,
+    >> fingerprints, as well as sequence and subfamily logos.
     >>
     >> Setting alignments of nucleotides and peptides for publication 
     >> or presentation purposes  is usually a time consuming two-step 
@@ -26,7 +27,7 @@
     >> ding modes.  TeXshade  combines  highest  flexibility  and the
     >> habitual TeX output quality--with reasonable time expenditure.
     >>
-    Copyright (C)  1999 - 2011  Eric Beitz
+    Copyright (C)  1999 - 2018  Eric Beitz
 
 
 
diff --git a/Master/texmf-dist/doc/latex/texshade/texshade.pdf b/Master/texmf-dist/doc/latex/texshade/texshade.pdf
index e0b6d09eb5f..f423a08595e 100644
--- a/Master/texmf-dist/doc/latex/texshade/texshade.pdf
+++ b/Master/texmf-dist/doc/latex/texshade/texshade.pdf
diff --git a/Master/texmf-dist/source/latex/texshade/texshade.dtx b/Master/texmf-dist/source/latex/texshade/texshade.dtx
index f399815966a..adf4e661c36 100644
--- a/Master/texmf-dist/source/latex/texshade/texshade.dtx
+++ b/Master/texmf-dist/source/latex/texshade/texshade.dtx
@@ -10,7 +10,7 @@
 % `README.txt' for further information!
 % 
 %
-% Copyright (C) 1999-2011 Eric Beitz
+% Copyright (C) 1999-2018 Eric Beitz
 % See the file texshade.txt
 % 
 %    \fi
@@ -393,6 +393,15 @@
 %                    Postscript color samples are shown in the manual.
 %                    }
 %
+%    \changes{1.25}{2011-12-01}{%
+%      Corrections:  aligments with many seqs produced wrong calculation
+%                    of threshold shading, corrected. 
+%      Introduction: new feature style |S-S| for disulfide bridges;
+%                    hooks in top feature lines can be drawn down to alignment.
+%                    }
+%
+%
+%
 %
 % \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
@@ -431,7 +440,7 @@
 %            for further information, updates and on-line documentation 
 %            see my homepage at
 %            \texttt{www.pharmazie.uni-kiel.de/chem/Prof\_Beitz/biotex.html} }}
-%    \date{\small v1.24; 2011/12/01\\[2pt]}
+%    \date{\small v1.25; 2018/01/17\\[2pt]}
 %    \maketitle
 %    \begin{abstract}
 %      Setting alignments of nucleotides and peptides for publication 
@@ -510,6 +519,16 @@
 %    
 %    \subsection{Version History}
 %
+%    \textbf{v1.25  2018/01/17}
+%    \medskip
+%
+%    \emph{Corrections}:  Aligments with many seqs produced wrong calculation
+%    of threshold shading,\footnote{Noted by Kathryn Parker.} corrected; minor bug fixes. 
+%
+%    \emph{Introduction}: A new feature style |S-S| for disulfide bridges is
+%    implemented; hooks in top feature lines can be drawn down to alignment.
+%    \medskip
+%
 %    \textbf{v1.24  2011/12/01}
 %    \medskip
 %
@@ -527,7 +546,7 @@
 %    \emph{Introductions:} 
 %    In diverse mode sequence positions where all residues match do not
 %    contain much information. A new command, 
-%    |\hideallmatchpositions|, \footnote{Requested by Matt Russell.}
+%    |\hideallmatchpositions|,\footnote{Requested by Matt Russell.}
 %    will remove all such positions from the alignment and hence condense
 %    the output considerably.
 %    \medskip
@@ -598,7 +617,6 @@
 %    output.\footnote{Suggestion by Yun He.}
 %    \medskip  
 %
-%    \newpage
 %
 %    \textbf{v1.19 2009/03/09}
 %    \medskip
@@ -887,7 +905,6 @@
 %    |{1,2,3,6,5,4,7}|.
 %    \bigskip
 %    
-%    \newpage
 %
 %    \textbf{v1.3a\&b 2000/7/28 \& 2000/7/30}
 %    \medskip
@@ -969,7 +986,7 @@
 %    length of the sequences. Therefore, the command `|\seqlength|' was
 %    introduced (\ref{seqlines}). (b) With `|\gapcolors|' (also 
 %    \ref{seqlines}) the
-%    color selection for gap symbols is independent from non conserved
+%    color selection for gap symbols is independent from non-conserved
 %    residues. (c) The divisions of the ruler where so far fixed to
 %    10. Now, this value is changeable by `|\rulersteps|' (again 
 %    \ref{seqlines}). (d) `|\hideresidues|' and `|\showresidues|' turn
@@ -1031,77 +1048,8 @@
 %    each \TeX{} system hides its default parameter file in a different
 %    place in the system. 
 %    
-%    In the following, an excerpt from the FAQ-list to \TeXshade{} is added. 
-%    This explains how 
-%    to increase the settings in Oz\TeX{} for the Macintosh, Mik\TeX{} 
-%    for Windows and te\TeX{} for *NIX \TeX{} distributions. Please contribute 
-%    to this list!
-%    
-%    \begin{enumerate}
-%    
-%    \item
-%    
-%    \textbf{Oz\TeX{} 4.0 for the Macintosh:}
-%    
-%    Find the file `OzTeX:TeX:Configs:Default'. This file contains
-%    all memory settings. Look for the section 
-%    `\% TeX parameters' and increase the values that \TeX{} complains
-%    about during the run. You will have to restart Oz\TeX{} before the
-%    changes are active.
-%    
-%    For older versions of Oz\TeX{} the configuration file has the 
-%    same name but the path is somewhat different.
 %    
 %    
-%    \item
-%    
-%    \textbf{te\TeX{} for *NIX:} (contributed by Joerg Daehn)
-%    
-%    Find the file: `/usr/share/texmf/web2c/texmf.cnf' or use 
-%    
-%    |locate texmf.cnf| at the command prompt to find it.
-%
-%    Login as super user. Backup `texmf.cnf' in case you destroy something and
-%    then open the `texmf.cnf' file in your favorite text editor and use its
-%    search function to locate |main_memory|. This variable is set to 384000.
-%    Change this to some higher value, i.e. 4000000 (works fine for me!). The
-%    total amount of memory should not exceed 8000000, so check the other
-%    values in that section. 
-%
-%    Next, you want to change the stack size. Search for |stack_size|. This
-%    will be set to 300. I changed it to 4000 and it works fine.
-%
-%    There might be complains by \TeX{} about further specific parameters such
-%    as |stack_size|. You find all those in the same file.
-%
-%    After this you have to run `texconfig init'.
-%
-%    Logout as root.
-%
-%    After this all should be set for large alignments. Happy \TeX{}ing!
-%
-%    The information on how to achieve this was derived from a mail in the
-%    te\TeX{} mail archive. The original question was posted by Pascal Francq and
-%    answered by Rolf Nieprasch.
-%
-%    
-%    \item
-%    
-%    \textbf{MiK\TeX{} for Windows:}
-%    
-%    The MiK\TeX{} documentation describes very detailed how the memory
-%    settings can be changed. In brief, you must locate the 
-%    configuration file `miktex/config/miktex.ini'. In the [MiKTeX] 
-%    section of this file you find all the parameters you need, e.\,g.\ 
-%    |mem_min|, |mem_max|, |buf_size|, |stack_size| etc.
-%    
-%    It appears, that the standard settings of MiK\TeX{} are bigger 
-%    than that of other \TeX{} installations, so it may not always be necessary 
-%    to increase the values.
-%    
-%    
-%    \end{enumerate}
-%    
 %    
 %
 %    \subsection{System requirements} \label{require}
@@ -1234,7 +1182,7 @@
 %    \end{verbatim}  
 %    }  
 %    
-%    This goes even furher. You can have \TeXshade{} select positions
+%    This goes even further. You can have \TeXshade{} select positions
 %    based on the 3D coordinates provided by a PDB file, e.\,g.\ show
 %    all residues that are within an 8 \AA{} radius around the
 %    $\alpha$-carbon of the residue at position 81:
@@ -2999,7 +2947,7 @@
 %
 %    \label{Llogocolor}\label{Lclearlogocolors}
 %    Logo colors can be turned to `Black' with the command
-%    |\clearlogocolors[|\meta{color}|}| with the optional parameter
+%    |\clearlogocolors[|\meta{color}|]| with the optional parameter
 %    not set. The optional parameter can be used to set all 
 %    residue colors to \meta{color}, e.g.\ |\clearlogocolors[Blue]|.
 %    User specific logo color sets are defined by using
@@ -3346,7 +3294,7 @@
 %    \medskip
 %
 %    
-%    It is helpful to show a ruler (probably single-stepped, see p.\,\pageref{Lshowruler}) to 
+%    It is helpful to show a ruler (e.g. single-stepped, see p.\,\pageref{Lshowruler}) to 
 %    label the residue positions. 
 %    
 %    The resulting gaps between sequence stretches are marked by a vertical rule, which
@@ -3915,14 +3863,15 @@
 %    |-->|& right arrow \\
 %    |'->|& right arrow with up hook \\
 %    |<-|$\vert$ & left \emph{maps to} arrow \\
-%    |<-o| & left arrow with ball at right end\\
+%    |<-o|& left arrow with ball at right end\\
 %    |<=>|& double arrow, two heads \\
 %    |,-,|& plain bar with down hooks\\
 %    $\vert$|=|$\vert$ & double bar with vertical ends\\
+%    |S-S|& labels disulfide bridges\\
 %    \end{tabular}
 %    \end{center}
 %    
-%    All combinations of the left-end-characters 
+%    Combinations of the left-end-characters 
 %    (|-=<',|$\vert$o), the middle-characters (|-=|),
 %    and the right-end-characters (|-=>',|$\vert$o) are
 %    allowed and produce the desired arrow or bar.
@@ -4427,7 +4376,7 @@
 %    existing file for the output. The great advantage of this method 
 %    is its flexibility. Due to the simple reason that the feature 
 %    file can be edited in the meantime. Thus, the user has the 
-%    ability to change the computer generated file according to his
+%    ability to change the computer-generated file according to his
 %    personal needs. On the other hand, one can force \TeXshade{} to
 %    write a new file every time by the optional argument |[make new]| in the 
 %    include command, e.\,g. |\includePHDsec[make new]{1}{AQP.phd}|.
@@ -6123,6 +6072,7 @@
 %       \> = |{helix[|\meta{helixcolor}|]}|\\
 %       \> = |{box[|\meta{framecolor,boxcolor}|][|\meta{length}|]:|\\
 %               \hspace{8.7cm}\meta{text}|[|\meta{textcolor}|]}|\\
+%       \> = |{S-S}|\\
 %       \> = arrows and bars (|-=<',|$\vert$|o|)(|-=|)(|-=>',|$\vert$|o|)\\
 %       \> = |{translate[|\meta{color}|]}|\\
 %       \> = |{bar[|\meta{min}|,|\meta{max}|]:|\\
@@ -6469,7 +6419,8 @@
 \openin\structurefile = hyperref.sty
 \ifeof\structurefile
  \else
-     \usepackage[dvips,colorlinks]{hyperref}
+%     \usepackage[dvips,colorlinks]{hyperref}
+     \usepackage[pdftex,colorlinks]{hyperref}
  \fi
 \closein\structurefile
 \DisableCrossrefs
@@ -6486,8 +6437,8 @@
 %    \begin{macrocode}
 %<*texshade>
 \NeedsTeXFormat{LaTeX2e}
-\ProvidesPackage{texshade}[2011/05/13 LaTeX TeXshade (v1.24)]
-\message{Package `texshade', Version 1.24 of 2011/12/01.}
+\ProvidesPackage{texshade}[2018/01/17 LaTeX TeXshade (v1.25)]
+\message{Package `texshade', Version 1.25 of 2018/01/17.}
 
 \PassOptionsToPackage{dvips}{color}
 \PassOptionsToPackage{dvips}{graphicx}
@@ -6567,6 +6518,7 @@
 \newlength\equal@height \newlength\temp@@length
 \newlength\vspace@legend
 \newlength\hspace@legend
+\newlength\bar@length
 
 \newif\ifletter       \newif\ifnumber
 \newif\ifnewres       \newif\ifall@shade
@@ -9075,7 +9027,7 @@
             \expandafter\xdef\csname hide@@@seq\first@\endcsname{kill}
             \ifnum\first@=\cons@num \xdef\cons@num{0} \fi
             \advance\killseq@count by -1
-            \seq@percent=100 \divide\seq@percent by \killseq@count
+%            \seq@percent=100 \divide\seq@percent by \killseq@count
          \fi
       \fi\fi
       \xdef\first@{\first@@ @}
@@ -9094,7 +9046,7 @@
             \expandafter\xdef\csname hide@@@seq\fourth@\endcsname{kill}
             \ifnum\fourth@=\cons@num \xdef\cons@num{0} \fi
             \advance\killseq@count by -1
-            \seq@percent=100 \divide\seq@percent by \killseq@count
+%            \seq@percent=100 \divide\seq@percent by \killseq@count
          \fi
       \fi\fi
       \killseq@
@@ -9596,22 +9548,33 @@
    \expandafter\xdef\csname stack@\bottop@\seq@\endcsname{\tmpstack}
 }
 \def\getarrow@shape#1#2#3#4&{%
-   \xdef\first@@{#1}\xdef\second@@{#2}\xdef\third@@{#3}
-   \if\first@@ v
-      \if\second@@ =
-      \else \xdef\style@{\first@@ v\third@@#4} \fi
+   \xdef\first@@{#1}\xdef\second@@{#2}\xdef\third@@{#3}\xdef\fourth@@{#4}
+   \ifx\temp@@\y@
+      \if\first@@ ` \xdef\first@@{a} \else
+      \if\first@@ ' \xdef\first@@{a} \else
+      \if\first@@ , \xdef\first@@{b} \else
+      \if\first@@ S \xdef\first@@{c} \xdef\second@@{-}
+      \fi\fi\fi\fi
+      \if\third@@ ` \xdef\third@@{a} \else
+      \if\third@@ ' \xdef\third@@{a} \else
+      \if\third@@ , \xdef\third@@{b} \else
+      \if\third@@ S \xdef\third@@{c} \xdef\second@@{-}
+      \fi\fi\fi\fi
+      \xdef\style@{\first@@ -\third@@\fourth@@}
+   \fi
+   \if\first@@ S
+      \xdef\style@{\first@@ -\third@@\fourth@@}
    \else
    \if\first@@ v
-      \if\second@@ =
-      \else \xdef\style@{\first@@ v\third@@#4} \fi
+      \if\second@@ = 
+      \else \xdef\style@{\first@@ v\third@@\fourth@@} \fi
    \else
-   \if\third@@ v
-      \if\second@@ =
-      \else \xdef\style@{\first@@ v\third@@#4} \fi
+   \if\third@@ S
+      \xdef\style@{\first@@ -\third@@\fourth@@}
    \else
    \if\third@@ v
       \if\second@@ =
-      \else \xdef\style@{\first@@ v\third@@#4} \fi
+      \else \xdef\style@{\first@@ v\third@@\fourth@@} \fi
    \fi\fi\fi\fi
 }
 \def\get@shape#1#2#3{%
@@ -12381,7 +12344,11 @@
          \fi
          \xdef\style@{cons[color]:cons[\f@color][0]}
       \else
-         \xdef\style@{#4} \expandafter\getarrow@shape\temp@
+         \xdef\style@{#4} \xdef\temp@@{n}
+         \expandafter\get@firstfill\temp@
+         \if\second@@ ^ \xdef\second@@{_} \fi
+         \if\second@@ _ \xdef\temp@{\fill@char} \xdef\temp@@{y}\fi
+         \expandafter\getarrow@shape\temp@
       \fi
       \fi
       \fi
@@ -14280,9 +14247,10 @@
        \advance\pos@sum by 1 \fi
   \ifnum\innerloopcount<\seq@count \repeat
 
-  \multiply\pos@sum by \seq@percent
+%  \multiply\pos@sum by \seq@percent
   \expandafter\xdef\csname pos\the\loopcount\endcsname{\the\pos@sum}
-  \expandafter\ifnum\csname pos\the\loopcount\endcsname<\thresh@ld
+%  \expandafter\ifnum\csname pos\the\loopcount\endcsname<\thresh@ld
+  \expandafter\ifnum\csname pos\the\loopcount\endcsname<\thresh@ld@
   \else
     \expandafter\ifnum\csname pos\the\loopcount\endcsname>\m@x
       \xdef\m@x{\csname pos\the\loopcount\endcsname}
@@ -14331,13 +14299,15 @@
   \expandafter\ifnum\csname pos\the\loopcount\endcsname=\seq@count
     \xdef\cons@seq{\the\loopcount} \xdef\match@case{2} \loopcount=1
   \else
-   \multiply\pos@sum by \seq@percent
+%   \multiply\pos@sum by \seq@percent
    \expandafter\xdef\csname pos\the\loopcount\endcsname{\the\pos@sum}
-   \expandafter\ifnum\csname pos\the\loopcount\endcsname<\thresh@ld
+%   \expandafter\ifnum\csname pos\the\loopcount\endcsname<\thresh@ld
+   \expandafter\ifnum\csname pos\the\loopcount\endcsname<\thresh@ld@
    \else
     \expandafter\ifnum\csname pos\the\loopcount\endcsname>\m@x
       \xdef\m@x{\csname pos\the\loopcount\endcsname}
-      \expandafter\ifnum\csname pos\the\loopcount\endcsname<\all@thresh@ld
+%      \expandafter\ifnum\csname pos\the\loopcount\endcsname<\all@thresh@ld
+      \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}
@@ -17870,7 +17840,7 @@
          \textcolor{\legend@fg}{%
          \ifgerm@n\kern2ex\legend@size{nicht konserviert}%
          \else\ifsp@nish\kern2ex\legend@size{no conservado}%
-         \else\kern2ex\legend@size{non conserved}\fi\fi}
+         \else\kern2ex\legend@size{non-conserved}\fi\fi}
          \newline\hbox{}\noindent%
          \ifsimmode%
          \ifnames@\ifnames@right\else\hbox to \name@width{\hss}\fi\fi
@@ -18359,6 +18329,8 @@
 \def\get@tripletfill#1#2#3#4&{%
    \multiply\temp@count by -1%
    \def\second@@{#1}\def\second@@@{#2}\def\second@@@@{#3}\def\fill@char{#4&}}
+
+
 \def\putfeature@style#1{%
    \residues@size%
    \setbox1=\hbox{\ensuremath{\overrightarrow{\hbox{}}}}%
@@ -18464,6 +18436,7 @@
        \fontseries{\featurestyles@series}%
        \fontshape{\featurestyles@shape}%
        \selectfont%
+       \xdef\last@{bottom}%
        \ifx\bottop@\temp@\xdef\last@{0.35}\else\xdef\last@{0}\fi%
        \kern0.15\box@width%
        \loopcount=0\relax%
@@ -18634,6 +18607,7 @@
         \ifx\bottop@\temp@ \xdef\last@{0.35}\else\xdef\last@{-0.55}\fi%
         \textcolor{\f@color}{%
         \raisebox{\last@\arrow@height}{%
+         \if\first@@ b \xdef\first@@{,}\fi%
          \if\first@@ ,%
             \rule{0.1\arrow@height}{\arrow@height}\kern-0.35\arrow@height%
          \else%
@@ -18645,10 +18619,15 @@
                   \rule[\arrow@height]%
                      {0.1\arrow@height}{\arrow@height}\kern-0.35\arrow@height%
                \else%
+               \if\first@@ '%
+                  \rule[\arrow@height]%
+                     {0.1\arrow@height}{\arrow@height}\kern-0.35\arrow@height%
+               \else%
                   \if\first@@ -%
                      \rule{0pt}{0pt}\kern-0.35\arrow@height%
                   \fi%
                \fi%
+               \fi%
             \fi%
          \fi%
          \if\third@@ v%
@@ -18709,6 +18688,7 @@
                  \xdef\last@{-0.25}\fi\fi\fi\fi%
         \textcolor{\f@color}{%
         \raisebox{\last@\arrow@height}{%
+         \if\first@@ b \xdef\first@@{,}\fi%
          \if\first@@ ,%
             \rule[-0.5\arrow@height]{0.1\arrow@height}{1.5\arrow@height}%
             \kern-0.1\arrow@height%
@@ -18717,7 +18697,8 @@
                \rule[-0.5\arrow@height]{0.1\arrow@height}{2.25\arrow@height}%
                \kern-0.1\arrow@height%
             \else%
-               \if\first@@ `\xdef\first@@{'}\fi%
+               \if\first@@ a \xdef\first@@{'}\fi%
+               \if\first@@ ` \xdef\first@@{'}\fi%
                \if\first@@ '%
                   \rule[0.4\arrow@height]%
                      {0.1\arrow@height}{1.5\arrow@height}%
@@ -18742,6 +18723,7 @@
             \rule[0.37\arrow@height]{\width@tmp}{0.1\arrow@height}%
             \kern-\width@tmp%
             \rule[0.9\arrow@height]{\width@tmp}{0.1\arrow@height}%
+            \if\first@@ b \xdef\first@@{,}\fi%
             \if\third@@ ,%
                \kern-0.05\arrow@height%
                \rule[-0.5\arrow@height]{0.1\arrow@height}{1.5\arrow@height}%
@@ -18750,10 +18732,16 @@
                   \kern-0.05\arrow@height%
                   \rule[-0.5\arrow@height]{0.1\arrow@height}{2.25\arrow@height}%
                \else%
-                  \if\third@@ `\xdef\third@@{'}\fi%
+                  \if\first@@ a \xdef\first@@{'}\fi%
+                  \if\third@@ ` \xdef\third@@{'}\fi%
                   \if\third@@ '%
                      \kern-0.05\arrow@height%
                      \rule[0.4\arrow@height]{0.1\arrow@height}{1.5\arrow@height}%
+                  \else%
+                  \if\third@@ a%
+                     \kern-0.05\arrow@height%
+                     \rule[0.4\arrow@height]{0.1\arrow@height}{1.5\arrow@height}%
+                  \fi%
                   \fi%
                \fi%
             \fi%
@@ -18765,9 +18753,25 @@
         \advance\width@tmp by -0.5\temp@@length%
         \if\first@@ o\xdef\first@@{O}\fi%
         \if\third@@ o\xdef\third@@{O}\fi%
+        \xdef\last@{bottom}%
+        \ifx\fe@turep@s\last@%
+           \vspace{-20pt}\message{(((-20pt)))}%
+        \fi%
         \textcolor{\f@color}{%
          \if\first@@ ,%
-         \rule{\temp@@length}{\arrow@height}\kern-\temp@@length%
+           \rule{\temp@@length}{\arrow@height}\kern-\temp@@length%
+         \else%
+         \if\first@@ b%
+           \xdef\last@{bottom}%
+           \ifx\fe@turep@s\last@%
+            \rule{\temp@@length}{\arrow@height}\kern-\temp@@length%
+           \else
+            \xdef\shift@feature{y}%
+            \kern-\temp@@length%
+            \rule[-\bar@length]{\temp@@length}{\bar@length}%
+            \kern-\temp@@length%
+            \rule{\temp@@length}{\arrow@height}\kern-\temp@@length%
+           \fi
          \else%
             \if\first@@ |%
                \rule{\temp@@length}{2\arrow@height}\kern-\temp@@length%
@@ -18776,6 +18780,52 @@
                 \raisebox{0.06ex}{\ensuremath{\bullet}}\kern-0.55ex%
                 \rule[\width@tmp]{0.65ex}{\temp@@length}%
               \else%
+              \if\first@@ S%
+                \xdef\last@{bottom}%
+                \ifx\fe@turep@s\last@%
+                   \advance\width@tmp by 0.5\temp@@length%
+                   \kern0.5\box@width%
+                   \kern-2\temp@@length%
+                   \rule[\width@tmp]{\temp@@length}{\arrow@height}%
+                   \advance\width@tmp by -0.5\temp@@length%
+                   \kern-\temp@@length%
+                   \rule[\width@tmp]{0.5\temp@@length}{\temp@@length}%
+                   \rule[\width@tmp]{0.5\box@width}{\temp@@length}%
+                \else%
+                   \kern0.5\box@width%
+                   \kern-2\temp@@length%
+                   \rule{\temp@@length}{\arrow@height}%
+                   \kern-\temp@@length%
+                   \rule[\width@tmp]{0.5\temp@@length}{\temp@@length}%
+                   \rule[\width@tmp]{0.5\box@width}{\temp@@length}%
+                \fi%
+              \else%
+              \if\first@@ c%
+                \xdef\last@{bottom}%
+                \ifx\fe@turep@s\last@%
+                   \advance\width@tmp by 0.5\temp@@length%
+                   \raisebox{\arrow@height}{\rule[\box@height]{0pt}{\bar@length}}%%%%%%%%%%%%%%%%%%%%%%%
+                   \kern0.5\box@width%
+                   \kern-2\temp@@length%
+                   \rule[2\arrow@height]{\temp@@length}{\bar@length}%%%%%%%%%%%%%%%%%%%%%%
+                   \kern-\temp@@length%%%%%%%%%%%%%%%%%%%%%%%%%
+                   \rule[\width@tmp]{\temp@@length}{\arrow@height}%
+                   \advance\width@tmp by -0.5\temp@@length%
+                   \kern-\temp@@length%
+                   \rule[\width@tmp]{0.5\temp@@length}{\temp@@length}%
+                   \rule[\width@tmp]{0.5\box@width}{\temp@@length}%
+                \else%
+                   \xdef\shift@feature{y}%
+                   \kern0.5\box@width%
+                   \kern-2\temp@@length%
+                   \rule[-\bar@length]{\temp@@length}{\bar@length}%
+                   \kern-\temp@@length%
+                   \rule{\temp@@length}{\arrow@height}%
+                   \kern-\temp@@length%
+                   \rule[\width@tmp]{0.5\temp@@length}{\temp@@length}%
+                   \rule[\width@tmp]{0.5\box@width}{\temp@@length}%
+                \fi%
+              \else%
                \if\first@@ <%
                  \raisebox{0.06ex}{\ensuremath{\blacktriangleleft}}\kern-0.35ex%
                \else
@@ -18787,13 +18837,20 @@
                 \fi%
                \fi%
               \fi%
+              \fi%
+              \fi%
             \fi%
          \fi%
+         \fi%
          \loopcount=\second@%
          \if\first@@ <\advance\loopcount by -1\relax\ifnum\loopcount<0 \loopcount=0\fi\fi%
          \if\third@@ >\advance\loopcount by -1\relax\ifnum\loopcount<0 \loopcount=0\fi\fi%
          \if\first@@ O\advance\loopcount by -1\relax\ifnum\loopcount<0 \loopcount=0\fi\fi%
          \if\third@@ O\advance\loopcount by -1\relax\ifnum\loopcount<0 \loopcount=0\fi\fi%
+         \if\first@@ S\advance\loopcount by -1\relax\ifnum\loopcount<0 \loopcount=0\fi\fi%
+         \if\third@@ S\advance\loopcount by -1\relax\ifnum\loopcount<0 \loopcount=0\fi\fi%
+         \if\first@@ c\advance\loopcount by -1\relax\ifnum\loopcount<0 \loopcount=0\fi\fi%
+         \if\third@@ c\advance\loopcount by -1\relax\ifnum\loopcount<0 \loopcount=0\fi\fi%
          \xdef\second@{\the\loopcount}%
          \rule[\width@tmp]{\second@\box@width}{\temp@@length}%
          \setbox1=\hbox{\residues@size{\fill@char}}%
@@ -18804,6 +18861,17 @@
          \if\third@@ ,%
          \kern-\temp@@length\rule{\temp@@length}{\arrow@height}%
          \else%
+         \if\third@@ b%
+           \xdef\last@{bottom}%
+           \ifx\fe@turep@s\last@%
+            \kern-\temp@@length\rule{\temp@@length}{\arrow@height}%
+           \else
+            \xdef\shift@feature{y}%
+            \kern-\temp@@length%
+            \rule[-\bar@length]{\temp@@length}{\bar@length}%
+            \kern-\temp@@length\rule{\temp@@length}{\arrow@height}%
+           \fi
+         \else%
             \if\third@@ |%
                \kern-\temp@@length\rule{\temp@@length}{2\arrow@height}%
             \else%
@@ -18811,6 +18879,31 @@
                 \rule[\width@tmp]{0.65ex}{\temp@@length}%
                 \kern-0.55ex\raisebox{0.06ex}{\ensuremath{\bullet}}%
               \else%
+              \if\third@@ S%
+                \rule[\width@tmp]{0.5\box@width}{\temp@@length}%
+                \rule[\width@tmp]{0.5\temp@@length}{\temp@@length}%
+                \xdef\last@{bottom}%
+                \ifx\fe@turep@s\last@%
+                  \advance\width@tmp by 0.5\temp@@length%
+                  \kern-\temp@@length\rule[\width@tmp]{\temp@@length}{\arrow@height}%
+                \else
+                  \kern-\temp@@length\rule{\temp@@length}{\arrow@height}%
+                \fi%
+              \else%
+              \if\third@@ c%
+                \xdef\shift@feature{y}%
+                \rule[\width@tmp]{0.5\box@width}{\temp@@length}%
+                \xdef\last@{bottom}%
+                \ifx\fe@turep@s\last@%
+                  \kern-\temp@@length%%%%%%%%%%%%%%%%%%%%%%%%%
+                  \rule[2\arrow@height]{\temp@@length}{\bar@length}%%%%%%%%%%%%%%%%%%%%%%
+                  \advance\width@tmp by 0.5\temp@@length%
+                  \kern-\temp@@length\rule[\width@tmp]{\temp@@length}{\arrow@height}%
+                \else
+                  \kern-\temp@@length\rule[-\bar@length]{\temp@@length}{\bar@length}%
+                  \kern-\temp@@length\rule{\temp@@length}{\arrow@height}%
+                \fi%
+              \else%
                \if\third@@ >%
                 \kern-0.35ex\raisebox{0.06ex}{\ensuremath{\blacktriangleright}}%
                \else
@@ -18821,7 +18914,10 @@
                 \fi%
                \fi%
               \fi%
-            \fi
+              \fi%
+              \fi%
+            \fi%
+         \fi%
          \fi}%
        \fi
       \fi
@@ -19622,10 +19718,23 @@
    \xdef\featureposttttop{1} \xdef\featureposbbbbottom{1}%
    \findc@nsensus%
    \noindent%
+   \setlength{\bar@length}{0pt}%
+   \xdef\fe@turep@s{top}%
    \ifnum\feature@ttttop=1
+      \advance\bar@length by \feature@tttop\baselineskip%
+      \advance\bar@length by \feature@ttop\baselineskip%
+      \advance\bar@length by \feature@top\baselineskip%
+      \multiply\bar@length by 2%
+      \advance\bar@length by \tttt@sp@ce%
+      \advance\bar@length by \ttt@sp@ce%
+      \advance\bar@length by \tt@sp@ce%
       \ifnum\featureonttttop=0 \xdef\feature@ttttop{0} \fi
       \xdef\bottop@{ttttop}%
+      \xdef\shift@feature{n}%
       \put@feature%
+      \advance\bar@length by -\baselineskip%
+      \ifx\shift@feature\y@ \vspace{-\bar@length}\fi%
+      \setlength{\bar@length}{0pt}%
       \vspace{\tttt@sp@ce}%
       \vspace{-\baselineskip}%
       \newline\hbox{}%
@@ -19633,9 +19742,18 @@
       \iffix@\ifttttopfeature \vspace{\tttt@sp@ce}\newline\hbox{}\newline\hbox{}\fi\fi
    \fi
    \ifnum\feature@tttop=1
+      \advance\bar@length by \feature@ttop\baselineskip%
+      \advance\bar@length by \feature@top\baselineskip%
+      \multiply\bar@length by 2%
+      \advance\bar@length by \ttt@sp@ce%
+      \advance\bar@length by \tt@sp@ce%
       \ifnum\featureontttop=0 \xdef\feature@tttop{0} \fi
       \xdef\bottop@{tttop}%
+      \xdef\shift@feature{n}%
       \put@feature%
+      \advance\bar@length by -\baselineskip%
+      \ifx\shift@feature\y@ \vspace{-\bar@length}\fi%
+      \setlength{\bar@length}{0pt}%
       \vspace{\ttt@sp@ce}%
       \vspace{-\baselineskip}%
       \newline\hbox{}%
@@ -19643,9 +19761,16 @@
       \iffix@\iftttopfeature \vspace{\ttt@sp@ce}\newline\hbox{}\newline\hbox{}\fi\fi
    \fi
    \ifnum\feature@ttop=1
+      \advance\bar@length by \feature@top\baselineskip%
+      \multiply\bar@length by 2%
+      \advance\bar@length by \tt@sp@ce\message{tt\the\bar@length tt}%
       \ifnum\featureonttop=0 \xdef\feature@ttop{0} \fi
       \xdef\bottop@{ttop}%
+      \xdef\shift@feature{n}%
       \put@feature%
+      \advance\bar@length by -\baselineskip%
+      \ifx\shift@feature\y@ \vspace{-\bar@length}\fi%
+      \setlength{\bar@length}{0pt}%
       \vspace{\tt@sp@ce}%
       \vspace{-\baselineskip}%
       \newline\hbox{}%
@@ -19761,6 +19886,9 @@
          \ifnum\ruler@rot=0 \vspace{0.25\baselineskip}\fi%
       \fi%
    \fi%
+   \xdef\fe@turep@s{bottom}%
+   \setlength{\bar@length}{0pt}%
+   \xdef\b@feature@count{0}
    \ifnum\feature@bottom=1 %
       \ifnum\featureonbottom=0 \xdef\feature@bottom{0}\fi%
       \xdef\bottop@{bottom}%
@@ -19770,6 +19898,9 @@
          \vspace{\b@r@stretch\box@height}%
       \fi%
       \put@feature%
+      \temp@@count=\b@feature@count%
+      \advance\temp@@count by 1%
+      \xdef\b@feature@count{\the\temp@@count}%
    \else
       \iffix@
       \if\bottom@stretch y%
@@ -19782,14 +19913,25 @@
       \fi%
    \fi%
    \ifnum\feature@bbottom=1 %
+      \advance\bar@length by \b@feature@count \baselineskip%
+      \multiply\bar@length by \b@r@stretch%
+      \multiply\bar@length by 2%
+      \advance\bar@length by \bb@sp@ce\message{bb\the\bar@length bb}%
       \ifnum\featureonbbottom=0 \xdef\feature@bbottom{0}\fi%
       \xdef\bottop@{bbottom}%
       \vspace{\bb@sp@ce}%
       \if\bbottom@stretch y%
+         \advance\bar@length by -\box@height%
+         \advance\bar@length by \b@r@stretch\box@height%
          \vspace{-\box@height}%
          \vspace{\b@r@stretch\box@height}%
       \fi%
+%      \vspace{-\bar@length}%%%%%%%%%%%%%%%%%%%%%%%
+      \setlength{\bar@length}{0pt}%%%%%%%%%%%%%%%%%%%%%%%
       \put@feature%
+      \temp@@count=\b@feature@count%
+      \advance\temp@@count by 1%
+      \xdef\b@feature@count{\the\temp@@count}%
    \else
       \iffix@
       \if\bbottom@stretch y%
@@ -19802,6 +19944,10 @@
       \fi
    \fi
    \ifnum\feature@bbbottom=1 %
+      \advance\bar@length by \b@feature@count\baselineskip%
+      \multiply\bar@length by \b@r@stretch%
+      \multiply\bar@length by 2%
+      \advance\bar@length by \bbb@sp@ce\message{bbb\the\bar@length bbb}%
       \ifnum\featureonbbbottom=0 \xdef\feature@bbbottom{0}\fi%
       \xdef\bottop@{bbbottom}%
       \vspace{\bbb@sp@ce}%
@@ -19810,6 +19956,9 @@
          \vspace{\b@r@stretch\box@height}%
       \fi%
       \put@feature%
+      \temp@@count=\b@feature@count%
+      \advance\temp@@count by 1%
+      \xdef\b@feature@count{\the\temp@@count}%
    \else
       \iffix@
       \if\bbbottom@stretch y%
@@ -19822,6 +19971,10 @@
       \fi
    \fi
    \ifnum\feature@bbbbottom=1 %
+      \advance\bar@length by \b@feature@count\baselineskip%
+      \multiply\bar@length by \b@r@stretch%
+      \multiply\bar@length by 2%
+      \advance\bar@length by \bbbb@sp@ce\message{bbbb\the\bar@length bbbb}%
       \ifnum\featureonbbbbottom=0 \xdef\feature@bbbbottom{0}\fi%
       \xdef\bottop@{bbbbottom}%
       \vspace{\bbbb@sp@ce}%
@@ -20679,8 +20832,8 @@
     \ifnum\loopcount<\seq@count \repeat
     \xdef\seq@order{\seq@order,@}
  \killseq@count=\seq@count
- \seq@percent=100
- \ifnum\seq@count>0 \divide\seq@percent by \seq@count \fi
+% \seq@percent=100
+% \ifnum\seq@count>0 \divide\seq@percent by \seq@count \fi
  \fi
  \fi
 }
@@ -20948,6 +21101,10 @@
            \caption[\c@pshort]{\c@p}
          \fi
       \fi
+      \loopcount = \thresh@ld \multiply\loopcount by \seq@count \divide\loopcount by 100
+      \xdef\thresh@ld@{\the\loopcount}
+      \loopcount = \all@thresh@ld \multiply\loopcount by \seq@count \divide\loopcount by 100
+      \xdef\all@thresh@ld@{\the\loopcount}
       \bgroup
          \ifx\out@put\y@\bigskip\fi
          \iffuncmode \show@consfalse \fi
diff --git a/Master/texmf-dist/tex/latex/texshade/texshade.sty b/Master/texmf-dist/tex/latex/texshade/texshade.sty
index e22dae05130..615108bfd03 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}[2011/05/13 LaTeX TeXshade (v1.24)]
-\message{Package `texshade', Version 1.24 of 2011/12/01.}
+\ProvidesPackage{texshade}[2018/01/17 LaTeX TeXshade (v1.25)]
+\message{Package `texshade', Version 1.25 of 2018/01/17.}
 
 \PassOptionsToPackage{dvips}{color}
 \PassOptionsToPackage{dvips}{graphicx}
@@ -94,6 +94,7 @@
 \newlength\equal@height \newlength\temp@@length
 \newlength\vspace@legend
 \newlength\hspace@legend
+\newlength\bar@length
 
 \newif\ifletter       \newif\ifnumber
 \newif\ifnewres       \newif\ifall@shade
@@ -2593,7 +2594,6 @@
             \expandafter\xdef\csname hide@@@seq\first@\endcsname{kill}
             \ifnum\first@=\cons@num \xdef\cons@num{0} \fi
             \advance\killseq@count by -1
-            \seq@percent=100 \divide\seq@percent by \killseq@count
          \fi
       \fi\fi
       \xdef\first@{\first@@ @}
@@ -2612,7 +2612,6 @@
             \expandafter\xdef\csname hide@@@seq\fourth@\endcsname{kill}
             \ifnum\fourth@=\cons@num \xdef\cons@num{0} \fi
             \advance\killseq@count by -1
-            \seq@percent=100 \divide\seq@percent by \killseq@count
          \fi
       \fi\fi
       \killseq@
@@ -3114,22 +3113,33 @@
    \expandafter\xdef\csname stack@\bottop@\seq@\endcsname{\tmpstack}
 }
 \def\getarrow@shape#1#2#3#4&{%
-   \xdef\first@@{#1}\xdef\second@@{#2}\xdef\third@@{#3}
-   \if\first@@ v
-      \if\second@@ =
-      \else \xdef\style@{\first@@ v\third@@#4} \fi
+   \xdef\first@@{#1}\xdef\second@@{#2}\xdef\third@@{#3}\xdef\fourth@@{#4}
+   \ifx\temp@@\y@
+      \if\first@@ ` \xdef\first@@{a} \else
+      \if\first@@ ' \xdef\first@@{a} \else
+      \if\first@@ , \xdef\first@@{b} \else
+      \if\first@@ S \xdef\first@@{c} \xdef\second@@{-}
+      \fi\fi\fi\fi
+      \if\third@@ ` \xdef\third@@{a} \else
+      \if\third@@ ' \xdef\third@@{a} \else
+      \if\third@@ , \xdef\third@@{b} \else
+      \if\third@@ S \xdef\third@@{c} \xdef\second@@{-}
+      \fi\fi\fi\fi
+      \xdef\style@{\first@@ -\third@@\fourth@@}
+   \fi
+   \if\first@@ S
+      \xdef\style@{\first@@ -\third@@\fourth@@}
    \else
    \if\first@@ v
       \if\second@@ =
-      \else \xdef\style@{\first@@ v\third@@#4} \fi
+      \else \xdef\style@{\first@@ v\third@@\fourth@@} \fi
    \else
-   \if\third@@ v
-      \if\second@@ =
-      \else \xdef\style@{\first@@ v\third@@#4} \fi
+   \if\third@@ S
+      \xdef\style@{\first@@ -\third@@\fourth@@}
    \else
    \if\third@@ v
       \if\second@@ =
-      \else \xdef\style@{\first@@ v\third@@#4} \fi
+      \else \xdef\style@{\first@@ v\third@@\fourth@@} \fi
    \fi\fi\fi\fi
 }
 \def\get@shape#1#2#3{%
@@ -5894,7 +5904,11 @@
          \fi
          \xdef\style@{cons[color]:cons[\f@color][0]}
       \else
-         \xdef\style@{#4} \expandafter\getarrow@shape\temp@
+         \xdef\style@{#4} \xdef\temp@@{n}
+         \expandafter\get@firstfill\temp@
+         \if\second@@ ^ \xdef\second@@{_} \fi
+         \if\second@@ _ \xdef\temp@{\fill@char} \xdef\temp@@{y}\fi
+         \expandafter\getarrow@shape\temp@
       \fi
       \fi
       \fi
@@ -7793,9 +7807,8 @@
        \advance\pos@sum by 1 \fi
   \ifnum\innerloopcount<\seq@count \repeat
 
-  \multiply\pos@sum by \seq@percent
   \expandafter\xdef\csname pos\the\loopcount\endcsname{\the\pos@sum}
-  \expandafter\ifnum\csname pos\the\loopcount\endcsname<\thresh@ld
+  \expandafter\ifnum\csname pos\the\loopcount\endcsname<\thresh@ld@
   \else
     \expandafter\ifnum\csname pos\the\loopcount\endcsname>\m@x
       \xdef\m@x{\csname pos\the\loopcount\endcsname}
@@ -7843,13 +7856,12 @@
   \expandafter\ifnum\csname pos\the\loopcount\endcsname=\seq@count
     \xdef\cons@seq{\the\loopcount} \xdef\match@case{2} \loopcount=1
   \else
-   \multiply\pos@sum by \seq@percent
    \expandafter\xdef\csname pos\the\loopcount\endcsname{\the\pos@sum}
-   \expandafter\ifnum\csname pos\the\loopcount\endcsname<\thresh@ld
+   \expandafter\ifnum\csname pos\the\loopcount\endcsname<\thresh@ld@
    \else
     \expandafter\ifnum\csname pos\the\loopcount\endcsname>\m@x
       \xdef\m@x{\csname pos\the\loopcount\endcsname}
-      \expandafter\ifnum\csname pos\the\loopcount\endcsname<\all@thresh@ld
+      \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}
@@ -11373,7 +11385,7 @@
          \textcolor{\legend@fg}{%
          \ifgerm@n\kern2ex\legend@size{nicht konserviert}%
          \else\ifsp@nish\kern2ex\legend@size{no conservado}%
-         \else\kern2ex\legend@size{non conserved}\fi\fi}
+         \else\kern2ex\legend@size{non-conserved}\fi\fi}
          \newline\hbox{}\noindent%
          \ifsimmode%
          \ifnames@\ifnames@right\else\hbox to \name@width{\hss}\fi\fi
@@ -11862,6 +11874,7 @@
 \def\get@tripletfill#1#2#3#4&{%
    \multiply\temp@count by -1%
    \def\second@@{#1}\def\second@@@{#2}\def\second@@@@{#3}\def\fill@char{#4&}}
+
 \def\putfeature@style#1{%
    \residues@size%
    \setbox1=\hbox{\ensuremath{\overrightarrow{\hbox{}}}}%
@@ -11967,6 +11980,7 @@
        \fontseries{\featurestyles@series}%
        \fontshape{\featurestyles@shape}%
        \selectfont%
+       \xdef\last@{bottom}%
        \ifx\bottop@\temp@\xdef\last@{0.35}\else\xdef\last@{0}\fi%
        \kern0.15\box@width%
        \loopcount=0\relax%
@@ -12137,6 +12151,7 @@
         \ifx\bottop@\temp@ \xdef\last@{0.35}\else\xdef\last@{-0.55}\fi%
         \textcolor{\f@color}{%
         \raisebox{\last@\arrow@height}{%
+         \if\first@@ b \xdef\first@@{,}\fi%
          \if\first@@ ,%
             \rule{0.1\arrow@height}{\arrow@height}\kern-0.35\arrow@height%
          \else%
@@ -12148,10 +12163,15 @@
                   \rule[\arrow@height]%
                      {0.1\arrow@height}{\arrow@height}\kern-0.35\arrow@height%
                \else%
+               \if\first@@ '%
+                  \rule[\arrow@height]%
+                     {0.1\arrow@height}{\arrow@height}\kern-0.35\arrow@height%
+               \else%
                   \if\first@@ -%
                      \rule{0pt}{0pt}\kern-0.35\arrow@height%
                   \fi%
                \fi%
+               \fi%
             \fi%
          \fi%
          \if\third@@ v%
@@ -12212,6 +12232,7 @@
                  \xdef\last@{-0.25}\fi\fi\fi\fi%
         \textcolor{\f@color}{%
         \raisebox{\last@\arrow@height}{%
+         \if\first@@ b \xdef\first@@{,}\fi%
          \if\first@@ ,%
             \rule[-0.5\arrow@height]{0.1\arrow@height}{1.5\arrow@height}%
             \kern-0.1\arrow@height%
@@ -12220,7 +12241,8 @@
                \rule[-0.5\arrow@height]{0.1\arrow@height}{2.25\arrow@height}%
                \kern-0.1\arrow@height%
             \else%
-               \if\first@@ `\xdef\first@@{'}\fi%
+               \if\first@@ a \xdef\first@@{'}\fi%
+               \if\first@@ ` \xdef\first@@{'}\fi%
                \if\first@@ '%
                   \rule[0.4\arrow@height]%
                      {0.1\arrow@height}{1.5\arrow@height}%
@@ -12245,6 +12267,7 @@
             \rule[0.37\arrow@height]{\width@tmp}{0.1\arrow@height}%
             \kern-\width@tmp%
             \rule[0.9\arrow@height]{\width@tmp}{0.1\arrow@height}%
+            \if\first@@ b \xdef\first@@{,}\fi%
             \if\third@@ ,%
                \kern-0.05\arrow@height%
                \rule[-0.5\arrow@height]{0.1\arrow@height}{1.5\arrow@height}%
@@ -12253,10 +12276,16 @@
                   \kern-0.05\arrow@height%
                   \rule[-0.5\arrow@height]{0.1\arrow@height}{2.25\arrow@height}%
                \else%
-                  \if\third@@ `\xdef\third@@{'}\fi%
+                  \if\first@@ a \xdef\first@@{'}\fi%
+                  \if\third@@ ` \xdef\third@@{'}\fi%
                   \if\third@@ '%
                      \kern-0.05\arrow@height%
                      \rule[0.4\arrow@height]{0.1\arrow@height}{1.5\arrow@height}%
+                  \else%
+                  \if\third@@ a%
+                     \kern-0.05\arrow@height%
+                     \rule[0.4\arrow@height]{0.1\arrow@height}{1.5\arrow@height}%
+                  \fi%
                   \fi%
                \fi%
             \fi%
@@ -12268,9 +12297,25 @@
         \advance\width@tmp by -0.5\temp@@length%
         \if\first@@ o\xdef\first@@{O}\fi%
         \if\third@@ o\xdef\third@@{O}\fi%
+        \xdef\last@{bottom}%
+        \ifx\fe@turep@s\last@%
+           \vspace{-20pt}\message{(((-20pt)))}%
+        \fi%
         \textcolor{\f@color}{%
          \if\first@@ ,%
-         \rule{\temp@@length}{\arrow@height}\kern-\temp@@length%
+           \rule{\temp@@length}{\arrow@height}\kern-\temp@@length%
+         \else%
+         \if\first@@ b%
+           \xdef\last@{bottom}%
+           \ifx\fe@turep@s\last@%
+            \rule{\temp@@length}{\arrow@height}\kern-\temp@@length%
+           \else
+            \xdef\shift@feature{y}%
+            \kern-\temp@@length%
+            \rule[-\bar@length]{\temp@@length}{\bar@length}%
+            \kern-\temp@@length%
+            \rule{\temp@@length}{\arrow@height}\kern-\temp@@length%
+           \fi
          \else%
             \if\first@@ |%
                \rule{\temp@@length}{2\arrow@height}\kern-\temp@@length%
@@ -12279,6 +12324,52 @@
                 \raisebox{0.06ex}{\ensuremath{\bullet}}\kern-0.55ex%
                 \rule[\width@tmp]{0.65ex}{\temp@@length}%
               \else%
+              \if\first@@ S%
+                \xdef\last@{bottom}%
+                \ifx\fe@turep@s\last@%
+                   \advance\width@tmp by 0.5\temp@@length%
+                   \kern0.5\box@width%
+                   \kern-2\temp@@length%
+                   \rule[\width@tmp]{\temp@@length}{\arrow@height}%
+                   \advance\width@tmp by -0.5\temp@@length%
+                   \kern-\temp@@length%
+                   \rule[\width@tmp]{0.5\temp@@length}{\temp@@length}%
+                   \rule[\width@tmp]{0.5\box@width}{\temp@@length}%
+                \else%
+                   \kern0.5\box@width%
+                   \kern-2\temp@@length%
+                   \rule{\temp@@length}{\arrow@height}%
+                   \kern-\temp@@length%
+                   \rule[\width@tmp]{0.5\temp@@length}{\temp@@length}%
+                   \rule[\width@tmp]{0.5\box@width}{\temp@@length}%
+                \fi%
+              \else%
+              \if\first@@ c%
+                \xdef\last@{bottom}%
+                \ifx\fe@turep@s\last@%
+                   \advance\width@tmp by 0.5\temp@@length%
+                   \raisebox{\arrow@height}{\rule[\box@height]{0pt}{\bar@length}}%%%%%%%%%%%%%%%%%%%%%%%
+                   \kern0.5\box@width%
+                   \kern-2\temp@@length%
+                   \rule[2\arrow@height]{\temp@@length}{\bar@length}%%%%%%%%%%%%%%%%%%%%%%
+                   \kern-\temp@@length%%%%%%%%%%%%%%%%%%%%%%%%%
+                   \rule[\width@tmp]{\temp@@length}{\arrow@height}%
+                   \advance\width@tmp by -0.5\temp@@length%
+                   \kern-\temp@@length%
+                   \rule[\width@tmp]{0.5\temp@@length}{\temp@@length}%
+                   \rule[\width@tmp]{0.5\box@width}{\temp@@length}%
+                \else%
+                   \xdef\shift@feature{y}%
+                   \kern0.5\box@width%
+                   \kern-2\temp@@length%
+                   \rule[-\bar@length]{\temp@@length}{\bar@length}%
+                   \kern-\temp@@length%
+                   \rule{\temp@@length}{\arrow@height}%
+                   \kern-\temp@@length%
+                   \rule[\width@tmp]{0.5\temp@@length}{\temp@@length}%
+                   \rule[\width@tmp]{0.5\box@width}{\temp@@length}%
+                \fi%
+              \else%
                \if\first@@ <%
                  \raisebox{0.06ex}{\ensuremath{\blacktriangleleft}}\kern-0.35ex%
                \else
@@ -12290,13 +12381,20 @@
                 \fi%
                \fi%
               \fi%
+              \fi%
+              \fi%
             \fi%
          \fi%
+         \fi%
          \loopcount=\second@%
          \if\first@@ <\advance\loopcount by -1\relax\ifnum\loopcount<0 \loopcount=0\fi\fi%
          \if\third@@ >\advance\loopcount by -1\relax\ifnum\loopcount<0 \loopcount=0\fi\fi%
          \if\first@@ O\advance\loopcount by -1\relax\ifnum\loopcount<0 \loopcount=0\fi\fi%
          \if\third@@ O\advance\loopcount by -1\relax\ifnum\loopcount<0 \loopcount=0\fi\fi%
+         \if\first@@ S\advance\loopcount by -1\relax\ifnum\loopcount<0 \loopcount=0\fi\fi%
+         \if\third@@ S\advance\loopcount by -1\relax\ifnum\loopcount<0 \loopcount=0\fi\fi%
+         \if\first@@ c\advance\loopcount by -1\relax\ifnum\loopcount<0 \loopcount=0\fi\fi%
+         \if\third@@ c\advance\loopcount by -1\relax\ifnum\loopcount<0 \loopcount=0\fi\fi%
          \xdef\second@{\the\loopcount}%
          \rule[\width@tmp]{\second@\box@width}{\temp@@length}%
          \setbox1=\hbox{\residues@size{\fill@char}}%
@@ -12307,6 +12405,17 @@
          \if\third@@ ,%
          \kern-\temp@@length\rule{\temp@@length}{\arrow@height}%
          \else%
+         \if\third@@ b%
+           \xdef\last@{bottom}%
+           \ifx\fe@turep@s\last@%
+            \kern-\temp@@length\rule{\temp@@length}{\arrow@height}%
+           \else
+            \xdef\shift@feature{y}%
+            \kern-\temp@@length%
+            \rule[-\bar@length]{\temp@@length}{\bar@length}%
+            \kern-\temp@@length\rule{\temp@@length}{\arrow@height}%
+           \fi
+         \else%
             \if\third@@ |%
                \kern-\temp@@length\rule{\temp@@length}{2\arrow@height}%
             \else%
@@ -12314,6 +12423,31 @@
                 \rule[\width@tmp]{0.65ex}{\temp@@length}%
                 \kern-0.55ex\raisebox{0.06ex}{\ensuremath{\bullet}}%
               \else%
+              \if\third@@ S%
+                \rule[\width@tmp]{0.5\box@width}{\temp@@length}%
+                \rule[\width@tmp]{0.5\temp@@length}{\temp@@length}%
+                \xdef\last@{bottom}%
+                \ifx\fe@turep@s\last@%
+                  \advance\width@tmp by 0.5\temp@@length%
+                  \kern-\temp@@length\rule[\width@tmp]{\temp@@length}{\arrow@height}%
+                \else
+                  \kern-\temp@@length\rule{\temp@@length}{\arrow@height}%
+                \fi%
+              \else%
+              \if\third@@ c%
+                \xdef\shift@feature{y}%
+                \rule[\width@tmp]{0.5\box@width}{\temp@@length}%
+                \xdef\last@{bottom}%
+                \ifx\fe@turep@s\last@%
+                  \kern-\temp@@length%%%%%%%%%%%%%%%%%%%%%%%%%
+                  \rule[2\arrow@height]{\temp@@length}{\bar@length}%%%%%%%%%%%%%%%%%%%%%%
+                  \advance\width@tmp by 0.5\temp@@length%
+                  \kern-\temp@@length\rule[\width@tmp]{\temp@@length}{\arrow@height}%
+                \else
+                  \kern-\temp@@length\rule[-\bar@length]{\temp@@length}{\bar@length}%
+                  \kern-\temp@@length\rule{\temp@@length}{\arrow@height}%
+                \fi%
+              \else%
                \if\third@@ >%
                 \kern-0.35ex\raisebox{0.06ex}{\ensuremath{\blacktriangleright}}%
                \else
@@ -12324,7 +12458,10 @@
                 \fi%
                \fi%
               \fi%
-            \fi
+              \fi%
+              \fi%
+            \fi%
+         \fi%
          \fi}%
        \fi
       \fi
@@ -13125,10 +13262,23 @@
    \xdef\featureposttttop{1} \xdef\featureposbbbbottom{1}%
    \findc@nsensus%
    \noindent%
+   \setlength{\bar@length}{0pt}%
+   \xdef\fe@turep@s{top}%
    \ifnum\feature@ttttop=1
+      \advance\bar@length by \feature@tttop\baselineskip%
+      \advance\bar@length by \feature@ttop\baselineskip%
+      \advance\bar@length by \feature@top\baselineskip%
+      \multiply\bar@length by 2%
+      \advance\bar@length by \tttt@sp@ce%
+      \advance\bar@length by \ttt@sp@ce%
+      \advance\bar@length by \tt@sp@ce%
       \ifnum\featureonttttop=0 \xdef\feature@ttttop{0} \fi
       \xdef\bottop@{ttttop}%
+      \xdef\shift@feature{n}%
       \put@feature%
+      \advance\bar@length by -\baselineskip%
+      \ifx\shift@feature\y@ \vspace{-\bar@length}\fi%
+      \setlength{\bar@length}{0pt}%
       \vspace{\tttt@sp@ce}%
       \vspace{-\baselineskip}%
       \newline\hbox{}%
@@ -13136,9 +13286,18 @@
       \iffix@\ifttttopfeature \vspace{\tttt@sp@ce}\newline\hbox{}\newline\hbox{}\fi\fi
    \fi
    \ifnum\feature@tttop=1
+      \advance\bar@length by \feature@ttop\baselineskip%
+      \advance\bar@length by \feature@top\baselineskip%
+      \multiply\bar@length by 2%
+      \advance\bar@length by \ttt@sp@ce%
+      \advance\bar@length by \tt@sp@ce%
       \ifnum\featureontttop=0 \xdef\feature@tttop{0} \fi
       \xdef\bottop@{tttop}%
+      \xdef\shift@feature{n}%
       \put@feature%
+      \advance\bar@length by -\baselineskip%
+      \ifx\shift@feature\y@ \vspace{-\bar@length}\fi%
+      \setlength{\bar@length}{0pt}%
       \vspace{\ttt@sp@ce}%
       \vspace{-\baselineskip}%
       \newline\hbox{}%
@@ -13146,9 +13305,16 @@
       \iffix@\iftttopfeature \vspace{\ttt@sp@ce}\newline\hbox{}\newline\hbox{}\fi\fi
    \fi
    \ifnum\feature@ttop=1
+      \advance\bar@length by \feature@top\baselineskip%
+      \multiply\bar@length by 2%
+      \advance\bar@length by \tt@sp@ce\message{tt\the\bar@length tt}%
       \ifnum\featureonttop=0 \xdef\feature@ttop{0} \fi
       \xdef\bottop@{ttop}%
+      \xdef\shift@feature{n}%
       \put@feature%
+      \advance\bar@length by -\baselineskip%
+      \ifx\shift@feature\y@ \vspace{-\bar@length}\fi%
+      \setlength{\bar@length}{0pt}%
       \vspace{\tt@sp@ce}%
       \vspace{-\baselineskip}%
       \newline\hbox{}%
@@ -13264,6 +13430,9 @@
          \ifnum\ruler@rot=0 \vspace{0.25\baselineskip}\fi%
       \fi%
    \fi%
+   \xdef\fe@turep@s{bottom}%
+   \setlength{\bar@length}{0pt}%
+   \xdef\b@feature@count{0}
    \ifnum\feature@bottom=1 %
       \ifnum\featureonbottom=0 \xdef\feature@bottom{0}\fi%
       \xdef\bottop@{bottom}%
@@ -13273,6 +13442,9 @@
          \vspace{\b@r@stretch\box@height}%
       \fi%
       \put@feature%
+      \temp@@count=\b@feature@count%
+      \advance\temp@@count by 1%
+      \xdef\b@feature@count{\the\temp@@count}%
    \else
       \iffix@
       \if\bottom@stretch y%
@@ -13285,14 +13457,24 @@
       \fi%
    \fi%
    \ifnum\feature@bbottom=1 %
+      \advance\bar@length by \b@feature@count \baselineskip%
+      \multiply\bar@length by \b@r@stretch%
+      \multiply\bar@length by 2%
+      \advance\bar@length by \bb@sp@ce\message{bb\the\bar@length bb}%
       \ifnum\featureonbbottom=0 \xdef\feature@bbottom{0}\fi%
       \xdef\bottop@{bbottom}%
       \vspace{\bb@sp@ce}%
       \if\bbottom@stretch y%
+         \advance\bar@length by -\box@height%
+         \advance\bar@length by \b@r@stretch\box@height%
          \vspace{-\box@height}%
          \vspace{\b@r@stretch\box@height}%
       \fi%
+      \setlength{\bar@length}{0pt}%%%%%%%%%%%%%%%%%%%%%%%
       \put@feature%
+      \temp@@count=\b@feature@count%
+      \advance\temp@@count by 1%
+      \xdef\b@feature@count{\the\temp@@count}%
    \else
       \iffix@
       \if\bbottom@stretch y%
@@ -13305,6 +13487,10 @@
       \fi
    \fi
    \ifnum\feature@bbbottom=1 %
+      \advance\bar@length by \b@feature@count\baselineskip%
+      \multiply\bar@length by \b@r@stretch%
+      \multiply\bar@length by 2%
+      \advance\bar@length by \bbb@sp@ce\message{bbb\the\bar@length bbb}%
       \ifnum\featureonbbbottom=0 \xdef\feature@bbbottom{0}\fi%
       \xdef\bottop@{bbbottom}%
       \vspace{\bbb@sp@ce}%
@@ -13313,6 +13499,9 @@
          \vspace{\b@r@stretch\box@height}%
       \fi%
       \put@feature%
+      \temp@@count=\b@feature@count%
+      \advance\temp@@count by 1%
+      \xdef\b@feature@count{\the\temp@@count}%
    \else
       \iffix@
       \if\bbbottom@stretch y%
@@ -13325,6 +13514,10 @@
       \fi
    \fi
    \ifnum\feature@bbbbottom=1 %
+      \advance\bar@length by \b@feature@count\baselineskip%
+      \multiply\bar@length by \b@r@stretch%
+      \multiply\bar@length by 2%
+      \advance\bar@length by \bbbb@sp@ce\message{bbbb\the\bar@length bbbb}%
       \ifnum\featureonbbbbottom=0 \xdef\feature@bbbbottom{0}\fi%
       \xdef\bottop@{bbbbottom}%
       \vspace{\bbbb@sp@ce}%
@@ -14181,8 +14374,6 @@
     \ifnum\loopcount<\seq@count \repeat
     \xdef\seq@order{\seq@order,@}
  \killseq@count=\seq@count
- \seq@percent=100
- \ifnum\seq@count>0 \divide\seq@percent by \seq@count \fi
  \fi
  \fi
 }
@@ -14450,6 +14641,10 @@
            \caption[\c@pshort]{\c@p}
          \fi
       \fi
+      \loopcount = \thresh@ld \multiply\loopcount by \seq@count \divide\loopcount by 100
+      \xdef\thresh@ld@{\the\loopcount}
+      \loopcount = \all@thresh@ld \multiply\loopcount by \seq@count \divide\loopcount by 100
+      \xdef\all@thresh@ld@{\the\loopcount}
       \bgroup
          \ifx\out@put\y@\bigskip\fi
          \iffuncmode \show@consfalse \fi