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fix in texshade.sty as suggested on TeXshade homepage at CTAN; version number bumped to 1.29.2

UBod authored on 24/06/2022 17:41:17
Showing4 changed files

... ...
@@ -1,8 +1,8 @@
1 1
 Package: msa
2 2
 Type: Package
3 3
 Title: Multiple Sequence Alignment
4
-Version: 1.29.1
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-Date: 2022-06-02
4
+Version: 1.29.2
5
+Date: 2022-06-24
6 6
 Author: Enrico Bonatesta, Christoph Horejs-Kainrath, Ulrich Bodenhofer
7 7
 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
8 8
 Description: The 'msa' package provides a unified R/Bioconductor interface to
... ...
@@ -1,6 +1,9 @@
1 1
 Change history of package msa:
2 2
 ==============================
3 3
 
4
+Version 1.29.2:
5
+- fix in texshade.sty as suggested on TeXshade homepage at CTAN
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+
4 7
 Version 1.29.1:
5 8
 - fix in argtable library (ClustalOmega) to avoid compilation errors on
6 9
   newest Mac OS
... ...
@@ -153,7 +153,12 @@
153 153
 \def\resn@m@tch{upper} \def\ressimm@tch{upper}
154 154
 \def\resm@tch{upper}   \def\res@llm@tch{upper}
155 155
 \def\tr@ns{translate}  \def\gr@ydef@ult{GrayDefault}
156
-\xdef\par@{\expandafter\string\par}
156
+%%%%REMOVED FOLLOWING LINE:
157
+%%%%\xdef\par@{\expandafter\string\par}
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+%%%%ADDED FOLLOWING TWO LINES (according to https://ctan.org/pkg/texshade)
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+\xdef\par@{\par}
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+\xdef\par@{\expandafter\string\par@}
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+%%%%
157 162
 \expandafter\def\csname fg@textcolor/\endcsname{White}
158 163
 \expandafter\def\csname fg@color/\endcsname{White}
159 164
 \expandafter\def\csname func@style/\endcsname{\csname textup\endcsname}
... ...
@@ -8,13 +8,13 @@
8 8
 %% 
9 9
 %% LaTeX package for typesetting nucleotide and peptide alignments
10 10
 %% 
11
-%% Copyright (C) 1999-2011 Eric Beitz
11
+%% Copyright (C) 1999-2021 Eric Beitz
12 12
 %% See the file texshade.txt
13 13
 %% 
14 14
 
15 15
 \NeedsTeXFormat{LaTeX2e}
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-\ProvidesPackage{texshade}[2011/05/13 LaTeX TeXshade (v1.24)]
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-\message{Package `texshade', Version 1.24 of 2011/12/01.}
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+\ProvidesPackage{texshade}[2021/04/01 LaTeX TeXshade (v1.26)]
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+\message{Package `texshade', Version 1.26 of 2021/04/01.}
18 18
 
19 19
 \PassOptionsToPackage{dvips}{color}
20 20
 \PassOptionsToPackage{dvips}{graphicx}
... ...
@@ -56,6 +56,7 @@
56 56
 \newread\structurefile  \newwrite\featurefile
57 57
 \newread\alignfile      \newread\sublogofile
58 58
 \newwrite\exp@rtfile
59
+\newwrite\exp@rt@chimerafile
59 60
 
60 61
 \expandafter\ifx\csname blacktriangleright\endcsname\relax
61 62
  \openin\structurefile = amssymb.sty
... ...
@@ -94,6 +95,7 @@
94 95
 \newlength\equal@height \newlength\temp@@length
95 96
 \newlength\vspace@legend
96 97
 \newlength\hspace@legend
98
+\newlength\bar@length
97 99
 
98 100
 \newif\ifletter       \newif\ifnumber
99 101
 \newif\ifnewres       \newif\ifall@shade
... ...
@@ -151,7 +153,12 @@
151 153
 \def\resn@m@tch{upper} \def\ressimm@tch{upper}
152 154
 \def\resm@tch{upper}   \def\res@llm@tch{upper}
153 155
 \def\tr@ns{translate}  \def\gr@ydef@ult{GrayDefault}
154
-\xdef\par@{\expandafter\string\par}
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+%%%%REMOVED FOLLOWING LINE:
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+%%%%\xdef\par@{\expandafter\string\par}
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+%%%%ADDED FOLLOWING TWO LINES (according to https://ctan.org/pkg/texshade)
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+\xdef\par@{\par}
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+\xdef\par@{\expandafter\string\par@}
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+%%%%
155 162
 \expandafter\def\csname fg@textcolor/\endcsname{White}
156 163
 \expandafter\def\csname fg@color/\endcsname{White}
157 164
 \expandafter\def\csname func@style/\endcsname{\csname textup\endcsname}
... ...
@@ -678,6 +685,16 @@
678 685
 \xdef\HydroV{37}  \xdef\HydroW{28}  \xdef\HydroX{N}
679 686
 \xdef\HydroY{9}   \xdef\HydroZ{N}
680 687
 
688
+\xdef\hardnessA{98}  \xdef\hardnessB{0}   \xdef\hardnessC{37}
689
+\xdef\hardnessD{100} \xdef\hardnessE{96} \xdef\hardnessF{48}
690
+\xdef\hardnessG{92}  \xdef\hardnessH{50} \xdef\hardnessI{98}
691
+\xdef\hardnessJ{86}   \xdef\hardnessK{73} \xdef\hardnessL{98}
692
+\xdef\hardnessM{25}  \xdef\hardnessN{86} \xdef\hardnessO{0}
693
+\xdef\hardnessP{91}   \xdef\hardnessQ{95} \xdef\hardnessR{69}
694
+\xdef\hardnessS{94}  \xdef\hardnessT{98}  \xdef\hardnessU{-34}
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+\xdef\hardnessV{98}  \xdef\hardnessW{0}  \xdef\hardnessX{0}
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+\xdef\hardnessY{28}   \xdef\hardnessZ{0}
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+
681 698
 \xdef\consCB{0}  \xdef\consCJ{0}  \xdef\consCO{0}  \xdef\consCU{0}  \xdef\consCX{0}  \xdef\consCZ{0}
682 699
 \expandafter\xdef\csname consC?\endcsname{0}
683 700
 
... ...
@@ -2593,7 +2610,6 @@
2593 2610
             \expandafter\xdef\csname hide@@@seq\first@\endcsname{kill}
2594 2611
             \ifnum\first@=\cons@num \xdef\cons@num{0} \fi
2595 2612
             \advance\killseq@count by -1
2596
-            \seq@percent=100 \divide\seq@percent by \killseq@count
2597 2613
          \fi
2598 2614
       \fi\fi
2599 2615
       \xdef\first@{\first@@ @}
... ...
@@ -2612,7 +2628,6 @@
2612 2628
             \expandafter\xdef\csname hide@@@seq\fourth@\endcsname{kill}
2613 2629
             \ifnum\fourth@=\cons@num \xdef\cons@num{0} \fi
2614 2630
             \advance\killseq@count by -1
2615
-            \seq@percent=100 \divide\seq@percent by \killseq@count
2616 2631
          \fi
2617 2632
       \fi\fi
2618 2633
       \killseq@
... ...
@@ -2893,8 +2908,17 @@
2893 2908
       \funcgroup{Leu, Val, Ile}{LVI}{Green}{White}{upper}{up}
2894 2909
       \funcgroup{Pro}{P}{Apricot}{White}{upper}{up}
2895 2910
    \else
2911
+   \xdef\second@{hardness}
2912
+   \ifx\temp@\second@
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+      \funcgroup{22-23 eV (ADEGILPQSTV) | 2$\times$ HOMO-LUMO gap}{ADEGILPQSTV}{White}{BlueRed5}{upper}{up}
2914
+      \funcgroup{21-22 eV (KN)}{KN}{White}{BlueRed20}{upper}{up}
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+      \funcgroup{20-21 eV (R)}{R}{Black}{BlueRed40}{upper}{up}
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+      \funcgroup{19-20 eV (CFH)}{CFH}{Black}{BlueRed60}{upper}{up}
2917
+      \funcgroup{18-19 eV (MY)}{MY}{White}{BlueRed80}{upper}{up}
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+      \funcgroup{17-18 eV (W)}{W}{White}{BlueRed100}{upper}{up}
2919
+   \else
2896 2920
    \message{<Unknown shading mode - clearing `funcgroups'>}
2897
-   \fi\fi\fi\fi\fi\fi\fi
2921
+   \fi\fi\fi\fi\fi\fi\fi\fi
2898 2922
 }
2899 2923
 \def\shadeallresidues{\all@fshadetrue}
2900 2924
 \def\get@fromstack#1;#2;#3;#4;#5@{%
... ...
@@ -3114,22 +3138,33 @@
3114 3138
    \expandafter\xdef\csname stack@\bottop@\seq@\endcsname{\tmpstack}
3115 3139
 }
3116 3140
 \def\getarrow@shape#1#2#3#4&{%
3117
-   \xdef\first@@{#1}\xdef\second@@{#2}\xdef\third@@{#3}
3118
-   \if\first@@ v
3119
-      \if\second@@ =
3120
-      \else \xdef\style@{\first@@ v\third@@#4} \fi
3141
+   \xdef\first@@{#1}\xdef\second@@{#2}\xdef\third@@{#3}\xdef\fourth@@{#4}
3142
+   \ifx\temp@@\y@
3143
+      \if\first@@ ` \xdef\first@@{a} \else
3144
+      \if\first@@ ' \xdef\first@@{a} \else
3145
+      \if\first@@ , \xdef\first@@{b} \else
3146
+      \if\first@@ S \xdef\first@@{c} \xdef\second@@{-}
3147
+      \fi\fi\fi\fi
3148
+      \if\third@@ ` \xdef\third@@{a} \else
3149
+      \if\third@@ ' \xdef\third@@{a} \else
3150
+      \if\third@@ , \xdef\third@@{b} \else
3151
+      \if\third@@ S \xdef\third@@{c} \xdef\second@@{-}
3152
+      \fi\fi\fi\fi
3153
+      \xdef\style@{\first@@ -\third@@\fourth@@}
3154
+   \fi
3155
+   \if\first@@ S
3156
+      \xdef\style@{\first@@ -\third@@\fourth@@}
3121 3157
    \else
3122 3158
    \if\first@@ v
3123 3159
       \if\second@@ =
3124
-      \else \xdef\style@{\first@@ v\third@@#4} \fi
3160
+      \else \xdef\style@{\first@@ v\third@@\fourth@@} \fi
3125 3161
    \else
3126
-   \if\third@@ v
3127
-      \if\second@@ =
3128
-      \else \xdef\style@{\first@@ v\third@@#4} \fi
3162
+   \if\third@@ S
3163
+      \xdef\style@{\first@@ -\third@@\fourth@@}
3129 3164
    \else
3130 3165
    \if\third@@ v
3131 3166
       \if\second@@ =
3132
-      \else \xdef\style@{\first@@ v\third@@#4} \fi
3167
+      \else \xdef\style@{\first@@ v\third@@\fourth@@} \fi
3133 3168
    \fi\fi\fi\fi
3134 3169
 }
3135 3170
 \def\get@shape#1#2#3{%
... ...
@@ -5894,7 +5929,11 @@
5894 5929
          \fi
5895 5930
          \xdef\style@{cons[color]:cons[\f@color][0]}
5896 5931
       \else
5897
-         \xdef\style@{#4} \expandafter\getarrow@shape\temp@
5932
+         \xdef\style@{#4} \xdef\temp@@{n}
5933
+         \expandafter\get@firstfill\temp@
5934
+         \if\second@@ ^ \xdef\second@@{_} \fi
5935
+         \if\second@@ _ \xdef\temp@{\fill@char} \xdef\temp@@{y}\fi
5936
+         \expandafter\getarrow@shape\temp@
5898 5937
       \fi
5899 5938
       \fi
5900 5939
       \fi
... ...
@@ -6382,7 +6421,17 @@
6382 6421
       \logocolor{EQ}{RoyalPurple}
6383 6422
       \logocolor{R}{RedViolet}
6384 6423
       \logocolor{K}{Black}
6385
-   \fi\fi\fi\fi\fi\fi\fi
6424
+   \else
6425
+   \xdef\second@{hardness}
6426
+   \ifx\first@\second@
6427
+      \clearlogocolors
6428
+      \logocolor{ADEGILPQSTV}{BlueRed5}
6429
+      \logocolor{KN}{BlueRed20}
6430
+      \logocolor{R}{BlueRed40}
6431
+      \logocolor{CFH}{BlueRed60}
6432
+      \logocolor{MY}{BlueRed80}
6433
+      \logocolor{W}{BlueRed100}
6434
+   \fi\fi\fi\fi\fi\fi\fi\fi
6386 6435
 }
6387 6436
 \newcommand\findsubfamily[2][n]{%
6388 6437
    \xdef\first@{#1}
... ...
@@ -7793,9 +7842,8 @@
7793 7842
        \advance\pos@sum by 1 \fi
7794 7843
   \ifnum\innerloopcount<\seq@count \repeat
7795 7844
 
7796
-  \multiply\pos@sum by \seq@percent
7797 7845
   \expandafter\xdef\csname pos\the\loopcount\endcsname{\the\pos@sum}
7798
-  \expandafter\ifnum\csname pos\the\loopcount\endcsname<\thresh@ld
7846
+  \expandafter\ifnum\csname pos\the\loopcount\endcsname<\thresh@ld@
7799 7847
   \else
7800 7848
     \expandafter\ifnum\csname pos\the\loopcount\endcsname>\m@x
7801 7849
       \xdef\m@x{\csname pos\the\loopcount\endcsname}
... ...
@@ -7843,13 +7891,12 @@
7843 7891
   \expandafter\ifnum\csname pos\the\loopcount\endcsname=\seq@count
7844 7892
     \xdef\cons@seq{\the\loopcount} \xdef\match@case{2} \loopcount=1
7845 7893
   \else
7846
-   \multiply\pos@sum by \seq@percent
7847 7894
    \expandafter\xdef\csname pos\the\loopcount\endcsname{\the\pos@sum}
7848
-   \expandafter\ifnum\csname pos\the\loopcount\endcsname<\thresh@ld
7895
+   \expandafter\ifnum\csname pos\the\loopcount\endcsname<\thresh@ld@
7849 7896
    \else
7850 7897
     \expandafter\ifnum\csname pos\the\loopcount\endcsname>\m@x
7851 7898
       \xdef\m@x{\csname pos\the\loopcount\endcsname}
7852
-      \expandafter\ifnum\csname pos\the\loopcount\endcsname<\all@thresh@ld
7899
+      \expandafter\ifnum\csname pos\the\loopcount\endcsname<\all@thresh@ld@
7853 7900
          \xdef\cons@seq{\the\loopcount} \xdef\match@case{1}
7854 7901
       \else
7855 7902
          \xdef\cons@seq{\the\loopcount} \xdef\match@case{2}
... ...
@@ -10431,6 +10478,7 @@
10431 10478
              \fi
10432 10479
              \fi
10433 10480
              \expandafter\xdef\csname res@count\the\loopcount\endcsname{\the\res@count}
10481
+             \ifnum\loopcount=\chimera@seqnum \xdef\chimera@stack{\chimera@stack \the\res@count,} \fi
10434 10482
              \ifnum\loopcount=\exp@rt@num \xdef\sixth@{\the\res@count}\xdef\seventh@{y}\fi
10435 10483
              \ifnum\loopcount=\rule@num\relax
10436 10484
               \expandafter\ifnum\csname res@count\rule@num\endcsname>\rule@tens
... ...
@@ -10574,6 +10622,7 @@
10574 10622
                            \the\innerloopcount}
10575 10623
          \else
10576 10624
           \ifnum\loopcount=\rule@num \xdef\ruler@{\ruler@ -} \fi
10625
+          \ifnum\loopcount=\chimera@seqnum \xdef\chimera@stack{\chimera@stack &,} \fi
10577 10626
           \ifx\collect@valtop\yes
10578 10627
           \ifnum\v@lseqtop=\loopcount
10579 10628
              \xdef\v@ltop{\v@ltop,N}
... ...
@@ -11373,7 +11422,7 @@
11373 11422
          \textcolor{\legend@fg}{%
11374 11423
          \ifgerm@n\kern2ex\legend@size{nicht konserviert}%
11375 11424
          \else\ifsp@nish\kern2ex\legend@size{no conservado}%
11376
-         \else\kern2ex\legend@size{non conserved}\fi\fi}
11425
+         \else\kern2ex\legend@size{non-conserved}\fi\fi}
11377 11426
          \newline\hbox{}\noindent%
11378 11427
          \ifsimmode%
11379 11428
          \ifnames@\ifnames@right\else\hbox to \name@width{\hss}\fi\fi
... ...
@@ -11862,6 +11911,7 @@
11862 11911
 \def\get@tripletfill#1#2#3#4&{%
11863 11912
    \multiply\temp@count by -1%
11864 11913
    \def\second@@{#1}\def\second@@@{#2}\def\second@@@@{#3}\def\fill@char{#4&}}
11914
+
11865 11915
 \def\putfeature@style#1{%
11866 11916
    \residues@size%
11867 11917
    \setbox1=\hbox{\ensuremath{\overrightarrow{\hbox{}}}}%
... ...
@@ -11967,6 +12017,7 @@
11967 12017
        \fontseries{\featurestyles@series}%
11968 12018
        \fontshape{\featurestyles@shape}%
11969 12019
        \selectfont%
12020
+       \xdef\last@{bottom}%
11970 12021
        \ifx\bottop@\temp@\xdef\last@{0.35}\else\xdef\last@{0}\fi%
11971 12022
        \kern0.15\box@width%
11972 12023
        \loopcount=0\relax%
... ...
@@ -12137,6 +12188,7 @@
12137 12188
         \ifx\bottop@\temp@ \xdef\last@{0.35}\else\xdef\last@{-0.55}\fi%
12138 12189
         \textcolor{\f@color}{%
12139 12190
         \raisebox{\last@\arrow@height}{%
12191
+         \if\first@@ b \xdef\first@@{,}\fi%
12140 12192
          \if\first@@ ,%
12141 12193
             \rule{0.1\arrow@height}{\arrow@height}\kern-0.35\arrow@height%
12142 12194
          \else%
... ...
@@ -12144,6 +12196,10 @@
12144 12196
                \rule{0.1\arrow@height}{2\arrow@height}\kern-0.35\arrow@height%
12145 12197
             \else%
12146 12198
                \if\first@@ `\xdef\first@@{'}\fi%
12199
+               \if\first@@ '%
12200
+                  \rule[\arrow@height]%
12201
+                     {0.1\arrow@height}{\arrow@height}\kern-0.35\arrow@height%
12202
+               \else%
12147 12203
                \if\first@@ '%
12148 12204
                   \rule[\arrow@height]%
12149 12205
                      {0.1\arrow@height}{\arrow@height}\kern-0.35\arrow@height%
... ...
@@ -12152,6 +12208,7 @@
12152 12208
                      \rule{0pt}{0pt}\kern-0.35\arrow@height%
12153 12209
                   \fi%
12154 12210
                \fi%
12211
+               \fi%
12155 12212
             \fi%
12156 12213
          \fi%
12157 12214
          \if\third@@ v%
... ...
@@ -12212,6 +12269,7 @@
12212 12269
                  \xdef\last@{-0.25}\fi\fi\fi\fi%
12213 12270
         \textcolor{\f@color}{%
12214 12271
         \raisebox{\last@\arrow@height}{%
12272
+         \if\first@@ b \xdef\first@@{,}\fi%
12215 12273
          \if\first@@ ,%
12216 12274
             \rule[-0.5\arrow@height]{0.1\arrow@height}{1.5\arrow@height}%
12217 12275
             \kern-0.1\arrow@height%
... ...
@@ -12220,7 +12278,8 @@
12220 12278
                \rule[-0.5\arrow@height]{0.1\arrow@height}{2.25\arrow@height}%
12221 12279
                \kern-0.1\arrow@height%
12222 12280
             \else%
12223
-               \if\first@@ `\xdef\first@@{'}\fi%
12281
+               \if\first@@ a \xdef\first@@{'}\fi%
12282
+               \if\first@@ ` \xdef\first@@{'}\fi%
12224 12283
                \if\first@@ '%
12225 12284
                   \rule[0.4\arrow@height]%
12226 12285
                      {0.1\arrow@height}{1.5\arrow@height}%
... ...
@@ -12245,6 +12304,7 @@
12245 12304
             \rule[0.37\arrow@height]{\width@tmp}{0.1\arrow@height}%
12246 12305
             \kern-\width@tmp%
12247 12306
             \rule[0.9\arrow@height]{\width@tmp}{0.1\arrow@height}%
12307
+            \if\first@@ b \xdef\first@@{,}\fi%
12248 12308
             \if\third@@ ,%
12249 12309
                \kern-0.05\arrow@height%
12250 12310
                \rule[-0.5\arrow@height]{0.1\arrow@height}{1.5\arrow@height}%
... ...
@@ -12253,10 +12313,16 @@
12253 12313
                   \kern-0.05\arrow@height%
12254 12314
                   \rule[-0.5\arrow@height]{0.1\arrow@height}{2.25\arrow@height}%
12255 12315
                \else%
12256
-                  \if\third@@ `\xdef\third@@{'}\fi%
12316
+                  \if\first@@ a \xdef\first@@{'}\fi%
12317
+                  \if\third@@ ` \xdef\third@@{'}\fi%
12257 12318
                   \if\third@@ '%
12258 12319
                      \kern-0.05\arrow@height%
12259 12320
                      \rule[0.4\arrow@height]{0.1\arrow@height}{1.5\arrow@height}%
12321
+                  \else%
12322
+                  \if\third@@ a%
12323
+                     \kern-0.05\arrow@height%
12324
+                     \rule[0.4\arrow@height]{0.1\arrow@height}{1.5\arrow@height}%
12325
+                  \fi%
12260 12326
                   \fi%
12261 12327
                \fi%
12262 12328
             \fi%
... ...
@@ -12268,9 +12334,25 @@
12268 12334
         \advance\width@tmp by -0.5\temp@@length%
12269 12335
         \if\first@@ o\xdef\first@@{O}\fi%
12270 12336
         \if\third@@ o\xdef\third@@{O}\fi%
12337
+        \xdef\last@{bottom}%
12338
+        \ifx\fe@turep@s\last@%
12339
+           \vspace{-20pt}\message{(((-20pt)))}%
12340
+        \fi%
12271 12341
         \textcolor{\f@color}{%
12272 12342
          \if\first@@ ,%
12273
-         \rule{\temp@@length}{\arrow@height}\kern-\temp@@length%
12343
+           \rule{\temp@@length}{\arrow@height}\kern-\temp@@length%
12344
+         \else%
12345
+         \if\first@@ b%
12346
+           \xdef\last@{bottom}%
12347
+           \ifx\fe@turep@s\last@%
12348
+            \rule{\temp@@length}{\arrow@height}\kern-\temp@@length%
12349
+           \else
12350
+            \xdef\shift@feature{y}%
12351
+            \kern-\temp@@length%
12352
+            \rule[-\bar@length]{\temp@@length}{\bar@length}%
12353
+            \kern-\temp@@length%
12354
+            \rule{\temp@@length}{\arrow@height}\kern-\temp@@length%
12355
+           \fi
12274 12356
          \else%
12275 12357
             \if\first@@ |%
12276 12358
                \rule{\temp@@length}{2\arrow@height}\kern-\temp@@length%
... ...
@@ -12278,6 +12360,52 @@
12278 12360
               \if\first@@ O%
12279 12361
                 \raisebox{0.06ex}{\ensuremath{\bullet}}\kern-0.55ex%
12280 12362
                 \rule[\width@tmp]{0.65ex}{\temp@@length}%
12363
+              \else%
12364
+              \if\first@@ S%
12365
+                \xdef\last@{bottom}%
12366
+                \ifx\fe@turep@s\last@%
12367
+                   \advance\width@tmp by 0.5\temp@@length%
12368
+                   \kern0.5\box@width%
12369
+                   \kern-2\temp@@length%
12370
+                   \rule[\width@tmp]{\temp@@length}{\arrow@height}%
12371
+                   \advance\width@tmp by -0.5\temp@@length%
12372
+                   \kern-\temp@@length%
12373
+                   \rule[\width@tmp]{0.5\temp@@length}{\temp@@length}%
12374
+                   \rule[\width@tmp]{0.5\box@width}{\temp@@length}%
12375
+                \else%
12376
+                   \kern0.5\box@width%
12377
+                   \kern-2\temp@@length%
12378
+                   \rule{\temp@@length}{\arrow@height}%
12379
+                   \kern-\temp@@length%
12380
+                   \rule[\width@tmp]{0.5\temp@@length}{\temp@@length}%
12381
+                   \rule[\width@tmp]{0.5\box@width}{\temp@@length}%
12382
+                \fi%
12383
+              \else%
12384
+              \if\first@@ c%
12385
+                \xdef\last@{bottom}%
12386
+                \ifx\fe@turep@s\last@%
12387
+                   \advance\width@tmp by 0.5\temp@@length%
12388
+                   \raisebox{\arrow@height}{\rule[\box@height]{0pt}{\bar@length}}%%%%%%%%%%%%%%%%%%%%%%%
12389
+                   \kern0.5\box@width%
12390
+                   \kern-2\temp@@length%
12391
+                   \rule[2\arrow@height]{\temp@@length}{\bar@length}%%%%%%%%%%%%%%%%%%%%%%
12392
+                   \kern-\temp@@length%%%%%%%%%%%%%%%%%%%%%%%%%
12393
+                   \rule[\width@tmp]{\temp@@length}{\arrow@height}%
12394
+                   \advance\width@tmp by -0.5\temp@@length%
12395
+                   \kern-\temp@@length%
12396
+                   \rule[\width@tmp]{0.5\temp@@length}{\temp@@length}%
12397
+                   \rule[\width@tmp]{0.5\box@width}{\temp@@length}%
12398
+                \else%
12399
+                   \xdef\shift@feature{y}%
12400
+                   \kern0.5\box@width%
12401
+                   \kern-2\temp@@length%
12402
+                   \rule[-\bar@length]{\temp@@length}{\bar@length}%
12403
+                   \kern-\temp@@length%
12404
+                   \rule{\temp@@length}{\arrow@height}%
12405
+                   \kern-\temp@@length%
12406
+                   \rule[\width@tmp]{0.5\temp@@length}{\temp@@length}%
12407
+                   \rule[\width@tmp]{0.5\box@width}{\temp@@length}%
12408
+                \fi%
12281 12409
               \else%
12282 12410
                \if\first@@ <%
12283 12411
                  \raisebox{0.06ex}{\ensuremath{\blacktriangleleft}}\kern-0.35ex%
... ...
@@ -12290,13 +12418,20 @@
12290 12418
                 \fi%
12291 12419
                \fi%
12292 12420
               \fi%
12421
+              \fi%
12422
+              \fi%
12293 12423
             \fi%
12294 12424
          \fi%
12425
+         \fi%
12295 12426
          \loopcount=\second@%
12296 12427
          \if\first@@ <\advance\loopcount by -1\relax\ifnum\loopcount<0 \loopcount=0\fi\fi%
12297 12428
          \if\third@@ >\advance\loopcount by -1\relax\ifnum\loopcount<0 \loopcount=0\fi\fi%
12298 12429
          \if\first@@ O\advance\loopcount by -1\relax\ifnum\loopcount<0 \loopcount=0\fi\fi%
12299 12430
          \if\third@@ O\advance\loopcount by -1\relax\ifnum\loopcount<0 \loopcount=0\fi\fi%
12431
+         \if\first@@ S\advance\loopcount by -1\relax\ifnum\loopcount<0 \loopcount=0\fi\fi%
12432
+         \if\third@@ S\advance\loopcount by -1\relax\ifnum\loopcount<0 \loopcount=0\fi\fi%
12433
+         \if\first@@ c\advance\loopcount by -1\relax\ifnum\loopcount<0 \loopcount=0\fi\fi%
12434
+         \if\third@@ c\advance\loopcount by -1\relax\ifnum\loopcount<0 \loopcount=0\fi\fi%
12300 12435
          \xdef\second@{\the\loopcount}%
12301 12436
          \rule[\width@tmp]{\second@\box@width}{\temp@@length}%
12302 12437
          \setbox1=\hbox{\residues@size{\fill@char}}%
... ...
@@ -12306,6 +12441,17 @@
12306 12441
          \hbox to \second@\box@width{\textcolor{\frame@color}{\residues@size{\hss\fill@char\hss}}}%
12307 12442
          \if\third@@ ,%
12308 12443
          \kern-\temp@@length\rule{\temp@@length}{\arrow@height}%
12444
+         \else%
12445
+         \if\third@@ b%
12446
+           \xdef\last@{bottom}%
12447
+           \ifx\fe@turep@s\last@%
12448
+            \kern-\temp@@length\rule{\temp@@length}{\arrow@height}%
12449
+           \else
12450
+            \xdef\shift@feature{y}%
12451
+            \kern-\temp@@length%
12452
+            \rule[-\bar@length]{\temp@@length}{\bar@length}%
12453
+            \kern-\temp@@length\rule{\temp@@length}{\arrow@height}%
12454
+           \fi
12309 12455
          \else%
12310 12456
             \if\third@@ |%
12311 12457
                \kern-\temp@@length\rule{\temp@@length}{2\arrow@height}%
... ...
@@ -12313,6 +12459,31 @@
12313 12459
               \if\third@@ O%
12314 12460
                 \rule[\width@tmp]{0.65ex}{\temp@@length}%
12315 12461
                 \kern-0.55ex\raisebox{0.06ex}{\ensuremath{\bullet}}%
12462
+              \else%
12463
+              \if\third@@ S%
12464
+                \rule[\width@tmp]{0.5\box@width}{\temp@@length}%
12465
+                \rule[\width@tmp]{0.5\temp@@length}{\temp@@length}%
12466
+                \xdef\last@{bottom}%
12467
+                \ifx\fe@turep@s\last@%
12468
+                  \advance\width@tmp by 0.5\temp@@length%
12469
+                  \kern-\temp@@length\rule[\width@tmp]{\temp@@length}{\arrow@height}%
12470
+                \else
12471
+                  \kern-\temp@@length\rule{\temp@@length}{\arrow@height}%
12472
+                \fi%
12473
+              \else%
12474
+              \if\third@@ c%
12475
+                \xdef\shift@feature{y}%
12476
+                \rule[\width@tmp]{0.5\box@width}{\temp@@length}%
12477
+                \xdef\last@{bottom}%
12478
+                \ifx\fe@turep@s\last@%
12479
+                  \kern-\temp@@length%%%%%%%%%%%%%%%%%%%%%%%%%
12480
+                  \rule[2\arrow@height]{\temp@@length}{\bar@length}%%%%%%%%%%%%%%%%%%%%%%
12481
+                  \advance\width@tmp by 0.5\temp@@length%
12482
+                  \kern-\temp@@length\rule[\width@tmp]{\temp@@length}{\arrow@height}%
12483
+                \else
12484
+                  \kern-\temp@@length\rule[-\bar@length]{\temp@@length}{\bar@length}%
12485
+                  \kern-\temp@@length\rule{\temp@@length}{\arrow@height}%
12486
+                \fi%
12316 12487
               \else%
12317 12488
                \if\third@@ >%
12318 12489
                 \kern-0.35ex\raisebox{0.06ex}{\ensuremath{\blacktriangleright}}%
... ...
@@ -12324,7 +12495,10 @@
12324 12495
                 \fi%
12325 12496
                \fi%
12326 12497
               \fi%
12327
-            \fi
12498
+              \fi%
12499
+              \fi%
12500
+            \fi%
12501
+         \fi%
12328 12502
          \fi}%
12329 12503
        \fi
12330 12504
       \fi
... ...
@@ -12731,9 +12905,550 @@
12731 12905
    \divide\loopcount by 100 %
12732 12906
    \xdef\third@{\the\loopcount}%
12733 12907
 }
12908
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
12909
+%%%%                         Chimera export routines                      %%%%
12910
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
12911
+\def\chimeraballScale#1{\xdef\chimerab@llSc@le{#1}}
12912
+\def\chimeraballscale#1{\xdef\chimerab@llSc@le{#1}}
12913
+\def\chimeraaxisdistance#1#2#3{\xdef\chimera@xdist@nce{#1}\xdef\chimera@ydist@nce{#2}\xdef\chimera@zdist@nce{#3}}
12914
+\def\memelabelcutoff#1{%
12915
+   \xdef\label@threshold@lower{#1}
12916
+   \setlength\temp@@length{1000sp}
12917
+   \setlength\temp@@length{\label@threshold@lower\temp@@length}
12918
+   \loopcount=\temp@@length
12919
+   \xdef\label@threshold@lowerIOOO{\the\loopcount}
12920
+   \xdef\label@threshold@lowerremainingIOOO{-\the\loopcount}
12921
+}
12922
+\def\chimera@color@get#1#2@{%
12923
+   \xdef\first@{#1}\xdef\third@{#2@}
12924
+   \ifx\first@\ampers@nd
12925
+   \else
12926
+      \ifnum`#1>96 \make@upper\fi
12927
+      \if\second@ O \else \expandafter\xdef\csname chimera@col@\first@\endcsname{\second@} \fi
12928
+      \expandafter\chimera@color@get\third@
12929
+   \fi
12930
+}
12931
+\def\memered#1{%
12932
+      \xdef\third@{#1&@}
12933
+      \xdef\second@{red}
12934
+      \expandafter\chimera@color@get\third@
12935
+}
12936
+\def\memeblue#1{%
12937
+      \xdef\third@{#1&@}
12938
+      \xdef\second@{blue}
12939
+      \expandafter\chimera@color@get\third@
12940
+}
12941
+\def\memeyellow#1{%
12942
+      \xdef\third@{#1&@}
12943
+      \xdef\second@{yellow}
12944
+      \expandafter\chimera@color@get\third@
12945
+}
12946
+\def\memeblack#1{%
12947
+      \xdef\third@{#1&@}
12948
+      \xdef\second@{black}
12949
+      \expandafter\chimera@color@get\third@
12950
+}
12951
+\def\memewhite#1{%
12952
+      \xdef\third@{#1&@}
12953
+      \xdef\second@{white}
12954
+      \expandafter\chimera@color@get\third@
12955
+}
12956
+\def\memenone#1{%
12957
+      \xdef\third@{#1&@}
12958
+      \xdef\second@{none}
12959
+      \expandafter\chimera@color@get\third@
12960
+}
12961
+\def\memeRed#1{\memered{#1}}
12962
+\def\memeBlue#1{\memeblue{#1}}
12963
+\def\memeYellow#1{\memeyellow{#1}}
12964
+\def\memeBlack#1{\memeblack{#1}}
12965
+\def\memeWhite#1{\memewhite{#1}}
12966
+\def\memeNone#1{\memenone{#1}}
12967
+\def\chimera@colors#1#2@{%
12968
+   \xdef\first@{#1}\xdef\third@{#2@}
12969
+   \ifx\first@\ampers@nd
12970
+   \else
12971
+      \xdef\second@{\csname chimera@col@\first@\endcsname}
12972
+      \expandafter\xdef\csname chimera@list@\second@\endcsname{\csname chimera@list@\second@\endcsname \first@}
12973
+      \expandafter\chimera@colors\third@
12974
+   \fi
12975
+}
12976
+\def\memeStandardcolors{%
12977
+   \xdef\chimera@col@A{white}
12978
+   \xdef\chimera@col@B{none}
12979
+   \xdef\chimera@col@C{yellow}
12980
+   \xdef\chimera@col@D{red}
12981
+   \xdef\chimera@col@E{red}
12982
+   \xdef\chimera@col@F{black}
12983
+   \xdef\chimera@col@G{yellow}
12984
+   \xdef\chimera@col@H{blue}
12985
+   \xdef\chimera@col@I{black}
12986
+   \xdef\chimera@col@J{none}
12987
+   \xdef\chimera@col@K{blue}
12988
+   \xdef\chimera@col@L{black}
12989
+   \xdef\chimera@col@M{black}
12990
+   \xdef\chimera@col@N{yellow}
12991
+   \xdef\chimera@col@O{none}
12992
+   \xdef\chimera@col@P{white}
12993
+   \xdef\chimera@col@Q{yellow}
12994
+   \xdef\chimera@col@R{blue}
12995
+   \xdef\chimera@col@S{yellow}
12996
+   \xdef\chimera@col@T{yellow}
12997
+   \xdef\chimera@col@U{none}
12998
+   \xdef\chimera@col@V{white}
12999
+   \xdef\chimera@col@W{black}
13000
+   \xdef\chimera@col@X{none}
13001
+   \xdef\chimera@col@Y{yellow}
13002
+   \xdef\chimera@col@Z{none}
13003
+}
13004
+\def\echostructurefile#1{\xdef\echo@filename{, e.g. #1}}
13005
+\def\chimerachain#1{\xdef\chimerach@in{.#1}}
13006
+\catcode`\"=6 \catcode`\#=12 \catcode`\~=12
13007
+\newcommand{\structurememe}[2][chimera.cmd]{%
13008
+   \ifx\exp@rt@chimera\n@
13009
+      \xdef\first@{"2 @} \expandafter\check@letter\first@
13010
+      \xdef\first@{"2}   \ifletter \get@name@number \fi
13011
+      \xdef\chimera@seqnum{\first@}
13012
+      \xdef\exp@rt@chimera{y}
13013
+      \xdef\first@{"1}
13014
+      \immediate\openout\exp@rt@chimerafile = \first@
13015
+   \fi
13016
+}
13017
+\def\init@chimera@file{%
13018
+      \xdef\chimera@list@red{} \xdef\chimera@list@blue{} \xdef\chimera@list@yellow{} \xdef\chimera@list@black{} \xdef\chimera@list@white{}
13019
+      \xdef\chimera@list@none{}
13020
+      \xdef\first@{ABCDEFGHIJKLMNOPQRSTUVWXYZ&@}
13021
+      \expandafter\chimera@colors\first@
13022
+      \immediate\write\exp@rt@chimerafile{############################################################}
13023
+      \immediate\write\exp@rt@chimerafile{###}
13024
+      \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }. O � o STRUCTURE MEME � . O o}
13025
+      \immediate\write\exp@rt@chimerafile{###}
13026
+      \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }Chimera command file generated from TeXshade logo data}
13027
+      \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }use '.cmd' or '.com' suffix}
13028
+      \immediate\write\exp@rt@chimerafile{###}
13029
+      \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }Reference sequence: '\csname newseqname\chimera@seqnum\endcsname'\echo@filename}
13030
+      \immediate\write\exp@rt@chimerafile{###}
13031
+      \immediate\write\exp@rt@chimerafile{############################################################}
13032
+      \immediate\write\exp@rt@chimerafile{}
13033
+      \immediate\write\exp@rt@chimerafile{############################################################}
13034
+      \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }residue colors: (set with \string\memeRed{residues}\unexpanded{ }etc.)}
13035
+      \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }\chimera@list@red \unexpanded{ }(Red)}
13036
+      \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }\chimera@list@blue \unexpanded{ }(Blue)}
13037
+      \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }\chimera@list@yellow \unexpanded{ }(Yellow)}
13038
+      \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }\chimera@list@black \unexpanded{ }(Black)}
13039
+      \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }\chimera@list@white \unexpanded{ }(White)}
13040
+      \immediate\write\exp@rt@chimerafile{############################################################}
13041
+      \immediate\write\exp@rt@chimerafile{}
13042
+      \immediate\write\exp@rt@chimerafile{############################################################}
13043
+      \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }residues in labels: (\string\memelabelcutoff{bit-value})}
13044
+      \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }\label@threshold@lower\unexpanded{ }bit required to appear}
13045
+      \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }> : . indicate 3, 2, and 1 bit levels}
13046
+      \immediate\write\exp@rt@chimerafile{############################################################}
13047
+      \immediate\write\exp@rt@chimerafile{}
13048
+      \immediate\write\exp@rt@chimerafile{############################################################}
13049
+      \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }initialize & load structure}
13050
+      \immediate\write\exp@rt@chimerafile{############################################################}
13051
+      \immediate\write\exp@rt@chimerafile{close session; background solid white;}
13052
+      \immediate\write\exp@rt@chimerafile{echo load structure file for '\csname newseqname\chimera@seqnum\endcsname'\echo@filename}
13053
+      \immediate\write\exp@rt@chimerafile{open #0; ~ribbon; ~surface}
13054
+      \immediate\write\exp@rt@chimerafile{}
13055
+      \immediate\write\exp@rt@chimerafile{############################################################}
13056
+      \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }to set ball scale, change factor ]0.0 - 1.0]}
13057
+      \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }in 'setattr m ballScale <factor> #0' below,}
13058
+      \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }or use the \string\chimeraballScale{factor}\unexpanded{ }command}
13059
+      \immediate\write\exp@rt@chimerafile{############################################################}
13060
+      \immediate\write\exp@rt@chimerafile{setattr m ballScale \chimerab@llSc@le \unexpanded{ }#0}
13061
+      \immediate\write\exp@rt@chimerafile{}
13062
+      \immediate\write\exp@rt@chimerafile{############################################################}
13063
+      \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }display alpha-carbons only}
13064
+      \immediate\write\exp@rt@chimerafile{############################################################}
13065
+      \immediate\write\exp@rt@chimerafile{represent bs @ca; show @ca}
13066
+      \immediate\write\exp@rt@chimerafile{}
13067
+      \ifshow@sublogo
13068
+            \immediate\write\exp@rt@chimerafile{############################################################}
13069
+            \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }duplicate structure;}
13070
+            \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }to alter direction or Angstrom distance, set}
13071
+            \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }'move <x, y, or z> 1 <distance> models #1' below,}
13072
+            \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }or use the \string\chimeraaxisdistance{x}{y}{z}\unexpanded{ }command}
13073
+            \immediate\write\exp@rt@chimerafile{############################################################}
13074
+            \immediate\write\exp@rt@chimerafile{combine #0}
13075
+            \ifnum\chimera@xdist@nce>0
13076
+               \immediate\write\exp@rt@chimerafile{move x 1 \chimera@xdist@nce \unexpanded{ }models #1}
13077
+            \fi
13078
+            \ifnum\chimera@ydist@nce>0
13079
+               \immediate\write\exp@rt@chimerafile{move y 1 \chimera@ydist@nce \unexpanded{ }models #1}
13080
+            \fi
13081
+            \ifnum\chimera@zdist@nce>0
13082
+               \immediate\write\exp@rt@chimerafile{move z 1 \chimera@zdist@nce \unexpanded{ }models #1}
13083
+            \fi
13084
+            \immediate\write\exp@rt@chimerafile{}
13085
+            \immediate\write\exp@rt@chimerafile{############################################################}
13086
+            \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }focus view and name structure models}
13087
+            \immediate\write\exp@rt@chimerafile{############################################################}
13088
+            \immediate\write\exp@rt@chimerafile{wait; focus #0#1}
13089
+            \ifx\sublogo@name@user\ampers@nd
13090
+                \immediate\write\exp@rt@chimerafile{setattr m name subfamily #0}
13091
+            \else
13092
+                \immediate\write\exp@rt@chimerafile{setattr m name '\sublogo@name@user' \unexpanded{ }#0}
13093
+            \fi
13094
+            \xdef\first@{\sublogo@name@neg &}
13095
+            \ifx\first@\ampers@nd
13096
+                \immediate\write\exp@rt@chimerafile{setattr m name remaining #1}
13097
+            \else
13098
+                \immediate\write\exp@rt@chimerafile{setattr m name '\sublogo@name@neg' \unexpanded{ }#1}
13099
+            \fi
13100
+     \else
13101
+            \immediate\write\exp@rt@chimerafile{\string ############################################################}
13102
+            \immediate\write\exp@rt@chimerafile{\string ###\unexpanded{ }\unexpanded{ }\unexpanded{ }name structure model}
13103
+            \immediate\write\exp@rt@chimerafile{\string ############################################################}
13104
+            \ifx\logo@name@user\ampers@nd
13105
+                \immediate\write\exp@rt@chimerafile{setattr m name logo #0}
13106
+            \else
13107
+                \immediate\write\exp@rt@chimerafile{setattr m name '\logo@name@user' \unexpanded{ }#0}
13108
+            \fi
13109
+      \fi
13110
+      \immediate\write\exp@rt@chimerafile{}
13111
+      \immediate\write\exp@rt@chimerafile{############################################################}
13112
+      \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }logo data}
13113
+      \immediate\write\exp@rt@chimerafile{############################################################}
13114
+}
13115
+\def\make@HEX{%
13116
+     \xdef\sixth@{\the\loopcount}%
13117
+     \divide\loopcount by 4096\relax%
13118
+     \ifnum\loopcount=10\relax%
13119
+        \xdef\seventh@{A}%
13120
+     \else%
13121
+     \ifnum\loopcount=11\relax%
13122
+        \xdef\seventh@{B}%
13123
+     \else%
13124
+     \ifnum\loopcount=12\relax%
13125
+        \xdef\seventh@{C}%
13126
+     \else%
13127
+     \ifnum\loopcount=13\relax%
13128
+        \xdef\seventh@{D}%
13129
+     \else%
13130
+     \ifnum\loopcount=14\relax%
13131
+        \xdef\seventh@{E}%
13132
+     \else%
13133
+     \ifnum\loopcount>14\relax%
13134
+        \xdef\seventh@{F}%
13135
+     \else%
13136
+        \xdef\seventh@{\the\loopcount}%
13137
+     \fi\fi\fi\fi\fi\fi%
13138
+     \multiply\loopcount by -4096\relax%
13139
+     \advance\loopcount by \sixth@%
13140
+     \xdef\sixth@{\the\loopcount}%
13141
+     \divide\loopcount by 256\relax%
13142
+     \ifnum\loopcount=10 \relax%
13143
+        \xdef\eighth@{A}%
13144
+     \else%
13145
+     \ifnum\loopcount=11 \relax%
13146
+        \xdef\eighth@{B}%
13147
+     \else%
13148
+     \ifnum\loopcount=12 \relax%
13149
+        \xdef\eighth@{C}%
13150
+     \else%
13151
+     \ifnum\loopcount=13 \relax%
13152
+        \xdef\eighth@{D}%
13153
+     \else%
13154
+     \ifnum\loopcount=14 \relax%
13155
+        \xdef\eighth@{E}%
13156
+     \else%
13157
+     \ifnum\loopcount>14 \relax%
13158
+        \xdef\eighth@{F}%
13159
+     \else%
13160
+        \xdef\eighth@{\the\loopcount}%
13161
+     \fi\fi\fi\fi\fi\fi%
13162
+     \xdef\seventh@{\seventh@\eighth@}%
13163
+     \multiply\loopcount by -256\relax%
13164
+     \advance\loopcount by \sixth@%
13165
+     \xdef\sixth@{\the\loopcount}%
13166
+     \divide\loopcount by 16\relax%
13167
+     \ifnum\loopcount=10\relax%
13168
+        \xdef\eighth@{A}%
13169
+     \else%
13170
+     \ifnum\loopcount=11\relax%
13171
+        \xdef\eighth@{B}%
13172
+     \else%
13173
+     \ifnum\loopcount=12\relax%
13174
+        \xdef\eighth@{C}%
13175
+     \else%
13176
+     \ifnum\loopcount=13\relax%
13177
+        \xdef\eighth@{D}%
13178
+     \else%
13179
+     \ifnum\loopcount=14\relax%
13180
+        \xdef\eighth@{E}%
13181
+     \else%
13182
+     \ifnum\loopcount>14\relax%
13183
+        \xdef\eighth@{F}%
13184
+     \else%
13185
+        \xdef\eighth@{\the\loopcount}%
13186
+     \fi\fi\fi\fi\fi\fi%
13187
+     \xdef\seventh@{\seventh@\eighth@}%
13188
+     \multiply\loopcount by -16\relax%
13189
+     \advance\loopcount by \sixth@\relax%
13190
+     \ifnum\loopcount=10\relax%
13191
+        \xdef\eighth@{A}%
13192
+     \else%
13193
+     \ifnum\loopcount=11\relax%
13194
+        \xdef\eighth@{B}%
13195
+     \else%
13196
+     \ifnum\loopcount=12\relax%
13197
+        \xdef\eighth@{C}%
13198
+     \else%
13199
+     \ifnum\loopcount=13\relax%
13200
+        \xdef\eighth@{D}%
13201
+     \else%
13202
+     \ifnum\loopcount=14\relax%
13203
+        \xdef\eighth@{E}%
13204
+     \else%
13205
+     \ifnum\loopcount>14\relax%
13206
+        \xdef\eighth@{F}%
13207
+     \else%
13208
+        \xdef\eighth@{\the\loopcount}%
13209
+     \fi\fi\fi\fi\fi\fi%
13210
+     \xdef\seventh@{\seventh@\eighth@}%
13211
+}
13212
+\def\write@chimera@data{%
13213
+      \ifnum\temp@count>0 \else\temp@count=1\relax\temp@@count=0\fi%
13214
+      \loopcount=\temp@count%
13215
+      \xdef\fourth@{\the\loopcount @}%
13216
+      \ifnum\loopcount>9999 \expandafter\decimal@A\fourth@ \else%
13217
+      \ifnum\loopcount>999  \expandafter\decimal@B\fourth@ \else%
13218
+      \ifnum\loopcount>99   \expandafter\decimal@C\fourth@ \else%
13219
+      \ifnum\loopcount>9    \expandafter\decimal@D\fourth@ \else%
13220
+                            \expandafter\decimal@E\fourth@%
13221
+      \fi\fi\fi\fi%
13222
+      \loopcount=\chimera@subfamily@col@black%
13223
+      \multiply\loopcount by 65535\relax%
13224
+      \divide\loopcount by \temp@count%
13225
+      \xdef\chimera@subfamily@col@black{\the\loopcount}%
13226
+      \loopcount=65535\relax%
13227
+      \advance\loopcount by -\chimera@subfamily@col@black%
13228
+      \xdef\temp@@{\the\loopcount}%
13229
+%%%%%%%%%%%%%%
13230
+%%%%%%%%%%%%%%
13231
+      \loopcount=\chimera@subfamily@col@blue\relax%
13232
+      \ifnum\chimera@subfamily@col@yellow>\loopcount\relax%
13233
+         \loopcount=\chimera@subfamily@col@yellow\relax%
13234
+      \else%
13235
+         \ifnum\chimera@subfamily@col@red>\loopcount\relax%
13236
+            \loopcount=\chimera@subfamily@col@red\relax%
13237
+         \fi%
13238
+      \fi%
13239
+      \xdef\max@yellow{\the\loopcount}%
13240
+      \ifnum\chimera@subfamily@col@blue<\chimera@subfamily@col@yellow\relax%
13241
+         \xdef\chimera@subfamily@col@green{\chimera@subfamily@col@blue}%
13242
+      \else%
13243
+         \xdef\chimera@subfamily@col@green{\chimera@subfamily@col@yellow}%
13244
+      \fi%
13245
+      \loopcount=\chimera@subfamily@col@yellow\relax%
13246
+      \advance\loopcount by -\chimera@subfamily@col@green%
13247
+      \xdef\chimera@subfamily@col@yellow{\the\loopcount}%
13248
+      \loopcount=\chimera@subfamily@col@blue\relax%
13249
+      \advance\loopcount by -\chimera@subfamily@col@green%
13250
+      \xdef\chimera@subfamily@col@blue{\the\loopcount}%
13251
+      \ifnum\chimera@subfamily@col@blue>0\relax%
13252
+         \ifnum\chimera@subfamily@col@green>0\relax%
13253
+            \loopcount=\chimera@subfamily@col@blue\relax%
13254
+            \multiply\loopcount by 2\relax \xdef\chimera@subfamily@col@blue{\the\loopcount}%
13255
+            \loopcount=\chimera@subfamily@col@green\relax%
13256
+            \multiply\loopcount by 2\relax \xdef\chimera@subfamily@col@green{\the\loopcount}%
13257
+         \fi%
13258
+      \fi%
13259
+      \loopcount=\chimera@subfamily@col@green\relax%
13260
+      \advance\loopcount by \chimera@subfamily@col@yellow%
13261
+      \xdef\chimera@subfamily@col@green{\the\loopcount}%
13262
+      \loopcount=\chimera@subfamily@col@red\relax%
13263
+      \advance\loopcount by \chimera@subfamily@col@yellow%
13264
+      \xdef\chimera@subfamily@col@red{\the\loopcount}%
13265
+      \loopcount=\chimera@subfamily@col@blue\relax%
13266
+      \ifnum\chimera@subfamily@col@green>\loopcount\relax%
13267
+         \loopcount=\chimera@subfamily@col@green\relax%
13268
+      \else%
13269
+         \ifnum\chimera@subfamily@col@red>\loopcount\relax%
13270
+            \loopcount=\chimera@subfamily@col@red\relax%
13271
+         \fi%
13272
+      \fi%
13273
+      \xdef\max@green{\the\loopcount}%
13274
+      \loopcount=\chimera@subfamily@col@blue%
13275
+      \ifnum\max@green>0\relax%
13276
+         \multiply\loopcount by \max@yellow%
13277
+         \divide\loopcount by \max@green%
13278
+      \fi%
13279
+      \advance\loopcount by \chimera@subfamily@col@white%
13280
+      \multiply\loopcount by \temp@@%
13281
+      \divide\loopcount by \temp@count%
13282
+      \make@HEX%
13283
+      \xdef\nineth@{\seventh@}%
13284
+      \loopcount=\chimera@subfamily@col@green%
13285
+      \ifnum\max@green>0\relax%
13286
+         \multiply\loopcount by \max@yellow%
13287
+         \divide\loopcount by \max@green%
13288
+      \fi%
13289
+      \advance\loopcount by \chimera@subfamily@col@white%
13290
+      \multiply\loopcount by \temp@@%
13291
+      \divide\loopcount by \temp@count%
13292
+      \make@HEX%
13293
+      \xdef\nineth@{\seventh@\nineth@}%
13294
+      \loopcount=\chimera@subfamily@col@red%
13295
+      \ifnum\max@green>0\relax%
13296
+         \multiply\loopcount by \max@yellow%
13297
+         \divide\loopcount by \max@green%
13298
+      \fi%
13299
+      \advance\loopcount by \chimera@subfamily@col@white%
13300
+      \multiply\loopcount by \temp@@%
13301
+      \divide\loopcount by \temp@count%
13302
+      \make@HEX%
13303
+      \xdef\nineth@{\seventh@\nineth@}%
13304
+                     \ifx\chimera@labelOne@set\n@%
13305
+                        \xdef\chimera@labelOne@set{y}%
13306
+                        \xdef\chimera@label@subfamily{.\chimera@label@subfamily}%
13307
+                     \fi%
13308
+      \immediate\write\exp@rt@chimerafile{setattr a radius \temp@ \unexpanded{} #0:\chimera@res@num\chimerach@in @ca}%
13309
+      \immediate\write\exp@rt@chimerafile{setattr a color #\nineth@ \unexpanded{} #0:\chimera@res@num\chimerach@in @ca}%
13310
+      \immediate\write\exp@rt@chimerafile{setattr a name '|| \chimera@label@subfamily' #0:\chimera@res@num\chimerach@in @ca}%
13311
+      \ifshow@sublogo
13312
+         \ifnum\temp@@count>0 \else\temp@@count=1\fi%
13313
+         \loopcount=\temp@@count%
13314
+         \xdef\fourth@{\the\loopcount @}%
13315
+         \ifnum\loopcount>9999 \expandafter\decimal@A\fourth@ \else%
13316
+         \ifnum\loopcount>999  \expandafter\decimal@B\fourth@ \else%
13317
+         \ifnum\loopcount>99   \expandafter\decimal@C\fourth@ \else%
13318
+         \ifnum\loopcount>9    \expandafter\decimal@D\fourth@ \else%
13319
+                               \expandafter\decimal@E\fourth@%
13320
+         \fi\fi\fi\fi%
13321
+         \loopcount=-\chimera@remaining@col@red\relax%
13322
+         \xdef\chimera@remaining@col@red{\the\loopcount}%
13323
+         \loopcount=-\chimera@remaining@col@yellow\relax%
13324
+         \xdef\chimera@remaining@col@yellow{\the\loopcount}%
13325
+         \loopcount=-\chimera@remaining@col@blue\relax%
13326
+         \xdef\chimera@remaining@col@blue{\the\loopcount}%
13327
+         \loopcount=-\chimera@remaining@col@white\relax%
13328
+         \xdef\chimera@remaining@col@white{\the\loopcount}%
13329
+         \loopcount=-\chimera@remaining@col@black%
13330
+         \multiply\loopcount by 65535\relax%
13331
+         \divide\loopcount by \temp@count%
13332
+         \xdef\chimera@remaining@col@black{\the\loopcount}%
13333
+         \loopcount=65535\relax%
13334
+         \advance\loopcount by -\chimera@remaining@col@black%
13335
+         \xdef\temp@@{\the\loopcount}%
13336
+         \loopcount=\chimera@remaining@col@blue\relax%
13337
+         \ifnum\chimera@remaining@col@yellow>\loopcount\relax%
13338
+            \loopcount=\chimera@remaining@col@yellow\relax%
13339
+         \else%
13340
+            \ifnum\chimera@remaining@col@red>\loopcount\relax%
13341
+               \loopcount=\chimera@remaining@col@red\relax%
13342
+            \fi%
13343
+         \fi%
13344
+         \xdef\max@yellow{\the\loopcount}%
13345
+         \ifnum\chimera@remaining@col@blue<\chimera@remaining@col@yellow\relax%
13346
+            \xdef\chimera@remaining@col@green{\chimera@remaining@col@blue}%
13347
+         \else%
13348
+            \xdef\chimera@remaining@col@green{\chimera@remaining@col@yellow}%
13349
+         \fi%
13350
+         \loopcount=\chimera@remaining@col@yellow\relax%
13351
+         \advance\loopcount by -\chimera@remaining@col@green%
13352
+         \xdef\chimera@remaining@col@yellow{\the\loopcount}%
13353
+         \loopcount=\chimera@remaining@col@blue\relax%
13354
+         \advance\loopcount by -\chimera@remaining@col@green%
13355
+         \xdef\chimera@remaining@col@blue{\the\loopcount}%
13356
+         \ifnum\chimera@remaining@col@blue>0\relax%
13357
+            \ifnum\chimera@remaining@col@green>0\relax%
13358
+               \loopcount=\chimera@remaining@col@blue\relax%
13359
+               \multiply\loopcount by 2\relax \xdef\chimera@remaining@col@blue{\the\loopcount}%
13360
+               \loopcount=\chimera@remaining@col@green\relax%
13361
+               \multiply\loopcount by 2\relax \xdef\chimera@remaining@col@green{\the\loopcount}%
13362
+            \fi%
13363
+         \fi%
13364
+         \loopcount=\chimera@remaining@col@green\relax%
13365
+         \advance\loopcount by \chimera@remaining@col@yellow%
13366
+         \xdef\chimera@remaining@col@green{\the\loopcount}%
13367
+         \loopcount=\chimera@remaining@col@red\relax%
13368
+         \advance\loopcount by \chimera@remaining@col@yellow%
13369
+         \xdef\chimera@remaining@col@red{\the\loopcount}%
13370
+         \loopcount=\chimera@remaining@col@blue\relax%
13371
+         \ifnum\chimera@remaining@col@green>\loopcount\relax%
13372
+            \loopcount=\chimera@remaining@col@green\relax%
13373
+         \else%
13374
+            \ifnum\chimera@remaining@col@red>\loopcount\relax%
13375
+               \loopcount=\chimera@remaining@col@red\relax%
13376
+            \fi%
13377
+         \fi%
13378
+         \xdef\max@green{\the\loopcount}%
13379
+         \loopcount=\chimera@remaining@col@blue%
13380
+         \ifnum\max@green>0\relax%
13381
+            \multiply\loopcount by \max@yellow%
13382
+            \divide\loopcount by \max@green%
13383
+         \fi%
13384
+         \advance\loopcount by \chimera@remaining@col@white%
13385
+         \multiply\loopcount by \temp@@%
13386
+         \divide\loopcount by \temp@count%
13387
+         \make@HEX%
13388
+         \xdef\nineth@{\seventh@}%
13389
+         \loopcount=\chimera@remaining@col@green%
13390
+         \ifnum\max@green>0\relax%
13391
+            \multiply\loopcount by \max@yellow%
13392
+            \divide\loopcount by \max@green%
13393
+         \fi%
13394
+         \advance\loopcount by \chimera@remaining@col@white%
13395
+         \multiply\loopcount by \temp@@%
13396
+         \divide\loopcount by \temp@count%
13397
+         \make@HEX%
13398
+         \xdef\nineth@{\seventh@\nineth@}%
13399
+         \loopcount=\chimera@remaining@col@red%
13400
+         \ifnum\max@green>0\relax%
13401
+            \multiply\loopcount by \max@yellow%
13402
+            \divide\loopcount by \max@green%
13403
+         \fi%
13404
+         \advance\loopcount by \chimera@remaining@col@white%
13405
+         \multiply\loopcount by \temp@@%
13406
+         \divide\loopcount by \temp@count%
13407
+         \make@HEX%
13408
+         \xdef\nineth@{\seventh@\nineth@}%
13409
+                     \ifx\chimera@label@remainingOne@set\n@%
13410
+                        \xdef\chimera@label@remainingOne@set{y}%
13411
+                        \xdef\chimera@label@remaining{.\chimera@label@remaining}%
13412
+                     \fi%
13413
+         \immediate\write\exp@rt@chimerafile{setattr a radius \temp@ \unexpanded{} #1:\chimera@res@num\chimerach@in @ca}%
13414
+         \immediate\write\exp@rt@chimerafile{setattr a color #\nineth@ \unexpanded{} #1:\chimera@res@num\chimerach@in @ca}%
13415
+         \immediate\write\exp@rt@chimerafile{setattr a name '|| \chimera@label@remaining' #1:\chimera@res@num\chimerach@in @ca}%
13416
+      \fi%
13417
+}
13418
+\catcode`\"=12 \catcode`\#=6 \catcode`\~=13
13419
+\def\get@chimera@res@num#1,#2@{\xdef\chimera@res@num{#1}\xdef\chimera@stack{#2}}
13420
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
13421
+%%%%                     Chimera export routines   end                %%%%
13422
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
12734 13423
 \def\next@logo#1:#2,#3@{%
12735 13424
    \xdef\first@{#1}\xdef\second@{#2}\xdef\last@{#3}%
12736 13425
    \ifx\first@\ampers@nd%
13426
+      \ifx\exp@rt@chimera\y@%
13427
+        \xdef\chimera@stack{\chimera@stack @}%
13428
+        \expandafter\get@chimera@res@num\chimera@stack%
13429
+        \ifx\chimera@res@num\ampers@nd%
13430
+        \else%
13431
+            \write@chimera@data%
13432
+        \fi%
13433
+        \xdef\chimera@label@subfamily{}%
13434
+        \xdef\chimera@label@remaining{}%
13435
+        \xdef\chimera@subfamily@col@red{0}%
13436
+        \xdef\chimera@subfamily@col@blue{0}%
13437
+        \xdef\chimera@subfamily@col@yellow{0}%
13438
+        \xdef\chimera@subfamily@col@black{0}%
13439
+        \xdef\chimera@subfamily@col@white{0}%
13440
+        \xdef\chimera@remaining@col@red{0}%
13441
+        \xdef\chimera@remaining@col@blue{0}%
13442
+        \xdef\chimera@remaining@col@yellow{0}%
13443
+        \xdef\chimera@remaining@col@black{0}%
13444
+        \xdef\chimera@remaining@col@white{0}%
13445
+        \xdef\chimera@labelOne@set{n}%
13446
+        \xdef\chimera@labelTwo@set{n}%
13447
+        \xdef\chimera@labelThree@set{n}%
13448
+        \xdef\chimera@label@remainingOne@set{n}%
13449
+        \xdef\chimera@label@remainingTwo@set{n}%
13450
+        \xdef\chimera@label@remainingThree@set{n}%
13451
+      \fi%
12737 13452
      \ifx\clear@logo\n@%
12738 13453
      \ifx\hide@sig\n@%
12739 13454
       \expandafter\firstchar@get\sublogo@sig%
... ...
@@ -12755,12 +13470,10 @@
12755 13470
      \fi%
12756 13471
      \fi%
12757 13472
      \temp@count=0%
13473
+     \temp@@count=0%
12758 13474
      \kern\box@width%
12759 13475
      \advance\outerloopcount by 1 %
12760 13476
    \else%
12761
-    \ifnum#2=1%
12762
-      \temp@count=0%
12763
-    \else%
12764 13477
       \if\seq@type N%
12765 13478
          \loopcount=\second@%
12766 13479
          \multiply\loopcount by 2%
... ...
@@ -12796,7 +13509,7 @@
12796 13509
       \fi\fi\fi\fi%
12797 13510
       \xdef\third@{\fl@g\temp@}%
12798 13511
       \ifnum\temp@count<0 %
12799
-         \ifnum\second@<0 \else\temp@count=0 \fi%
13512
+         \ifnum\second@<0 \else\temp@@count=-\temp@count\relax\temp@count=0 \fi%
12800 13513
       \fi%
12801 13514
       \ifnum\temp@count>0 %
12802 13515
          \loopcount=\temp@count \xdef\fl@g{}%
... ...
@@ -12823,7 +13536,64 @@
12823 13536
          \kern-\box@width%
12824 13537
       \fi%
12825 13538
       \advance\temp@count by \second@%
12826
-    \fi%
13539
+      \xdef\temp@{\the\temp@count}%
13540
+      \ifx\exp@rt@chimera\y@%
13541
+         \xdef\temp@@{\csname chimera@col@\first@\endcsname}%
13542
+         \ifnum\second@<0 %
13543
+            \xdef\temp@@@{\csname chimera@remaining@col@\temp@@\endcsname}%
13544
+            \temp@count=\temp@@@%
13545
+            \advance\temp@count by \second@%
13546
+            \expandafter\xdef\csname chimera@remaining@col@\temp@@\endcsname{\the\temp@count}%
13547
+            \ifnum\second@<\label@threshold@lowerremainingIOOO%
13548
+                  \ifnum\second@<-999%
13549
+                     \ifx\chimera@label@remainingOne@set\n@%
13550
+                        \xdef\chimera@label@remainingOne@set{y}%
13551
+                        \xdef\chimera@label@remaining{.\chimera@label@remaining}%
13552
+                     \fi%
13553
+                  \fi%
13554
+                  \ifnum\second@<-1999%
13555
+                     \ifx\chimera@label@remainingTwo@set\n@%
13556
+                        \xdef\chimera@label@remainingTwo@set{y}%
13557
+                        \xdef\chimera@label@remaining{:\chimera@label@remaining}%
13558
+                     \fi%
13559
+                  \fi%
13560
+                  \ifnum\second@<-2999%
13561
+                     \ifx\chimera@label@remainingThree@set\n@%
13562
+                        \xdef\chimera@label@remainingThree@set{y}%
13563
+                        \xdef\chimera@label@remaining{>\chimera@label@remaining}%
13564
+                     \fi%
13565
+                  \fi%
13566
+                  \xdef\chimera@label@remaining{\first@\chimera@label@remaining}%
13567
+            \fi%
13568
+         \else%
13569
+            \xdef\temp@@@{\csname chimera@subfamily@col@\temp@@\endcsname}%
13570
+            \temp@count=\temp@@@%
13571
+            \advance\temp@count by \second@%
13572
+            \expandafter\xdef\csname chimera@subfamily@col@\temp@@\endcsname{\the\temp@count}%
13573
+            \ifnum\second@>\label@threshold@lowerIOOO%
13574
+                  \ifnum\second@>999%
13575
+                     \ifx\chimera@labelOne@set\n@%
13576
+                        \xdef\chimera@labelOne@set{y}%
13577
+                        \xdef\chimera@label@subfamily{.\chimera@label@subfamily}%
13578
+                     \fi%
13579
+                  \fi%
13580
+                  \ifnum\second@>1999%
13581
+                     \ifx\chimera@labelTwo@set\n@%
13582
+                        \xdef\chimera@labelTwo@set{y}%
13583
+                        \xdef\chimera@label@subfamily{:\chimera@label@subfamily}%
13584
+                     \fi%
13585
+                  \fi%
13586
+                  \ifnum\second@>2999%
13587
+                     \ifx\chimera@labelThree@set\n@%
13588
+                        \xdef\chimera@labelThree@set{y}%
13589
+                        \xdef\chimera@label@subfamily{>\chimera@label@subfamily}%
13590
+                     \fi%
13591
+                  \fi%
13592
+                  \xdef\chimera@label@subfamily{\first@\chimera@label@subfamily}%
13593
+            \fi%
13594
+         \fi%
13595
+      \fi%
13596
+      \temp@count=\temp@%
12827 13597
    \fi%
12828 13598
    \xdef\temp@{\last@.}%
12829 13599
    \ifx\temp@\d@t%
... ...
@@ -13125,10 +13895,23 @@
13125 13895
    \xdef\featureposttttop{1} \xdef\featureposbbbbottom{1}%
13126 13896
    \findc@nsensus%
13127 13897
    \noindent%
13898
+   \setlength{\bar@length}{0pt}%
13899
+   \xdef\fe@turep@s{top}%
13128 13900
    \ifnum\feature@ttttop=1
13901
+      \advance\bar@length by \feature@tttop\baselineskip%
13902
+      \advance\bar@length by \feature@ttop\baselineskip%
13903
+      \advance\bar@length by \feature@top\baselineskip%
13904
+      \multiply\bar@length by 2%
13905
+      \advance\bar@length by \tttt@sp@ce%
13906
+      \advance\bar@length by \ttt@sp@ce%
13907
+      \advance\bar@length by \tt@sp@ce%
13129 13908
       \ifnum\featureonttttop=0 \xdef\feature@ttttop{0} \fi
13130 13909
       \xdef\bottop@{ttttop}%
13910
+      \xdef\shift@feature{n}%
13131 13911
       \put@feature%
13912
+      \advance\bar@length by -\baselineskip%
13913
+      \ifx\shift@feature\y@ \vspace{-\bar@length}\fi%
13914
+      \setlength{\bar@length}{0pt}%
13132 13915
       \vspace{\tttt@sp@ce}%
13133 13916
       \vspace{-\baselineskip}%
13134 13917
       \newline\hbox{}%
... ...
@@ -13136,9 +13919,18 @@
13136 13919
       \iffix@\ifttttopfeature \vspace{\tttt@sp@ce}\newline\hbox{}\newline\hbox{}\fi\fi
13137 13920
    \fi
13138 13921
    \ifnum\feature@tttop=1
13922
+      \advance\bar@length by \feature@ttop\baselineskip%
13923
+      \advance\bar@length by \feature@top\baselineskip%
13924
+      \multiply\bar@length by 2%
13925
+      \advance\bar@length by \ttt@sp@ce%
13926
+      \advance\bar@length by \tt@sp@ce%
13139 13927
       \ifnum\featureontttop=0 \xdef\feature@tttop{0} \fi
13140 13928
       \xdef\bottop@{tttop}%
13929
+      \xdef\shift@feature{n}%
13141 13930
       \put@feature%
13931
+      \advance\bar@length by -\baselineskip%
13932
+      \ifx\shift@feature\y@ \vspace{-\bar@length}\fi%
13933
+      \setlength{\bar@length}{0pt}%
13142 13934
       \vspace{\ttt@sp@ce}%
13143 13935
       \vspace{-\baselineskip}%
13144 13936
       \newline\hbox{}%
... ...
@@ -13146,9 +13938,16 @@
13146 13938
       \iffix@\iftttopfeature \vspace{\ttt@sp@ce}\newline\hbox{}\newline\hbox{}\fi\fi
13147 13939
    \fi
13148 13940
    \ifnum\feature@ttop=1
13941
+      \advance\bar@length by \feature@top\baselineskip%
13942
+      \multiply\bar@length by 2%
13943
+      \advance\bar@length by \tt@sp@ce\message{tt\the\bar@length tt}%
13149 13944
       \ifnum\featureonttop=0 \xdef\feature@ttop{0} \fi
13150 13945
       \xdef\bottop@{ttop}%
13946
+      \xdef\shift@feature{n}%
13151 13947
       \put@feature%
13948
+      \advance\bar@length by -\baselineskip%
13949
+      \ifx\shift@feature\y@ \vspace{-\bar@length}\fi%
13950
+      \setlength{\bar@length}{0pt}%
13152 13951
       \vspace{\tt@sp@ce}%
13153 13952
       \vspace{-\baselineskip}%
13154 13953
       \newline\hbox{}%
... ...
@@ -13264,6 +14063,9 @@
13264 14063
          \ifnum\ruler@rot=0 \vspace{0.25\baselineskip}\fi%
13265 14064
       \fi%
13266 14065
    \fi%
14066
+   \xdef\fe@turep@s{bottom}%
14067
+   \setlength{\bar@length}{0pt}%
14068
+   \xdef\b@feature@count{0}
13267 14069
    \ifnum\feature@bottom=1 %
13268 14070
       \ifnum\featureonbottom=0 \xdef\feature@bottom{0}\fi%
13269 14071
       \xdef\bottop@{bottom}%
... ...
@@ -13273,6 +14075,9 @@
13273 14075
          \vspace{\b@r@stretch\box@height}%
13274 14076
       \fi%
13275 14077
       \put@feature%
14078
+      \temp@@count=\b@feature@count%
14079
+      \advance\temp@@count by 1%
14080
+      \xdef\b@feature@count{\the\temp@@count}%
13276 14081
    \else
13277 14082
       \iffix@
13278 14083
       \if\bottom@stretch y%
... ...
@@ -13285,14 +14090,24 @@
13285 14090
       \fi%
13286 14091
    \fi%
13287 14092
    \ifnum\feature@bbottom=1 %
14093
+      \advance\bar@length by \b@feature@count \baselineskip%
14094
+      \multiply\bar@length by \b@r@stretch%
14095
+      \multiply\bar@length by 2%
14096
+      \advance\bar@length by \bb@sp@ce\message{bb\the\bar@length bb}%
13288 14097
       \ifnum\featureonbbottom=0 \xdef\feature@bbottom{0}\fi%
13289 14098
       \xdef\bottop@{bbottom}%
13290 14099
       \vspace{\bb@sp@ce}%
13291 14100
       \if\bbottom@stretch y%
14101
+         \advance\bar@length by -\box@height%
14102
+         \advance\bar@length by \b@r@stretch\box@height%
13292 14103
          \vspace{-\box@height}%
13293 14104
          \vspace{\b@r@stretch\box@height}%
13294 14105
       \fi%
14106
+      \setlength{\bar@length}{0pt}%
13295 14107
       \put@feature%
14108
+      \temp@@count=\b@feature@count%
14109
+      \advance\temp@@count by 1%
14110
+      \xdef\b@feature@count{\the\temp@@count}%
13296 14111
    \else
13297 14112
       \iffix@
13298 14113
       \if\bbottom@stretch y%
... ...
@@ -13305,6 +14120,10 @@
13305 14120
       \fi
13306 14121
    \fi
13307 14122
    \ifnum\feature@bbbottom=1 %
14123
+      \advance\bar@length by \b@feature@count\baselineskip%
14124
+      \multiply\bar@length by \b@r@stretch%
14125
+      \multiply\bar@length by 2%
14126
+      \advance\bar@length by \bbb@sp@ce\message{bbb\the\bar@length bbb}%
13308 14127
       \ifnum\featureonbbbottom=0 \xdef\feature@bbbottom{0}\fi%
13309 14128
       \xdef\bottop@{bbbottom}%
13310 14129
       \vspace{\bbb@sp@ce}%
... ...
@@ -13313,6 +14132,9 @@
13313 14132
          \vspace{\b@r@stretch\box@height}%
13314 14133
       \fi%
13315 14134
       \put@feature%
14135
+      \temp@@count=\b@feature@count%
14136
+      \advance\temp@@count by 1%
14137
+      \xdef\b@feature@count{\the\temp@@count}%
13316 14138
    \else
13317 14139
       \iffix@
13318 14140
       \if\bbbottom@stretch y%
... ...
@@ -13325,6 +14147,10 @@
13325 14147
       \fi
13326 14148
    \fi
13327 14149
    \ifnum\feature@bbbbottom=1 %
14150
+      \advance\bar@length by \b@feature@count\baselineskip%
14151
+      \multiply\bar@length by \b@r@stretch%
14152
+      \multiply\bar@length by 2%
14153
+      \advance\bar@length by \bbbb@sp@ce\message{bbbb\the\bar@length bbbb}%
13328 14154
       \ifnum\featureonbbbbottom=0 \xdef\feature@bbbbottom{0}\fi%
13329 14155
       \xdef\bottop@{bbbbottom}%
13330 14156
       \vspace{\bbbb@sp@ce}%
... ...
@@ -14030,6 +14856,7 @@
14030 14856
     \fi
14031 14857
     \ifshow@sublogo \closein\sublogofile \fi
14032 14858
     \ifx\exp@rt\y@ \closeout\exp@rtfile \fi
14859
+    \ifx\exp@rt@chimera\y@ \closeout\exp@rt@chimerafile \fi%
14033 14860
     \closein\alignfile
14034 14861
     \message{)}
14035 14862
 }
... ...
@@ -14181,8 +15008,6 @@
14181 15008
     \ifnum\loopcount<\seq@count \repeat
14182 15009
     \xdef\seq@order{\seq@order,@}
14183 15010
  \killseq@count=\seq@count
14184
- \seq@percent=100
14185
- \ifnum\seq@count>0 \divide\seq@percent by \seq@count \fi
14186 15011
  \fi
14187 15012
  \fi
14188 15013
 }
... ...
@@ -14450,6 +15275,18 @@
14450 15275
            \caption[\c@pshort]{\c@p}
14451 15276
          \fi
14452 15277
       \fi
15278
+      \loopcount = \thresh@ld \multiply\loopcount by \seq@count \divide\loopcount by 100
15279
+      \xdef\thresh@ld@{\the\loopcount}
15280
+      \loopcount = \all@thresh@ld \multiply\loopcount by \seq@count \divide\loopcount by 100
15281
+      \xdef\all@thresh@ld@{\the\loopcount}
15282
+      \if\exp@rt@chimera\y@%
15283
+         \ifshow@logo%
15284
+             \init@chimera@file%
15285
+         \else%
15286
+         \ifshow@sublogo%
15287
+             \init@chimera@file%
15288
+         \fi\fi%
15289
+      \fi%
14453 15290
       \bgroup
14454 15291
          \ifx\out@put\y@\bigskip\fi
14455 15292
          \iffuncmode \show@consfalse \fi
... ...
@@ -14607,6 +15444,32 @@
14607 15444
 \expandafter\xdef\csname group@num1\endcsname{0}
14608 15445
 \expandafter\xdef\csname group@num2\endcsname{0}
14609 15446
 \xdef\exp@rt@num{0}       \xdef\exp@rt{n}
15447
+\xdef\exp@rt@chimera@num{1}   \xdef\exp@rt@chimera{n} \xdef\chimera@stack{}
15448
+\xdef\chimerab@llSc@le{1.0}
15449
+\memelabelcutoff{0.1}
15450
+\xdef\chimera@labelOne@set{n}
15451
+\xdef\chimera@labelTwo@set{n}
15452
+\xdef\chimera@labelThree@set{n}
15453
+\xdef\chimera@labelOne@remaining@set{n}
15454
+\xdef\chimera@labelTwo@remaining@set{n}
15455
+\xdef\chimera@labelThree@remaining@set{n}
15456
+\xdef\chimera@xdist@nce{0} \xdef\chimera@ydist@nce{40} \xdef\chimera@zdist@nce{0}
15457
+\xdef\chimerach@in{} \xdef\chimera@seqnum{0}
15458
+\xdef\chimera@label@subfamily{} \xdef\chimera@label@remaining{}
15459
+\memeStandardcolors
15460
+\xdef\chimera@subfamily@col@red{0}%
15461
+\xdef\chimera@subfamily@col@blue{0}%
15462
+\xdef\chimera@subfamily@col@yellow{0}%
15463
+\xdef\chimera@subfamily@col@black{0}%
15464
+\xdef\chimera@subfamily@col@white{0}%
15465
+\xdef\chimera@subfamily@col@none{0}%
15466
+\xdef\chimera@remaining@col@red{0}%
15467
+\xdef\chimera@remaining@col@blue{0}%
15468
+\xdef\chimera@remaining@col@yellow{0}%
15469
+\xdef\chimera@remaining@col@black{0}%
15470
+\xdef\chimera@remaining@col@white{0}%
15471
+\xdef\chimera@remaining@col@none{0}%
15472
+\xdef\echo@filename{}
14610 15473
 \xdef\divref@{0}
14611 15474
 \xdef\all@thresh@ld{100}  \all@shadefalse
14612 15475
 \hidefeaturenames         \hidefeaturestylenames