| ... | ... |
@@ -1,8 +1,8 @@ |
| 1 | 1 |
Package: msa |
| 2 | 2 |
Type: Package |
| 3 | 3 |
Title: Multiple Sequence Alignment |
| 4 |
-Version: 1.23.0 |
|
| 5 |
-Date: 2020-08-12 |
|
| 4 |
+Version: 1.23.1 |
|
| 5 |
+Date: 2021-04-29 |
|
| 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 +1,18 @@ |
| 1 | 1 |
Change history of package msa: |
| 2 | 2 |
============================== |
| 3 | 3 |
|
| 4 |
+Version 1.24.0: |
|
| 5 |
+- release as part of Bioconductor 3.13 |
|
| 6 |
+ |
|
| 7 |
+Version 1.23.1: |
|
| 8 |
+- updated texshade.sty to newest version |
|
| 9 |
+ |
|
| 10 |
+Version 1.23.0: |
|
| 11 |
+- new branch for Bioconductor 3.13 devel |
|
| 12 |
+ |
|
| 13 |
+Version 1.22.0: |
|
| 14 |
+- release as part of Bioconductor 3.12 |
|
| 15 |
+ |
|
| 4 | 16 |
Version 1.21.1: |
| 5 | 17 |
- changed msaClustalW() examples to run smoothly on Windows with R 4.0.x |
| 6 | 18 |
- added warning to msaClustalW() help page regarding cluster="upgma" on |
| 7 | 19 |
new file mode 100644 |
| ... | ... |
@@ -0,0 +1,19 @@ |
| 1 |
+ |
|
| 2 |
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
|
| 3 |
+%%%%% %%%%% |
|
| 4 |
+%%%%% Ciliate macronuclear genetic code definitions %%%%% |
|
| 5 |
+%%%%% %%%%% |
|
| 6 |
+%%%%% Only exchanges compared to the standard code must be defined. %%%%% |
|
| 7 |
+%%%%% %%%%% |
|
| 8 |
+%%%%% (The last codon of the list is used for backtranslations %%%%% |
|
| 9 |
+%%%%% from protein to DNA sequences---therefore the wobbles) %%%%% |
|
| 10 |
+%%%%% %%%%% |
|
| 11 |
+%%%%% %%%%% |
|
| 12 |
+%%%%% Activate these definitions for your alignment by the following %%%%% |
|
| 13 |
+%%%%% command in the texshade environment: %%%%% |
|
| 14 |
+%%%%% %%%%% |
|
| 15 |
+%%%%% \geneticcode{ciliate} %%%%%
|
|
| 16 |
+%%%%% %%%%% |
|
| 17 |
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
|
| 18 |
+ |
|
| 19 |
+\codon{Q}{TAA,TAG,UAA,UAG,YAR}
|
| 0 | 20 |
new file mode 100644 |
| ... | ... |
@@ -0,0 +1,34 @@ |
| 1 |
+ |
|
| 2 |
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
|
| 3 |
+%%%%% %%%%% |
|
| 4 |
+%%%%% Standard genetic code definitions %%%%% |
|
| 5 |
+%%%%% %%%%% |
|
| 6 |
+%%%%% (The last codon of each list is used for backtranslations %%%%% |
|
| 7 |
+%%%%% from protein to DNA sequences---therefore the wobbles) %%%%% |
|
| 8 |
+%%%%% %%%%% |
|
| 9 |
+%%%%% These definitions are default in TeXshade. %%%%% |
|
| 10 |
+%%%%% There is no need to load them. This is an example file only. %%%%% |
|
| 11 |
+%%%%% %%%%% |
|
| 12 |
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
|
| 13 |
+ |
|
| 14 |
+\codon{A}{GCA,GCG,GCC,GCT,GCU,GCN}
|
|
| 15 |
+\codon{C}{TGC,TGT,UGC,UGU,TGY}
|
|
| 16 |
+\codon{D}{GAC,GAT,GAU,GAY}
|
|
| 17 |
+\codon{E}{GAA,GAG,GAR}
|
|
| 18 |
+\codon{F}{TTC,TTT,UUC,UUU,TTY}
|
|
| 19 |
+\codon{G}{GGA,GGG,GGC,GGT,GGU,GGN}
|
|
| 20 |
+\codon{H}{CAC,CAT,CAY}
|
|
| 21 |
+\codon{I}{ATA,ATC,ATT,AUA,AUC,AUU,ATH}
|
|
| 22 |
+\codon{K}{AAA,AAG,AAG,AAR}
|
|
| 23 |
+\codon{L}{CTA,CTG,CTC,CTT,TTA,TTG,CUG,CUG,CUC,CUU,UUA,UUG,YTN}
|
|
| 24 |
+\codon{M}{ATG,AUG,ATG}
|
|
| 25 |
+\codon{N}{AAC,AAT,AAU,AAY}
|
|
| 26 |
+\codon{P}{CCA,CCG,CCC,CCT,CCU,CCN}
|
|
| 27 |
+\codon{Q}{CAA,CAG,CAR}
|
|
| 28 |
+\codon{R}{AGA,AGG,CGA,CGG,CGC,CGT,CGU,MGN}
|
|
| 29 |
+\codon{S}{TCT,TCC,TCG,TCA,AGT,AGC,UCU,UCC,UCG,UCA,AGU,WSN}
|
|
| 30 |
+\codon{T}{ACT,ACC,ACG,ACA,ACU,ACN}
|
|
| 31 |
+\codon{V}{GTA,GTG,GTC,GTT,GUA,GUG,GUC,GUU,GTN}
|
|
| 32 |
+\codon{W}{TGG,UGG,TGG}
|
|
| 33 |
+\codon{Y}{TAC,TAT,UAC,UAU,TAY}
|
|
| 34 |
+\codon{.}{TAA,TAG,TGA,UAA,UAG,UGA,TRR}
|
| ... | ... |
@@ -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}
|
| 16 |
-\ProvidesPackage{texshade}[2011/05/13 LaTeX TeXshade (v1.24)]
|
|
| 17 |
-\message{Package `texshade', Version 1.24 of 2011/12/01.}
|
|
| 16 |
+\ProvidesPackage{texshade}[2021/04/01 LaTeX TeXshade (v1.26)]
|
|
| 17 |
+\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 |
| ... | ... |
@@ -678,6 +680,16 @@ |
| 678 | 680 |
\xdef\HydroV{37} \xdef\HydroW{28} \xdef\HydroX{N}
|
| 679 | 681 |
\xdef\HydroY{9} \xdef\HydroZ{N}
|
| 680 | 682 |
|
| 683 |
+\xdef\hardnessA{98} \xdef\hardnessB{0} \xdef\hardnessC{37}
|
|
| 684 |
+\xdef\hardnessD{100} \xdef\hardnessE{96} \xdef\hardnessF{48}
|
|
| 685 |
+\xdef\hardnessG{92} \xdef\hardnessH{50} \xdef\hardnessI{98}
|
|
| 686 |
+\xdef\hardnessJ{86} \xdef\hardnessK{73} \xdef\hardnessL{98}
|
|
| 687 |
+\xdef\hardnessM{25} \xdef\hardnessN{86} \xdef\hardnessO{0}
|
|
| 688 |
+\xdef\hardnessP{91} \xdef\hardnessQ{95} \xdef\hardnessR{69}
|
|
| 689 |
+\xdef\hardnessS{94} \xdef\hardnessT{98} \xdef\hardnessU{-34}
|
|
| 690 |
+\xdef\hardnessV{98} \xdef\hardnessW{0} \xdef\hardnessX{0}
|
|
| 691 |
+\xdef\hardnessY{28} \xdef\hardnessZ{0}
|
|
| 692 |
+ |
|
| 681 | 693 |
\xdef\consCB{0} \xdef\consCJ{0} \xdef\consCO{0} \xdef\consCU{0} \xdef\consCX{0} \xdef\consCZ{0}
|
| 682 | 694 |
\expandafter\xdef\csname consC?\endcsname{0}
|
| 683 | 695 |
|
| ... | ... |
@@ -2593,7 +2605,6 @@ |
| 2593 | 2605 |
\expandafter\xdef\csname hide@@@seq\first@\endcsname{kill}
|
| 2594 | 2606 |
\ifnum\first@=\cons@num \xdef\cons@num{0} \fi
|
| 2595 | 2607 |
\advance\killseq@count by -1 |
| 2596 |
- \seq@percent=100 \divide\seq@percent by \killseq@count |
|
| 2597 | 2608 |
\fi |
| 2598 | 2609 |
\fi\fi |
| 2599 | 2610 |
\xdef\first@{\first@@ @}
|
| ... | ... |
@@ -2612,7 +2623,6 @@ |
| 2612 | 2623 |
\expandafter\xdef\csname hide@@@seq\fourth@\endcsname{kill}
|
| 2613 | 2624 |
\ifnum\fourth@=\cons@num \xdef\cons@num{0} \fi
|
| 2614 | 2625 |
\advance\killseq@count by -1 |
| 2615 |
- \seq@percent=100 \divide\seq@percent by \killseq@count |
|
| 2616 | 2626 |
\fi |
| 2617 | 2627 |
\fi\fi |
| 2618 | 2628 |
\killseq@ |
| ... | ... |
@@ -2893,8 +2903,17 @@ |
| 2893 | 2903 |
\funcgroup{Leu, Val, Ile}{LVI}{Green}{White}{upper}{up}
|
| 2894 | 2904 |
\funcgroup{Pro}{P}{Apricot}{White}{upper}{up}
|
| 2895 | 2905 |
\else |
| 2906 |
+ \xdef\second@{hardness}
|
|
| 2907 |
+ \ifx\temp@\second@ |
|
| 2908 |
+ \funcgroup{22-23 eV (ADEGILPQSTV) | 2$\times$ HOMO-LUMO gap}{ADEGILPQSTV}{White}{BlueRed5}{upper}{up}
|
|
| 2909 |
+ \funcgroup{21-22 eV (KN)}{KN}{White}{BlueRed20}{upper}{up}
|
|
| 2910 |
+ \funcgroup{20-21 eV (R)}{R}{Black}{BlueRed40}{upper}{up}
|
|
| 2911 |
+ \funcgroup{19-20 eV (CFH)}{CFH}{Black}{BlueRed60}{upper}{up}
|
|
| 2912 |
+ \funcgroup{18-19 eV (MY)}{MY}{White}{BlueRed80}{upper}{up}
|
|
| 2913 |
+ \funcgroup{17-18 eV (W)}{W}{White}{BlueRed100}{upper}{up}
|
|
| 2914 |
+ \else |
|
| 2896 | 2915 |
\message{<Unknown shading mode - clearing `funcgroups'>}
|
| 2897 |
- \fi\fi\fi\fi\fi\fi\fi |
|
| 2916 |
+ \fi\fi\fi\fi\fi\fi\fi\fi |
|
| 2898 | 2917 |
} |
| 2899 | 2918 |
\def\shadeallresidues{\all@fshadetrue}
|
| 2900 | 2919 |
\def\get@fromstack#1;#2;#3;#4;#5@{%
|
| ... | ... |
@@ -3114,22 +3133,33 @@ |
| 3114 | 3133 |
\expandafter\xdef\csname stack@\bottop@\seq@\endcsname{\tmpstack}
|
| 3115 | 3134 |
} |
| 3116 | 3135 |
\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
|
|
| 3136 |
+ \xdef\first@@{#1}\xdef\second@@{#2}\xdef\third@@{#3}\xdef\fourth@@{#4}
|
|
| 3137 |
+ \ifx\temp@@\y@ |
|
| 3138 |
+ \if\first@@ ` \xdef\first@@{a} \else
|
|
| 3139 |
+ \if\first@@ ' \xdef\first@@{a} \else
|
|
| 3140 |
+ \if\first@@ , \xdef\first@@{b} \else
|
|
| 3141 |
+ \if\first@@ S \xdef\first@@{c} \xdef\second@@{-}
|
|
| 3142 |
+ \fi\fi\fi\fi |
|
| 3143 |
+ \if\third@@ ` \xdef\third@@{a} \else
|
|
| 3144 |
+ \if\third@@ ' \xdef\third@@{a} \else
|
|
| 3145 |
+ \if\third@@ , \xdef\third@@{b} \else
|
|
| 3146 |
+ \if\third@@ S \xdef\third@@{c} \xdef\second@@{-}
|
|
| 3147 |
+ \fi\fi\fi\fi |
|
| 3148 |
+ \xdef\style@{\first@@ -\third@@\fourth@@}
|
|
| 3149 |
+ \fi |
|
| 3150 |
+ \if\first@@ S |
|
| 3151 |
+ \xdef\style@{\first@@ -\third@@\fourth@@}
|
|
| 3121 | 3152 |
\else |
| 3122 | 3153 |
\if\first@@ v |
| 3123 | 3154 |
\if\second@@ = |
| 3124 |
- \else \xdef\style@{\first@@ v\third@@#4} \fi
|
|
| 3155 |
+ \else \xdef\style@{\first@@ v\third@@\fourth@@} \fi
|
|
| 3125 | 3156 |
\else |
| 3126 |
- \if\third@@ v |
|
| 3127 |
- \if\second@@ = |
|
| 3128 |
- \else \xdef\style@{\first@@ v\third@@#4} \fi
|
|
| 3157 |
+ \if\third@@ S |
|
| 3158 |
+ \xdef\style@{\first@@ -\third@@\fourth@@}
|
|
| 3129 | 3159 |
\else |
| 3130 | 3160 |
\if\third@@ v |
| 3131 | 3161 |
\if\second@@ = |
| 3132 |
- \else \xdef\style@{\first@@ v\third@@#4} \fi
|
|
| 3162 |
+ \else \xdef\style@{\first@@ v\third@@\fourth@@} \fi
|
|
| 3133 | 3163 |
\fi\fi\fi\fi |
| 3134 | 3164 |
} |
| 3135 | 3165 |
\def\get@shape#1#2#3{%
|
| ... | ... |
@@ -5894,7 +5924,11 @@ |
| 5894 | 5924 |
\fi |
| 5895 | 5925 |
\xdef\style@{cons[color]:cons[\f@color][0]}
|
| 5896 | 5926 |
\else |
| 5897 |
- \xdef\style@{#4} \expandafter\getarrow@shape\temp@
|
|
| 5927 |
+ \xdef\style@{#4} \xdef\temp@@{n}
|
|
| 5928 |
+ \expandafter\get@firstfill\temp@ |
|
| 5929 |
+ \if\second@@ ^ \xdef\second@@{_} \fi
|
|
| 5930 |
+ \if\second@@ _ \xdef\temp@{\fill@char} \xdef\temp@@{y}\fi
|
|
| 5931 |
+ \expandafter\getarrow@shape\temp@ |
|
| 5898 | 5932 |
\fi |
| 5899 | 5933 |
\fi |
| 5900 | 5934 |
\fi |
| ... | ... |
@@ -6382,7 +6416,17 @@ |
| 6382 | 6416 |
\logocolor{EQ}{RoyalPurple}
|
| 6383 | 6417 |
\logocolor{R}{RedViolet}
|
| 6384 | 6418 |
\logocolor{K}{Black}
|
| 6385 |
- \fi\fi\fi\fi\fi\fi\fi |
|
| 6419 |
+ \else |
|
| 6420 |
+ \xdef\second@{hardness}
|
|
| 6421 |
+ \ifx\first@\second@ |
|
| 6422 |
+ \clearlogocolors |
|
| 6423 |
+ \logocolor{ADEGILPQSTV}{BlueRed5}
|
|
| 6424 |
+ \logocolor{KN}{BlueRed20}
|
|
| 6425 |
+ \logocolor{R}{BlueRed40}
|
|
| 6426 |
+ \logocolor{CFH}{BlueRed60}
|
|
| 6427 |
+ \logocolor{MY}{BlueRed80}
|
|
| 6428 |
+ \logocolor{W}{BlueRed100}
|
|
| 6429 |
+ \fi\fi\fi\fi\fi\fi\fi\fi |
|
| 6386 | 6430 |
} |
| 6387 | 6431 |
\newcommand\findsubfamily[2][n]{%
|
| 6388 | 6432 |
\xdef\first@{#1}
|
| ... | ... |
@@ -7793,9 +7837,8 @@ |
| 7793 | 7837 |
\advance\pos@sum by 1 \fi |
| 7794 | 7838 |
\ifnum\innerloopcount<\seq@count \repeat |
| 7795 | 7839 |
|
| 7796 |
- \multiply\pos@sum by \seq@percent |
|
| 7797 | 7840 |
\expandafter\xdef\csname pos\the\loopcount\endcsname{\the\pos@sum}
|
| 7798 |
- \expandafter\ifnum\csname pos\the\loopcount\endcsname<\thresh@ld |
|
| 7841 |
+ \expandafter\ifnum\csname pos\the\loopcount\endcsname<\thresh@ld@ |
|
| 7799 | 7842 |
\else |
| 7800 | 7843 |
\expandafter\ifnum\csname pos\the\loopcount\endcsname>\m@x |
| 7801 | 7844 |
\xdef\m@x{\csname pos\the\loopcount\endcsname}
|
| ... | ... |
@@ -7843,13 +7886,12 @@ |
| 7843 | 7886 |
\expandafter\ifnum\csname pos\the\loopcount\endcsname=\seq@count |
| 7844 | 7887 |
\xdef\cons@seq{\the\loopcount} \xdef\match@case{2} \loopcount=1
|
| 7845 | 7888 |
\else |
| 7846 |
- \multiply\pos@sum by \seq@percent |
|
| 7847 | 7889 |
\expandafter\xdef\csname pos\the\loopcount\endcsname{\the\pos@sum}
|
| 7848 |
- \expandafter\ifnum\csname pos\the\loopcount\endcsname<\thresh@ld |
|
| 7890 |
+ \expandafter\ifnum\csname pos\the\loopcount\endcsname<\thresh@ld@ |
|
| 7849 | 7891 |
\else |
| 7850 | 7892 |
\expandafter\ifnum\csname pos\the\loopcount\endcsname>\m@x |
| 7851 | 7893 |
\xdef\m@x{\csname pos\the\loopcount\endcsname}
|
| 7852 |
- \expandafter\ifnum\csname pos\the\loopcount\endcsname<\all@thresh@ld |
|
| 7894 |
+ \expandafter\ifnum\csname pos\the\loopcount\endcsname<\all@thresh@ld@ |
|
| 7853 | 7895 |
\xdef\cons@seq{\the\loopcount} \xdef\match@case{1}
|
| 7854 | 7896 |
\else |
| 7855 | 7897 |
\xdef\cons@seq{\the\loopcount} \xdef\match@case{2}
|
| ... | ... |
@@ -10431,6 +10473,7 @@ |
| 10431 | 10473 |
\fi |
| 10432 | 10474 |
\fi |
| 10433 | 10475 |
\expandafter\xdef\csname res@count\the\loopcount\endcsname{\the\res@count}
|
| 10476 |
+ \ifnum\loopcount=\chimera@seqnum \xdef\chimera@stack{\chimera@stack \the\res@count,} \fi
|
|
| 10434 | 10477 |
\ifnum\loopcount=\exp@rt@num \xdef\sixth@{\the\res@count}\xdef\seventh@{y}\fi
|
| 10435 | 10478 |
\ifnum\loopcount=\rule@num\relax |
| 10436 | 10479 |
\expandafter\ifnum\csname res@count\rule@num\endcsname>\rule@tens |
| ... | ... |
@@ -10574,6 +10617,7 @@ |
| 10574 | 10617 |
\the\innerloopcount} |
| 10575 | 10618 |
\else |
| 10576 | 10619 |
\ifnum\loopcount=\rule@num \xdef\ruler@{\ruler@ -} \fi
|
| 10620 |
+ \ifnum\loopcount=\chimera@seqnum \xdef\chimera@stack{\chimera@stack &,} \fi
|
|
| 10577 | 10621 |
\ifx\collect@valtop\yes |
| 10578 | 10622 |
\ifnum\v@lseqtop=\loopcount |
| 10579 | 10623 |
\xdef\v@ltop{\v@ltop,N}
|
| ... | ... |
@@ -11373,7 +11417,7 @@ |
| 11373 | 11417 |
\textcolor{\legend@fg}{%
|
| 11374 | 11418 |
\ifgerm@n\kern2ex\legend@size{nicht konserviert}%
|
| 11375 | 11419 |
\else\ifsp@nish\kern2ex\legend@size{no conservado}%
|
| 11376 |
- \else\kern2ex\legend@size{non conserved}\fi\fi}
|
|
| 11420 |
+ \else\kern2ex\legend@size{non-conserved}\fi\fi}
|
|
| 11377 | 11421 |
\newline\hbox{}\noindent%
|
| 11378 | 11422 |
\ifsimmode% |
| 11379 | 11423 |
\ifnames@\ifnames@right\else\hbox to \name@width{\hss}\fi\fi
|
| ... | ... |
@@ -11862,6 +11906,7 @@ |
| 11862 | 11906 |
\def\get@tripletfill#1#2#3#4&{%
|
| 11863 | 11907 |
\multiply\temp@count by -1% |
| 11864 | 11908 |
\def\second@@{#1}\def\second@@@{#2}\def\second@@@@{#3}\def\fill@char{#4&}}
|
| 11909 |
+ |
|
| 11865 | 11910 |
\def\putfeature@style#1{%
|
| 11866 | 11911 |
\residues@size% |
| 11867 | 11912 |
\setbox1=\hbox{\ensuremath{\overrightarrow{\hbox{}}}}%
|
| ... | ... |
@@ -11967,6 +12012,7 @@ |
| 11967 | 12012 |
\fontseries{\featurestyles@series}%
|
| 11968 | 12013 |
\fontshape{\featurestyles@shape}%
|
| 11969 | 12014 |
\selectfont% |
| 12015 |
+ \xdef\last@{bottom}%
|
|
| 11970 | 12016 |
\ifx\bottop@\temp@\xdef\last@{0.35}\else\xdef\last@{0}\fi%
|
| 11971 | 12017 |
\kern0.15\box@width% |
| 11972 | 12018 |
\loopcount=0\relax% |
| ... | ... |
@@ -12137,6 +12183,7 @@ |
| 12137 | 12183 |
\ifx\bottop@\temp@ \xdef\last@{0.35}\else\xdef\last@{-0.55}\fi%
|
| 12138 | 12184 |
\textcolor{\f@color}{%
|
| 12139 | 12185 |
\raisebox{\last@\arrow@height}{%
|
| 12186 |
+ \if\first@@ b \xdef\first@@{,}\fi%
|
|
| 12140 | 12187 |
\if\first@@ ,% |
| 12141 | 12188 |
\rule{0.1\arrow@height}{\arrow@height}\kern-0.35\arrow@height%
|
| 12142 | 12189 |
\else% |
| ... | ... |
@@ -12144,6 +12191,10 @@ |
| 12144 | 12191 |
\rule{0.1\arrow@height}{2\arrow@height}\kern-0.35\arrow@height%
|
| 12145 | 12192 |
\else% |
| 12146 | 12193 |
\if\first@@ `\xdef\first@@{'}\fi%
|
| 12194 |
+ \if\first@@ '% |
|
| 12195 |
+ \rule[\arrow@height]% |
|
| 12196 |
+ {0.1\arrow@height}{\arrow@height}\kern-0.35\arrow@height%
|
|
| 12197 |
+ \else% |
|
| 12147 | 12198 |
\if\first@@ '% |
| 12148 | 12199 |
\rule[\arrow@height]% |
| 12149 | 12200 |
{0.1\arrow@height}{\arrow@height}\kern-0.35\arrow@height%
|
| ... | ... |
@@ -12152,6 +12203,7 @@ |
| 12152 | 12203 |
\rule{0pt}{0pt}\kern-0.35\arrow@height%
|
| 12153 | 12204 |
\fi% |
| 12154 | 12205 |
\fi% |
| 12206 |
+ \fi% |
|
| 12155 | 12207 |
\fi% |
| 12156 | 12208 |
\fi% |
| 12157 | 12209 |
\if\third@@ v% |
| ... | ... |
@@ -12212,6 +12264,7 @@ |
| 12212 | 12264 |
\xdef\last@{-0.25}\fi\fi\fi\fi%
|
| 12213 | 12265 |
\textcolor{\f@color}{%
|
| 12214 | 12266 |
\raisebox{\last@\arrow@height}{%
|
| 12267 |
+ \if\first@@ b \xdef\first@@{,}\fi%
|
|
| 12215 | 12268 |
\if\first@@ ,% |
| 12216 | 12269 |
\rule[-0.5\arrow@height]{0.1\arrow@height}{1.5\arrow@height}%
|
| 12217 | 12270 |
\kern-0.1\arrow@height% |
| ... | ... |
@@ -12220,7 +12273,8 @@ |
| 12220 | 12273 |
\rule[-0.5\arrow@height]{0.1\arrow@height}{2.25\arrow@height}%
|
| 12221 | 12274 |
\kern-0.1\arrow@height% |
| 12222 | 12275 |
\else% |
| 12223 |
- \if\first@@ `\xdef\first@@{'}\fi%
|
|
| 12276 |
+ \if\first@@ a \xdef\first@@{'}\fi%
|
|
| 12277 |
+ \if\first@@ ` \xdef\first@@{'}\fi%
|
|
| 12224 | 12278 |
\if\first@@ '% |
| 12225 | 12279 |
\rule[0.4\arrow@height]% |
| 12226 | 12280 |
{0.1\arrow@height}{1.5\arrow@height}%
|
| ... | ... |
@@ -12245,6 +12299,7 @@ |
| 12245 | 12299 |
\rule[0.37\arrow@height]{\width@tmp}{0.1\arrow@height}%
|
| 12246 | 12300 |
\kern-\width@tmp% |
| 12247 | 12301 |
\rule[0.9\arrow@height]{\width@tmp}{0.1\arrow@height}%
|
| 12302 |
+ \if\first@@ b \xdef\first@@{,}\fi%
|
|
| 12248 | 12303 |
\if\third@@ ,% |
| 12249 | 12304 |
\kern-0.05\arrow@height% |
| 12250 | 12305 |
\rule[-0.5\arrow@height]{0.1\arrow@height}{1.5\arrow@height}%
|
| ... | ... |
@@ -12253,10 +12308,16 @@ |
| 12253 | 12308 |
\kern-0.05\arrow@height% |
| 12254 | 12309 |
\rule[-0.5\arrow@height]{0.1\arrow@height}{2.25\arrow@height}%
|
| 12255 | 12310 |
\else% |
| 12256 |
- \if\third@@ `\xdef\third@@{'}\fi%
|
|
| 12311 |
+ \if\first@@ a \xdef\first@@{'}\fi%
|
|
| 12312 |
+ \if\third@@ ` \xdef\third@@{'}\fi%
|
|
| 12257 | 12313 |
\if\third@@ '% |
| 12258 | 12314 |
\kern-0.05\arrow@height% |
| 12259 | 12315 |
\rule[0.4\arrow@height]{0.1\arrow@height}{1.5\arrow@height}%
|
| 12316 |
+ \else% |
|
| 12317 |
+ \if\third@@ a% |
|
| 12318 |
+ \kern-0.05\arrow@height% |
|
| 12319 |
+ \rule[0.4\arrow@height]{0.1\arrow@height}{1.5\arrow@height}%
|
|
| 12320 |
+ \fi% |
|
| 12260 | 12321 |
\fi% |
| 12261 | 12322 |
\fi% |
| 12262 | 12323 |
\fi% |
| ... | ... |
@@ -12268,9 +12329,25 @@ |
| 12268 | 12329 |
\advance\width@tmp by -0.5\temp@@length% |
| 12269 | 12330 |
\if\first@@ o\xdef\first@@{O}\fi%
|
| 12270 | 12331 |
\if\third@@ o\xdef\third@@{O}\fi%
|
| 12332 |
+ \xdef\last@{bottom}%
|
|
| 12333 |
+ \ifx\fe@turep@s\last@% |
|
| 12334 |
+ \vspace{-20pt}\message{(((-20pt)))}%
|
|
| 12335 |
+ \fi% |
|
| 12271 | 12336 |
\textcolor{\f@color}{%
|
| 12272 | 12337 |
\if\first@@ ,% |
| 12273 |
- \rule{\temp@@length}{\arrow@height}\kern-\temp@@length%
|
|
| 12338 |
+ \rule{\temp@@length}{\arrow@height}\kern-\temp@@length%
|
|
| 12339 |
+ \else% |
|
| 12340 |
+ \if\first@@ b% |
|
| 12341 |
+ \xdef\last@{bottom}%
|
|
| 12342 |
+ \ifx\fe@turep@s\last@% |
|
| 12343 |
+ \rule{\temp@@length}{\arrow@height}\kern-\temp@@length%
|
|
| 12344 |
+ \else |
|
| 12345 |
+ \xdef\shift@feature{y}%
|
|
| 12346 |
+ \kern-\temp@@length% |
|
| 12347 |
+ \rule[-\bar@length]{\temp@@length}{\bar@length}%
|
|
| 12348 |
+ \kern-\temp@@length% |
|
| 12349 |
+ \rule{\temp@@length}{\arrow@height}\kern-\temp@@length%
|
|
| 12350 |
+ \fi |
|
| 12274 | 12351 |
\else% |
| 12275 | 12352 |
\if\first@@ |% |
| 12276 | 12353 |
\rule{\temp@@length}{2\arrow@height}\kern-\temp@@length%
|
| ... | ... |
@@ -12278,6 +12355,52 @@ |
| 12278 | 12355 |
\if\first@@ O% |
| 12279 | 12356 |
\raisebox{0.06ex}{\ensuremath{\bullet}}\kern-0.55ex%
|
| 12280 | 12357 |
\rule[\width@tmp]{0.65ex}{\temp@@length}%
|
| 12358 |
+ \else% |
|
| 12359 |
+ \if\first@@ S% |
|
| 12360 |
+ \xdef\last@{bottom}%
|
|
| 12361 |
+ \ifx\fe@turep@s\last@% |
|
| 12362 |
+ \advance\width@tmp by 0.5\temp@@length% |
|
| 12363 |
+ \kern0.5\box@width% |
|
| 12364 |
+ \kern-2\temp@@length% |
|
| 12365 |
+ \rule[\width@tmp]{\temp@@length}{\arrow@height}%
|
|
| 12366 |
+ \advance\width@tmp by -0.5\temp@@length% |
|
| 12367 |
+ \kern-\temp@@length% |
|
| 12368 |
+ \rule[\width@tmp]{0.5\temp@@length}{\temp@@length}%
|
|
| 12369 |
+ \rule[\width@tmp]{0.5\box@width}{\temp@@length}%
|
|
| 12370 |
+ \else% |
|
| 12371 |
+ \kern0.5\box@width% |
|
| 12372 |
+ \kern-2\temp@@length% |
|
| 12373 |
+ \rule{\temp@@length}{\arrow@height}%
|
|
| 12374 |
+ \kern-\temp@@length% |
|
| 12375 |
+ \rule[\width@tmp]{0.5\temp@@length}{\temp@@length}%
|
|
| 12376 |
+ \rule[\width@tmp]{0.5\box@width}{\temp@@length}%
|
|
| 12377 |
+ \fi% |
|
| 12378 |
+ \else% |
|
| 12379 |
+ \if\first@@ c% |
|
| 12380 |
+ \xdef\last@{bottom}%
|
|
| 12381 |
+ \ifx\fe@turep@s\last@% |
|
| 12382 |
+ \advance\width@tmp by 0.5\temp@@length% |
|
| 12383 |
+ \raisebox{\arrow@height}{\rule[\box@height]{0pt}{\bar@length}}%%%%%%%%%%%%%%%%%%%%%%%
|
|
| 12384 |
+ \kern0.5\box@width% |
|
| 12385 |
+ \kern-2\temp@@length% |
|
| 12386 |
+ \rule[2\arrow@height]{\temp@@length}{\bar@length}%%%%%%%%%%%%%%%%%%%%%%
|
|
| 12387 |
+ \kern-\temp@@length%%%%%%%%%%%%%%%%%%%%%%%%% |
|
| 12388 |
+ \rule[\width@tmp]{\temp@@length}{\arrow@height}%
|
|
| 12389 |
+ \advance\width@tmp by -0.5\temp@@length% |
|
| 12390 |
+ \kern-\temp@@length% |
|
| 12391 |
+ \rule[\width@tmp]{0.5\temp@@length}{\temp@@length}%
|
|
| 12392 |
+ \rule[\width@tmp]{0.5\box@width}{\temp@@length}%
|
|
| 12393 |
+ \else% |
|
| 12394 |
+ \xdef\shift@feature{y}%
|
|
| 12395 |
+ \kern0.5\box@width% |
|
| 12396 |
+ \kern-2\temp@@length% |
|
| 12397 |
+ \rule[-\bar@length]{\temp@@length}{\bar@length}%
|
|
| 12398 |
+ \kern-\temp@@length% |
|
| 12399 |
+ \rule{\temp@@length}{\arrow@height}%
|
|
| 12400 |
+ \kern-\temp@@length% |
|
| 12401 |
+ \rule[\width@tmp]{0.5\temp@@length}{\temp@@length}%
|
|
| 12402 |
+ \rule[\width@tmp]{0.5\box@width}{\temp@@length}%
|
|
| 12403 |
+ \fi% |
|
| 12281 | 12404 |
\else% |
| 12282 | 12405 |
\if\first@@ <% |
| 12283 | 12406 |
\raisebox{0.06ex}{\ensuremath{\blacktriangleleft}}\kern-0.35ex%
|
| ... | ... |
@@ -12290,13 +12413,20 @@ |
| 12290 | 12413 |
\fi% |
| 12291 | 12414 |
\fi% |
| 12292 | 12415 |
\fi% |
| 12416 |
+ \fi% |
|
| 12417 |
+ \fi% |
|
| 12293 | 12418 |
\fi% |
| 12294 | 12419 |
\fi% |
| 12420 |
+ \fi% |
|
| 12295 | 12421 |
\loopcount=\second@% |
| 12296 | 12422 |
\if\first@@ <\advance\loopcount by -1\relax\ifnum\loopcount<0 \loopcount=0\fi\fi% |
| 12297 | 12423 |
\if\third@@ >\advance\loopcount by -1\relax\ifnum\loopcount<0 \loopcount=0\fi\fi% |
| 12298 | 12424 |
\if\first@@ O\advance\loopcount by -1\relax\ifnum\loopcount<0 \loopcount=0\fi\fi% |
| 12299 | 12425 |
\if\third@@ O\advance\loopcount by -1\relax\ifnum\loopcount<0 \loopcount=0\fi\fi% |
| 12426 |
+ \if\first@@ S\advance\loopcount by -1\relax\ifnum\loopcount<0 \loopcount=0\fi\fi% |
|
| 12427 |
+ \if\third@@ S\advance\loopcount by -1\relax\ifnum\loopcount<0 \loopcount=0\fi\fi% |
|
| 12428 |
+ \if\first@@ c\advance\loopcount by -1\relax\ifnum\loopcount<0 \loopcount=0\fi\fi% |
|
| 12429 |
+ \if\third@@ c\advance\loopcount by -1\relax\ifnum\loopcount<0 \loopcount=0\fi\fi% |
|
| 12300 | 12430 |
\xdef\second@{\the\loopcount}%
|
| 12301 | 12431 |
\rule[\width@tmp]{\second@\box@width}{\temp@@length}%
|
| 12302 | 12432 |
\setbox1=\hbox{\residues@size{\fill@char}}%
|
| ... | ... |
@@ -12306,6 +12436,17 @@ |
| 12306 | 12436 |
\hbox to \second@\box@width{\textcolor{\frame@color}{\residues@size{\hss\fill@char\hss}}}%
|
| 12307 | 12437 |
\if\third@@ ,% |
| 12308 | 12438 |
\kern-\temp@@length\rule{\temp@@length}{\arrow@height}%
|
| 12439 |
+ \else% |
|
| 12440 |
+ \if\third@@ b% |
|
| 12441 |
+ \xdef\last@{bottom}%
|
|
| 12442 |
+ \ifx\fe@turep@s\last@% |
|
| 12443 |
+ \kern-\temp@@length\rule{\temp@@length}{\arrow@height}%
|
|
| 12444 |
+ \else |
|
| 12445 |
+ \xdef\shift@feature{y}%
|
|
| 12446 |
+ \kern-\temp@@length% |
|
| 12447 |
+ \rule[-\bar@length]{\temp@@length}{\bar@length}%
|
|
| 12448 |
+ \kern-\temp@@length\rule{\temp@@length}{\arrow@height}%
|
|
| 12449 |
+ \fi |
|
| 12309 | 12450 |
\else% |
| 12310 | 12451 |
\if\third@@ |% |
| 12311 | 12452 |
\kern-\temp@@length\rule{\temp@@length}{2\arrow@height}%
|
| ... | ... |
@@ -12313,6 +12454,31 @@ |
| 12313 | 12454 |
\if\third@@ O% |
| 12314 | 12455 |
\rule[\width@tmp]{0.65ex}{\temp@@length}%
|
| 12315 | 12456 |
\kern-0.55ex\raisebox{0.06ex}{\ensuremath{\bullet}}%
|
| 12457 |
+ \else% |
|
| 12458 |
+ \if\third@@ S% |
|
| 12459 |
+ \rule[\width@tmp]{0.5\box@width}{\temp@@length}%
|
|
| 12460 |
+ \rule[\width@tmp]{0.5\temp@@length}{\temp@@length}%
|
|
| 12461 |
+ \xdef\last@{bottom}%
|
|
| 12462 |
+ \ifx\fe@turep@s\last@% |
|
| 12463 |
+ \advance\width@tmp by 0.5\temp@@length% |
|
| 12464 |
+ \kern-\temp@@length\rule[\width@tmp]{\temp@@length}{\arrow@height}%
|
|
| 12465 |
+ \else |
|
| 12466 |
+ \kern-\temp@@length\rule{\temp@@length}{\arrow@height}%
|
|
| 12467 |
+ \fi% |
|
| 12468 |
+ \else% |
|
| 12469 |
+ \if\third@@ c% |
|
| 12470 |
+ \xdef\shift@feature{y}%
|
|
| 12471 |
+ \rule[\width@tmp]{0.5\box@width}{\temp@@length}%
|
|
| 12472 |
+ \xdef\last@{bottom}%
|
|
| 12473 |
+ \ifx\fe@turep@s\last@% |
|
| 12474 |
+ \kern-\temp@@length%%%%%%%%%%%%%%%%%%%%%%%%% |
|
| 12475 |
+ \rule[2\arrow@height]{\temp@@length}{\bar@length}%%%%%%%%%%%%%%%%%%%%%%
|
|
| 12476 |
+ \advance\width@tmp by 0.5\temp@@length% |
|
| 12477 |
+ \kern-\temp@@length\rule[\width@tmp]{\temp@@length}{\arrow@height}%
|
|
| 12478 |
+ \else |
|
| 12479 |
+ \kern-\temp@@length\rule[-\bar@length]{\temp@@length}{\bar@length}%
|
|
| 12480 |
+ \kern-\temp@@length\rule{\temp@@length}{\arrow@height}%
|
|
| 12481 |
+ \fi% |
|
| 12316 | 12482 |
\else% |
| 12317 | 12483 |
\if\third@@ >% |
| 12318 | 12484 |
\kern-0.35ex\raisebox{0.06ex}{\ensuremath{\blacktriangleright}}%
|
| ... | ... |
@@ -12324,7 +12490,10 @@ |
| 12324 | 12490 |
\fi% |
| 12325 | 12491 |
\fi% |
| 12326 | 12492 |
\fi% |
| 12327 |
- \fi |
|
| 12493 |
+ \fi% |
|
| 12494 |
+ \fi% |
|
| 12495 |
+ \fi% |
|
| 12496 |
+ \fi% |
|
| 12328 | 12497 |
\fi}% |
| 12329 | 12498 |
\fi |
| 12330 | 12499 |
\fi |
| ... | ... |
@@ -12731,9 +12900,550 @@ |
| 12731 | 12900 |
\divide\loopcount by 100 % |
| 12732 | 12901 |
\xdef\third@{\the\loopcount}%
|
| 12733 | 12902 |
} |
| 12903 |
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
|
| 12904 |
+%%%% Chimera export routines %%%% |
|
| 12905 |
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
|
| 12906 |
+\def\chimeraballScale#1{\xdef\chimerab@llSc@le{#1}}
|
|
| 12907 |
+\def\chimeraballscale#1{\xdef\chimerab@llSc@le{#1}}
|
|
| 12908 |
+\def\chimeraaxisdistance#1#2#3{\xdef\chimera@xdist@nce{#1}\xdef\chimera@ydist@nce{#2}\xdef\chimera@zdist@nce{#3}}
|
|
| 12909 |
+\def\memelabelcutoff#1{%
|
|
| 12910 |
+ \xdef\label@threshold@lower{#1}
|
|
| 12911 |
+ \setlength\temp@@length{1000sp}
|
|
| 12912 |
+ \setlength\temp@@length{\label@threshold@lower\temp@@length}
|
|
| 12913 |
+ \loopcount=\temp@@length |
|
| 12914 |
+ \xdef\label@threshold@lowerIOOO{\the\loopcount}
|
|
| 12915 |
+ \xdef\label@threshold@lowerremainingIOOO{-\the\loopcount}
|
|
| 12916 |
+} |
|
| 12917 |
+\def\chimera@color@get#1#2@{%
|
|
| 12918 |
+ \xdef\first@{#1}\xdef\third@{#2@}
|
|
| 12919 |
+ \ifx\first@\ampers@nd |
|
| 12920 |
+ \else |
|
| 12921 |
+ \ifnum`#1>96 \make@upper\fi |
|
| 12922 |
+ \if\second@ O \else \expandafter\xdef\csname chimera@col@\first@\endcsname{\second@} \fi
|
|
| 12923 |
+ \expandafter\chimera@color@get\third@ |
|
| 12924 |
+ \fi |
|
| 12925 |
+} |
|
| 12926 |
+\def\memered#1{%
|
|
| 12927 |
+ \xdef\third@{#1&@}
|
|
| 12928 |
+ \xdef\second@{red}
|
|
| 12929 |
+ \expandafter\chimera@color@get\third@ |
|
| 12930 |
+} |
|
| 12931 |
+\def\memeblue#1{%
|
|
| 12932 |
+ \xdef\third@{#1&@}
|
|
| 12933 |
+ \xdef\second@{blue}
|
|
| 12934 |
+ \expandafter\chimera@color@get\third@ |
|
| 12935 |
+} |
|
| 12936 |
+\def\memeyellow#1{%
|
|
| 12937 |
+ \xdef\third@{#1&@}
|
|
| 12938 |
+ \xdef\second@{yellow}
|
|
| 12939 |
+ \expandafter\chimera@color@get\third@ |
|
| 12940 |
+} |
|
| 12941 |
+\def\memeblack#1{%
|
|
| 12942 |
+ \xdef\third@{#1&@}
|
|
| 12943 |
+ \xdef\second@{black}
|
|
| 12944 |
+ \expandafter\chimera@color@get\third@ |
|
| 12945 |
+} |
|
| 12946 |
+\def\memewhite#1{%
|
|
| 12947 |
+ \xdef\third@{#1&@}
|
|
| 12948 |
+ \xdef\second@{white}
|
|
| 12949 |
+ \expandafter\chimera@color@get\third@ |
|
| 12950 |
+} |
|
| 12951 |
+\def\memenone#1{%
|
|
| 12952 |
+ \xdef\third@{#1&@}
|
|
| 12953 |
+ \xdef\second@{none}
|
|
| 12954 |
+ \expandafter\chimera@color@get\third@ |
|
| 12955 |
+} |
|
| 12956 |
+\def\memeRed#1{\memered{#1}}
|
|
| 12957 |
+\def\memeBlue#1{\memeblue{#1}}
|
|
| 12958 |
+\def\memeYellow#1{\memeyellow{#1}}
|
|
| 12959 |
+\def\memeBlack#1{\memeblack{#1}}
|
|
| 12960 |
+\def\memeWhite#1{\memewhite{#1}}
|
|
| 12961 |
+\def\memeNone#1{\memenone{#1}}
|
|
| 12962 |
+\def\chimera@colors#1#2@{%
|
|
| 12963 |
+ \xdef\first@{#1}\xdef\third@{#2@}
|
|
| 12964 |
+ \ifx\first@\ampers@nd |
|
| 12965 |
+ \else |
|
| 12966 |
+ \xdef\second@{\csname chimera@col@\first@\endcsname}
|
|
| 12967 |
+ \expandafter\xdef\csname chimera@list@\second@\endcsname{\csname chimera@list@\second@\endcsname \first@}
|
|
| 12968 |
+ \expandafter\chimera@colors\third@ |
|
| 12969 |
+ \fi |
|
| 12970 |
+} |
|
| 12971 |
+\def\memeStandardcolors{%
|
|
| 12972 |
+ \xdef\chimera@col@A{white}
|
|
| 12973 |
+ \xdef\chimera@col@B{none}
|
|
| 12974 |
+ \xdef\chimera@col@C{yellow}
|
|
| 12975 |
+ \xdef\chimera@col@D{red}
|
|
| 12976 |
+ \xdef\chimera@col@E{red}
|
|
| 12977 |
+ \xdef\chimera@col@F{black}
|
|
| 12978 |
+ \xdef\chimera@col@G{yellow}
|
|
| 12979 |
+ \xdef\chimera@col@H{blue}
|
|
| 12980 |
+ \xdef\chimera@col@I{black}
|
|
| 12981 |
+ \xdef\chimera@col@J{none}
|
|
| 12982 |
+ \xdef\chimera@col@K{blue}
|
|
| 12983 |
+ \xdef\chimera@col@L{black}
|
|
| 12984 |
+ \xdef\chimera@col@M{black}
|
|
| 12985 |
+ \xdef\chimera@col@N{yellow}
|
|
| 12986 |
+ \xdef\chimera@col@O{none}
|
|
| 12987 |
+ \xdef\chimera@col@P{white}
|
|
| 12988 |
+ \xdef\chimera@col@Q{yellow}
|
|
| 12989 |
+ \xdef\chimera@col@R{blue}
|
|
| 12990 |
+ \xdef\chimera@col@S{yellow}
|
|
| 12991 |
+ \xdef\chimera@col@T{yellow}
|
|
| 12992 |
+ \xdef\chimera@col@U{none}
|
|
| 12993 |
+ \xdef\chimera@col@V{white}
|
|
| 12994 |
+ \xdef\chimera@col@W{black}
|
|
| 12995 |
+ \xdef\chimera@col@X{none}
|
|
| 12996 |
+ \xdef\chimera@col@Y{yellow}
|
|
| 12997 |
+ \xdef\chimera@col@Z{none}
|
|
| 12998 |
+} |
|
| 12999 |
+\def\echostructurefile#1{\xdef\echo@filename{, e.g. #1}}
|
|
| 13000 |
+\def\chimerachain#1{\xdef\chimerach@in{.#1}}
|
|
| 13001 |
+\catcode`\"=6 \catcode`\#=12 \catcode`\~=12 |
|
| 13002 |
+\newcommand{\structurememe}[2][chimera.cmd]{%
|
|
| 13003 |
+ \ifx\exp@rt@chimera\n@ |
|
| 13004 |
+ \xdef\first@{"2 @} \expandafter\check@letter\first@
|
|
| 13005 |
+ \xdef\first@{"2} \ifletter \get@name@number \fi
|
|
| 13006 |
+ \xdef\chimera@seqnum{\first@}
|
|
| 13007 |
+ \xdef\exp@rt@chimera{y}
|
|
| 13008 |
+ \xdef\first@{"1}
|
|
| 13009 |
+ \immediate\openout\exp@rt@chimerafile = \first@ |
|
| 13010 |
+ \fi |
|
| 13011 |
+} |
|
| 13012 |
+\def\init@chimera@file{%
|
|
| 13013 |
+ \xdef\chimera@list@red{} \xdef\chimera@list@blue{} \xdef\chimera@list@yellow{} \xdef\chimera@list@black{} \xdef\chimera@list@white{}
|
|
| 13014 |
+ \xdef\chimera@list@none{}
|
|
| 13015 |
+ \xdef\first@{ABCDEFGHIJKLMNOPQRSTUVWXYZ&@}
|
|
| 13016 |
+ \expandafter\chimera@colors\first@ |
|
| 13017 |
+ \immediate\write\exp@rt@chimerafile{############################################################}
|
|
| 13018 |
+ \immediate\write\exp@rt@chimerafile{###}
|
|
| 13019 |
+ \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }. O � o STRUCTURE MEME � . O o}
|
|
| 13020 |
+ \immediate\write\exp@rt@chimerafile{###}
|
|
| 13021 |
+ \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }Chimera command file generated from TeXshade logo data}
|
|
| 13022 |
+ \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }use '.cmd' or '.com' suffix}
|
|
| 13023 |
+ \immediate\write\exp@rt@chimerafile{###}
|
|
| 13024 |
+ \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }Reference sequence: '\csname newseqname\chimera@seqnum\endcsname'\echo@filename}
|
|
| 13025 |
+ \immediate\write\exp@rt@chimerafile{###}
|
|
| 13026 |
+ \immediate\write\exp@rt@chimerafile{############################################################}
|
|
| 13027 |
+ \immediate\write\exp@rt@chimerafile{}
|
|
| 13028 |
+ \immediate\write\exp@rt@chimerafile{############################################################}
|
|
| 13029 |
+ \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }residue colors: (set with \string\memeRed{residues}\unexpanded{ }etc.)}
|
|
| 13030 |
+ \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }\chimera@list@red \unexpanded{ }(Red)}
|
|
| 13031 |
+ \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }\chimera@list@blue \unexpanded{ }(Blue)}
|
|
| 13032 |
+ \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }\chimera@list@yellow \unexpanded{ }(Yellow)}
|
|
| 13033 |
+ \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }\chimera@list@black \unexpanded{ }(Black)}
|
|
| 13034 |
+ \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }\chimera@list@white \unexpanded{ }(White)}
|
|
| 13035 |
+ \immediate\write\exp@rt@chimerafile{############################################################}
|
|
| 13036 |
+ \immediate\write\exp@rt@chimerafile{}
|
|
| 13037 |
+ \immediate\write\exp@rt@chimerafile{############################################################}
|
|
| 13038 |
+ \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }residues in labels: (\string\memelabelcutoff{bit-value})}
|
|
| 13039 |
+ \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }\label@threshold@lower\unexpanded{ }bit required to appear}
|
|
| 13040 |
+ \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }> : . indicate 3, 2, and 1 bit levels}
|
|
| 13041 |
+ \immediate\write\exp@rt@chimerafile{############################################################}
|
|
| 13042 |
+ \immediate\write\exp@rt@chimerafile{}
|
|
| 13043 |
+ \immediate\write\exp@rt@chimerafile{############################################################}
|
|
| 13044 |
+ \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }initialize & load structure}
|
|
| 13045 |
+ \immediate\write\exp@rt@chimerafile{############################################################}
|
|
| 13046 |
+ \immediate\write\exp@rt@chimerafile{close session; background solid white;}
|
|
| 13047 |
+ \immediate\write\exp@rt@chimerafile{echo load structure file for '\csname newseqname\chimera@seqnum\endcsname'\echo@filename}
|
|
| 13048 |
+ \immediate\write\exp@rt@chimerafile{open #0; ~ribbon; ~surface}
|
|
| 13049 |
+ \immediate\write\exp@rt@chimerafile{}
|
|
| 13050 |
+ \immediate\write\exp@rt@chimerafile{############################################################}
|
|
| 13051 |
+ \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }to set ball scale, change factor ]0.0 - 1.0]}
|
|
| 13052 |
+ \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }in 'setattr m ballScale <factor> #0' below,}
|
|
| 13053 |
+ \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }or use the \string\chimeraballScale{factor}\unexpanded{ }command}
|
|
| 13054 |
+ \immediate\write\exp@rt@chimerafile{############################################################}
|
|
| 13055 |
+ \immediate\write\exp@rt@chimerafile{setattr m ballScale \chimerab@llSc@le \unexpanded{ }#0}
|
|
| 13056 |
+ \immediate\write\exp@rt@chimerafile{}
|
|
| 13057 |
+ \immediate\write\exp@rt@chimerafile{############################################################}
|
|
| 13058 |
+ \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }display alpha-carbons only}
|
|
| 13059 |
+ \immediate\write\exp@rt@chimerafile{############################################################}
|
|
| 13060 |
+ \immediate\write\exp@rt@chimerafile{represent bs @ca; show @ca}
|
|
| 13061 |
+ \immediate\write\exp@rt@chimerafile{}
|
|
| 13062 |
+ \ifshow@sublogo |
|
| 13063 |
+ \immediate\write\exp@rt@chimerafile{############################################################}
|
|
| 13064 |
+ \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }duplicate structure;}
|
|
| 13065 |
+ \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }to alter direction or Angstrom distance, set}
|
|
| 13066 |
+ \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }'move <x, y, or z> 1 <distance> models #1' below,}
|
|
| 13067 |
+ \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }or use the \string\chimeraaxisdistance{x}{y}{z}\unexpanded{ }command}
|
|
| 13068 |
+ \immediate\write\exp@rt@chimerafile{############################################################}
|
|
| 13069 |
+ \immediate\write\exp@rt@chimerafile{combine #0}
|
|
| 13070 |
+ \ifnum\chimera@xdist@nce>0 |
|
| 13071 |
+ \immediate\write\exp@rt@chimerafile{move x 1 \chimera@xdist@nce \unexpanded{ }models #1}
|
|
| 13072 |
+ \fi |
|
| 13073 |
+ \ifnum\chimera@ydist@nce>0 |
|
| 13074 |
+ \immediate\write\exp@rt@chimerafile{move y 1 \chimera@ydist@nce \unexpanded{ }models #1}
|
|
| 13075 |
+ \fi |
|
| 13076 |
+ \ifnum\chimera@zdist@nce>0 |
|
| 13077 |
+ \immediate\write\exp@rt@chimerafile{move z 1 \chimera@zdist@nce \unexpanded{ }models #1}
|
|
| 13078 |
+ \fi |
|
| 13079 |
+ \immediate\write\exp@rt@chimerafile{}
|
|
| 13080 |
+ \immediate\write\exp@rt@chimerafile{############################################################}
|
|
| 13081 |
+ \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }focus view and name structure models}
|
|
| 13082 |
+ \immediate\write\exp@rt@chimerafile{############################################################}
|
|
| 13083 |
+ \immediate\write\exp@rt@chimerafile{wait; focus #0#1}
|
|
| 13084 |
+ \ifx\sublogo@name@user\ampers@nd |
|
| 13085 |
+ \immediate\write\exp@rt@chimerafile{setattr m name subfamily #0}
|
|
| 13086 |
+ \else |
|
| 13087 |
+ \immediate\write\exp@rt@chimerafile{setattr m name '\sublogo@name@user' \unexpanded{ }#0}
|
|
| 13088 |
+ \fi |
|
| 13089 |
+ \xdef\first@{\sublogo@name@neg &}
|
|
| 13090 |
+ \ifx\first@\ampers@nd |
|
| 13091 |
+ \immediate\write\exp@rt@chimerafile{setattr m name remaining #1}
|
|
| 13092 |
+ \else |
|
| 13093 |
+ \immediate\write\exp@rt@chimerafile{setattr m name '\sublogo@name@neg' \unexpanded{ }#1}
|
|
| 13094 |
+ \fi |
|
| 13095 |
+ \else |
|
| 13096 |
+ \immediate\write\exp@rt@chimerafile{\string ############################################################}
|
|
| 13097 |
+ \immediate\write\exp@rt@chimerafile{\string ###\unexpanded{ }\unexpanded{ }\unexpanded{ }name structure model}
|
|
| 13098 |
+ \immediate\write\exp@rt@chimerafile{\string ############################################################}
|
|
| 13099 |
+ \ifx\logo@name@user\ampers@nd |
|
| 13100 |
+ \immediate\write\exp@rt@chimerafile{setattr m name logo #0}
|
|
| 13101 |
+ \else |
|
| 13102 |
+ \immediate\write\exp@rt@chimerafile{setattr m name '\logo@name@user' \unexpanded{ }#0}
|
|
| 13103 |
+ \fi |
|
| 13104 |
+ \fi |
|
| 13105 |
+ \immediate\write\exp@rt@chimerafile{}
|
|
| 13106 |
+ \immediate\write\exp@rt@chimerafile{############################################################}
|
|
| 13107 |
+ \immediate\write\exp@rt@chimerafile{###\unexpanded{ }\unexpanded{ }\unexpanded{ }logo data}
|
|
| 13108 |
+ \immediate\write\exp@rt@chimerafile{############################################################}
|
|
| 13109 |
+} |
|
| 13110 |
+\def\make@HEX{%
|
|
| 13111 |
+ \xdef\sixth@{\the\loopcount}%
|
|
| 13112 |
+ \divide\loopcount by 4096\relax% |
|
| 13113 |
+ \ifnum\loopcount=10\relax% |
|
| 13114 |
+ \xdef\seventh@{A}%
|
|
| 13115 |
+ \else% |
|
| 13116 |
+ \ifnum\loopcount=11\relax% |
|
| 13117 |
+ \xdef\seventh@{B}%
|
|
| 13118 |
+ \else% |
|
| 13119 |
+ \ifnum\loopcount=12\relax% |
|
| 13120 |
+ \xdef\seventh@{C}%
|
|
| 13121 |
+ \else% |
|
| 13122 |
+ \ifnum\loopcount=13\relax% |
|
| 13123 |
+ \xdef\seventh@{D}%
|
|
| 13124 |
+ \else% |
|
| 13125 |
+ \ifnum\loopcount=14\relax% |
|
| 13126 |
+ \xdef\seventh@{E}%
|
|
| 13127 |
+ \else% |
|
| 13128 |
+ \ifnum\loopcount>14\relax% |
|
| 13129 |
+ \xdef\seventh@{F}%
|
|
| 13130 |
+ \else% |
|
| 13131 |
+ \xdef\seventh@{\the\loopcount}%
|
|
| 13132 |
+ \fi\fi\fi\fi\fi\fi% |
|
| 13133 |
+ \multiply\loopcount by -4096\relax% |
|
| 13134 |
+ \advance\loopcount by \sixth@% |
|
| 13135 |
+ \xdef\sixth@{\the\loopcount}%
|
|
| 13136 |
+ \divide\loopcount by 256\relax% |
|
| 13137 |
+ \ifnum\loopcount=10 \relax% |
|
| 13138 |
+ \xdef\eighth@{A}%
|
|
| 13139 |
+ \else% |
|
| 13140 |
+ \ifnum\loopcount=11 \relax% |
|
| 13141 |
+ \xdef\eighth@{B}%
|
|
| 13142 |
+ \else% |
|
| 13143 |
+ \ifnum\loopcount=12 \relax% |
|
| 13144 |
+ \xdef\eighth@{C}%
|
|
| 13145 |
+ \else% |
|
| 13146 |
+ \ifnum\loopcount=13 \relax% |
|
| 13147 |
+ \xdef\eighth@{D}%
|
|
| 13148 |
+ \else% |
|
| 13149 |
+ \ifnum\loopcount=14 \relax% |
|
| 13150 |
+ \xdef\eighth@{E}%
|
|
| 13151 |
+ \else% |
|
| 13152 |
+ \ifnum\loopcount>14 \relax% |
|
| 13153 |
+ \xdef\eighth@{F}%
|
|
| 13154 |
+ \else% |
|
| 13155 |
+ \xdef\eighth@{\the\loopcount}%
|
|
| 13156 |
+ \fi\fi\fi\fi\fi\fi% |
|
| 13157 |
+ \xdef\seventh@{\seventh@\eighth@}%
|
|
| 13158 |
+ \multiply\loopcount by -256\relax% |
|
| 13159 |
+ \advance\loopcount by \sixth@% |
|
| 13160 |
+ \xdef\sixth@{\the\loopcount}%
|
|
| 13161 |
+ \divide\loopcount by 16\relax% |
|
| 13162 |
+ \ifnum\loopcount=10\relax% |
|
| 13163 |
+ \xdef\eighth@{A}%
|
|
| 13164 |
+ \else% |
|
| 13165 |
+ \ifnum\loopcount=11\relax% |
|
| 13166 |
+ \xdef\eighth@{B}%
|
|
| 13167 |
+ \else% |
|
| 13168 |
+ \ifnum\loopcount=12\relax% |
|
| 13169 |
+ \xdef\eighth@{C}%
|
|
| 13170 |
+ \else% |
|
| 13171 |
+ \ifnum\loopcount=13\relax% |
|
| 13172 |
+ \xdef\eighth@{D}%
|
|
| 13173 |
+ \else% |
|
| 13174 |
+ \ifnum\loopcount=14\relax% |
|
| 13175 |
+ \xdef\eighth@{E}%
|
|
| 13176 |
+ \else% |
|
| 13177 |
+ \ifnum\loopcount>14\relax% |
|
| 13178 |
+ \xdef\eighth@{F}%
|
|
| 13179 |
+ \else% |
|
| 13180 |
+ \xdef\eighth@{\the\loopcount}%
|
|
| 13181 |
+ \fi\fi\fi\fi\fi\fi% |
|
| 13182 |
+ \xdef\seventh@{\seventh@\eighth@}%
|
|
| 13183 |
+ \multiply\loopcount by -16\relax% |
|
| 13184 |
+ \advance\loopcount by \sixth@\relax% |
|
| 13185 |
+ \ifnum\loopcount=10\relax% |
|
| 13186 |
+ \xdef\eighth@{A}%
|
|
| 13187 |
+ \else% |
|
| 13188 |
+ \ifnum\loopcount=11\relax% |
|
| 13189 |
+ \xdef\eighth@{B}%
|
|
| 13190 |
+ \else% |
|
| 13191 |
+ \ifnum\loopcount=12\relax% |
|
| 13192 |
+ \xdef\eighth@{C}%
|
|
| 13193 |
+ \else% |
|
| 13194 |
+ \ifnum\loopcount=13\relax% |
|
| 13195 |
+ \xdef\eighth@{D}%
|
|
| 13196 |
+ \else% |
|
| 13197 |
+ \ifnum\loopcount=14\relax% |
|
| 13198 |
+ \xdef\eighth@{E}%
|
|
| 13199 |
+ \else% |
|
| 13200 |
+ \ifnum\loopcount>14\relax% |
|
| 13201 |
+ \xdef\eighth@{F}%
|
|
| 13202 |
+ \else% |
|
| 13203 |
+ \xdef\eighth@{\the\loopcount}%
|
|
| 13204 |
+ \fi\fi\fi\fi\fi\fi% |
|
| 13205 |
+ \xdef\seventh@{\seventh@\eighth@}%
|
|
| 13206 |
+} |
|
| 13207 |
+\def\write@chimera@data{%
|
|
| 13208 |
+ \ifnum\temp@count>0 \else\temp@count=1\relax\temp@@count=0\fi% |
|
| 13209 |
+ \loopcount=\temp@count% |
|
| 13210 |
+ \xdef\fourth@{\the\loopcount @}%
|
|
| 13211 |
+ \ifnum\loopcount>9999 \expandafter\decimal@A\fourth@ \else% |
|
| 13212 |
+ \ifnum\loopcount>999 \expandafter\decimal@B\fourth@ \else% |
|
| 13213 |
+ \ifnum\loopcount>99 \expandafter\decimal@C\fourth@ \else% |
|
| 13214 |
+ \ifnum\loopcount>9 \expandafter\decimal@D\fourth@ \else% |
|
| 13215 |
+ \expandafter\decimal@E\fourth@% |
|
| 13216 |
+ \fi\fi\fi\fi% |
|
| 13217 |
+ \loopcount=\chimera@subfamily@col@black% |
|
| 13218 |
+ \multiply\loopcount by 65535\relax% |
|
| 13219 |
+ \divide\loopcount by \temp@count% |
|
| 13220 |
+ \xdef\chimera@subfamily@col@black{\the\loopcount}%
|
|
| 13221 |
+ \loopcount=65535\relax% |
|
| 13222 |
+ \advance\loopcount by -\chimera@subfamily@col@black% |
|
| 13223 |
+ \xdef\temp@@{\the\loopcount}%
|
|
| 13224 |
+%%%%%%%%%%%%%% |
|
| 13225 |
+%%%%%%%%%%%%%% |
|
| 13226 |
+ \loopcount=\chimera@subfamily@col@blue\relax% |
|
| 13227 |
+ \ifnum\chimera@subfamily@col@yellow>\loopcount\relax% |
|
| 13228 |
+ \loopcount=\chimera@subfamily@col@yellow\relax% |
|
| 13229 |
+ \else% |
|
| 13230 |
+ \ifnum\chimera@subfamily@col@red>\loopcount\relax% |
|
| 13231 |
+ \loopcount=\chimera@subfamily@col@red\relax% |
|
| 13232 |
+ \fi% |
|
| 13233 |
+ \fi% |
|
| 13234 |
+ \xdef\max@yellow{\the\loopcount}%
|
|
| 13235 |
+ \ifnum\chimera@subfamily@col@blue<\chimera@subfamily@col@yellow\relax% |
|
| 13236 |
+ \xdef\chimera@subfamily@col@green{\chimera@subfamily@col@blue}%
|
|
| 13237 |
+ \else% |
|
| 13238 |
+ \xdef\chimera@subfamily@col@green{\chimera@subfamily@col@yellow}%
|
|
| 13239 |
+ \fi% |
|
| 13240 |
+ \loopcount=\chimera@subfamily@col@yellow\relax% |
|
| 13241 |
+ \advance\loopcount by -\chimera@subfamily@col@green% |
|
| 13242 |
+ \xdef\chimera@subfamily@col@yellow{\the\loopcount}%
|
|
| 13243 |
+ \loopcount=\chimera@subfamily@col@blue\relax% |
|
| 13244 |
+ \advance\loopcount by -\chimera@subfamily@col@green% |
|
| 13245 |
+ \xdef\chimera@subfamily@col@blue{\the\loopcount}%
|
|
| 13246 |
+ \ifnum\chimera@subfamily@col@blue>0\relax% |
|
| 13247 |
+ \ifnum\chimera@subfamily@col@green>0\relax% |
|
| 13248 |
+ \loopcount=\chimera@subfamily@col@blue\relax% |
|
| 13249 |
+ \multiply\loopcount by 2\relax \xdef\chimera@subfamily@col@blue{\the\loopcount}%
|
|
| 13250 |
+ \loopcount=\chimera@subfamily@col@green\relax% |
|
| 13251 |
+ \multiply\loopcount by 2\relax \xdef\chimera@subfamily@col@green{\the\loopcount}%
|
|
| 13252 |
+ \fi% |
|
| 13253 |
+ \fi% |
|
| 13254 |
+ \loopcount=\chimera@subfamily@col@green\relax% |
|
| 13255 |
+ \advance\loopcount by \chimera@subfamily@col@yellow% |
|
| 13256 |
+ \xdef\chimera@subfamily@col@green{\the\loopcount}%
|
|
| 13257 |
+ \loopcount=\chimera@subfamily@col@red\relax% |
|
| 13258 |
+ \advance\loopcount by \chimera@subfamily@col@yellow% |
|
| 13259 |
+ \xdef\chimera@subfamily@col@red{\the\loopcount}%
|
|
| 13260 |
+ \loopcount=\chimera@subfamily@col@blue\relax% |
|
| 13261 |
+ \ifnum\chimera@subfamily@col@green>\loopcount\relax% |
|
| 13262 |
+ \loopcount=\chimera@subfamily@col@green\relax% |
|
| 13263 |
+ \else% |
|
| 13264 |
+ \ifnum\chimera@subfamily@col@red>\loopcount\relax% |
|
| 13265 |
+ \loopcount=\chimera@subfamily@col@red\relax% |
|
| 13266 |
+ \fi% |
|
| 13267 |
+ \fi% |
|
| 13268 |
+ \xdef\max@green{\the\loopcount}%
|
|
| 13269 |
+ \loopcount=\chimera@subfamily@col@blue% |
|
| 13270 |
+ \ifnum\max@green>0\relax% |
|
| 13271 |
+ \multiply\loopcount by \max@yellow% |
|
| 13272 |
+ \divide\loopcount by \max@green% |
|
| 13273 |
+ \fi% |
|
| 13274 |
+ \advance\loopcount by \chimera@subfamily@col@white% |
|
| 13275 |
+ \multiply\loopcount by \temp@@% |
|
| 13276 |
+ \divide\loopcount by \temp@count% |
|
| 13277 |
+ \make@HEX% |
|
| 13278 |
+ \xdef\nineth@{\seventh@}%
|
|
| 13279 |
+ \loopcount=\chimera@subfamily@col@green% |
|
| 13280 |
+ \ifnum\max@green>0\relax% |
|
| 13281 |
+ \multiply\loopcount by \max@yellow% |
|
| 13282 |
+ \divide\loopcount by \max@green% |
|
| 13283 |
+ \fi% |
|
| 13284 |
+ \advance\loopcount by \chimera@subfamily@col@white% |
|
| 13285 |
+ \multiply\loopcount by \temp@@% |
|
| 13286 |
+ \divide\loopcount by \temp@count% |
|
| 13287 |
+ \make@HEX% |
|
| 13288 |
+ \xdef\nineth@{\seventh@\nineth@}%
|
|
| 13289 |
+ \loopcount=\chimera@subfamily@col@red% |
|
| 13290 |
+ \ifnum\max@green>0\relax% |
|
| 13291 |
+ \multiply\loopcount by \max@yellow% |
|
| 13292 |
+ \divide\loopcount by \max@green% |
|
| 13293 |
+ \fi% |
|
| 13294 |
+ \advance\loopcount by \chimera@subfamily@col@white% |
|
| 13295 |
+ \multiply\loopcount by \temp@@% |
|
| 13296 |
+ \divide\loopcount by \temp@count% |
|
| 13297 |
+ \make@HEX% |
|
| 13298 |
+ \xdef\nineth@{\seventh@\nineth@}%
|
|
| 13299 |
+ \ifx\chimera@labelOne@set\n@% |
|
| 13300 |
+ \xdef\chimera@labelOne@set{y}%
|
|
| 13301 |
+ \xdef\chimera@label@subfamily{.\chimera@label@subfamily}%
|
|
| 13302 |
+ \fi% |
|
| 13303 |
+ \immediate\write\exp@rt@chimerafile{setattr a radius \temp@ \unexpanded{} #0:\chimera@res@num\chimerach@in @ca}%
|
|
| 13304 |
+ \immediate\write\exp@rt@chimerafile{setattr a color #\nineth@ \unexpanded{} #0:\chimera@res@num\chimerach@in @ca}%
|
|
| 13305 |
+ \immediate\write\exp@rt@chimerafile{setattr a name '|| \chimera@label@subfamily' #0:\chimera@res@num\chimerach@in @ca}%
|
|
| 13306 |
+ \ifshow@sublogo |
|
| 13307 |
+ \ifnum\temp@@count>0 \else\temp@@count=1\fi% |
|
| 13308 |
+ \loopcount=\temp@@count% |
|
| 13309 |
+ \xdef\fourth@{\the\loopcount @}%
|
|
| 13310 |
+ \ifnum\loopcount>9999 \expandafter\decimal@A\fourth@ \else% |
|
| 13311 |
+ \ifnum\loopcount>999 \expandafter\decimal@B\fourth@ \else% |
|
| 13312 |
+ \ifnum\loopcount>99 \expandafter\decimal@C\fourth@ \else% |
|
| 13313 |
+ \ifnum\loopcount>9 \expandafter\decimal@D\fourth@ \else% |
|
| 13314 |
+ \expandafter\decimal@E\fourth@% |
|
| 13315 |
+ \fi\fi\fi\fi% |
|
| 13316 |
+ \loopcount=-\chimera@remaining@col@red\relax% |
|
| 13317 |
+ \xdef\chimera@remaining@col@red{\the\loopcount}%
|
|
| 13318 |
+ \loopcount=-\chimera@remaining@col@yellow\relax% |
|
| 13319 |
+ \xdef\chimera@remaining@col@yellow{\the\loopcount}%
|
|
| 13320 |
+ \loopcount=-\chimera@remaining@col@blue\relax% |
|
| 13321 |
+ \xdef\chimera@remaining@col@blue{\the\loopcount}%
|
|
| 13322 |
+ \loopcount=-\chimera@remaining@col@white\relax% |
|
| 13323 |
+ \xdef\chimera@remaining@col@white{\the\loopcount}%
|
|
| 13324 |
+ \loopcount=-\chimera@remaining@col@black% |
|
| 13325 |
+ \multiply\loopcount by 65535\relax% |
|
| 13326 |
+ \divide\loopcount by \temp@count% |
|
| 13327 |
+ \xdef\chimera@remaining@col@black{\the\loopcount}%
|
|
| 13328 |
+ \loopcount=65535\relax% |
|
| 13329 |
+ \advance\loopcount by -\chimera@remaining@col@black% |
|
| 13330 |
+ \xdef\temp@@{\the\loopcount}%
|
|
| 13331 |
+ \loopcount=\chimera@remaining@col@blue\relax% |
|
| 13332 |
+ \ifnum\chimera@remaining@col@yellow>\loopcount\relax% |
|
| 13333 |
+ \loopcount=\chimera@remaining@col@yellow\relax% |
|
| 13334 |
+ \else% |
|
| 13335 |
+ \ifnum\chimera@remaining@col@red>\loopcount\relax% |
|
| 13336 |
+ \loopcount=\chimera@remaining@col@red\relax% |
|
| 13337 |
+ \fi% |
|
| 13338 |
+ \fi% |
|
| 13339 |
+ \xdef\max@yellow{\the\loopcount}%
|
|
| 13340 |
+ \ifnum\chimera@remaining@col@blue<\chimera@remaining@col@yellow\relax% |
|
| 13341 |
+ \xdef\chimera@remaining@col@green{\chimera@remaining@col@blue}%
|
|
| 13342 |
+ \else% |
|
| 13343 |
+ \xdef\chimera@remaining@col@green{\chimera@remaining@col@yellow}%
|
|
| 13344 |
+ \fi% |
|
| 13345 |
+ \loopcount=\chimera@remaining@col@yellow\relax% |
|
| 13346 |
+ \advance\loopcount by -\chimera@remaining@col@green% |
|
| 13347 |
+ \xdef\chimera@remaining@col@yellow{\the\loopcount}%
|
|
| 13348 |
+ \loopcount=\chimera@remaining@col@blue\relax% |
|
| 13349 |
+ \advance\loopcount by -\chimera@remaining@col@green% |
|
| 13350 |
+ \xdef\chimera@remaining@col@blue{\the\loopcount}%
|
|
| 13351 |
+ \ifnum\chimera@remaining@col@blue>0\relax% |
|
| 13352 |
+ \ifnum\chimera@remaining@col@green>0\relax% |
|
| 13353 |
+ \loopcount=\chimera@remaining@col@blue\relax% |
|
| 13354 |
+ \multiply\loopcount by 2\relax \xdef\chimera@remaining@col@blue{\the\loopcount}%
|
|
| 13355 |
+ \loopcount=\chimera@remaining@col@green\relax% |
|
| 13356 |
+ \multiply\loopcount by 2\relax \xdef\chimera@remaining@col@green{\the\loopcount}%
|
|
| 13357 |
+ \fi% |
|
| 13358 |
+ \fi% |
|
| 13359 |
+ \loopcount=\chimera@remaining@col@green\relax% |
|
| 13360 |
+ \advance\loopcount by \chimera@remaining@col@yellow% |
|
| 13361 |
+ \xdef\chimera@remaining@col@green{\the\loopcount}%
|
|
| 13362 |
+ \loopcount=\chimera@remaining@col@red\relax% |
|
| 13363 |
+ \advance\loopcount by \chimera@remaining@col@yellow% |
|
| 13364 |
+ \xdef\chimera@remaining@col@red{\the\loopcount}%
|
|
| 13365 |
+ \loopcount=\chimera@remaining@col@blue\relax% |
|
| 13366 |
+ \ifnum\chimera@remaining@col@green>\loopcount\relax% |
|
| 13367 |
+ \loopcount=\chimera@remaining@col@green\relax% |
|
| 13368 |
+ \else% |
|
| 13369 |
+ \ifnum\chimera@remaining@col@red>\loopcount\relax% |
|
| 13370 |
+ \loopcount=\chimera@remaining@col@red\relax% |
|
| 13371 |
+ \fi% |
|
| 13372 |
+ \fi% |
|
| 13373 |
+ \xdef\max@green{\the\loopcount}%
|
|
| 13374 |
+ \loopcount=\chimera@remaining@col@blue% |
|
| 13375 |
+ \ifnum\max@green>0\relax% |
|
| 13376 |
+ \multiply\loopcount by \max@yellow% |
|
| 13377 |
+ \divide\loopcount by \max@green% |
|
| 13378 |
+ \fi% |
|
| 13379 |
+ \advance\loopcount by \chimera@remaining@col@white% |
|
| 13380 |
+ \multiply\loopcount by \temp@@% |
|
| 13381 |
+ \divide\loopcount by \temp@count% |
|
| 13382 |
+ \make@HEX% |
|
| 13383 |
+ \xdef\nineth@{\seventh@}%
|
|
| 13384 |
+ \loopcount=\chimera@remaining@col@green% |
|
| 13385 |
+ \ifnum\max@green>0\relax% |
|
| 13386 |
+ \multiply\loopcount by \max@yellow% |
|
| 13387 |
+ \divide\loopcount by \max@green% |
|
| 13388 |
+ \fi% |
|
| 13389 |
+ \advance\loopcount by \chimera@remaining@col@white% |
|
| 13390 |
+ \multiply\loopcount by \temp@@% |
|
| 13391 |
+ \divide\loopcount by \temp@count% |
|
| 13392 |
+ \make@HEX% |
|
| 13393 |
+ \xdef\nineth@{\seventh@\nineth@}%
|
|
| 13394 |
+ \loopcount=\chimera@remaining@col@red% |
|
| 13395 |
+ \ifnum\max@green>0\relax% |
|
| 13396 |
+ \multiply\loopcount by \max@yellow% |
|
| 13397 |
+ \divide\loopcount by \max@green% |
|
| 13398 |
+ \fi% |
|
| 13399 |
+ \advance\loopcount by \chimera@remaining@col@white% |
|
| 13400 |
+ \multiply\loopcount by \temp@@% |
|
| 13401 |
+ \divide\loopcount by \temp@count% |
|
| 13402 |
+ \make@HEX% |
|
| 13403 |
+ \xdef\nineth@{\seventh@\nineth@}%
|
|
| 13404 |
+ \ifx\chimera@label@remainingOne@set\n@% |
|
| 13405 |
+ \xdef\chimera@label@remainingOne@set{y}%
|
|
| 13406 |
+ \xdef\chimera@label@remaining{.\chimera@label@remaining}%
|
|
| 13407 |
+ \fi% |
|
| 13408 |
+ \immediate\write\exp@rt@chimerafile{setattr a radius \temp@ \unexpanded{} #1:\chimera@res@num\chimerach@in @ca}%
|
|
| 13409 |
+ \immediate\write\exp@rt@chimerafile{setattr a color #\nineth@ \unexpanded{} #1:\chimera@res@num\chimerach@in @ca}%
|
|
| 13410 |
+ \immediate\write\exp@rt@chimerafile{setattr a name '|| \chimera@label@remaining' #1:\chimera@res@num\chimerach@in @ca}%
|
|
| 13411 |
+ \fi% |
|
| 13412 |
+} |
|
| 13413 |
+\catcode`\"=12 \catcode`\#=6 \catcode`\~=13 |
|
| 13414 |
+\def\get@chimera@res@num#1,#2@{\xdef\chimera@res@num{#1}\xdef\chimera@stack{#2}}
|
|
| 13415 |
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
|
| 13416 |
+%%%% Chimera export routines end %%%% |
|
| 13417 |
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
|
| 12734 | 13418 |
\def\next@logo#1:#2,#3@{%
|
| 12735 | 13419 |
\xdef\first@{#1}\xdef\second@{#2}\xdef\last@{#3}%
|
| 12736 | 13420 |
\ifx\first@\ampers@nd% |
| 13421 |
+ \ifx\exp@rt@chimera\y@% |
|
| 13422 |
+ \xdef\chimera@stack{\chimera@stack @}%
|
|
| 13423 |
+ \expandafter\get@chimera@res@num\chimera@stack% |
|
| 13424 |
+ \ifx\chimera@res@num\ampers@nd% |
|
| 13425 |
+ \else% |
|
| 13426 |
+ \write@chimera@data% |
|
| 13427 |
+ \fi% |
|
| 13428 |
+ \xdef\chimera@label@subfamily{}%
|
|
| 13429 |
+ \xdef\chimera@label@remaining{}%
|
|
| 13430 |
+ \xdef\chimera@subfamily@col@red{0}%
|
|
| 13431 |
+ \xdef\chimera@subfamily@col@blue{0}%
|
|
| 13432 |
+ \xdef\chimera@subfamily@col@yellow{0}%
|
|
| 13433 |
+ \xdef\chimera@subfamily@col@black{0}%
|
|
| 13434 |
+ \xdef\chimera@subfamily@col@white{0}%
|
|
| 13435 |
+ \xdef\chimera@remaining@col@red{0}%
|
|
| 13436 |
+ \xdef\chimera@remaining@col@blue{0}%
|
|
| 13437 |
+ \xdef\chimera@remaining@col@yellow{0}%
|
|
| 13438 |
+ \xdef\chimera@remaining@col@black{0}%
|
|
| 13439 |
+ \xdef\chimera@remaining@col@white{0}%
|
|
| 13440 |
+ \xdef\chimera@labelOne@set{n}%
|
|
| 13441 |
+ \xdef\chimera@labelTwo@set{n}%
|
|
| 13442 |
+ \xdef\chimera@labelThree@set{n}%
|
|
| 13443 |
+ \xdef\chimera@label@remainingOne@set{n}%
|
|
| 13444 |
+ \xdef\chimera@label@remainingTwo@set{n}%
|
|
| 13445 |
+ \xdef\chimera@label@remainingThree@set{n}%
|
|
| 13446 |
+ \fi% |
|
| 12737 | 13447 |
\ifx\clear@logo\n@% |
| 12738 | 13448 |
\ifx\hide@sig\n@% |
| 12739 | 13449 |
\expandafter\firstchar@get\sublogo@sig% |
| ... | ... |
@@ -12755,12 +13465,10 @@ |
| 12755 | 13465 |
\fi% |
| 12756 | 13466 |
\fi% |
| 12757 | 13467 |
\temp@count=0% |
| 13468 |
+ \temp@@count=0% |
|
| 12758 | 13469 |
\kern\box@width% |
| 12759 | 13470 |
\advance\outerloopcount by 1 % |
| 12760 | 13471 |
\else% |
| 12761 |
- \ifnum#2=1% |
|
| 12762 |
- \temp@count=0% |
|
| 12763 |
- \else% |
|
| 12764 | 13472 |
\if\seq@type N% |
| 12765 | 13473 |
\loopcount=\second@% |
| 12766 | 13474 |
\multiply\loopcount by 2% |
| ... | ... |
@@ -12796,7 +13504,7 @@ |
| 12796 | 13504 |
\fi\fi\fi\fi% |
| 12797 | 13505 |
\xdef\third@{\fl@g\temp@}%
|
| 12798 | 13506 |
\ifnum\temp@count<0 % |
| 12799 |
- \ifnum\second@<0 \else\temp@count=0 \fi% |
|
| 13507 |
+ \ifnum\second@<0 \else\temp@@count=-\temp@count\relax\temp@count=0 \fi% |
|
| 12800 | 13508 |
\fi% |
| 12801 | 13509 |
\ifnum\temp@count>0 % |
| 12802 | 13510 |
\loopcount=\temp@count \xdef\fl@g{}%
|
| ... | ... |
@@ -12823,7 +13531,64 @@ |
| 12823 | 13531 |
\kern-\box@width% |
| 12824 | 13532 |
\fi% |
| 12825 | 13533 |
\advance\temp@count by \second@% |
| 12826 |
- \fi% |
|
| 13534 |
+ \xdef\temp@{\the\temp@count}%
|
|
| 13535 |
+ \ifx\exp@rt@chimera\y@% |
|
| 13536 |
+ \xdef\temp@@{\csname chimera@col@\first@\endcsname}%
|
|
| 13537 |
+ \ifnum\second@<0 % |
|
| 13538 |
+ \xdef\temp@@@{\csname chimera@remaining@col@\temp@@\endcsname}%
|
|
| 13539 |
+ \temp@count=\temp@@@% |
|
| 13540 |
+ \advance\temp@count by \second@% |
|
| 13541 |
+ \expandafter\xdef\csname chimera@remaining@col@\temp@@\endcsname{\the\temp@count}%
|
|
| 13542 |
+ \ifnum\second@<\label@threshold@lowerremainingIOOO% |
|
| 13543 |
+ \ifnum\second@<-999% |
|
| 13544 |
+ \ifx\chimera@label@remainingOne@set\n@% |
|
| 13545 |
+ \xdef\chimera@label@remainingOne@set{y}%
|
|
| 13546 |
+ \xdef\chimera@label@remaining{.\chimera@label@remaining}%
|
|
| 13547 |
+ \fi% |
|
| 13548 |
+ \fi% |
|
| 13549 |
+ \ifnum\second@<-1999% |
|
| 13550 |
+ \ifx\chimera@label@remainingTwo@set\n@% |
|
| 13551 |
+ \xdef\chimera@label@remainingTwo@set{y}%
|
|
| 13552 |
+ \xdef\chimera@label@remaining{:\chimera@label@remaining}%
|
|
| 13553 |
+ \fi% |
|
| 13554 |
+ \fi% |
|
| 13555 |
+ \ifnum\second@<-2999% |
|
| 13556 |
+ \ifx\chimera@label@remainingThree@set\n@% |
|
| 13557 |
+ \xdef\chimera@label@remainingThree@set{y}%
|
|
| 13558 |
+ \xdef\chimera@label@remaining{>\chimera@label@remaining}%
|
|
| 13559 |
+ \fi% |
|
| 13560 |
+ \fi% |
|
| 13561 |
+ \xdef\chimera@label@remaining{\first@\chimera@label@remaining}%
|
|
| 13562 |
+ \fi% |
|
| 13563 |
+ \else% |
|
| 13564 |
+ \xdef\temp@@@{\csname chimera@subfamily@col@\temp@@\endcsname}%
|
|
| 13565 |
+ \temp@count=\temp@@@% |
|
| 13566 |
+ \advance\temp@count by \second@% |
|
| 13567 |
+ \expandafter\xdef\csname chimera@subfamily@col@\temp@@\endcsname{\the\temp@count}%
|
|
| 13568 |
+ \ifnum\second@>\label@threshold@lowerIOOO% |
|
| 13569 |
+ \ifnum\second@>999% |
|
| 13570 |
+ \ifx\chimera@labelOne@set\n@% |
|
| 13571 |
+ \xdef\chimera@labelOne@set{y}%
|
|
| 13572 |
+ \xdef\chimera@label@subfamily{.\chimera@label@subfamily}%
|
|
| 13573 |
+ \fi% |
|
| 13574 |
+ \fi% |
|
| 13575 |
+ \ifnum\second@>1999% |
|
| 13576 |
+ \ifx\chimera@labelTwo@set\n@% |
|
| 13577 |
+ \xdef\chimera@labelTwo@set{y}%
|
|
| 13578 |
+ \xdef\chimera@label@subfamily{:\chimera@label@subfamily}%
|
|
| 13579 |
+ \fi% |
|
| 13580 |
+ \fi% |
|
| 13581 |
+ \ifnum\second@>2999% |
|
| 13582 |
+ \ifx\chimera@labelThree@set\n@% |
|
| 13583 |
+ \xdef\chimera@labelThree@set{y}%
|
|
| 13584 |
+ \xdef\chimera@label@subfamily{>\chimera@label@subfamily}%
|
|
| 13585 |
+ \fi% |
|
| 13586 |
+ \fi% |
|
| 13587 |
+ \xdef\chimera@label@subfamily{\first@\chimera@label@subfamily}%
|
|
| 13588 |
+ \fi% |
|
| 13589 |
+ \fi% |
|
| 13590 |
+ \fi% |
|
| 13591 |
+ \temp@count=\temp@% |
|
| 12827 | 13592 |
\fi% |
| 12828 | 13593 |
\xdef\temp@{\last@.}%
|
| 12829 | 13594 |
\ifx\temp@\d@t% |
| ... | ... |
@@ -13125,10 +13890,23 @@ |
| 13125 | 13890 |
\xdef\featureposttttop{1} \xdef\featureposbbbbottom{1}%
|
| 13126 | 13891 |
\findc@nsensus% |
| 13127 | 13892 |
\noindent% |
| 13893 |
+ \setlength{\bar@length}{0pt}%
|
|
| 13894 |
+ \xdef\fe@turep@s{top}%
|
|
| 13128 | 13895 |
\ifnum\feature@ttttop=1 |
| 13896 |
+ \advance\bar@length by \feature@tttop\baselineskip% |
|
| 13897 |
+ \advance\bar@length by \feature@ttop\baselineskip% |
|
| 13898 |
+ \advance\bar@length by \feature@top\baselineskip% |
|
| 13899 |
+ \multiply\bar@length by 2% |
|
| 13900 |
+ \advance\bar@length by \tttt@sp@ce% |
|
| 13901 |
+ \advance\bar@length by \ttt@sp@ce% |
|
| 13902 |
+ \advance\bar@length by \tt@sp@ce% |
|
| 13129 | 13903 |
\ifnum\featureonttttop=0 \xdef\feature@ttttop{0} \fi
|
| 13130 | 13904 |
\xdef\bottop@{ttttop}%
|
| 13905 |
+ \xdef\shift@feature{n}%
|
|
| 13131 | 13906 |
\put@feature% |
| 13907 |
+ \advance\bar@length by -\baselineskip% |
|
| 13908 |
+ \ifx\shift@feature\y@ \vspace{-\bar@length}\fi%
|
|
| 13909 |
+ \setlength{\bar@length}{0pt}%
|
|
| 13132 | 13910 |
\vspace{\tttt@sp@ce}%
|
| 13133 | 13911 |
\vspace{-\baselineskip}%
|
| 13134 | 13912 |
\newline\hbox{}%
|
| ... | ... |
@@ -13136,9 +13914,18 @@ |
| 13136 | 13914 |
\iffix@\ifttttopfeature \vspace{\tttt@sp@ce}\newline\hbox{}\newline\hbox{}\fi\fi
|
| 13137 | 13915 |
\fi |
| 13138 | 13916 |
\ifnum\feature@tttop=1 |
| 13917 |
+ \advance\bar@length by \feature@ttop\baselineskip% |
|
| 13918 |
+ \advance\bar@length by \feature@top\baselineskip% |
|
| 13919 |
+ \multiply\bar@length by 2% |
|
| 13920 |
+ \advance\bar@length by \ttt@sp@ce% |
|
| 13921 |
+ \advance\bar@length by \tt@sp@ce% |
|
| 13139 | 13922 |
\ifnum\featureontttop=0 \xdef\feature@tttop{0} \fi
|
| 13140 | 13923 |
\xdef\bottop@{tttop}%
|
| 13924 |
+ \xdef\shift@feature{n}%
|
|
| 13141 | 13925 |
\put@feature% |
| 13926 |
+ \advance\bar@length by -\baselineskip% |
|
| 13927 |
+ \ifx\shift@feature\y@ \vspace{-\bar@length}\fi%
|
|
| 13928 |
+ \setlength{\bar@length}{0pt}%
|
|
| 13142 | 13929 |
\vspace{\ttt@sp@ce}%
|
| 13143 | 13930 |
\vspace{-\baselineskip}%
|
| 13144 | 13931 |
\newline\hbox{}%
|
| ... | ... |
@@ -13146,9 +13933,16 @@ |
| 13146 | 13933 |
\iffix@\iftttopfeature \vspace{\ttt@sp@ce}\newline\hbox{}\newline\hbox{}\fi\fi
|
| 13147 | 13934 |
\fi |
| 13148 | 13935 |
\ifnum\feature@ttop=1 |
| 13936 |
+ \advance\bar@length by \feature@top\baselineskip% |
|
| 13937 |
+ \multiply\bar@length by 2% |
|
| 13938 |
+ \advance\bar@length by \tt@sp@ce\message{tt\the\bar@length tt}%
|
|
| 13149 | 13939 |
\ifnum\featureonttop=0 \xdef\feature@ttop{0} \fi
|
| 13150 | 13940 |
\xdef\bottop@{ttop}%
|
| 13941 |
+ \xdef\shift@feature{n}%
|
|
| 13151 | 13942 |
\put@feature% |
| 13943 |
+ \advance\bar@length by -\baselineskip% |
|
| 13944 |
+ \ifx\shift@feature\y@ \vspace{-\bar@length}\fi%
|
|
| 13945 |
+ \setlength{\bar@length}{0pt}%
|
|
| 13152 | 13946 |
\vspace{\tt@sp@ce}%
|
| 13153 | 13947 |
\vspace{-\baselineskip}%
|
| 13154 | 13948 |
\newline\hbox{}%
|
| ... | ... |
@@ -13264,6 +14058,9 @@ |
| 13264 | 14058 |
\ifnum\ruler@rot=0 \vspace{0.25\baselineskip}\fi%
|
| 13265 | 14059 |
\fi% |
| 13266 | 14060 |
\fi% |
| 14061 |
+ \xdef\fe@turep@s{bottom}%
|
|
| 14062 |
+ \setlength{\bar@length}{0pt}%
|
|
| 14063 |
+ \xdef\b@feature@count{0}
|
|
| 13267 | 14064 |
\ifnum\feature@bottom=1 % |
| 13268 | 14065 |
\ifnum\featureonbottom=0 \xdef\feature@bottom{0}\fi%
|
| 13269 | 14066 |
\xdef\bottop@{bottom}%
|
| ... | ... |
@@ -13273,6 +14070,9 @@ |
| 13273 | 14070 |
\vspace{\b@r@stretch\box@height}%
|
| 13274 | 14071 |
\fi% |
| 13275 | 14072 |
\put@feature% |
| 14073 |
+ \temp@@count=\b@feature@count% |
|
| 14074 |
+ \advance\temp@@count by 1% |
|
| 14075 |
+ \xdef\b@feature@count{\the\temp@@count}%
|
|
| 13276 | 14076 |
\else |
| 13277 | 14077 |
\iffix@ |
| 13278 | 14078 |
\if\bottom@stretch y% |
| ... | ... |
@@ -13285,14 +14085,24 @@ |
| 13285 | 14085 |
\fi% |
| 13286 | 14086 |
\fi% |
| 13287 | 14087 |
\ifnum\feature@bbottom=1 % |
| 14088 |
+ \advance\bar@length by \b@feature@count \baselineskip% |
|
| 14089 |
+ \multiply\bar@length by \b@r@stretch% |
|
| 14090 |
+ \multiply\bar@length by 2% |
|
| 14091 |
+ \advance\bar@length by \bb@sp@ce\message{bb\the\bar@length bb}%
|
|
| 13288 | 14092 |
\ifnum\featureonbbottom=0 \xdef\feature@bbottom{0}\fi%
|
| 13289 | 14093 |
\xdef\bottop@{bbottom}%
|
| 13290 | 14094 |
\vspace{\bb@sp@ce}%
|
| 13291 | 14095 |
\if\bbottom@stretch y% |
| 14096 |
+ \advance\bar@length by -\box@height% |
|
| 14097 |
+ \advance\bar@length by \b@r@stretch\box@height% |
|
| 13292 | 14098 |
\vspace{-\box@height}%
|
| 13293 | 14099 |
\vspace{\b@r@stretch\box@height}%
|
| 13294 | 14100 |
\fi% |
| 14101 |
+ \setlength{\bar@length}{0pt}%
|
|
| 13295 | 14102 |
\put@feature% |
| 14103 |
+ \temp@@count=\b@feature@count% |
|
| 14104 |
+ \advance\temp@@count by 1% |
|
| 14105 |
+ \xdef\b@feature@count{\the\temp@@count}%
|
|
| 13296 | 14106 |
\else |
| 13297 | 14107 |
\iffix@ |
| 13298 | 14108 |
\if\bbottom@stretch y% |
| ... | ... |
@@ -13305,6 +14115,10 @@ |
| 13305 | 14115 |
\fi |
| 13306 | 14116 |
\fi |
| 13307 | 14117 |
\ifnum\feature@bbbottom=1 % |
| 14118 |
+ \advance\bar@length by \b@feature@count\baselineskip% |
|
| 14119 |
+ \multiply\bar@length by \b@r@stretch% |
|
| 14120 |
+ \multiply\bar@length by 2% |
|
| 14121 |
+ \advance\bar@length by \bbb@sp@ce\message{bbb\the\bar@length bbb}%
|
|
| 13308 | 14122 |
\ifnum\featureonbbbottom=0 \xdef\feature@bbbottom{0}\fi%
|
| 13309 | 14123 |
\xdef\bottop@{bbbottom}%
|
| 13310 | 14124 |
\vspace{\bbb@sp@ce}%
|
| ... | ... |
@@ -13313,6 +14127,9 @@ |
| 13313 | 14127 |
\vspace{\b@r@stretch\box@height}%
|
| 13314 | 14128 |
\fi% |
| 13315 | 14129 |
\put@feature% |
| 14130 |
+ \temp@@count=\b@feature@count% |
|
| 14131 |
+ \advance\temp@@count by 1% |
|
| 14132 |
+ \xdef\b@feature@count{\the\temp@@count}%
|
|
| 13316 | 14133 |
\else |
| 13317 | 14134 |
\iffix@ |
| 13318 | 14135 |
\if\bbbottom@stretch y% |
| ... | ... |
@@ -13325,6 +14142,10 @@ |
| 13325 | 14142 |
\fi |
| 13326 | 14143 |
\fi |
| 13327 | 14144 |
\ifnum\feature@bbbbottom=1 % |
| 14145 |
+ \advance\bar@length by \b@feature@count\baselineskip% |
|
| 14146 |
+ \multiply\bar@length by \b@r@stretch% |
|
| 14147 |
+ \multiply\bar@length by 2% |
|
| 14148 |
+ \advance\bar@length by \bbbb@sp@ce\message{bbbb\the\bar@length bbbb}%
|
|
| 13328 | 14149 |
\ifnum\featureonbbbbottom=0 \xdef\feature@bbbbottom{0}\fi%
|
| 13329 | 14150 |
\xdef\bottop@{bbbbottom}%
|
| 13330 | 14151 |
\vspace{\bbbb@sp@ce}%
|
| ... | ... |
@@ -14030,6 +14851,7 @@ |
| 14030 | 14851 |
\fi |
| 14031 | 14852 |
\ifshow@sublogo \closein\sublogofile \fi |
| 14032 | 14853 |
\ifx\exp@rt\y@ \closeout\exp@rtfile \fi |
| 14854 |
+ \ifx\exp@rt@chimera\y@ \closeout\exp@rt@chimerafile \fi% |
|
| 14033 | 14855 |
\closein\alignfile |
| 14034 | 14856 |
\message{)}
|
| 14035 | 14857 |
} |
| ... | ... |
@@ -14181,8 +15003,6 @@ |
| 14181 | 15003 |
\ifnum\loopcount<\seq@count \repeat |
| 14182 | 15004 |
\xdef\seq@order{\seq@order,@}
|
| 14183 | 15005 |
\killseq@count=\seq@count |
| 14184 |
- \seq@percent=100 |
|
| 14185 |
- \ifnum\seq@count>0 \divide\seq@percent by \seq@count \fi |
|
| 14186 | 15006 |
\fi |
| 14187 | 15007 |
\fi |
| 14188 | 15008 |
} |
| ... | ... |
@@ -14450,6 +15270,18 @@ |
| 14450 | 15270 |
\caption[\c@pshort]{\c@p}
|
| 14451 | 15271 |
\fi |
| 14452 | 15272 |
\fi |
| 15273 |
+ \loopcount = \thresh@ld \multiply\loopcount by \seq@count \divide\loopcount by 100 |
|
| 15274 |
+ \xdef\thresh@ld@{\the\loopcount}
|
|
| 15275 |
+ \loopcount = \all@thresh@ld \multiply\loopcount by \seq@count \divide\loopcount by 100 |
|
| 15276 |
+ \xdef\all@thresh@ld@{\the\loopcount}
|
|
| 15277 |
+ \if\exp@rt@chimera\y@% |
|
| 15278 |
+ \ifshow@logo% |
|
| 15279 |
+ \init@chimera@file% |
|
| 15280 |
+ \else% |
|
| 15281 |
+ \ifshow@sublogo% |
|
| 15282 |
+ \init@chimera@file% |
|
| 15283 |
+ \fi\fi% |
|
| 15284 |
+ \fi% |
|
| 14453 | 15285 |
\bgroup |
| 14454 | 15286 |
\ifx\out@put\y@\bigskip\fi |
| 14455 | 15287 |
\iffuncmode \show@consfalse \fi |
| ... | ... |
@@ -14607,6 +15439,32 @@ |
| 14607 | 15439 |
\expandafter\xdef\csname group@num1\endcsname{0}
|
| 14608 | 15440 |
\expandafter\xdef\csname group@num2\endcsname{0}
|
| 14609 | 15441 |
\xdef\exp@rt@num{0} \xdef\exp@rt{n}
|
| 15442 |
+\xdef\exp@rt@chimera@num{1} \xdef\exp@rt@chimera{n} \xdef\chimera@stack{}
|
|
| 15443 |
+\xdef\chimerab@llSc@le{1.0}
|
|
| 15444 |
+\memelabelcutoff{0.1}
|
|
| 15445 |
+\xdef\chimera@labelOne@set{n}
|
|
| 15446 |
+\xdef\chimera@labelTwo@set{n}
|
|
| 15447 |
+\xdef\chimera@labelThree@set{n}
|
|
| 15448 |
+\xdef\chimera@labelOne@remaining@set{n}
|
|
| 15449 |
+\xdef\chimera@labelTwo@remaining@set{n}
|
|
| 15450 |
+\xdef\chimera@labelThree@remaining@set{n}
|
|
| 15451 |
+\xdef\chimera@xdist@nce{0} \xdef\chimera@ydist@nce{40} \xdef\chimera@zdist@nce{0}
|
|
| 15452 |
+\xdef\chimerach@in{} \xdef\chimera@seqnum{0}
|
|
| 15453 |
+\xdef\chimera@label@subfamily{} \xdef\chimera@label@remaining{}
|
|
| 15454 |
+\memeStandardcolors |
|
| 15455 |
+\xdef\chimera@subfamily@col@red{0}%
|
|
| 15456 |
+\xdef\chimera@subfamily@col@blue{0}%
|
|
| 15457 |
+\xdef\chimera@subfamily@col@yellow{0}%
|
|
| 15458 |
+\xdef\chimera@subfamily@col@black{0}%
|
|
| 15459 |
+\xdef\chimera@subfamily@col@white{0}%
|
|
| 15460 |
+\xdef\chimera@subfamily@col@none{0}%
|
|
| 15461 |
+\xdef\chimera@remaining@col@red{0}%
|
|
| 15462 |
+\xdef\chimera@remaining@col@blue{0}%
|
|
| 15463 |
+\xdef\chimera@remaining@col@yellow{0}%
|
|
| 15464 |
+\xdef\chimera@remaining@col@black{0}%
|
|
| 15465 |
+\xdef\chimera@remaining@col@white{0}%
|
|
| 15466 |
+\xdef\chimera@remaining@col@none{0}%
|
|
| 15467 |
+\xdef\echo@filename{}
|
|
| 14610 | 15468 |
\xdef\divref@{0}
|
