BioPerl
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deobfuscator/Deobfuscator/cgi-bin/deob_interface.cgi view on Meta::CPAN
$sort_order = param('sort_order') ? param('sort_order') : 'by method';
# define some styles
my $style1
= qq{style="border-collapse:collapse;border:solid black 1px;font-family:verdana;font-size:10px;background-color:lightgrey;padding:3"};
my $style2
= qq{style="border-collapse:collapse;border:solid black 1px;font-family:verdana;font-size:10px;padding:3"};
my $style3
= qq{style="border-collapse:collapse;border:solid black 1px;font-family:verdana;font-size:14px;padding:3"};
my $style4
= qq{style="border-collapse:collapse;border:0px;font-family:verdana;font-size:18px;font-weight:bold;padding:3"};
my $style5 = qq{style="font-family:verdana;font-size:14px;padding:3"};
# Open file containing all Bioperl package names
open my $MODS, '<', $PERLMODULES
or die "Could not read list of Perl module names '$PERLMODULES': $!\n";
# Open BerkeleyDB by getting hash references
$ref_BerkeleyDB_packages = Deobfuscator::open_db($BerkeleyDB_packages);
$ref_BerkeleyDB_methods = Deobfuscator::open_db($BerkeleyDB_methods);
ide/bioperl-mode/site-lisp/bioperl-init.el view on Meta::CPAN
(define-key map "i" 'imenu)
(define-key map "P" 'bioperl-view-parents-this-buffer)
(define-key map "B" 'bioperl-view-parents-this-buffer)
(define-key map "\C-m" 'bioperl-view-pod)
(define-key map "\C-\M-m" 'bioperl-view-pod-method)))
map )
;; and now, a total kludge.
(view-mode))
(defface pod-section-face
'( (t (:weight bold :foreground "maroon3") ) )
"Highlight for pod section names.")
(defvar pod-section-face 'pod-section-face)
(defface pod-bioperl-identifier-face
'( (t (:foreground "blue3" :weight bold)))
"Highlight for bioperl identifiers")
(defvar pod-bioperl-identifier-face 'pod-bioperl-identifier-face)
(defface pod-method-pod-tag-face
'( (t (:foreground "blue4")) )
"Highlight for method pod tags (Title, Usage, etc.)")
(defvar pod-method-pod-tag-face 'pod-method-pod-tag-face)
(defface pod-blue-man-face
'( (t (:background "blue" :foreground "dark blue")))
"My world is blue.")
(defvar pod-blue-man-face 'pod-blue-man-face)
(defface pod-subsec-header-face
'( (t (:weight bold :slant italic :foreground "blue4")))
"Highlight pod subsection headers")
(defvar pod-subsec-header-face 'pod-subsec-header-face)
(defface pod-method-subsec-face
'( (t (:slant italic :foreground "maroon4")))
"Highlight for APPENDIX subsections")
(defvar pod-method-subsec-face 'pod-method-subsec-face)
(defface pod-method-name-face
'( (t (:weight bold) ) )
"Highlight pod method names")
(defvar pod-method-name-face 'pod-method-name-face)
(defface pod-key-value-arg-face
'( (t (:slant italic :foreground "green3")) )
"Highlight for key-value keys (-something)" )
(defvar pod-key-value-arg-face 'pod-key-value-arg-face)
(defface pod-deref-symb-face
'( (t (:weight bold :foreground "blue4")))
"Highlight '->' ")
(defvar pod-deref-symb-face 'pod-deref-symb-face)
(defface pod-assoc-symb-face
'( (t (:weight bold :foreground "green3")))
"Highlight '=>' ")
(defvar pod-assoc-symb-face 'pod-assoc-symb-face)
(defvar bioperl-pod-font-lock-keywords
'(
;; rudimentary perl syntax highlighting
("[%$][{]?\\([a-zA-Z0-9_]+\\)[}]?" 1 font-lock-variable-name-face)
("[^a-zA-Z0-9]@[{]?\\([a-zA-Z0-9_]+\\)[}]?" 1 font-lock-variable-name-face)
("\\>->\\<" . pod-deref-symb-face)
("\\(?:\\s \\|\\>\\)\\(=>\\)\\(?:\\s \\|\\<\\|[\'\"]\\)" 1 pod-assoc-symb-face)
t/data/Bird_Ovomucoids.nex view on Meta::CPAN
Struthio_camelus VKYPNTNEEGKEVVLPKILSPIGSDGVYSNELANIEYTNVSK??????FAT--VDDYKPVPLDYMLDSKTSNKNNVVESSGTLRHFGK [86]
Rhea_americana .............L..E..N.V.T................?.D?????...--...H...S.E..........D.....N...S.... [86]
Pterocnemia_pennata .............L..E..N.V.A..................DHD?EV...--...H...S.E..........D.....N...S.... [86]
Casuarius_casuarius ........D....L.....N.........DD......A....DHDKEV...--..E....SPE.......N..DS....N...G.... [86]
Dromaius_novaehollandiae ........D....L.....N..........D......A..??D?????...--.......S.E.......N..D.....N...G.... [86]
Nothoprocta_cinerascens .....A.D.....P...TP...A.NA.FGS....V....I..DHDK?????T-..G...AT.E.F..NQ.A..A....KNV....L.. [87]
Eudromia_elegans .R.....D.....P...TP..V.AN....S....V....I?.?????????S-I.G...AT.EFF..NQ....A.A..KNV..N.I.E [87]
Pygoscelis_adeliae_f .TF..........LVT.......T..................DHDKEVI..--.......S.E..............D.N...S.... [86]
Pygoscelis_adeliae_y .T...........LVT.......T..................DHDKEVI..--.......S.E..............D.N...S.... [86]
Spheniscus_humboldti .T.S.........LIT.......T..................D?DKEVI..--I......S.E..............D.N.I.S.... [86]
Phalacrocorax_sulcirostris .S.SK.......ALVT.......T..............KI..DHDKEVI..--.......S.E.............AD.N...S.... [86]
Anhinga_novaehollandeae .L.S.........LVT.......T................T.DHDKEVI.S--.......S.E..............D.N...S.... [86]
Nycticorax_nycticorax .T.S.A....R..LVT.......A..........M....I..DHDGEVIV.--.......SPEN.V.......D..AD.N...S.... [86]
Chauna_chavaria .R...........L.T.T.....T..................DRDKEAV..--......AT.E....NQ....S...D.N...S.... [86]
Anseranas_semipalmata .R...S.......L.T.D...................A....DHDKEAV..--..E...AT.E....NQ........D.N...S.... [86]
Dendrocygna_arcuata .RF..........L.T.E...V.................I..D?DKEAV..--......AT.E....N..G......D.N...S.... [86]
Dendrocygna_autumnalis .RF..........L.T.D.....................I..DHDKEAV..--......AT.E....N..G......D.N...S.... [86]
Dendrocygna_eytoni_d .RF..........L.T.DVI.V............L....I..DHDKEAV..--....R.DT.E....N..G......D.N...S.... [86]
Dendrocygna_eytoni_e .RF..........L.T.DVI.V............L....I..DHDKEAV..--..E.R.DT.E....N..G......D.N...S.... [86]
Dendrocygna_viduata .RFS.........L.T.E...V.................I..D?D?EAV..--......AT.E....N..G.R....D.N...S.... [86]
t/data/Bird_Ovomucoids.nex view on Meta::CPAN
TRANSLATE
1 Struthio_camelus,
2 Rhea_americana,
3 Pterocnemia_pennata,
4 Casuarius_casuarius,
5 Dromaius_novaehollandiae,
6 Nothoprocta_cinerascens,
7 Eudromia_elegans,
8 Pygoscelis_adeliae_f,
9 Pygoscelis_adeliae_y,
10 Spheniscus_humboldti,
11 Phalacrocorax_sulcirostris,
12 Anhinga_novaehollandeae,
13 Nycticorax_nycticorax,
14 Chauna_chavaria,
15 Anseranas_semipalmata,
16 Dendrocygna_arcuata,
17 Dendrocygna_autumnalis,
18 Dendrocygna_eytoni_d,
19 Dendrocygna_eytoni_e,
20 Dendrocygna_viduata,
t/data/mini-AE001405.gb view on Meta::CPAN
PUBMED 9804551
REFERENCE 2 (bases 1 to 11389)
AUTHORS Gardner,M.J., Hall,N., Fung,E., White,O., Berriman,M., Hyman,R.W.,
Carlton,J.M., Pain,A., Nelson,K.E., Bowman,S., Paulsen,I.T.,
James,K., Eisen,J.A., Rutherford,K., Salzberg,S.L., Craig,A.,
Kyes,S., Chan,M.S., Nene,V., Shallom,S.J., Suh,B., Peterson,J.,
Angiuoli,S., Pertea,M., Allen,J., Selengut,J., Haft,D.,
Mather,M.W., Vaidya,A.B., Martin,D.M., Fairlamb,A.H.,
Fraunholz,M.J., Roos,D.S., Ralph,S.A., McFadden,G.I.,
Cummings,L.M., Subramanian,G.M., Mungall,C., Venter,J.C.,
Carucci,D.J., Hoffman,S.L., Newbold,C., Davis,R.W., Fraser,C.M. and
Barrell,B.
TITLE Genome sequence of the human malaria parasite Plasmodium falciparum
JOURNAL Nature 419 (6906), 498-511 (2002)
PUBMED 12368864
REFERENCE 3 (bases 1 to 11389)
AUTHORS Gardner,M.J.
TITLE Direct Submission
JOURNAL Submitted (02-OCT-2002) The Institute for Genomic Research, 9712
Medical Center Dr, Rockville, MD 20850, USA
COMMENT On Oct 4, 2002 this sequence version replaced gi:3845224.
t/data/tol-2010-02-18.nhx view on Meta::CPAN
(((aquifex[&&NHX:TOL=59615],calderobacterium[&&NHX:TOL=59616],hydrogenobacter[&&NHX:TOL=59617],thermocrinis[&&NHX:TOL=59618],hydrogenothermus[&&NHX:TOL=59619],persephonella[&&NHX:TOL=59620],sulfurihydrogenibium[&&NHX:TOL=59621],balnearium[&&NHX:TOL=5...
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