Bio-Phylo
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lib/Bio/Phylo/Forest/DrawNodeRole.pm view on Meta::CPAN
=item set_clade_label_font()
Type : Mutator
Title : set_clade_label_font
Usage : $node->set_clade_label_font({ '-face' => 'Verdana' });
Function: Sets font properties for the clade label
Returns : $self
Args : {
'-face' => 'Verdana', # Arial, Times, etc.
'-weight' => 'bold',
'-style' => 'italic',
'-colour' => 'red',
}
=back
=head2 ACCESSORS
=over
lib/Bio/Phylo/Util/Logger.pm view on Meta::CPAN
our ( %VERBOSITY, $PREFIX, %STYLE );
our $STYLE = 'detailed';
our $COLORED = 1; # new default: we use colors
our $TRACEBACK = 0;
our @EXPORT_OK = qw(DEBUG INFO WARN ERROR FATAL VERBOSE);
our %EXPORT_TAGS = ( 'simple' => [@EXPORT_OK], 'levels' => [@EXPORT_OK] );
our %COLORS = (
'DEBUG' => 'blue',
'INFO' => 'green',
'WARN' => 'yellow',
'ERROR' => 'bold red',
'FATAL' => 'red',
);
BEGIN {
# compute the path to the root of Bio::Phylo,
# use that as the default prefix
my $package = __PACKAGE__;
my $file = __FILE__;
$package =~ s/::/\//g;
t/14-nexus.t view on Meta::CPAN
20 Synthliboramphus_hypoleucus,
21 Synthliboramphus_antiquus,
22 Synthliboramphus_wumizusume,
23 Podiceps_cristatus,
24 Pygoscelis_papua,
25 Pygoscelis_antarctica,
26 Pygoscelis_adeliae,
27 Aptenodytes_forsteri,
28 Aptenodytes_patagonicus,
29 Eudyptula_minor,
30 Spheniscus_humboldti,
31 Spheniscus_mendiculus,
32 Spheniscus_magellanicus,
33 Spheniscus_demersus,
34 Megadyptes_antipodes,
35 Eudyptes_pachyrhynchus,
36 Eudyptes_chrysocome,
37 Eudyptes_chrysolophus,
38 Eudyptes_sclateri;
tree tree.0.16248.085507 = (((((1:0.0252829964,((37:0.0923922678,36:0.0227291363):0.0214856938,(30:0.0985772880,0:0.0009462633):0.0085211709):0.0179755543):0.0205001767,(7:0.0424374264,((9:0.0669529421,14:0.0573991137):0.0739853752,((20:0.067712522...
end;
BAYES_PHYLOGENIES
;
my $bayes_phylogenies_newick =
'(((((Uria_lomvia:0.025283,((Eudyptes_chrysolophus:0.0923923,Eudyptes_chrysocome:0.0227291):0.0214857,(Spheniscus_humboldti:0.0985773,Uria_aalge:0.000946263):0.00852117):0.0179756):0.0205002,(Fratercula_cirrhata:0.0424374,((Fratercula_arctica:0.06695...
################################################################################
################################################################################
################################################################################
################################################################################
# Done defining nexus tokens, let's try to parse them.
print "--------------------------------------------------------------------\n";
eval { parse( '-format' => 'nexus', '-string' => $testparse ) };
if ($@) {
print $@->trace->as_string;
die $@;
t/32-tolweb.t view on Meta::CPAN
</NODE>
<NODE EXTINCT="0" ID="131619" CONFIDENCE="0" PHYLESIS="0" LEAF="1" HASPAGE="0" ANCESTORWITHPAGE="113128" ITALICIZENAME="1" INCOMPLETESUBGROUPS="0" SHOWAUTHORITY="1" SHOWAUTHORITYCONTAINING="1" IS_NEW_COMBINATION="0" COMBINATION_DATE="nu...
<NAME><![CDATA[Bembidion guamani]]></NAME>
<DESCRIPTION></DESCRIPTION>
<AUTHORITY><![CDATA[Moret & Toledano]]></AUTHORITY>
<NAMECOMMENT></NAMECOMMENT>
<COMBINATION_AUTHOR></COMBINATION_AUTHOR>
<AUTHDATE>2002</AUTHDATE>
</NODE>
<NODE EXTINCT="0" ID="131620" CONFIDENCE="0" PHYLESIS="0" LEAF="1" HASPAGE="0" ANCESTORWITHPAGE="113128" ITALICIZENAME="1" INCOMPLETESUBGROUPS="0" SHOWAUTHORITY="1" SHOWAUTHORITYCONTAINING="1" IS_NEW_COMBINATION="0" COMBINATION_DATE="nu...
<NAME><![CDATA[Bembidion humboldti]]></NAME>
<DESCRIPTION></DESCRIPTION>
<AUTHORITY><![CDATA[Moret & Toledano]]></AUTHORITY>
<NAMECOMMENT></NAMECOMMENT>
<COMBINATION_AUTHOR></COMBINATION_AUTHOR>
<AUTHDATE>2002</AUTHDATE>
</NODE>
<NODE EXTINCT="0" ID="131621" CONFIDENCE="0" PHYLESIS="0" LEAF="1" HASPAGE="0" ANCESTORWITHPAGE="113128" ITALICIZENAME="1" INCOMPLETESUBGROUPS="0" SHOWAUTHORITY="1" SHOWAUTHORITYCONTAINING="1" IS_NEW_COMBINATION="0" COMBINATION_DATE="nu...
<NAME><![CDATA[Bembidion illuchi]]></NAME>
<DESCRIPTION></DESCRIPTION>
<AUTHORITY><![CDATA[Moret & Toledano]]></AUTHORITY>
t/32-tolweb.t view on Meta::CPAN
<COMMENTS></COMMENTS>
</OTHERNAME>
<OTHERNAME ISIMPORTANT="0" ISPREFERRED="0" SEQUENCE="1" DATE="1880" ITALICIZENAME="1">
<NAME><![CDATA[Bembidion parvicolle]]></NAME>
<AUTHORITY><![CDATA[Sahlberg, J.]]></AUTHORITY>
<COMMENTS></COMMENTS>
</OTHERNAME>
</OTHERNAMES>
</NODE>
<NODE EXTINCT="0" ID="23755" CONFIDENCE="0" PHYLESIS="0" LEAF="1" HASPAGE="0" ANCESTORWITHPAGE="23690" ITALICIZENAME="1" INCOMPLETESUBGROUPS="0" SHOWAUTHORITY="1" SHOWAUTHORITYCONTAINING="1" IS_NEW_COMBINATION="0" COMBINATION_DATE="null" CH...
<NAME><![CDATA[Bembidion humboldtense]]></NAME>
<DESCRIPTION></DESCRIPTION>
<AUTHORITY><![CDATA[Blaisdell]]></AUTHORITY>
<NAMECOMMENT></NAMECOMMENT>
<COMBINATION_AUTHOR></COMBINATION_AUTHOR>
<AUTHDATE>1902</AUTHDATE>
<OTHERNAMES>
<OTHERNAME ISIMPORTANT="0" ISPREFERRED="0" SEQUENCE="0" DATE="1920" ITALICIZENAME="1">
<NAME><![CDATA[Bembidion humboldtiense]]></NAME>
<AUTHORITY><![CDATA[Leng]]></AUTHORITY>
<COMMENTS></COMMENTS>
</OTHERNAME>
<OTHERNAME ISIMPORTANT="0" ISPREFERRED="0" SEQUENCE="1" DATE="1953" ITALICIZENAME="1">
<NAME><![CDATA[Bembidion chetcoens]]></NAME>
<AUTHORITY><![CDATA[Hatch]]></AUTHORITY>
<COMMENTS></COMMENTS>
</OTHERNAME>
</OTHERNAMES>
</NODE>
t/32-tolweb.t view on Meta::CPAN
</NODE>
<NODE EXTINCT="0" ID="132155" CONFIDENCE="0" PHYLESIS="0" LEAF="1" HASPAGE="0" ANCESTORWITHPAGE="23703" ITALICIZENAME="1" INCOMPLETESUBGROUPS="0" SHOWAUTHORITY="1" SHOWAUTHORITYCONTAINING="1" IS_NEW_COMBINATION="0" COMBINATION_DATE="null" C...
<NAME><![CDATA[Bembidion consummatum]]></NAME>
<DESCRIPTION></DESCRIPTION>
<AUTHORITY><![CDATA[Bates]]></AUTHORITY>
<NAMECOMMENT></NAMECOMMENT>
<COMBINATION_AUTHOR></COMBINATION_AUTHOR>
<AUTHDATE>1873</AUTHDATE>
<OTHERNAMES>
<OTHERNAME ISIMPORTANT="0" ISPREFERRED="0" SEQUENCE="0" DATE="1966" ITALICIZENAME="1">
<NAME><![CDATA[Bembidion boldi]]></NAME>
<AUTHORITY><![CDATA[Jedlicka]]></AUTHORITY>
<COMMENTS></COMMENTS>
</OTHERNAME>
</OTHERNAMES>
</NODE>
<NODE EXTINCT="0" ID="132156" CONFIDENCE="0" PHYLESIS="0" LEAF="1" HASPAGE="0" ANCESTORWITHPAGE="23703" ITALICIZENAME="1" INCOMPLETESUBGROUPS="0" SHOWAUTHORITY="1" SHOWAUTHORITYCONTAINING="1" IS_NEW_COMBINATION="0" COMBINATION_DATE="null" C...
<NAME><![CDATA[Bembidion delerei]]></NAME>
<DESCRIPTION></DESCRIPTION>
<AUTHORITY><![CDATA[Fassati]]></AUTHORITY>
<NAMECOMMENT></NAMECOMMENT>
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