Bio-Phylo

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lib/Bio/Phylo/Manual.pod  view on Meta::CPAN

and find out what might have gone wrong starting from your script drilling
into the module code.

 # exception caught.
 if ( UNIVERSAL::isa( $@, 'Bio::Phylo::Util::Exceptions::BadNumber' ) ) {

    # prints stack trace in addition to error
    warn $@->error, "\n, $@->trace->as_string, "\n";

    # further metadata from exception object
    warn join ' ',  $@->euid, $@->egid, $@->uid, $@->gid, $@->pid, $@->time;
    exit;
 }

As a new feature (from v.0.17 onwards) exceptions have become more descriptive,
with a generic explanation of what the thrown exception class typically means
added to the error message, and stack traces are printed out by default.

=item Exception types

Several exception classes are defined. The type of the thrown exception should

lib/Bio/Phylo/Util/Exceptions.pm  view on Meta::CPAN

    my %args  = @_;
    my $self  = {

        #		'error'       => $args{'error'},
        #		'description' => $args{'description'},
        'trace' => Bio::Phylo::Util::StackTrace->new,
        'time'  => CORE::time(),
        'pid'   => $$,
        'uid'   => $<,
        'euid'  => $>,
        'gid'   => $(,
        'egid'  => $),
        %args
    };
    return bless $self, $class;
}

sub as_string {
    my $self        = shift;
    my $error       = $self->error;
    my $description = $self->description;
    my $class       = ref $self;

t/32-tolweb.t  view on Meta::CPAN

        <AUTHDATE>1986</AUTHDATE>
        <OTHERNAMES>
          <OTHERNAME ISIMPORTANT="0" ISPREFERRED="0" SEQUENCE="0" DATE="1986" ITALICIZENAME="1">
            <NAME><![CDATA[Chinoperyphus]]></NAME>
            <AUTHORITY><![CDATA[Vysoky]]></AUTHORITY>
            <COMMENTS></COMMENTS>
          </OTHERNAME>
        </OTHERNAMES>
        <NODES>
          <NODE EXTINCT="0" ID="132113" CONFIDENCE="0" PHYLESIS="0" LEAF="1" HASPAGE="0" ANCESTORWITHPAGE="357" ITALICIZENAME="1" INCOMPLETESUBGROUPS="0" SHOWAUTHORITY="1" SHOWAUTHORITYCONTAINING="1" IS_NEW_COMBINATION="0" COMBINATION_DATE="null" CHI...
            <NAME><![CDATA[Bembidion algidum]]></NAME>
            <DESCRIPTION></DESCRIPTION>
            <AUTHORITY><![CDATA[Andrewes]]></AUTHORITY>
            <NAMECOMMENT></NAMECOMMENT>
            <COMBINATION_AUTHOR></COMBINATION_AUTHOR>
            <AUTHDATE>1935</AUTHDATE>
          </NODE>
          <NODE EXTINCT="0" ID="132114" CONFIDENCE="0" PHYLESIS="0" LEAF="1" HASPAGE="0" ANCESTORWITHPAGE="357" ITALICIZENAME="1" INCOMPLETESUBGROUPS="0" SHOWAUTHORITY="1" SHOWAUTHORITYCONTAINING="1" IS_NEW_COMBINATION="0" COMBINATION_DATE="null" CHI...
            <NAME><![CDATA[Bembidion altestriatum]]></NAME>
            <DESCRIPTION></DESCRIPTION>
            <AUTHORITY><![CDATA[Netolitzky]]></AUTHORITY>

t/32-tolweb.t  view on Meta::CPAN

                <NODES>
                  <NODE EXTINCT="0" ID="131734" CONFIDENCE="0" PHYLESIS="0" LEAF="1" HASPAGE="0" ANCESTORWITHPAGE="23687" ITALICIZENAME="1" INCOMPLETESUBGROUPS="0" SHOWAUTHORITY="1" SHOWAUTHORITYCONTAINING="1" IS_NEW_COMBINATION="0" COMBINATION_DATE=...
                    <NAME><![CDATA[Bembidion gebleri gebleri]]></NAME>
                    <DESCRIPTION></DESCRIPTION>
                    <AUTHORITY><![CDATA[Gebler]]></AUTHORITY>
                    <NAMECOMMENT></NAMECOMMENT>
                    <COMBINATION_AUTHOR></COMBINATION_AUTHOR>
                    <AUTHDATE>1833</AUTHDATE>
                    <OTHERNAMES>
                      <OTHERNAME ISIMPORTANT="0" ISPREFERRED="0" SEQUENCE="0" DATE="1880" ITALICIZENAME="1">
                        <NAME><![CDATA[Bembidion gebler frigidum]]></NAME>
                        <AUTHORITY><![CDATA[Sahlberg, J.]]></AUTHORITY>
                        <COMMENTS></COMMENTS>
                      </OTHERNAME>
                      <OTHERNAME ISIMPORTANT="0" ISPREFERRED="0" SEQUENCE="1" DATE="1943" ITALICIZENAME="1">
                        <NAME><![CDATA[Bembidion gebler jenseni]]></NAME>
                        <AUTHORITY><![CDATA[Netolitzky]]></AUTHORITY>
                        <COMMENTS></COMMENTS>
                      </OTHERNAME>
                    </OTHERNAMES>
                  </NODE>

t/57-nhx.t  view on Meta::CPAN

		my $obs = $node->get_meta_object( 'nhx:' . $key );
		ok( $obs eq $exp, "$key: $obs eq $exp" );
	}
}
ok( unparse(
	'-format' => 'nhx',
	'-phylo'  => $tree,
), 'unparse to NHX' );

__DATA__
(((((155657|estExt_Genewise1.C_15140004:5.3435[&&NHX:D=N:G=155657|estExt_Genewise1.C_15140004:T=283909],jgi|Helro1|186101:100000[&&NHX:D=N:G=jgi|Helro1|186101:T=6412])Annelida:0.0000[&&NHX:D=N:B=27:T=6340],222316:2.9506[&&NHX:D=N:G=222316:T=225164])L...