• Your recent searches
BioPerl-Run
10 results

 view release on metacpan or  search on metacpan

lib/Bio/Tools/Run/Phylo/Phylip/Consense.pm  view on Meta::CPAN 

	
package Bio::Tools::Run::Phylo::Phylip::Consense;

use vars qw($AUTOLOAD @ISA $PROGRAM $PROGRAMDIR $PROGRAMNAME
	    @CONSENSE_PARAMS @OTHER_SWITCHES
	    %OK_FIELD);
use strict;
use Bio::SimpleAlign;
use Bio::TreeIO;
use Bio::Tools::Run::Phylo::Phylip::Base;
use Bio::Tools::Run::Phylo::Phylip::PhylipConf qw(%Menu);
use IO::String;
use Cwd;


# inherit from Phylip::Base which has some methods for dealing with
# Phylip specifics
@ISA = qw(Bio::Tools::Run::Phylo::Phylip::Base);

# You will need to enable the Consense program. This
# can be done in (at least) 3 ways:

lib/Bio/Tools/Run/Phylo/Phylip/Consense.pm  view on Meta::CPAN 

    my ($attr, $value, $self);

    #do nothing for now
    $self = shift;
    my $param_string = "";
    my $rooted = 0;

    #for case where type is Ml
    my $Ml = 0;
    my $frac = 0.5;
    my %menu = %{$Menu{$self->version}->{'CONSENSE'}};

    foreach  my $attr ( @CONSENSE_PARAMS) {
    	$value = $self->$attr();
    	next unless (defined $value);
    	if ($attr =~/ROOTED/i){
        $rooted = 1;
        $param_string .= $menu{'ROOTED'};
      }
      elsif($attr =~/OUTGROUP/i){
          if($rooted == 1){

lib/Bio/Tools/Run/Phylo/Phylip/DrawGram.pm  view on Meta::CPAN 


# Let the code begin...


package Bio::Tools::Run::Phylo::Phylip::DrawGram;
use vars qw($AUTOLOAD @ISA $PROGRAM $PROGRAMDIR $PROGRAMNAME
	    $FONTFILE @DRAW_PARAMS @OTHER_SWITCHES
	    %OK_FIELD %DEFAULT);
use strict;
use Bio::Tools::Run::Phylo::Phylip::Base;
use Bio::Tools::Run::Phylo::Phylip::PhylipConf qw(%Menu);
use Cwd;
# inherit from Phylip::Base which has some methods for dealing with
# Phylip specifics
@ISA = qw(Bio::Tools::Run::Phylo::Phylip::Base);

# You will need to enable the neighbor program. This
# can be done in (at least) 3 ways:
#
# 1. define an environmental variable PHYLIPDIR:
# export PHYLIPDIR=/home/shawnh/PHYLIP/bin

lib/Bio/Tools/Run/Phylo/Phylip/DrawGram.pm  view on Meta::CPAN 

=cut

sub _setparams {
    my ($attr, $value, $self);

    #do nothing for now
    $self = shift;
    my $param_string = "";
    my $cat = 0;
    my ($hmargin,$vmargin);
    my %menu = %{$Menu{$self->version}->{'DRAWGRAM'}};
    foreach  my $attr ( @DRAW_PARAMS) {	
	$value = $self->$attr();
	next unless defined $value;
	my @vals;
	if( ref($value) ) {
	    ($value,@vals) = @$value;
	}
	$attr = uc($attr);
	if( ! exists $menu{$attr} ) {
	    $self->warn("unknown parameter $attr, known params are ".

lib/Bio/Tools/Run/Phylo/Phylip/DrawTree.pm  view on Meta::CPAN 

				$FONTFILE @DRAW_PARAMS @OTHER_SWITCHES
				%OK_FIELD %DEFAULT);
use strict;
# inherit from Phylip::Base which has some methods for dealing with
# Phylip specifics
use Bio::Tools::Run::Phylo::Phylip::Base;
use Cwd;

@ISA = qw( Bio::Tools::Run::Phylo::Phylip::Base );

use Bio::Tools::Run::Phylo::Phylip::PhylipConf qw(%Menu);

# You will need to enable the neighbor program. This
# can be done in (at least) 3 ways:
#
# 1. define an environmental variable PHYLIPDIR:
# export PHYLIPDIR=/home/shawnh/PHYLIP/bin
#
# 2. include a definition of an environmental variable PHYLIPDIR in
# every script that will use DrawTree.pm.
# $ENV{PHYLIPDIR} = '/home/shawnh/PHYLIP/bin';

lib/Bio/Tools/Run/Phylo/Phylip/DrawTree.pm  view on Meta::CPAN 



sub _setparams {
	my ($attr, $value, $self);

	#do nothing for now
	$self = shift;
	my $param_string = "";
	my $cat = 0;
	my ($hmargin,$vmargin);
	my %menu = %{$Menu{$self->version}->{'DRAWTREE'}};
	foreach  my $attr ( @DRAW_PARAMS) {	
		$value = $self->$attr();
		next unless defined $value;
		my @vals;
		if( ref($value) ) {
			($value,@vals) = @$value;
		}
		$attr = uc($attr);
		if( ! exists $menu{$attr} ) {
			$self->warn("unknown parameter $attr, known params are ".

lib/Bio/Tools/Run/Phylo/Phylip/Neighbor.pm  view on Meta::CPAN 

use vars qw($AUTOLOAD @ISA $PROGRAM $PROGRAMDIR $PROGRAMNAME
	    @NEIGHBOR_PARAMS @OTHER_SWITCHES
	    %OK_FIELD);
use strict;
use Bio::SimpleAlign;
use Bio::AlignIO;
use Bio::TreeIO;
use Bio::Root::Root;
use Bio::Root::IO;
use Bio::Tools::Run::Phylo::Phylip::Base;
use Bio::Tools::Run::Phylo::Phylip::PhylipConf qw(%Menu);

use Cwd;
			    
# inherit from Phylip::Base which has some methods for dealing with
# Phylip specifics
@ISA = qw(Bio::Tools::Run::Phylo::Phylip::Base);

# You will need to enable the neighbor program. This
# can be done in (at least) 3 ways:
#

lib/Bio/Tools/Run/Phylo/Phylip/Neighbor.pm  view on Meta::CPAN 

=cut

sub _setparams {
    my ($attr, $value, $self);

    #do nothing for now
    $self = shift;
    my $param_string = "";
    my $type ="";
    my $version = $self->version;
    my %menu = %{$Menu{$version}->{'NEIGHBOR'}};

    foreach  my $attr ( @NEIGHBOR_PARAMS) {
    	$value = $self->$attr();
    	next unless (defined $value && $value);
  	  if ($attr =~/TYPE/i){
	     if ($value=~/UPGMA/i){
    		$type = "UPGMA";
    		$param_string .= $menu{'TYPE'}{'UPGMA'};
       }
	    }

lib/Bio/Tools/Run/Phylo/Phylip/PhylipConf.pm  view on Meta::CPAN 


# POD documentation - main docs before the code

=head1 NAME

Bio::Tools::Run::Phylo::Phylip::PhylipConf

=head1 SYNOPSIS

  use Bio::Tools::Run::Phylo::Phylip::PhylipConf;
  my %menu = %{$Bio::Tools::Run::Phylo::Phylip::PhylipConf::Menu->{$version}->{'PROTDIST'}};

=head1 DESCRIPTION

A configuration for managing menu configuration differences 
between version 3.5 and 3.6

=head1 FEEDBACK

=head2 Mailing Lists

lib/Bio/Tools/Run/Phylo/Phylip/PhylipConf.pm  view on Meta::CPAN 

methods. Internal methods are usually preceded with a _

=cut

#'

package Bio::Tools::Run::Phylo::Phylip::PhylipConf;

use strict;
use Exporter;
use vars qw(@ISA %Menu %FileName $RESOLUTIONX $RESOLUTIONY @EXPORT_OK);
use base 'Exporter';

$RESOLUTIONX = 300;
$RESOLUTIONY = 300;

@EXPORT_OK = qw(%FileName %Menu);

%FileName = (
              "3.5"=>{'OUTFILE'=>'outfile',
                      'TREEFILE'=>'treefile',
                      'PLOTFILE'=>'plotfile',
                     },
              "3.6"=>{'OUTFILE'=>'outfile',
                      'TREEFILE'=>'outtree',
                      'PLOTFILE'=>'plotfile',
                     },
);
                      
%Menu = 
    (
     "3.5" => {
	 'PROTDIST' => {
	     'MODEL'  => {
		 'CAT'   =>"P\nP\n",
		 'KIMURA'=>"P\n",
	     },
	     'GENCODE'=>  {
		 'ALLOWED'=>"UMVFY",
		 'OPTION' =>"C\n",

lib/Bio/Tools/Run/Phylo/Phylip/ProtDist.pm  view on Meta::CPAN 

package Bio::Tools::Run::Phylo::Phylip::ProtDist;

use vars qw($AUTOLOAD @ISA $PROGRAM $PROGRAMDIR $PROGRAMNAME
	    @PROTDIST_PARAMS @OTHER_SWITCHES
	    %OK_FIELD);
use strict;
use Bio::SimpleAlign;
use Bio::AlignIO;
use Bio::TreeIO;
use Bio::Tools::Run::Phylo::Phylip::Base;
use Bio::Tools::Run::Phylo::Phylip::PhylipConf qw(%Menu);
use Bio::Tools::Phylo::Phylip::ProtDist;
use Cwd;


# inherit from Phylip::Base which has some methods for dealing with
# Phylip specifics
@ISA = qw(Bio::Tools::Run::Phylo::Phylip::Base);

# You will need to enable the protdist program. This
# can be done in (at least) 3 ways:

lib/Bio/Tools/Run/Phylo/Phylip/ProtDist.pm  view on Meta::CPAN 


=cut

sub _setparams {
    my ($attr, $value, $self);

    #do nothing for now
    $self = shift;
    my $param_string = "";
    my $cat = 0;
    my %menu = %{$Menu{$self->version}->{'PROTDIST'}};

    foreach  my $attr ( @PROTDIST_PARAMS) {
    	$value = $self->$attr();
    	next unless (defined $value);
    	if ($attr =~/MODEL/i){
	    if ($value=~/CAT/i){
		$cat = 1;
	    }
	    $param_string .= $menu{'MODEL'}{$value};
	}

lib/Bio/Tools/Run/Phylo/Phylip/ProtPars.pm  view on Meta::CPAN 

	    @PROTPARS_PARAMS @OTHER_SWITCHES
	    %OK_FIELD);
use strict;
use Bio::SimpleAlign;
use Cwd;
use Bio::AlignIO;
use Bio::TreeIO;
use Bio::Root::Root;
use Bio::Root::IO;
use Bio::Tools::Run::Phylo::Phylip::Base;
use Bio::Tools::Run::Phylo::Phylip::PhylipConf qw(%Menu);

@ISA = qw(Bio::Tools::Run::Phylo::Phylip::Base);

# You will need to enable the protpars program. This
# can be done in (at least) two ways:
#
# 1. define an environmental variable PHYLIPDIR:
# export PHYLIPDIR=/home/shawnh/PHYLIP/bin
#
# 2. include a definition of an environmental variable CLUSTALDIR in

lib/Bio/Tools/Run/Phylo/Phylip/ProtPars.pm  view on Meta::CPAN 

 Args    : name of calling object

=cut

sub _setparams {
    my ($attr, $value, $self);

    $self = shift;
    my $param_string = "";
    
    my %menu = %{$Menu{$self->version}->{'PROTPARS'}};

    for $attr ( @PROTPARS_PARAMS) {
        $value = $self->$attr();
        next unless (defined $value);
	      if ($attr =~/JUMBLE/i){
      		my ($seed,$itr) = split(",",$value);
      		$param_string .=$menu{'JUMBLE'}."$seed\n$itr\n";
      	}
        else {
          $param_string .= $menu{uc $attr}."$value\n";

lib/Bio/Tools/Run/Phylo/Phylip/SeqBoot.pm  view on Meta::CPAN 

package Bio::Tools::Run::Phylo::Phylip::SeqBoot;

use vars qw($AUTOLOAD @ISA $PROGRAM $PROGRAMDIR $PROGRAMNAME
	    @SEQBOOT_PARAMS @OTHER_SWITCHES
	    %OK_FIELD);
use strict;
use Bio::SimpleAlign;
use Bio::AlignIO;
use Bio::TreeIO;
use Bio::Tools::Run::Phylo::Phylip::Base;
use Bio::Tools::Run::Phylo::Phylip::PhylipConf qw(%Menu);
use Bio::Matrix::PhylipDist;
use Cwd;


# inherit from Phylip::Base which has some methods for dealing with
# Phylip specifics
@ISA = qw(Bio::Tools::Run::Phylo::Phylip::Base);

# You will need to enable the SeqBoot program. This
# can be done in (at least) 3 ways:

lib/Bio/Tools/Run/Phylo/Phylip/SeqBoot.pm  view on Meta::CPAN 

=cut

sub _setparams {
    my ($attr, $value, $self);

    #do nothing for now
    $self = shift;
    my $param_string = "";
    my $cat = 0;
    my $gene_freq = 0;
    my %menu = %{$Menu{$self->version}->{'SEQBOOT'}};

    foreach  my $attr ( @SEQBOOT_PARAMS) {
    	$value = $self->$attr();
    	next unless (defined $value);
    	if ($attr =~/REPLICATES/i){
        if( $value !~ /(\d+(\.\d+)?)/ ) {
            $self->warn("Expected a number in  $attr\n");
            next;
        }
		   $param_string .= $menu{'REPLICATES'}."$value\n";

t/SoapEU-unit.t  view on Meta::CPAN 

             { 'db' => 1 },
             { 'tool' => 1 },
             { 'email' => 1 }
             ] } , 'einfo request parameters');
    is_deeply( $wsdl->response_parameters('einfo'),
           {'eInfoResult' =>
            [ {'ERROR' => 1},
              {'DbList' => [{'DbName|' => 1 }]},
              {'DbInfo' => [
                   {'DbName' => 1 },
                   {'MenuName' => 1},
                   {'Description' => 1},
                   {'Count' => 1},
                   {'LastUpdate' => 1},
                   {'FieldList' => [
                    {'Field' => [
                     {'Name' => 1},
                     {'FullName' => 1},
                     {'Description' => 1},
                     {'TermCount' => 1},
                     {'IsDate' => 1},
                     {'IsNumerical' => 1},
                     {'SingleToken' => 1},
                     {'Hierarchy' => 1},
                     {'IsHidden' => 1}
                     ]}
                    ]},
                   {'LinkList' => [
                    {'Link' => [
                     {'Name' => 1},
                     {'Menu' => 1},
                     {'Description' => 1},
                     {'DbTo' => 1}
                     ]}
                    ]}
                   ]}
             ]}, 'einfo response parameters');
    is_deeply( $wsdl->request_parameters('egquery'),
           { 'eGqueryRequest' => [
             { 'term' => 1 },
             { 'tool' => 1 },
             { 'email' => 1 }
             ] } , 'egquery request parameters');
    is_deeply( $wsdl->response_parameters('egquery'),
           { 'Result' => [
             { 'Term' => 1 },
             { 'eGQueryResult' => [
                   {'ERROR' => 1},
                   {'ResultItem' => [
                    {'DbName' => 1},
                    {'MenuName' => 1},
                    {'Count' => 1},
                    {'Status' => 1}
                    ]}
                   ]}
             ]} , 'egquery response parameters');

    # ESoap

    ok my $dumfac = Bio::DB::ESoap->new( -util => 'run_eLink',
                         -wsdl_file => test_input_file('eutils.wsdl') ), "dummy ESoap factory";

t/data/eutils.wsdl  view on Meta::CPAN 

      <xs:complexType>
	<xs:sequence>
	  <xs:element name="Term" type="xs:string"/>
	  <xs:element name="eGQueryResult" type="tns:eGQueryResultType"/>
	</xs:sequence>
      </xs:complexType>
    </xs:element>
    <xs:complexType name="ResultItemType">
      <xs:sequence>
	<xs:element name="DbName" type="xs:string"/>
	<xs:element name="MenuName" type="xs:string"/>
	<xs:element name="Count" type="xs:string"/>
	<xs:element name="Status" type="xs:string"/>
      </xs:sequence>
    </xs:complexType>
    <xs:complexType name="eGQueryResultType">
      <xs:sequence>
	<xs:element name="ERROR" type="xs:string" minOccurs="0"/>
	<xs:element name="ResultItem" type="tns:ResultItemType" maxOccurs="unbounded"/>
      </xs:sequence>
    </xs:complexType>

t/data/eutils.wsdl  view on Meta::CPAN 

    </xs:element>
  </xs:schema>
  
  <xs:schema targetNamespace="http://www.ncbi.nlm.nih.gov/soap/eutils/einfo" xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:tns="http://www.ncbi.nlm.nih.gov/soap/eutils/einfo" elementFormDefault="qualified"	>
    
    <!--   version="2.0" -->
    <!--   http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eInfo_020511.dtd  date: 2006-12-04 -->
    <xs:complexType name="DbInfoType">
      <xs:sequence>
	<xs:element name="DbName" type="xs:string"/>
	<xs:element name="MenuName" type="xs:string"/>
	<xs:element name="Description" type="xs:string"/>
	<xs:element name="Count" type="xs:string"/>
	<xs:element name="LastUpdate" type="xs:string"/>
	<xs:element name="FieldList" type="tns:FieldListType"/>
	<xs:element name="LinkList" type="tns:LinkListType" minOccurs="0"/>
      </xs:sequence>
    </xs:complexType>
    <xs:complexType name="DbListType">
      <xs:choice>
	<xs:element name="DbName" type="xs:string" minOccurs="0" maxOccurs="unbounded"/>

t/data/eutils.wsdl  view on Meta::CPAN 

      </xs:sequence>
    </xs:complexType>
    <xs:complexType name="FieldListType">
      <xs:sequence>
	<xs:element name="Field" type="tns:FieldType" minOccurs="0" maxOccurs="unbounded"/>
      </xs:sequence>
    </xs:complexType>
    <xs:complexType name="LinkType">
      <xs:sequence>
	<xs:element name="Name" type="xs:string"/>
	<xs:element name="Menu" type="xs:string"/>
	<xs:element name="Description" type="xs:string"/>
	<xs:element name="DbTo" type="xs:string"/>
      </xs:sequence>
    </xs:complexType>
    <xs:complexType name="LinkListType">
      <xs:sequence>
	<xs:element name="Link" type="tns:LinkType" minOccurs="0" maxOccurs="unbounded"/>
      </xs:sequence>
    </xs:complexType>

t/data/eutils.wsdl  view on Meta::CPAN 

    <xs:complexType name="LinkType">
      <xs:sequence>
	<xs:element name="Id" type="tns:IdType"/>
	<xs:element ref="tns:Score" minOccurs="0"/>
      </xs:sequence>
    </xs:complexType>
    <xs:complexType name="LinkInfoType">
      <xs:sequence>
	<xs:element ref="tns:DbTo"/>
	<xs:element ref="tns:LinkName"/>
	<xs:element ref="tns:MenuTag" minOccurs="0"/>
	<xs:element ref="tns:HtmlTag" minOccurs="0"/>
	<xs:element ref="tns:Url" minOccurs="0"/>
	<xs:element ref="tns:Priority"/>
      </xs:sequence>
    </xs:complexType>
    <xs:element name="LinkName" type="xs:string"/>
    
    
    <!-- TOO complex for Axis2
	 <xs:complexType name="LinkSetType">

t/data/eutils.wsdl  view on Meta::CPAN 

    <xs:complexType name="LinkSetDbHistoryType">
      <xs:sequence>
	<xs:element ref="tns:DbTo"/>
	<xs:element ref="tns:LinkName"/>
	<xs:element ref="tns:QueryKey"  minOccurs="0"/>
	<xs:element ref="tns:Info"  minOccurs="0"/>
	<xs:element ref="tns:ERROR" minOccurs="0"/>
      </xs:sequence>
    </xs:complexType>
    
    <xs:element name="MenuTag" type="xs:string"/>
    <xs:element name="Name" type="xs:string"/>
    <xs:element name="NameAbbr" type="xs:string"/>
    <xs:complexType name="ObjUrlType">
      <xs:sequence>
	<xs:element ref="tns:Url"/>
	<xs:element ref="tns:IconUrl" minOccurs="0"/>
	<xs:element ref="tns:LinkName" minOccurs="0"/>
	<xs:element ref="tns:SubjectType" minOccurs="0" maxOccurs="unbounded"/>
	<xs:element ref="tns:Category" minOccurs="0" maxOccurs="unbounded"/>
	<xs:element ref="tns:Attribute" minOccurs="0" maxOccurs="unbounded"/>



( run in 1.387 second using v1.01-cache-2.11-cpan-49f99fa48dc )