CaCORE

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examples/caBIOtest.pl  view on Meta::CPAN

		print "ClinicalTrialProtocol id= " . $a->getId . "\n";

	}
}
# test CaBIO 7: Query by Big Id
#
print "test CaBIO 1: query by Big Id\n";

# instantiate a SecurityToken domain object and sets the value of symbol attribute to NAT2.
$gene = new CaCORE::CaBIO::Gene;
$gene->setBigid("hdl://2500.1.PMEUQUCCL5/ONSXKL4KEL");

# the eval...warn... construct is recommended, if error is encountered during webservice call, this will
# trap the exception and allows for error handling, and prevent the program from exiting.
eval{
	#
	# This call encapsulates the webservice invocation to the caCORE server, and converts
	# the returned XML into list of Chromosome objects
	# Parameter 1 indicates target class, Chromosome, to be retrieved
	# Parameter 2 indicates search criteria. In this case, is the genes associated with the chromosome.
	#

html/CaBIO.html  view on Meta::CPAN

<dd>
<p>data type: <code>string</code></p>
</dd>
</li>
<dt><strong><a name="item_nscnumber">NSCNumber</a></strong>

<dd>
<p>data type: <code>long</code></p>
</dd>
</li>
<dt><strong><a name="item_bigid">bigid</a></strong>

<dd>
<p>data type: <code>string</code></p>
</dd>
</li>
<dt><strong><a name="item_comment">comment</a></strong>

<dd>
<p>data type: <code>string</code></p>
</dd>

html/CaBIO.html  view on Meta::CPAN

<h2><a name="synopsis">SYNOPSIS</a></h2>
<p>See <a href="/CaCORE/ApplicationService.html">the CaCORE::ApplicationService manpage</a>.</p>
<p>
</p>
<h2><a name="description">DESCRIPTION</a></h2>
<p>
</p>
<h2><a name="attributes_of_anomaly">ATTRIBUTES of Anomaly</a></h2>
<p>The following are all the attributes of the Anomaly object and their data types:</p>
<dl>
<dt><strong>bigid</strong>

<dd>
<p>data type: <code>string</code></p>
</dd>
</li>
<dt><strong><a name="item_description">description</a></strong>

<dd>
<p>data type: <code>string</code></p>
</dd>

html/CaBIO.html  view on Meta::CPAN

<h2><a name="synopsis">SYNOPSIS</a></h2>
<p>See <a href="/CaCORE/ApplicationService.html">the CaCORE::ApplicationService manpage</a>.</p>
<p>
</p>
<h2><a name="description">DESCRIPTION</a></h2>
<p>
</p>
<h2><a name="attributes_of_chromosome">ATTRIBUTES of Chromosome</a></h2>
<p>The following are all the attributes of the Chromosome object and their data types:</p>
<dl>
<dt><strong>bigid</strong>

<dd>
<p>data type: <code>string</code></p>
</dd>
</li>
<dt><strong>id</strong>

<dd>
<p>data type: <code>long</code></p>
</dd>

html/CaBIO.html  view on Meta::CPAN

<dd>
<p>data type: <code>string</code></p>
</dd>
</li>
<dt><strong><a name="item_piname">PIName</a></strong>

<dd>
<p>data type: <code>string</code></p>
</dd>
</li>
<dt><strong>bigid</strong>

<dd>
<p>data type: <code>string</code></p>
</dd>
</li>
<dt><strong><a name="item_currentstatus">currentStatus</a></strong>

<dd>
<p>data type: <code>string</code></p>
</dd>

html/CaBIO.html  view on Meta::CPAN

<h2><a name="synopsis">SYNOPSIS</a></h2>
<p>See <a href="/CaCORE/ApplicationService.html">the CaCORE::ApplicationService manpage</a>.</p>
<p>
</p>
<h2><a name="description">DESCRIPTION</a></h2>
<p>
</p>
<h2><a name="attributes_of_clone">ATTRIBUTES of Clone</a></h2>
<p>The following are all the attributes of the Clone object and their data types:</p>
<dl>
<dt><strong>bigid</strong>

<dd>
<p>data type: <code>string</code></p>
</dd>
</li>
<dt><strong>id</strong>

<dd>
<p>data type: <code>long</code></p>
</dd>

html/CaBIO.html  view on Meta::CPAN

<h2><a name="synopsis">SYNOPSIS</a></h2>
<p>See <a href="/CaCORE/ApplicationService.html">the CaCORE::ApplicationService manpage</a>.</p>
<p>
</p>
<h2><a name="description">DESCRIPTION</a></h2>
<p>
</p>
<h2><a name="attributes_of_clonerelativelocation">ATTRIBUTES of CloneRelativeLocation</a></h2>
<p>The following are all the attributes of the CloneRelativeLocation object and their data types:</p>
<dl>
<dt><strong>bigid</strong>

<dd>
<p>data type: <code>string</code></p>
</dd>
</li>
<dt><strong>id</strong>

<dd>
<p>data type: <code>long</code></p>
</dd>

html/CaBIO.html  view on Meta::CPAN

<h2><a name="synopsis">SYNOPSIS</a></h2>
<p>See <a href="/CaCORE/ApplicationService.html">the CaCORE::ApplicationService manpage</a>.</p>
<p>
</p>
<h2><a name="description">DESCRIPTION</a></h2>
<p>
</p>
<h2><a name="attributes_of_cytoband">ATTRIBUTES of Cytoband</a></h2>
<p>The following are all the attributes of the Cytoband object and their data types:</p>
<dl>
<dt><strong>bigid</strong>

<dd>
<p>data type: <code>string</code></p>
</dd>
</li>
<dt><strong>id</strong>

<dd>
<p>data type: <code>long</code></p>
</dd>

html/CaBIO.html  view on Meta::CPAN

<h2><a name="synopsis">SYNOPSIS</a></h2>
<p>See <a href="/CaCORE/ApplicationService.html">the CaCORE::ApplicationService manpage</a>.</p>
<p>
</p>
<h2><a name="description">DESCRIPTION</a></h2>
<p>
</p>
<h2><a name="attributes_of_cytogeneticlocation">ATTRIBUTES of CytogeneticLocation</a></h2>
<p>The following are all the attributes of the CytogeneticLocation object and their data types:</p>
<dl>
<dt><strong>bigid</strong>

<dd>
<p>data type: <code>string</code></p>
</dd>
</li>
<dt><strong><a name="item_endcytobandlocid">endCytobandLocId</a></strong>

<dd>
<p>data type: <code>long</code></p>
</dd>

html/CaBIO.html  view on Meta::CPAN

<h2><a name="synopsis">SYNOPSIS</a></h2>
<p>See <a href="/CaCORE/ApplicationService.html">the CaCORE::ApplicationService manpage</a>.</p>
<p>
</p>
<h2><a name="description">DESCRIPTION</a></h2>
<p>
</p>
<h2><a name="attributes_of_diseaseontology">ATTRIBUTES of DiseaseOntology</a></h2>
<p>The following are all the attributes of the DiseaseOntology object and their data types:</p>
<dl>
<dt><strong>bigid</strong>

<dd>
<p>data type: <code>string</code></p>
</dd>
</li>
<dt><strong>id</strong>

<dd>
<p>data type: <code>long</code></p>
</dd>

html/CaBIO.html  view on Meta::CPAN

<h2><a name="synopsis">SYNOPSIS</a></h2>
<p>See <a href="/CaCORE/ApplicationService.html">the CaCORE::ApplicationService manpage</a>.</p>
<p>
</p>
<h2><a name="description">DESCRIPTION</a></h2>
<p>
</p>
<h2><a name="attributes_of_diseaseontologyrelationship">ATTRIBUTES of DiseaseOntologyRelationship</a></h2>
<p>The following are all the attributes of the DiseaseOntologyRelationship object and their data types:</p>
<dl>
<dt><strong>bigid</strong>

<dd>
<p>data type: <code>string</code></p>
</dd>
</li>
<dt><strong>id</strong>

<dd>
<p>data type: <code>long</code></p>
</dd>

html/CaBIO.html  view on Meta::CPAN

<h2><a name="synopsis">SYNOPSIS</a></h2>
<p>See <a href="/CaCORE/ApplicationService.html">the CaCORE::ApplicationService manpage</a>.</p>
<p>
</p>
<h2><a name="description">DESCRIPTION</a></h2>
<p>
</p>
<h2><a name="attributes_of_gene">ATTRIBUTES of Gene</a></h2>
<p>The following are all the attributes of the Gene object and their data types:</p>
<dl>
<dt><strong>bigid</strong>

<dd>
<p>data type: <code>string</code></p>
</dd>
</li>
<dt><strong><a name="item_clusterid">clusterId</a></strong>

<dd>
<p>data type: <code>long</code></p>
</dd>

html/CaBIO.html  view on Meta::CPAN

<h2><a name="synopsis">SYNOPSIS</a></h2>
<p>See <a href="/CaCORE/ApplicationService.html">the CaCORE::ApplicationService manpage</a>.</p>
<p>
</p>
<h2><a name="description">DESCRIPTION</a></h2>
<p>
</p>
<h2><a name="attributes_of_genealias">ATTRIBUTES of GeneAlias</a></h2>
<p>The following are all the attributes of the GeneAlias object and their data types:</p>
<dl>
<dt><strong>bigid</strong>

<dd>
<p>data type: <code>string</code></p>
</dd>
</li>
<dt><strong>id</strong>

<dd>
<p>data type: <code>long</code></p>
</dd>

html/CaBIO.html  view on Meta::CPAN

<h2><a name="synopsis">SYNOPSIS</a></h2>
<p>See <a href="/CaCORE/ApplicationService.html">the CaCORE::ApplicationService manpage</a>.</p>
<p>
</p>
<h2><a name="description">DESCRIPTION</a></h2>
<p>
</p>
<h2><a name="attributes_of_geneontology">ATTRIBUTES of GeneOntology</a></h2>
<p>The following are all the attributes of the GeneOntology object and their data types:</p>
<dl>
<dt><strong>bigid</strong>

<dd>
<p>data type: <code>string</code></p>
</dd>
</li>
<dt><strong>id</strong>

<dd>
<p>data type: <code>long</code></p>
</dd>

html/CaBIO.html  view on Meta::CPAN

<h2><a name="synopsis">SYNOPSIS</a></h2>
<p>See <a href="/CaCORE/ApplicationService.html">the CaCORE::ApplicationService manpage</a>.</p>
<p>
</p>
<h2><a name="description">DESCRIPTION</a></h2>
<p>
</p>
<h2><a name="attributes_of_geneontologyrelationship">ATTRIBUTES of GeneOntologyRelationship</a></h2>
<p>The following are all the attributes of the GeneOntologyRelationship object and their data types:</p>
<dl>
<dt><strong>bigid</strong>

<dd>
<p>data type: <code>string</code></p>
</dd>
</li>
<dt><strong>id</strong>

<dd>
<p>data type: <code>long</code></p>
</dd>

html/CaBIO.html  view on Meta::CPAN

<h2><a name="synopsis">SYNOPSIS</a></h2>
<p>See <a href="/CaCORE/ApplicationService.html">the CaCORE::ApplicationService manpage</a>.</p>
<p>
</p>
<h2><a name="description">DESCRIPTION</a></h2>
<p>
</p>
<h2><a name="attributes_of_generelativelocation">ATTRIBUTES of GeneRelativeLocation</a></h2>
<p>The following are all the attributes of the GeneRelativeLocation object and their data types:</p>
<dl>
<dt><strong>bigid</strong>

<dd>
<p>data type: <code>string</code></p>
</dd>
</li>
<dt><strong>id</strong>

<dd>
<p>data type: <code>long</code></p>
</dd>

html/CaBIO.html  view on Meta::CPAN

</p>
<h2><a name="attributes_of_genericarray">ATTRIBUTES of GenericArray</a></h2>
<p>The following are all the attributes of the GenericArray object and their data types:</p>
<dl>
<dt><strong><a name="item_arrayname">arrayName</a></strong>

<dd>
<p>data type: <code>string</code></p>
</dd>
</li>
<dt><strong>bigid</strong>

<dd>
<p>data type: <code>string</code></p>
</dd>
</li>
<dt><strong>id</strong>

<dd>
<p>data type: <code>long</code></p>
</dd>

html/CaBIO.html  view on Meta::CPAN

<h2><a name="synopsis">SYNOPSIS</a></h2>
<p>See <a href="/CaCORE/ApplicationService.html">the CaCORE::ApplicationService manpage</a>.</p>
<p>
</p>
<h2><a name="description">DESCRIPTION</a></h2>
<p>
</p>
<h2><a name="attributes_of_genericreporter">ATTRIBUTES of GenericReporter</a></h2>
<p>The following are all the attributes of the GenericReporter object and their data types:</p>
<dl>
<dt><strong>bigid</strong>

<dd>
<p>data type: <code>string</code></p>
</dd>
</li>
<dt><strong>id</strong>

<dd>
<p>data type: <code>long</code></p>
</dd>

html/CaBIO.html  view on Meta::CPAN

<h2><a name="synopsis">SYNOPSIS</a></h2>
<p>See <a href="/CaCORE/ApplicationService.html">the CaCORE::ApplicationService manpage</a>.</p>
<p>
</p>
<h2><a name="description">DESCRIPTION</a></h2>
<p>
</p>
<h2><a name="attributes_of_homologousassociation">ATTRIBUTES of HomologousAssociation</a></h2>
<p>The following are all the attributes of the HomologousAssociation object and their data types:</p>
<dl>
<dt><strong>bigid</strong>

<dd>
<p>data type: <code>string</code></p>
</dd>
</li>
<dt><strong><a name="item_homologousid">homologousId</a></strong>

<dd>
<p>data type: <code>long</code></p>
</dd>

html/CaBIO.html  view on Meta::CPAN

<h2><a name="synopsis">SYNOPSIS</a></h2>
<p>See <a href="/CaCORE/ApplicationService.html">the CaCORE::ApplicationService manpage</a>.</p>
<p>
</p>
<h2><a name="description">DESCRIPTION</a></h2>
<p>
</p>
<h2><a name="attributes_of_library">ATTRIBUTES of Library</a></h2>
<p>The following are all the attributes of the Library object and their data types:</p>
<dl>
<dt><strong>bigid</strong>

<dd>
<p>data type: <code>string</code></p>
</dd>
</li>
<dt><strong><a name="item_cloneproducer">cloneProducer</a></strong>

<dd>
<p>data type: <code>string</code></p>
</dd>

html/CaBIO.html  view on Meta::CPAN

<dd>
<p>data type: <code>string</code></p>
</dd>
</li>
<dt><strong><a name="item_accessionnumberversion">accessionNumberVersion</a></strong>

<dd>
<p>data type: <code>string</code></p>
</dd>
</li>
<dt><strong>bigid</strong>

<dd>
<p>data type: <code>string</code></p>
</dd>
</li>
<dt><strong>id</strong>

<dd>
<p>data type: <code>long</code></p>
</dd>

html/CaBIO.html  view on Meta::CPAN

<h2><a name="synopsis">SYNOPSIS</a></h2>
<p>See <a href="/CaCORE/ApplicationService.html">the CaCORE::ApplicationService manpage</a>.</p>
<p>
</p>
<h2><a name="description">DESCRIPTION</a></h2>
<p>
</p>
<h2><a name="attributes_of_organontology">ATTRIBUTES of OrganOntology</a></h2>
<p>The following are all the attributes of the OrganOntology object and their data types:</p>
<dl>
<dt><strong>bigid</strong>

<dd>
<p>data type: <code>string</code></p>
</dd>
</li>
<dt><strong>id</strong>

<dd>
<p>data type: <code>long</code></p>
</dd>

html/CaBIO.html  view on Meta::CPAN

<h2><a name="synopsis">SYNOPSIS</a></h2>
<p>See <a href="/CaCORE/ApplicationService.html">the CaCORE::ApplicationService manpage</a>.</p>
<p>
</p>
<h2><a name="description">DESCRIPTION</a></h2>
<p>
</p>
<h2><a name="attributes_of_organontologyrelationship">ATTRIBUTES of OrganOntologyRelationship</a></h2>
<p>The following are all the attributes of the OrganOntologyRelationship object and their data types:</p>
<dl>
<dt><strong>bigid</strong>

<dd>
<p>data type: <code>string</code></p>
</dd>
</li>
<dt><strong>id</strong>

<dd>
<p>data type: <code>long</code></p>
</dd>

html/CaBIO.html  view on Meta::CPAN

<h2><a name="synopsis">SYNOPSIS</a></h2>
<p>See <a href="/CaCORE/ApplicationService.html">the CaCORE::ApplicationService manpage</a>.</p>
<p>
</p>
<h2><a name="description">DESCRIPTION</a></h2>
<p>
</p>
<h2><a name="attributes_of_pathway">ATTRIBUTES of Pathway</a></h2>
<p>The following are all the attributes of the Pathway object and their data types:</p>
<dl>
<dt><strong>bigid</strong>

<dd>
<p>data type: <code>string</code></p>
</dd>
</li>
<dt><strong>description</strong>

<dd>
<p>data type: <code>string</code></p>
</dd>

html/CaBIO.html  view on Meta::CPAN

<h2><a name="synopsis">SYNOPSIS</a></h2>
<p>See <a href="/CaCORE/ApplicationService.html">the CaCORE::ApplicationService manpage</a>.</p>
<p>
</p>
<h2><a name="description">DESCRIPTION</a></h2>
<p>
</p>
<h2><a name="attributes_of_populationfrequency">ATTRIBUTES of PopulationFrequency</a></h2>
<p>The following are all the attributes of the PopulationFrequency object and their data types:</p>
<dl>
<dt><strong>bigid</strong>

<dd>
<p>data type: <code>string</code></p>
</dd>
</li>
<dt><strong><a name="item_ethnicity">ethnicity</a></strong>

<dd>
<p>data type: <code>string</code></p>
</dd>

html/CaBIO.html  view on Meta::CPAN

<h2><a name="synopsis">SYNOPSIS</a></h2>
<p>See <a href="/CaCORE/ApplicationService.html">the CaCORE::ApplicationService manpage</a>.</p>
<p>
</p>
<h2><a name="description">DESCRIPTION</a></h2>
<p>
</p>
<h2><a name="attributes_of_protein">ATTRIBUTES of Protein</a></h2>
<p>The following are all the attributes of the Protein object and their data types:</p>
<dl>
<dt><strong>bigid</strong>

<dd>
<p>data type: <code>string</code></p>
</dd>
</li>
<dt><strong><a name="item_copyrightstatement">copyrightStatement</a></strong>

<dd>
<p>data type: <code>string</code></p>
</dd>

html/CaBIO.html  view on Meta::CPAN

<h2><a name="synopsis">SYNOPSIS</a></h2>
<p>See <a href="/CaCORE/ApplicationService.html">the CaCORE::ApplicationService manpage</a>.</p>
<p>
</p>
<h2><a name="description">DESCRIPTION</a></h2>
<p>
</p>
<h2><a name="attributes_of_proteinalias">ATTRIBUTES of ProteinAlias</a></h2>
<p>The following are all the attributes of the ProteinAlias object and their data types:</p>
<dl>
<dt><strong>bigid</strong>

<dd>
<p>data type: <code>string</code></p>
</dd>
</li>
<dt><strong>id</strong>

<dd>
<p>data type: <code>long</code></p>
</dd>

html/CaBIO.html  view on Meta::CPAN

<h2><a name="synopsis">SYNOPSIS</a></h2>
<p>See <a href="/CaCORE/ApplicationService.html">the CaCORE::ApplicationService manpage</a>.</p>
<p>
</p>
<h2><a name="description">DESCRIPTION</a></h2>
<p>
</p>
<h2><a name="attributes_of_proteinsequence">ATTRIBUTES of ProteinSequence</a></h2>
<p>The following are all the attributes of the ProteinSequence object and their data types:</p>
<dl>
<dt><strong>bigid</strong>

<dd>
<p>data type: <code>string</code></p>
</dd>
</li>
<dt><strong><a name="item_checksum">checkSum</a></strong>

<dd>
<p>data type: <code>string</code></p>
</dd>

html/CaBIO.html  view on Meta::CPAN

<h2><a name="synopsis">SYNOPSIS</a></h2>
<p>See <a href="/CaCORE/ApplicationService.html">the CaCORE::ApplicationService manpage</a>.</p>
<p>
</p>
<h2><a name="description">DESCRIPTION</a></h2>
<p>
</p>
<h2><a name="attributes_of_protocol">ATTRIBUTES of Protocol</a></h2>
<p>The following are all the attributes of the Protocol object and their data types:</p>
<dl>
<dt><strong>bigid</strong>

<dd>
<p>data type: <code>string</code></p>
</dd>
</li>
<dt><strong>description</strong>

<dd>
<p>data type: <code>string</code></p>
</dd>

html/CaBIO.html  view on Meta::CPAN

</dd>
</li>
<dt><strong><a name="item_imtcode">IMTCODE</a></strong>

<dd>
<p>data type: <code>long</code>

</p>
</dd>
</li>
<dt><strong>bigid</strong>

<dd>
<p>data type: <code>string</code>

</p>
</dd>
</li>
<dt><strong><a name="item_diseasecategory">diseaseCategory</a></strong>

<dd>

html/CaBIO.html  view on Meta::CPAN

</dd>
</li>
<dt><strong><a name="item_alleleb">alleleB</a></strong>

<dd>
<p>data type: <code>string</code>

</p>
</dd>
</li>
<dt><strong>bigid</strong>

<dd>
<p>data type: <code>string</code>

</p>
</dd>
</li>
<dt><strong>id</strong>

<dd>

html/CaBIO.html  view on Meta::CPAN

<p>
</p>
<h2><a name="description">DESCRIPTION</a></h2>
<p>
</p>
<h2><a name="attributes_of_target">ATTRIBUTES of Target</a></h2>
<p>The following are all the attributes of the Target object and their data types:

</p>
<dl>
<dt><strong>bigid</strong>

<dd>
<p>data type: <code>string</code>

</p>
</dd>
</li>
<dt><strong>id</strong>

<dd>

html/CaBIO.html  view on Meta::CPAN

</p>
<dl>
<dt><strong><a name="item_abbreviation">abbreviation</a></strong>

<dd>
<p>data type: <code>string</code>

</p>
</dd>
</li>
<dt><strong>bigid</strong>

<dd>
<p>data type: <code>string</code>

</p>
</dd>
</li>
<dt><strong><a name="item_commonname">commonName</a></strong>

<dd>

html/CaBIO.html  view on Meta::CPAN

<p>
</p>
<h2><a name="description">DESCRIPTION</a></h2>
<p>
</p>
<h2><a name="attributes_of_vocabulary">ATTRIBUTES of Vocabulary</a></h2>
<p>The following are all the attributes of the Vocabulary object and their data types:

</p>
<dl>
<dt><strong>bigid</strong>

<dd>
<p>data type: <code>string</code>

</p>
</dd>
</li>
<dt><strong><a name="item_coreterm">coreTerm</a></strong>

<dd>

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

	$result .= $tmpstr;

	# alleleB;
	if( defined( $self->getAlleleB ) ) {
		$tmpstr = "<alleleB xsi:type=\"xsd:string\">" . $self->getAlleleB . "</alleleB>";
	} else {
		$tmpstr = "<alleleB xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
	}
	$result .= $tmpstr;

	# bigid;
	if( defined( $self->getBigid ) ) {
		$tmpstr = "<bigid xsi:type=\"xsd:string\">" . $self->getBigid . "</bigid>";
	} else {
		$tmpstr = "<bigid xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
	}
	$result .= $tmpstr;

	# id;
	if( defined( $self->getId ) ) {
		$tmpstr = "<id xsi:type=\"xsd:long\">" . $self->getId . "</id>";
	} else {
		$tmpstr = "<id xsi:type=\"xsd:long\" xsi:nil=\"true\" />";
	}
	$result .= $tmpstr;

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

# parse a given xml node, construct one SNP object
# param: xml node
# returns: one SNP object
sub fromWSXMLNode {
	my $SNPNode = $_[1];
	
	## begin ELEMENT_NODE children ##
		my $DBSNPID;
		my $alleleA;
		my $alleleB;
		my $bigid;
		my $id;
		my $validationStatus;
	## end ELEMENT_NODE children ##

	# get all children for this node
	for my $childrenNode ($SNPNode->getChildNodes) {
	    if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
		if( ! defined($childrenNode->getFirstChild) ){ next; };
		my $textNode = $childrenNode->getFirstChild;
		## begin iterate ELEMENT_NODE ##

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

		}
			elsif ($childrenNode->getNodeName eq "DBSNPID") {
				$DBSNPID=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "alleleA") {
				$alleleA=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "alleleB") {
				$alleleB=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "bigid") {
				$bigid=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "id") {
				$id=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "validationStatus") {
				$validationStatus=$textNode->getNodeValue;
			}
		## end iterate ELEMENT_NODE ##
	    }
	}
	my $newobj = new CaCORE::CaBIO::SNP;
	## begin set attr ##
		$newobj->setDBSNPID($DBSNPID);
		$newobj->setAlleleA($alleleA);
		$newobj->setAlleleB($alleleB);
		$newobj->setBigid($bigid);
		$newobj->setId($id);
		$newobj->setValidationStatus($validationStatus);
	## end set attr ##
	
	return $newobj;
}

## begin getters and setters ##

sub getDBSNPID {

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

sub getAlleleB {
	my $self = shift;
	return $self->{alleleB};
}

sub setAlleleB {
	my $self = shift;
	$self->{alleleB} = shift;
}

sub getBigid {
	my $self = shift;
	return $self->{bigid};
}

sub setBigid {
	my $self = shift;
	$self->{bigid} = shift;
}

sub getId {
	my $self = shift;
	return $self->{id};
}

sub setId {
	my $self = shift;
	$self->{id} = shift;

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

	
	## begin attribute to XML ##
	# abbreviation;
	if( defined( $self->getAbbreviation ) ) {
		$tmpstr = "<abbreviation xsi:type=\"xsd:string\">" . $self->getAbbreviation . "</abbreviation>";
	} else {
		$tmpstr = "<abbreviation xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
	}
	$result .= $tmpstr;

	# bigid;
	if( defined( $self->getBigid ) ) {
		$tmpstr = "<bigid xsi:type=\"xsd:string\">" . $self->getBigid . "</bigid>";
	} else {
		$tmpstr = "<bigid xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
	}
	$result .= $tmpstr;

	# commonName;
	if( defined( $self->getCommonName ) ) {
		$tmpstr = "<commonName xsi:type=\"xsd:string\">" . $self->getCommonName . "</commonName>";
	} else {
		$tmpstr = "<commonName xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
	}
	$result .= $tmpstr;

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

}

# parse a given xml node, construct one Taxon object
# param: xml node
# returns: one Taxon object
sub fromWSXMLNode {
	my $TaxonNode = $_[1];
	
	## begin ELEMENT_NODE children ##
		my $abbreviation;
		my $bigid;
		my $commonName;
		my $ethnicityStrain;
		my $id;
		my $scientificName;
	## end ELEMENT_NODE children ##

	# get all children for this node
	for my $childrenNode ($TaxonNode->getChildNodes) {
	    if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
		if( ! defined($childrenNode->getFirstChild) ){ next; };
		my $textNode = $childrenNode->getFirstChild;
		## begin iterate ELEMENT_NODE ##
		if (0) {
			# do nothing, just a place holder for "if" component
		}
			elsif ($childrenNode->getNodeName eq "abbreviation") {
				$abbreviation=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "bigid") {
				$bigid=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "commonName") {
				$commonName=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "ethnicityStrain") {
				$ethnicityStrain=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "id") {
				$id=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "scientificName") {
				$scientificName=$textNode->getNodeValue;
			}
		## end iterate ELEMENT_NODE ##
	    }
	}
	my $newobj = new CaCORE::CaBIO::Taxon;
	## begin set attr ##
		$newobj->setAbbreviation($abbreviation);
		$newobj->setBigid($bigid);
		$newobj->setCommonName($commonName);
		$newobj->setEthnicityStrain($ethnicityStrain);
		$newobj->setId($id);
		$newobj->setScientificName($scientificName);
	## end set attr ##
	
	return $newobj;
}

## begin getters and setters ##

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

sub getAbbreviation {
	my $self = shift;
	return $self->{abbreviation};
}

sub setAbbreviation {
	my $self = shift;
	$self->{abbreviation} = shift;
}

sub getBigid {
	my $self = shift;
	return $self->{bigid};
}

sub setBigid {
	my $self = shift;
	$self->{bigid} = shift;
}

sub getCommonName {
	my $self = shift;
	return $self->{commonName};
}

sub setCommonName {
	my $self = shift;
	$self->{commonName} = shift;

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

	my $current_id = shift;
	my $l = shift;
	my %worklist = %$l;
	
	# prefix portion of the xml
	$result .= "<multiRef id=\"id" . $assigned_id ."\" soapenc:root=\"0\" soapenv:encodingStyle=\"http://schemas.xmlsoap.org/soap/encoding/\" xsi:type=\"ns" . $current_id . ":Chromosome\" xmlns:soapenc=\"http://schemas.xmlsoap.org/soap/encoding/\" xmlns...
	my $tmpstr = "";
	$current_id ++;
	
	## begin attribute to XML ##
	# bigid;
	if( defined( $self->getBigid ) ) {
		$tmpstr = "<bigid xsi:type=\"xsd:string\">" . $self->getBigid . "</bigid>";
	} else {
		$tmpstr = "<bigid xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
	}
	$result .= $tmpstr;

	# id;
	if( defined( $self->getId ) ) {
		$tmpstr = "<id xsi:type=\"xsd:long\">" . $self->getId . "</id>";
	} else {
		$tmpstr = "<id xsi:type=\"xsd:long\" xsi:nil=\"true\" />";
	}
	$result .= $tmpstr;

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

	return @obj_list;
}

# parse a given xml node, construct one Chromosome object
# param: xml node
# returns: one Chromosome object
sub fromWSXMLNode {
	my $ChromosomeNode = $_[1];
	
	## begin ELEMENT_NODE children ##
		my $bigid;
		my $id;
		my $number;
	## end ELEMENT_NODE children ##

	# get all children for this node
	for my $childrenNode ($ChromosomeNode->getChildNodes) {
	    if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
		if( ! defined($childrenNode->getFirstChild) ){ next; };
		my $textNode = $childrenNode->getFirstChild;
		## begin iterate ELEMENT_NODE ##
		if (0) {
			# do nothing, just a place holder for "if" component
		}
			elsif ($childrenNode->getNodeName eq "bigid") {
				$bigid=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "id") {
				$id=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "number") {
				$number=$textNode->getNodeValue;
			}
		## end iterate ELEMENT_NODE ##
	    }
	}
	my $newobj = new CaCORE::CaBIO::Chromosome;
	## begin set attr ##
		$newobj->setBigid($bigid);
		$newobj->setId($id);
		$newobj->setNumber($number);
	## end set attr ##
	
	return $newobj;
}

## begin getters and setters ##

sub getBigid {
	my $self = shift;
	return $self->{bigid};
}

sub setBigid {
	my $self = shift;
	$self->{bigid} = shift;
}

sub getId {
	my $self = shift;
	return $self->{id};
}

sub setId {
	my $self = shift;
	$self->{id} = shift;

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

	my $current_id = shift;
	my $l = shift;
	my %worklist = %$l;
	
	# prefix portion of the xml
	$result .= "<multiRef id=\"id" . $assigned_id ."\" soapenc:root=\"0\" soapenv:encodingStyle=\"http://schemas.xmlsoap.org/soap/encoding/\" xsi:type=\"ns" . $current_id . ":Gene\" xmlns:soapenc=\"http://schemas.xmlsoap.org/soap/encoding/\" xmlns:ns" ....
	my $tmpstr = "";
	$current_id ++;
	
	## begin attribute to XML ##
	# bigid;
	if( defined( $self->getBigid ) ) {
		$tmpstr = "<bigid xsi:type=\"xsd:string\">" . $self->getBigid . "</bigid>";
	} else {
		$tmpstr = "<bigid xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
	}
	$result .= $tmpstr;

	# clusterId;
	if( defined( $self->getClusterId ) ) {
		$tmpstr = "<clusterId xsi:type=\"xsd:long\">" . $self->getClusterId . "</clusterId>";
	} else {
		$tmpstr = "<clusterId xsi:type=\"xsd:long\" xsi:nil=\"true\" />";
	}
	$result .= $tmpstr;

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

	return @obj_list;
}

# parse a given xml node, construct one Gene object
# param: xml node
# returns: one Gene object
sub fromWSXMLNode {
	my $GeneNode = $_[1];
	
	## begin ELEMENT_NODE children ##
		my $bigid;
		my $clusterId;
		my $fullName;
		my $id;
		my $symbol;
	## end ELEMENT_NODE children ##

	# get all children for this node
	for my $childrenNode ($GeneNode->getChildNodes) {
	    if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
		if( ! defined($childrenNode->getFirstChild) ){ next; };
		my $textNode = $childrenNode->getFirstChild;
		## begin iterate ELEMENT_NODE ##
		if (0) {
			# do nothing, just a place holder for "if" component
		}
			elsif ($childrenNode->getNodeName eq "bigid") {
				$bigid=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "clusterId") {
				$clusterId=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "fullName") {
				$fullName=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "id") {
				$id=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "symbol") {
				$symbol=$textNode->getNodeValue;
			}
		## end iterate ELEMENT_NODE ##
	    }
	}
	my $newobj = new CaCORE::CaBIO::Gene;
	## begin set attr ##
		$newobj->setBigid($bigid);
		$newobj->setClusterId($clusterId);
		$newobj->setFullName($fullName);
		$newobj->setId($id);
		$newobj->setSymbol($symbol);
	## end set attr ##
	
	return $newobj;
}

## begin getters and setters ##

sub getBigid {
	my $self = shift;
	return $self->{bigid};
}

sub setBigid {
	my $self = shift;
	$self->{bigid} = shift;
}

sub getClusterId {
	my $self = shift;
	return $self->{clusterId};
}

sub setClusterId {
	my $self = shift;
	$self->{clusterId} = shift;

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

	my $current_id = shift;
	my $l = shift;
	my %worklist = %$l;
	
	# prefix portion of the xml
	$result .= "<multiRef id=\"id" . $assigned_id ."\" soapenc:root=\"0\" soapenv:encodingStyle=\"http://schemas.xmlsoap.org/soap/encoding/\" xsi:type=\"ns" . $current_id . ":Protocol\" xmlns:soapenc=\"http://schemas.xmlsoap.org/soap/encoding/\" xmlns:n...
	my $tmpstr = "";
	$current_id ++;
	
	## begin attribute to XML ##
	# bigid;
	if( defined( $self->getBigid ) ) {
		$tmpstr = "<bigid xsi:type=\"xsd:string\">" . $self->getBigid . "</bigid>";
	} else {
		$tmpstr = "<bigid xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
	}
	$result .= $tmpstr;

	# description;
	if( defined( $self->getDescription ) ) {
		$tmpstr = "<description xsi:type=\"xsd:string\">" . $self->getDescription . "</description>";
	} else {
		$tmpstr = "<description xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
	}
	$result .= $tmpstr;

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

	return @obj_list;
}

# parse a given xml node, construct one Protocol object
# param: xml node
# returns: one Protocol object
sub fromWSXMLNode {
	my $ProtocolNode = $_[1];
	
	## begin ELEMENT_NODE children ##
		my $bigid;
		my $description;
		my $id;
		my $name;
		my $type;
	## end ELEMENT_NODE children ##

	# get all children for this node
	for my $childrenNode ($ProtocolNode->getChildNodes) {
	    if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
		if( ! defined($childrenNode->getFirstChild) ){ next; };
		my $textNode = $childrenNode->getFirstChild;
		## begin iterate ELEMENT_NODE ##
		if (0) {
			# do nothing, just a place holder for "if" component
		}
			elsif ($childrenNode->getNodeName eq "bigid") {
				$bigid=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "description") {
				$description=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "id") {
				$id=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "name") {
				$name=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "type") {
				$type=$textNode->getNodeValue;
			}
		## end iterate ELEMENT_NODE ##
	    }
	}
	my $newobj = new CaCORE::CaBIO::Protocol;
	## begin set attr ##
		$newobj->setBigid($bigid);
		$newobj->setDescription($description);
		$newobj->setId($id);
		$newobj->setName($name);
		$newobj->setType($type);
	## end set attr ##
	
	return $newobj;
}

## begin getters and setters ##

sub getBigid {
	my $self = shift;
	return $self->{bigid};
}

sub setBigid {
	my $self = shift;
	$self->{bigid} = shift;
}

sub getDescription {
	my $self = shift;
	return $self->{description};
}

sub setDescription {
	my $self = shift;
	$self->{description} = shift;

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

	my $current_id = shift;
	my $l = shift;
	my %worklist = %$l;
	
	# prefix portion of the xml
	$result .= "<multiRef id=\"id" . $assigned_id ."\" soapenc:root=\"0\" soapenv:encodingStyle=\"http://schemas.xmlsoap.org/soap/encoding/\" xsi:type=\"ns" . $current_id . ":Library\" xmlns:soapenc=\"http://schemas.xmlsoap.org/soap/encoding/\" xmlns:ns...
	my $tmpstr = "";
	$current_id ++;
	
	## begin attribute to XML ##
	# bigid;
	if( defined( $self->getBigid ) ) {
		$tmpstr = "<bigid xsi:type=\"xsd:string\">" . $self->getBigid . "</bigid>";
	} else {
		$tmpstr = "<bigid xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
	}
	$result .= $tmpstr;

	# cloneProducer;
	if( defined( $self->getCloneProducer ) ) {
		$tmpstr = "<cloneProducer xsi:type=\"xsd:string\">" . $self->getCloneProducer . "</cloneProducer>";
	} else {
		$tmpstr = "<cloneProducer xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
	}
	$result .= $tmpstr;

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

	return @obj_list;
}

# parse a given xml node, construct one Library object
# param: xml node
# returns: one Library object
sub fromWSXMLNode {
	my $LibraryNode = $_[1];
	
	## begin ELEMENT_NODE children ##
		my $bigid;
		my $cloneProducer;
		my $cloneVector;
		my $cloneVectorType;
		my $clonesToDate;
		my $creationDate;
		my $description;
		my $id;
		my $keyword;
		my $labHost;
		my $name;

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

	# get all children for this node
	for my $childrenNode ($LibraryNode->getChildNodes) {
	    if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
		if( ! defined($childrenNode->getFirstChild) ){ next; };
		my $textNode = $childrenNode->getFirstChild;
		## begin iterate ELEMENT_NODE ##
		if (0) {
			# do nothing, just a place holder for "if" component
		}
			elsif ($childrenNode->getNodeName eq "bigid") {
				$bigid=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "cloneProducer") {
				$cloneProducer=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "cloneVector") {
				$cloneVector=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "cloneVectorType") {
				$cloneVectorType=$textNode->getNodeValue;
			}

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

				$type=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "uniGeneId") {
				$uniGeneId=$textNode->getNodeValue;
			}
		## end iterate ELEMENT_NODE ##
	    }
	}
	my $newobj = new CaCORE::CaBIO::Library;
	## begin set attr ##
		$newobj->setBigid($bigid);
		$newobj->setCloneProducer($cloneProducer);
		$newobj->setCloneVector($cloneVector);
		$newobj->setCloneVectorType($cloneVectorType);
		$newobj->setClonesToDate($clonesToDate);
		$newobj->setCreationDate($creationDate);
		$newobj->setDescription($description);
		$newobj->setId($id);
		$newobj->setKeyword($keyword);
		$newobj->setLabHost($labHost);
		$newobj->setName($name);

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

		$newobj->setSequencesToDate($sequencesToDate);
		$newobj->setType($type);
		$newobj->setUniGeneId($uniGeneId);
	## end set attr ##
	
	return $newobj;
}

## begin getters and setters ##

sub getBigid {
	my $self = shift;
	return $self->{bigid};
}

sub setBigid {
	my $self = shift;
	$self->{bigid} = shift;
}

sub getCloneProducer {
	my $self = shift;
	return $self->{cloneProducer};
}

sub setCloneProducer {
	my $self = shift;
	$self->{cloneProducer} = shift;

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

	my $current_id = shift;
	my $l = shift;
	my %worklist = %$l;
	
	# prefix portion of the xml
	$result .= "<multiRef id=\"id" . $assigned_id ."\" soapenc:root=\"0\" soapenv:encodingStyle=\"http://schemas.xmlsoap.org/soap/encoding/\" xsi:type=\"ns" . $current_id . ":Clone\" xmlns:soapenc=\"http://schemas.xmlsoap.org/soap/encoding/\" xmlns:ns" ...
	my $tmpstr = "";
	$current_id ++;
	
	## begin attribute to XML ##
	# bigid;
	if( defined( $self->getBigid ) ) {
		$tmpstr = "<bigid xsi:type=\"xsd:string\">" . $self->getBigid . "</bigid>";
	} else {
		$tmpstr = "<bigid xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
	}
	$result .= $tmpstr;

	# id;
	if( defined( $self->getId ) ) {
		$tmpstr = "<id xsi:type=\"xsd:long\">" . $self->getId . "</id>";
	} else {
		$tmpstr = "<id xsi:type=\"xsd:long\" xsi:nil=\"true\" />";
	}
	$result .= $tmpstr;

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

	return @obj_list;
}

# parse a given xml node, construct one Clone object
# param: xml node
# returns: one Clone object
sub fromWSXMLNode {
	my $CloneNode = $_[1];
	
	## begin ELEMENT_NODE children ##
		my $bigid;
		my $id;
		my $insertSize;
		my $name;
		my $type;
	## end ELEMENT_NODE children ##

	# get all children for this node
	for my $childrenNode ($CloneNode->getChildNodes) {
	    if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
		if( ! defined($childrenNode->getFirstChild) ){ next; };
		my $textNode = $childrenNode->getFirstChild;
		## begin iterate ELEMENT_NODE ##
		if (0) {
			# do nothing, just a place holder for "if" component
		}
			elsif ($childrenNode->getNodeName eq "bigid") {
				$bigid=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "id") {
				$id=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "insertSize") {
				$insertSize=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "name") {
				$name=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "type") {
				$type=$textNode->getNodeValue;
			}
		## end iterate ELEMENT_NODE ##
	    }
	}
	my $newobj = new CaCORE::CaBIO::Clone;
	## begin set attr ##
		$newobj->setBigid($bigid);
		$newobj->setId($id);
		$newobj->setInsertSize($insertSize);
		$newobj->setName($name);
		$newobj->setType($type);
	## end set attr ##
	
	return $newobj;
}

## begin getters and setters ##

sub getBigid {
	my $self = shift;
	return $self->{bigid};
}

sub setBigid {
	my $self = shift;
	$self->{bigid} = shift;
}

sub getId {
	my $self = shift;
	return $self->{id};
}

sub setId {
	my $self = shift;
	$self->{id} = shift;

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

	my $current_id = shift;
	my $l = shift;
	my %worklist = %$l;
	
	# prefix portion of the xml
	$result .= "<multiRef id=\"id" . $assigned_id ."\" soapenc:root=\"0\" soapenv:encodingStyle=\"http://schemas.xmlsoap.org/soap/encoding/\" xsi:type=\"ns" . $current_id . ":CloneRelativeLocation\" xmlns:soapenc=\"http://schemas.xmlsoap.org/soap/encodi...
	my $tmpstr = "";
	$current_id ++;
	
	## begin attribute to XML ##
	# bigid;
	if( defined( $self->getBigid ) ) {
		$tmpstr = "<bigid xsi:type=\"xsd:string\">" . $self->getBigid . "</bigid>";
	} else {
		$tmpstr = "<bigid xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
	}
	$result .= $tmpstr;

	# id;
	if( defined( $self->getId ) ) {
		$tmpstr = "<id xsi:type=\"xsd:long\">" . $self->getId . "</id>";
	} else {
		$tmpstr = "<id xsi:type=\"xsd:long\" xsi:nil=\"true\" />";
	}
	$result .= $tmpstr;

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

	return @obj_list;
}

# parse a given xml node, construct one CloneRelativeLocation object
# param: xml node
# returns: one CloneRelativeLocation object
sub fromWSXMLNode {
	my $CloneRelativeLocationNode = $_[1];
	
	## begin ELEMENT_NODE children ##
		my $bigid;
		my $id;
		my $type;
	## end ELEMENT_NODE children ##

	# get all children for this node
	for my $childrenNode ($CloneRelativeLocationNode->getChildNodes) {
	    if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
		if( ! defined($childrenNode->getFirstChild) ){ next; };
		my $textNode = $childrenNode->getFirstChild;
		## begin iterate ELEMENT_NODE ##
		if (0) {
			# do nothing, just a place holder for "if" component
		}
			elsif ($childrenNode->getNodeName eq "bigid") {
				$bigid=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "id") {
				$id=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "type") {
				$type=$textNode->getNodeValue;
			}
		## end iterate ELEMENT_NODE ##
	    }
	}
	my $newobj = new CaCORE::CaBIO::CloneRelativeLocation;
	## begin set attr ##
		$newobj->setBigid($bigid);
		$newobj->setId($id);
		$newobj->setType($type);
	## end set attr ##
	
	return $newobj;
}

## begin getters and setters ##

sub getBigid {
	my $self = shift;
	return $self->{bigid};
}

sub setBigid {
	my $self = shift;
	$self->{bigid} = shift;
}

sub getId {
	my $self = shift;
	return $self->{id};
}

sub setId {
	my $self = shift;
	$self->{id} = shift;

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

	$result .= $tmpstr;

	# accessionNumberVersion;
	if( defined( $self->getAccessionNumberVersion ) ) {
		$tmpstr = "<accessionNumberVersion xsi:type=\"xsd:string\">" . $self->getAccessionNumberVersion . "</accessionNumberVersion>";
	} else {
		$tmpstr = "<accessionNumberVersion xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
	}
	$result .= $tmpstr;

	# bigid;
	if( defined( $self->getBigid ) ) {
		$tmpstr = "<bigid xsi:type=\"xsd:string\">" . $self->getBigid . "</bigid>";
	} else {
		$tmpstr = "<bigid xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
	}
	$result .= $tmpstr;

	# id;
	if( defined( $self->getId ) ) {
		$tmpstr = "<id xsi:type=\"xsd:long\">" . $self->getId . "</id>";
	} else {
		$tmpstr = "<id xsi:type=\"xsd:long\" xsi:nil=\"true\" />";
	}
	$result .= $tmpstr;

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

# parse a given xml node, construct one NucleicAcidSequence object
# param: xml node
# returns: one NucleicAcidSequence object
sub fromWSXMLNode {
	my $NucleicAcidSequenceNode = $_[1];
	
	## begin ELEMENT_NODE children ##
		my $accessionNumber;
		my $accessionNumberVersion;
		my $bigid;
		my $id;
		my $length;
		my $type;
		my $value;
	## end ELEMENT_NODE children ##

	# get all children for this node
	for my $childrenNode ($NucleicAcidSequenceNode->getChildNodes) {
	    if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
		if( ! defined($childrenNode->getFirstChild) ){ next; };

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

		## begin iterate ELEMENT_NODE ##
		if (0) {
			# do nothing, just a place holder for "if" component
		}
			elsif ($childrenNode->getNodeName eq "accessionNumber") {
				$accessionNumber=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "accessionNumberVersion") {
				$accessionNumberVersion=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "bigid") {
				$bigid=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "id") {
				$id=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "length") {
				$length=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "type") {
				$type=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "value") {
				$value=$textNode->getNodeValue;
			}
		## end iterate ELEMENT_NODE ##
	    }
	}
	my $newobj = new CaCORE::CaBIO::NucleicAcidSequence;
	## begin set attr ##
		$newobj->setAccessionNumber($accessionNumber);
		$newobj->setAccessionNumberVersion($accessionNumberVersion);
		$newobj->setBigid($bigid);
		$newobj->setId($id);
		$newobj->setLength($length);
		$newobj->setType($type);
		$newobj->setValue($value);
	## end set attr ##
	
	return $newobj;
}

## begin getters and setters ##

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

sub getAccessionNumberVersion {
	my $self = shift;
	return $self->{accessionNumberVersion};
}

sub setAccessionNumberVersion {
	my $self = shift;
	$self->{accessionNumberVersion} = shift;
}

sub getBigid {
	my $self = shift;
	return $self->{bigid};
}

sub setBigid {
	my $self = shift;
	$self->{bigid} = shift;
}

sub getId {
	my $self = shift;
	return $self->{id};
}

sub setId {
	my $self = shift;
	$self->{id} = shift;

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

	my $current_id = shift;
	my $l = shift;
	my %worklist = %$l;
	
	# prefix portion of the xml
	$result .= "<multiRef id=\"id" . $assigned_id ."\" soapenc:root=\"0\" soapenv:encodingStyle=\"http://schemas.xmlsoap.org/soap/encoding/\" xsi:type=\"ns" . $current_id . ":DiseaseOntology\" xmlns:soapenc=\"http://schemas.xmlsoap.org/soap/encoding/\" ...
	my $tmpstr = "";
	$current_id ++;
	
	## begin attribute to XML ##
	# bigid;
	if( defined( $self->getBigid ) ) {
		$tmpstr = "<bigid xsi:type=\"xsd:string\">" . $self->getBigid . "</bigid>";
	} else {
		$tmpstr = "<bigid xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
	}
	$result .= $tmpstr;

	# id;
	if( defined( $self->getId ) ) {
		$tmpstr = "<id xsi:type=\"xsd:long\">" . $self->getId . "</id>";
	} else {
		$tmpstr = "<id xsi:type=\"xsd:long\" xsi:nil=\"true\" />";
	}
	$result .= $tmpstr;

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

	return @obj_list;
}

# parse a given xml node, construct one DiseaseOntology object
# param: xml node
# returns: one DiseaseOntology object
sub fromWSXMLNode {
	my $DiseaseOntologyNode = $_[1];
	
	## begin ELEMENT_NODE children ##
		my $bigid;
		my $id;
		my $name;
	## end ELEMENT_NODE children ##

	# get all children for this node
	for my $childrenNode ($DiseaseOntologyNode->getChildNodes) {
	    if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
		if( ! defined($childrenNode->getFirstChild) ){ next; };
		my $textNode = $childrenNode->getFirstChild;
		## begin iterate ELEMENT_NODE ##
		if (0) {
			# do nothing, just a place holder for "if" component
		}
			elsif ($childrenNode->getNodeName eq "bigid") {
				$bigid=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "id") {
				$id=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "name") {
				$name=$textNode->getNodeValue;
			}
		## end iterate ELEMENT_NODE ##
	    }
	}
	my $newobj = new CaCORE::CaBIO::DiseaseOntology;
	## begin set attr ##
		$newobj->setBigid($bigid);
		$newobj->setId($id);
		$newobj->setName($name);
	## end set attr ##
	
	return $newobj;
}

## begin getters and setters ##

sub getBigid {
	my $self = shift;
	return $self->{bigid};
}

sub setBigid {
	my $self = shift;
	$self->{bigid} = shift;
}

sub getId {
	my $self = shift;
	return $self->{id};
}

sub setId {
	my $self = shift;
	$self->{id} = shift;

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

	my $current_id = shift;
	my $l = shift;
	my %worklist = %$l;
	
	# prefix portion of the xml
	$result .= "<multiRef id=\"id" . $assigned_id ."\" soapenc:root=\"0\" soapenv:encodingStyle=\"http://schemas.xmlsoap.org/soap/encoding/\" xsi:type=\"ns" . $current_id . ":GeneRelativeLocation\" xmlns:soapenc=\"http://schemas.xmlsoap.org/soap/encodin...
	my $tmpstr = "";
	$current_id ++;
	
	## begin attribute to XML ##
	# bigid;
	if( defined( $self->getBigid ) ) {
		$tmpstr = "<bigid xsi:type=\"xsd:string\">" . $self->getBigid . "</bigid>";
	} else {
		$tmpstr = "<bigid xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
	}
	$result .= $tmpstr;

	# id;
	if( defined( $self->getId ) ) {
		$tmpstr = "<id xsi:type=\"xsd:long\">" . $self->getId . "</id>";
	} else {
		$tmpstr = "<id xsi:type=\"xsd:long\" xsi:nil=\"true\" />";
	}
	$result .= $tmpstr;

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

	return @obj_list;
}

# parse a given xml node, construct one GeneRelativeLocation object
# param: xml node
# returns: one GeneRelativeLocation object
sub fromWSXMLNode {
	my $GeneRelativeLocationNode = $_[1];
	
	## begin ELEMENT_NODE children ##
		my $bigid;
		my $id;
		my $type;
	## end ELEMENT_NODE children ##

	# get all children for this node
	for my $childrenNode ($GeneRelativeLocationNode->getChildNodes) {
	    if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
		if( ! defined($childrenNode->getFirstChild) ){ next; };
		my $textNode = $childrenNode->getFirstChild;
		## begin iterate ELEMENT_NODE ##
		if (0) {
			# do nothing, just a place holder for "if" component
		}
			elsif ($childrenNode->getNodeName eq "bigid") {
				$bigid=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "id") {
				$id=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "type") {
				$type=$textNode->getNodeValue;
			}
		## end iterate ELEMENT_NODE ##
	    }
	}
	my $newobj = new CaCORE::CaBIO::GeneRelativeLocation;
	## begin set attr ##
		$newobj->setBigid($bigid);
		$newobj->setId($id);
		$newobj->setType($type);
	## end set attr ##
	
	return $newobj;
}

## begin getters and setters ##

sub getBigid {
	my $self = shift;
	return $self->{bigid};
}

sub setBigid {
	my $self = shift;
	$self->{bigid} = shift;
}

sub getId {
	my $self = shift;
	return $self->{id};
}

sub setId {
	my $self = shift;
	$self->{id} = shift;

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

	my $current_id = shift;
	my $l = shift;
	my %worklist = %$l;
	
	# prefix portion of the xml
	$result .= "<multiRef id=\"id" . $assigned_id ."\" soapenc:root=\"0\" soapenv:encodingStyle=\"http://schemas.xmlsoap.org/soap/encoding/\" xsi:type=\"ns" . $current_id . ":PopulationFrequency\" xmlns:soapenc=\"http://schemas.xmlsoap.org/soap/encoding...
	my $tmpstr = "";
	$current_id ++;
	
	## begin attribute to XML ##
	# bigid;
	if( defined( $self->getBigid ) ) {
		$tmpstr = "<bigid xsi:type=\"xsd:string\">" . $self->getBigid . "</bigid>";
	} else {
		$tmpstr = "<bigid xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
	}
	$result .= $tmpstr;

	# ethnicity;
	if( defined( $self->getEthnicity ) ) {
		$tmpstr = "<ethnicity xsi:type=\"xsd:string\">" . $self->getEthnicity . "</ethnicity>";
	} else {
		$tmpstr = "<ethnicity xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
	}
	$result .= $tmpstr;

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

	return @obj_list;
}

# parse a given xml node, construct one PopulationFrequency object
# param: xml node
# returns: one PopulationFrequency object
sub fromWSXMLNode {
	my $PopulationFrequencyNode = $_[1];
	
	## begin ELEMENT_NODE children ##
		my $bigid;
		my $ethnicity;
		my $id;
		my $majorAllele;
		my $majorFrequency;
		my $minorAllele;
		my $minorFrequency;
		my $type;
	## end ELEMENT_NODE children ##

	# get all children for this node
	for my $childrenNode ($PopulationFrequencyNode->getChildNodes) {
	    if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
		if( ! defined($childrenNode->getFirstChild) ){ next; };
		my $textNode = $childrenNode->getFirstChild;
		## begin iterate ELEMENT_NODE ##
		if (0) {
			# do nothing, just a place holder for "if" component
		}
			elsif ($childrenNode->getNodeName eq "bigid") {
				$bigid=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "ethnicity") {
				$ethnicity=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "id") {
				$id=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "majorAllele") {
				$majorAllele=$textNode->getNodeValue;
			}

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

				$minorFrequency=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "type") {
				$type=$textNode->getNodeValue;
			}
		## end iterate ELEMENT_NODE ##
	    }
	}
	my $newobj = new CaCORE::CaBIO::PopulationFrequency;
	## begin set attr ##
		$newobj->setBigid($bigid);
		$newobj->setEthnicity($ethnicity);
		$newobj->setId($id);
		$newobj->setMajorAllele($majorAllele);
		$newobj->setMajorFrequency($majorFrequency);
		$newobj->setMinorAllele($minorAllele);
		$newobj->setMinorFrequency($minorFrequency);
		$newobj->setType($type);
	## end set attr ##
	
	return $newobj;
}

## begin getters and setters ##

sub getBigid {
	my $self = shift;
	return $self->{bigid};
}

sub setBigid {
	my $self = shift;
	$self->{bigid} = shift;
}

sub getEthnicity {
	my $self = shift;
	return $self->{ethnicity};
}

sub setEthnicity {
	my $self = shift;
	$self->{ethnicity} = shift;

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

	my $current_id = shift;
	my $l = shift;
	my %worklist = %$l;
	
	# prefix portion of the xml
	$result .= "<multiRef id=\"id" . $assigned_id ."\" soapenc:root=\"0\" soapenv:encodingStyle=\"http://schemas.xmlsoap.org/soap/encoding/\" xsi:type=\"ns" . $current_id . ":HomologousAssociation\" xmlns:soapenc=\"http://schemas.xmlsoap.org/soap/encodi...
	my $tmpstr = "";
	$current_id ++;
	
	## begin attribute to XML ##
	# bigid;
	if( defined( $self->getBigid ) ) {
		$tmpstr = "<bigid xsi:type=\"xsd:string\">" . $self->getBigid . "</bigid>";
	} else {
		$tmpstr = "<bigid xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
	}
	$result .= $tmpstr;

	# homologousId;
	if( defined( $self->getHomologousId ) ) {
		$tmpstr = "<homologousId xsi:type=\"xsd:long\">" . $self->getHomologousId . "</homologousId>";
	} else {
		$tmpstr = "<homologousId xsi:type=\"xsd:long\" xsi:nil=\"true\" />";
	}
	$result .= $tmpstr;

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

	return @obj_list;
}

# parse a given xml node, construct one HomologousAssociation object
# param: xml node
# returns: one HomologousAssociation object
sub fromWSXMLNode {
	my $HomologousAssociationNode = $_[1];
	
	## begin ELEMENT_NODE children ##
		my $bigid;
		my $homologousId;
		my $id;
		my $similarityPercentage;
	## end ELEMENT_NODE children ##

	# get all children for this node
	for my $childrenNode ($HomologousAssociationNode->getChildNodes) {
	    if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
		if( ! defined($childrenNode->getFirstChild) ){ next; };
		my $textNode = $childrenNode->getFirstChild;
		## begin iterate ELEMENT_NODE ##
		if (0) {
			# do nothing, just a place holder for "if" component
		}
			elsif ($childrenNode->getNodeName eq "bigid") {
				$bigid=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "homologousId") {
				$homologousId=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "id") {
				$id=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "similarityPercentage") {
				$similarityPercentage=$textNode->getNodeValue;
			}
		## end iterate ELEMENT_NODE ##
	    }
	}
	my $newobj = new CaCORE::CaBIO::HomologousAssociation;
	## begin set attr ##
		$newobj->setBigid($bigid);
		$newobj->setHomologousId($homologousId);
		$newobj->setId($id);
		$newobj->setSimilarityPercentage($similarityPercentage);
	## end set attr ##
	
	return $newobj;
}

## begin getters and setters ##

sub getBigid {
	my $self = shift;
	return $self->{bigid};
}

sub setBigid {
	my $self = shift;
	$self->{bigid} = shift;
}

sub getHomologousId {
	my $self = shift;
	return $self->{homologousId};
}

sub setHomologousId {
	my $self = shift;
	$self->{homologousId} = shift;

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

	my $current_id = shift;
	my $l = shift;
	my %worklist = %$l;
	
	# prefix portion of the xml
	$result .= "<multiRef id=\"id" . $assigned_id ."\" soapenc:root=\"0\" soapenv:encodingStyle=\"http://schemas.xmlsoap.org/soap/encoding/\" xsi:type=\"ns" . $current_id . ":Cytoband\" xmlns:soapenc=\"http://schemas.xmlsoap.org/soap/encoding/\" xmlns:n...
	my $tmpstr = "";
	$current_id ++;
	
	## begin attribute to XML ##
	# bigid;
	if( defined( $self->getBigid ) ) {
		$tmpstr = "<bigid xsi:type=\"xsd:string\">" . $self->getBigid . "</bigid>";
	} else {
		$tmpstr = "<bigid xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
	}
	$result .= $tmpstr;

	# id;
	if( defined( $self->getId ) ) {
		$tmpstr = "<id xsi:type=\"xsd:long\">" . $self->getId . "</id>";
	} else {
		$tmpstr = "<id xsi:type=\"xsd:long\" xsi:nil=\"true\" />";
	}
	$result .= $tmpstr;

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

	return @obj_list;
}

# parse a given xml node, construct one Cytoband object
# param: xml node
# returns: one Cytoband object
sub fromWSXMLNode {
	my $CytobandNode = $_[1];
	
	## begin ELEMENT_NODE children ##
		my $bigid;
		my $id;
		my $name;
	## end ELEMENT_NODE children ##

	# get all children for this node
	for my $childrenNode ($CytobandNode->getChildNodes) {
	    if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
		if( ! defined($childrenNode->getFirstChild) ){ next; };
		my $textNode = $childrenNode->getFirstChild;
		## begin iterate ELEMENT_NODE ##
		if (0) {
			# do nothing, just a place holder for "if" component
		}
			elsif ($childrenNode->getNodeName eq "bigid") {
				$bigid=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "id") {
				$id=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "name") {
				$name=$textNode->getNodeValue;
			}
		## end iterate ELEMENT_NODE ##
	    }
	}
	my $newobj = new CaCORE::CaBIO::Cytoband;
	## begin set attr ##
		$newobj->setBigid($bigid);
		$newobj->setId($id);
		$newobj->setName($name);
	## end set attr ##
	
	return $newobj;
}

## begin getters and setters ##

sub getBigid {
	my $self = shift;
	return $self->{bigid};
}

sub setBigid {
	my $self = shift;
	$self->{bigid} = shift;
}

sub getId {
	my $self = shift;
	return $self->{id};
}

sub setId {
	my $self = shift;
	$self->{id} = shift;

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

	my $current_id = shift;
	my $l = shift;
	my %worklist = %$l;
	
	# prefix portion of the xml
	$result .= "<multiRef id=\"id" . $assigned_id ."\" soapenc:root=\"0\" soapenv:encodingStyle=\"http://schemas.xmlsoap.org/soap/encoding/\" xsi:type=\"ns" . $current_id . ":GeneOntology\" xmlns:soapenc=\"http://schemas.xmlsoap.org/soap/encoding/\" xml...
	my $tmpstr = "";
	$current_id ++;
	
	## begin attribute to XML ##
	# bigid;
	if( defined( $self->getBigid ) ) {
		$tmpstr = "<bigid xsi:type=\"xsd:string\">" . $self->getBigid . "</bigid>";
	} else {
		$tmpstr = "<bigid xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
	}
	$result .= $tmpstr;

	# id;
	if( defined( $self->getId ) ) {
		$tmpstr = "<id xsi:type=\"xsd:long\">" . $self->getId . "</id>";
	} else {
		$tmpstr = "<id xsi:type=\"xsd:long\" xsi:nil=\"true\" />";
	}
	$result .= $tmpstr;

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

	return @obj_list;
}

# parse a given xml node, construct one GeneOntology object
# param: xml node
# returns: one GeneOntology object
sub fromWSXMLNode {
	my $GeneOntologyNode = $_[1];
	
	## begin ELEMENT_NODE children ##
		my $bigid;
		my $id;
		my $name;
	## end ELEMENT_NODE children ##

	# get all children for this node
	for my $childrenNode ($GeneOntologyNode->getChildNodes) {
	    if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
		if( ! defined($childrenNode->getFirstChild) ){ next; };
		my $textNode = $childrenNode->getFirstChild;
		## begin iterate ELEMENT_NODE ##
		if (0) {
			# do nothing, just a place holder for "if" component
		}
			elsif ($childrenNode->getNodeName eq "bigid") {
				$bigid=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "id") {
				$id=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "name") {
				$name=$textNode->getNodeValue;
			}
		## end iterate ELEMENT_NODE ##
	    }
	}
	my $newobj = new CaCORE::CaBIO::GeneOntology;
	## begin set attr ##
		$newobj->setBigid($bigid);
		$newobj->setId($id);
		$newobj->setName($name);
	## end set attr ##
	
	return $newobj;
}

## begin getters and setters ##

sub getBigid {
	my $self = shift;
	return $self->{bigid};
}

sub setBigid {
	my $self = shift;
	$self->{bigid} = shift;
}

sub getId {
	my $self = shift;
	return $self->{id};
}

sub setId {
	my $self = shift;
	$self->{id} = shift;

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

	my $current_id = shift;
	my $l = shift;
	my %worklist = %$l;
	
	# prefix portion of the xml
	$result .= "<multiRef id=\"id" . $assigned_id ."\" soapenc:root=\"0\" soapenv:encodingStyle=\"http://schemas.xmlsoap.org/soap/encoding/\" xsi:type=\"ns" . $current_id . ":OrganOntology\" xmlns:soapenc=\"http://schemas.xmlsoap.org/soap/encoding/\" xm...
	my $tmpstr = "";
	$current_id ++;
	
	## begin attribute to XML ##
	# bigid;
	if( defined( $self->getBigid ) ) {
		$tmpstr = "<bigid xsi:type=\"xsd:string\">" . $self->getBigid . "</bigid>";
	} else {
		$tmpstr = "<bigid xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
	}
	$result .= $tmpstr;

	# id;
	if( defined( $self->getId ) ) {
		$tmpstr = "<id xsi:type=\"xsd:long\">" . $self->getId . "</id>";
	} else {
		$tmpstr = "<id xsi:type=\"xsd:long\" xsi:nil=\"true\" />";
	}
	$result .= $tmpstr;

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

	return @obj_list;
}

# parse a given xml node, construct one OrganOntology object
# param: xml node
# returns: one OrganOntology object
sub fromWSXMLNode {
	my $OrganOntologyNode = $_[1];
	
	## begin ELEMENT_NODE children ##
		my $bigid;
		my $id;
		my $name;
	## end ELEMENT_NODE children ##

	# get all children for this node
	for my $childrenNode ($OrganOntologyNode->getChildNodes) {
	    if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
		if( ! defined($childrenNode->getFirstChild) ){ next; };
		my $textNode = $childrenNode->getFirstChild;
		## begin iterate ELEMENT_NODE ##
		if (0) {
			# do nothing, just a place holder for "if" component
		}
			elsif ($childrenNode->getNodeName eq "bigid") {
				$bigid=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "id") {
				$id=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "name") {
				$name=$textNode->getNodeValue;
			}
		## end iterate ELEMENT_NODE ##
	    }
	}
	my $newobj = new CaCORE::CaBIO::OrganOntology;
	## begin set attr ##
		$newobj->setBigid($bigid);
		$newobj->setId($id);
		$newobj->setName($name);
	## end set attr ##
	
	return $newobj;
}

## begin getters and setters ##

sub getBigid {
	my $self = shift;
	return $self->{bigid};
}

sub setBigid {
	my $self = shift;
	$self->{bigid} = shift;
}

sub getId {
	my $self = shift;
	return $self->{id};
}

sub setId {
	my $self = shift;
	$self->{id} = shift;

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

	my $current_id = shift;
	my $l = shift;
	my %worklist = %$l;
	
	# prefix portion of the xml
	$result .= "<multiRef id=\"id" . $assigned_id ."\" soapenc:root=\"0\" soapenv:encodingStyle=\"http://schemas.xmlsoap.org/soap/encoding/\" xsi:type=\"ns" . $current_id . ":ProteinSequence\" xmlns:soapenc=\"http://schemas.xmlsoap.org/soap/encoding/\" ...
	my $tmpstr = "";
	$current_id ++;
	
	## begin attribute to XML ##
	# bigid;
	if( defined( $self->getBigid ) ) {
		$tmpstr = "<bigid xsi:type=\"xsd:string\">" . $self->getBigid . "</bigid>";
	} else {
		$tmpstr = "<bigid xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
	}
	$result .= $tmpstr;

	# checkSum;
	if( defined( $self->getCheckSum ) ) {
		$tmpstr = "<checkSum xsi:type=\"xsd:string\">" . $self->getCheckSum . "</checkSum>";
	} else {
		$tmpstr = "<checkSum xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
	}
	$result .= $tmpstr;

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

	return @obj_list;
}

# parse a given xml node, construct one ProteinSequence object
# param: xml node
# returns: one ProteinSequence object
sub fromWSXMLNode {
	my $ProteinSequenceNode = $_[1];
	
	## begin ELEMENT_NODE children ##
		my $bigid;
		my $checkSum;
		my $id;
		my $length;
		my $molecularWeightInDaltons;
		my $value;
	## end ELEMENT_NODE children ##

	# get all children for this node
	for my $childrenNode ($ProteinSequenceNode->getChildNodes) {
	    if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
		if( ! defined($childrenNode->getFirstChild) ){ next; };
		my $textNode = $childrenNode->getFirstChild;
		## begin iterate ELEMENT_NODE ##
		if (0) {
			# do nothing, just a place holder for "if" component
		}
			elsif ($childrenNode->getNodeName eq "bigid") {
				$bigid=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "checkSum") {
				$checkSum=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "id") {
				$id=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "length") {
				$length=$textNode->getNodeValue;
			}

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

				$molecularWeightInDaltons=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "value") {
				$value=$textNode->getNodeValue;
			}
		## end iterate ELEMENT_NODE ##
	    }
	}
	my $newobj = new CaCORE::CaBIO::ProteinSequence;
	## begin set attr ##
		$newobj->setBigid($bigid);
		$newobj->setCheckSum($checkSum);
		$newobj->setId($id);
		$newobj->setLength($length);
		$newobj->setMolecularWeightInDaltons($molecularWeightInDaltons);
		$newobj->setValue($value);
	## end set attr ##
	
	return $newobj;
}

## begin getters and setters ##

sub getBigid {
	my $self = shift;
	return $self->{bigid};
}

sub setBigid {
	my $self = shift;
	$self->{bigid} = shift;
}

sub getCheckSum {
	my $self = shift;
	return $self->{checkSum};
}

sub setCheckSum {
	my $self = shift;
	$self->{checkSum} = shift;

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

	my $current_id = shift;
	my $l = shift;
	my %worklist = %$l;
	
	# prefix portion of the xml
	$result .= "<multiRef id=\"id" . $assigned_id ."\" soapenc:root=\"0\" soapenv:encodingStyle=\"http://schemas.xmlsoap.org/soap/encoding/\" xsi:type=\"ns" . $current_id . ":Protein\" xmlns:soapenc=\"http://schemas.xmlsoap.org/soap/encoding/\" xmlns:ns...
	my $tmpstr = "";
	$current_id ++;
	
	## begin attribute to XML ##
	# bigid;
	if( defined( $self->getBigid ) ) {
		$tmpstr = "<bigid xsi:type=\"xsd:string\">" . $self->getBigid . "</bigid>";
	} else {
		$tmpstr = "<bigid xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
	}
	$result .= $tmpstr;

	# copyrightStatement;
	if( defined( $self->getCopyrightStatement ) ) {
		$tmpstr = "<copyrightStatement xsi:type=\"xsd:string\">" . $self->getCopyrightStatement . "</copyrightStatement>";
	} else {
		$tmpstr = "<copyrightStatement xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
	}
	$result .= $tmpstr;

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

	return @obj_list;
}

# parse a given xml node, construct one Protein object
# param: xml node
# returns: one Protein object
sub fromWSXMLNode {
	my $ProteinNode = $_[1];
	
	## begin ELEMENT_NODE children ##
		my $bigid;
		my $copyrightStatement;
		my $id;
		my $name;
		my $primaryAccession;
		my $uniProtCode;
		my @keywords = ();
		my @secondaryAccession = ();
	## end ELEMENT_NODE children ##

	# get all children for this node
	for my $childrenNode ($ProteinNode->getChildNodes) {
	    if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
		if( ! defined($childrenNode->getFirstChild) ){ next; };
		my $textNode = $childrenNode->getFirstChild;
		## begin iterate ELEMENT_NODE ##
		if (0) {
			# do nothing, just a place holder for "if" component
		}
			elsif ($childrenNode->getNodeName eq "bigid") {
				$bigid=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "copyrightStatement") {
				$copyrightStatement=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "id") {
				$id=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "name") {
				$name=$textNode->getNodeValue;
			}

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

					if( ! defined($node->getFirstChild) ){ next; };
					my $txnode = $node->getFirstChild;
					push @secondaryAccession, $txnode->getNodeValue;
				}
			}
		## end iterate ELEMENT_NODE ##
	    }
	}
	my $newobj = new CaCORE::CaBIO::Protein;
	## begin set attr ##
		$newobj->setBigid($bigid);
		$newobj->setCopyrightStatement($copyrightStatement);
		$newobj->setId($id);
		$newobj->setName($name);
		$newobj->setPrimaryAccession($primaryAccession);
		$newobj->setUniProtCode($uniProtCode);
		$newobj->setKeywordsCollection(@keywords);
		$newobj->setSecondaryAccessionCollection(@secondaryAccession);
	## end set attr ##
	
	return $newobj;
}

## begin getters and setters ##

sub getBigid {
	my $self = shift;
	return $self->{bigid};
}

sub setBigid {
	my $self = shift;
	$self->{bigid} = shift;
}

sub getCopyrightStatement {
	my $self = shift;
	return $self->{copyrightStatement};
}

sub setCopyrightStatement {
	my $self = shift;
	$self->{copyrightStatement} = shift;

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

	my $current_id = shift;
	my $l = shift;
	my %worklist = %$l;
	
	# prefix portion of the xml
	$result .= "<multiRef id=\"id" . $assigned_id ."\" soapenc:root=\"0\" soapenv:encodingStyle=\"http://schemas.xmlsoap.org/soap/encoding/\" xsi:type=\"ns" . $current_id . ":ProteinAlias\" xmlns:soapenc=\"http://schemas.xmlsoap.org/soap/encoding/\" xml...
	my $tmpstr = "";
	$current_id ++;
	
	## begin attribute to XML ##
	# bigid;
	if( defined( $self->getBigid ) ) {
		$tmpstr = "<bigid xsi:type=\"xsd:string\">" . $self->getBigid . "</bigid>";
	} else {
		$tmpstr = "<bigid xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
	}
	$result .= $tmpstr;

	# id;
	if( defined( $self->getId ) ) {
		$tmpstr = "<id xsi:type=\"xsd:long\">" . $self->getId . "</id>";
	} else {
		$tmpstr = "<id xsi:type=\"xsd:long\" xsi:nil=\"true\" />";
	}
	$result .= $tmpstr;

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

	return @obj_list;
}

# parse a given xml node, construct one ProteinAlias object
# param: xml node
# returns: one ProteinAlias object
sub fromWSXMLNode {
	my $ProteinAliasNode = $_[1];
	
	## begin ELEMENT_NODE children ##
		my $bigid;
		my $id;
		my $name;
	## end ELEMENT_NODE children ##

	# get all children for this node
	for my $childrenNode ($ProteinAliasNode->getChildNodes) {
	    if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
		if( ! defined($childrenNode->getFirstChild) ){ next; };
		my $textNode = $childrenNode->getFirstChild;
		## begin iterate ELEMENT_NODE ##
		if (0) {
			# do nothing, just a place holder for "if" component
		}
			elsif ($childrenNode->getNodeName eq "bigid") {
				$bigid=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "id") {
				$id=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "name") {
				$name=$textNode->getNodeValue;
			}
		## end iterate ELEMENT_NODE ##
	    }
	}
	my $newobj = new CaCORE::CaBIO::ProteinAlias;
	## begin set attr ##
		$newobj->setBigid($bigid);
		$newobj->setId($id);
		$newobj->setName($name);
	## end set attr ##
	
	return $newobj;
}

## begin getters and setters ##

sub getBigid {
	my $self = shift;
	return $self->{bigid};
}

sub setBigid {
	my $self = shift;
	$self->{bigid} = shift;
}

sub getId {
	my $self = shift;
	return $self->{id};
}

sub setId {
	my $self = shift;
	$self->{id} = shift;

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

	my $current_id = shift;
	my $l = shift;
	my %worklist = %$l;
	
	# prefix portion of the xml
	$result .= "<multiRef id=\"id" . $assigned_id ."\" soapenc:root=\"0\" soapenv:encodingStyle=\"http://schemas.xmlsoap.org/soap/encoding/\" xsi:type=\"ns" . $current_id . ":Target\" xmlns:soapenc=\"http://schemas.xmlsoap.org/soap/encoding/\" xmlns:ns"...
	my $tmpstr = "";
	$current_id ++;
	
	## begin attribute to XML ##
	# bigid;
	if( defined( $self->getBigid ) ) {
		$tmpstr = "<bigid xsi:type=\"xsd:string\">" . $self->getBigid . "</bigid>";
	} else {
		$tmpstr = "<bigid xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
	}
	$result .= $tmpstr;

	# id;
	if( defined( $self->getId ) ) {
		$tmpstr = "<id xsi:type=\"xsd:long\">" . $self->getId . "</id>";
	} else {
		$tmpstr = "<id xsi:type=\"xsd:long\" xsi:nil=\"true\" />";
	}
	$result .= $tmpstr;

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

	return @obj_list;
}

# parse a given xml node, construct one Target object
# param: xml node
# returns: one Target object
sub fromWSXMLNode {
	my $TargetNode = $_[1];
	
	## begin ELEMENT_NODE children ##
		my $bigid;
		my $id;
		my $name;
		my $type;
	## end ELEMENT_NODE children ##

	# get all children for this node
	for my $childrenNode ($TargetNode->getChildNodes) {
	    if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
		if( ! defined($childrenNode->getFirstChild) ){ next; };
		my $textNode = $childrenNode->getFirstChild;
		## begin iterate ELEMENT_NODE ##
		if (0) {
			# do nothing, just a place holder for "if" component
		}
			elsif ($childrenNode->getNodeName eq "bigid") {
				$bigid=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "id") {
				$id=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "name") {
				$name=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "type") {
				$type=$textNode->getNodeValue;
			}
		## end iterate ELEMENT_NODE ##
	    }
	}
	my $newobj = new CaCORE::CaBIO::Target;
	## begin set attr ##
		$newobj->setBigid($bigid);
		$newobj->setId($id);
		$newobj->setName($name);
		$newobj->setType($type);
	## end set attr ##
	
	return $newobj;
}

## begin getters and setters ##

sub getBigid {
	my $self = shift;
	return $self->{bigid};
}

sub setBigid {
	my $self = shift;
	$self->{bigid} = shift;
}

sub getId {
	my $self = shift;
	return $self->{id};
}

sub setId {
	my $self = shift;
	$self->{id} = shift;

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

	my $current_id = shift;
	my $l = shift;
	my %worklist = %$l;
	
	# prefix portion of the xml
	$result .= "<multiRef id=\"id" . $assigned_id ."\" soapenc:root=\"0\" soapenv:encodingStyle=\"http://schemas.xmlsoap.org/soap/encoding/\" xsi:type=\"ns" . $current_id . ":GeneAlias\" xmlns:soapenc=\"http://schemas.xmlsoap.org/soap/encoding/\" xmlns:...
	my $tmpstr = "";
	$current_id ++;
	
	## begin attribute to XML ##
	# bigid;
	if( defined( $self->getBigid ) ) {
		$tmpstr = "<bigid xsi:type=\"xsd:string\">" . $self->getBigid . "</bigid>";
	} else {
		$tmpstr = "<bigid xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
	}
	$result .= $tmpstr;

	# id;
	if( defined( $self->getId ) ) {
		$tmpstr = "<id xsi:type=\"xsd:long\">" . $self->getId . "</id>";
	} else {
		$tmpstr = "<id xsi:type=\"xsd:long\" xsi:nil=\"true\" />";
	}
	$result .= $tmpstr;

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

	return @obj_list;
}

# parse a given xml node, construct one GeneAlias object
# param: xml node
# returns: one GeneAlias object
sub fromWSXMLNode {
	my $GeneAliasNode = $_[1];
	
	## begin ELEMENT_NODE children ##
		my $bigid;
		my $id;
		my $name;
		my $type;
	## end ELEMENT_NODE children ##

	# get all children for this node
	for my $childrenNode ($GeneAliasNode->getChildNodes) {
	    if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
		if( ! defined($childrenNode->getFirstChild) ){ next; };
		my $textNode = $childrenNode->getFirstChild;
		## begin iterate ELEMENT_NODE ##
		if (0) {
			# do nothing, just a place holder for "if" component
		}
			elsif ($childrenNode->getNodeName eq "bigid") {
				$bigid=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "id") {
				$id=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "name") {
				$name=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "type") {
				$type=$textNode->getNodeValue;
			}
		## end iterate ELEMENT_NODE ##
	    }
	}
	my $newobj = new CaCORE::CaBIO::GeneAlias;
	## begin set attr ##
		$newobj->setBigid($bigid);
		$newobj->setId($id);
		$newobj->setName($name);
		$newobj->setType($type);
	## end set attr ##
	
	return $newobj;
}

## begin getters and setters ##

sub getBigid {
	my $self = shift;
	return $self->{bigid};
}

sub setBigid {
	my $self = shift;
	$self->{bigid} = shift;
}

sub getId {
	my $self = shift;
	return $self->{id};
}

sub setId {
	my $self = shift;
	$self->{id} = shift;

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

	
	## begin attribute to XML ##
	# arrayName;
	if( defined( $self->getArrayName ) ) {
		$tmpstr = "<arrayName xsi:type=\"xsd:string\">" . $self->getArrayName . "</arrayName>";
	} else {
		$tmpstr = "<arrayName xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
	}
	$result .= $tmpstr;

	# bigid;
	if( defined( $self->getBigid ) ) {
		$tmpstr = "<bigid xsi:type=\"xsd:string\">" . $self->getBigid . "</bigid>";
	} else {
		$tmpstr = "<bigid xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
	}
	$result .= $tmpstr;

	# id;
	if( defined( $self->getId ) ) {
		$tmpstr = "<id xsi:type=\"xsd:long\">" . $self->getId . "</id>";
	} else {
		$tmpstr = "<id xsi:type=\"xsd:long\" xsi:nil=\"true\" />";
	}
	$result .= $tmpstr;

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

}

# parse a given xml node, construct one GenericArray object
# param: xml node
# returns: one GenericArray object
sub fromWSXMLNode {
	my $GenericArrayNode = $_[1];
	
	## begin ELEMENT_NODE children ##
		my $arrayName;
		my $bigid;
		my $id;
		my $platform;
		my $type;
	## end ELEMENT_NODE children ##

	# get all children for this node
	for my $childrenNode ($GenericArrayNode->getChildNodes) {
	    if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
		if( ! defined($childrenNode->getFirstChild) ){ next; };
		my $textNode = $childrenNode->getFirstChild;
		## begin iterate ELEMENT_NODE ##
		if (0) {
			# do nothing, just a place holder for "if" component
		}
			elsif ($childrenNode->getNodeName eq "arrayName") {
				$arrayName=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "bigid") {
				$bigid=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "id") {
				$id=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "platform") {
				$platform=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "type") {
				$type=$textNode->getNodeValue;
			}
		## end iterate ELEMENT_NODE ##
	    }
	}
	my $newobj = new CaCORE::CaBIO::GenericArray;
	## begin set attr ##
		$newobj->setArrayName($arrayName);
		$newobj->setBigid($bigid);
		$newobj->setId($id);
		$newobj->setPlatform($platform);
		$newobj->setType($type);
	## end set attr ##
	
	return $newobj;
}

## begin getters and setters ##

sub getArrayName {
	my $self = shift;
	return $self->{arrayName};
}

sub setArrayName {
	my $self = shift;
	$self->{arrayName} = shift;
}

sub getBigid {
	my $self = shift;
	return $self->{bigid};
}

sub setBigid {
	my $self = shift;
	$self->{bigid} = shift;
}

sub getId {
	my $self = shift;
	return $self->{id};
}

sub setId {
	my $self = shift;
	$self->{id} = shift;

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

	my $current_id = shift;
	my $l = shift;
	my %worklist = %$l;
	
	# prefix portion of the xml
	$result .= "<multiRef id=\"id" . $assigned_id ."\" soapenc:root=\"0\" soapenv:encodingStyle=\"http://schemas.xmlsoap.org/soap/encoding/\" xsi:type=\"ns" . $current_id . ":Vocabulary\" xmlns:soapenc=\"http://schemas.xmlsoap.org/soap/encoding/\" xmlns...
	my $tmpstr = "";
	$current_id ++;
	
	## begin attribute to XML ##
	# bigid;
	if( defined( $self->getBigid ) ) {
		$tmpstr = "<bigid xsi:type=\"xsd:string\">" . $self->getBigid . "</bigid>";
	} else {
		$tmpstr = "<bigid xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
	}
	$result .= $tmpstr;

	# coreTerm;
	if( defined( $self->getCoreTerm ) ) {
		$tmpstr = "<coreTerm xsi:type=\"xsd:string\">" . $self->getCoreTerm . "</coreTerm>";
	} else {
		$tmpstr = "<coreTerm xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
	}
	$result .= $tmpstr;

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

	return @obj_list;
}

# parse a given xml node, construct one Vocabulary object
# param: xml node
# returns: one Vocabulary object
sub fromWSXMLNode {
	my $VocabularyNode = $_[1];
	
	## begin ELEMENT_NODE children ##
		my $bigid;
		my $coreTerm;
		my $generalTerm;
		my $id;
	## end ELEMENT_NODE children ##

	# get all children for this node
	for my $childrenNode ($VocabularyNode->getChildNodes) {
	    if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
		if( ! defined($childrenNode->getFirstChild) ){ next; };
		my $textNode = $childrenNode->getFirstChild;
		## begin iterate ELEMENT_NODE ##
		if (0) {
			# do nothing, just a place holder for "if" component
		}
			elsif ($childrenNode->getNodeName eq "bigid") {
				$bigid=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "coreTerm") {
				$coreTerm=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "generalTerm") {
				$generalTerm=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "id") {
				$id=$textNode->getNodeValue;
			}
		## end iterate ELEMENT_NODE ##
	    }
	}
	my $newobj = new CaCORE::CaBIO::Vocabulary;
	## begin set attr ##
		$newobj->setBigid($bigid);
		$newobj->setCoreTerm($coreTerm);
		$newobj->setGeneralTerm($generalTerm);
		$newobj->setId($id);
	## end set attr ##
	
	return $newobj;
}

## begin getters and setters ##

sub getBigid {
	my $self = shift;
	return $self->{bigid};
}

sub setBigid {
	my $self = shift;
	$self->{bigid} = shift;
}

sub getCoreTerm {
	my $self = shift;
	return $self->{coreTerm};
}

sub setCoreTerm {
	my $self = shift;
	$self->{coreTerm} = shift;

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

	my $current_id = shift;
	my $l = shift;
	my %worklist = %$l;
	
	# prefix portion of the xml
	$result .= "<multiRef id=\"id" . $assigned_id ."\" soapenc:root=\"0\" soapenv:encodingStyle=\"http://schemas.xmlsoap.org/soap/encoding/\" xsi:type=\"ns" . $current_id . ":OrganOntologyRelationship\" xmlns:soapenc=\"http://schemas.xmlsoap.org/soap/en...
	my $tmpstr = "";
	$current_id ++;
	
	## begin attribute to XML ##
	# bigid;
	if( defined( $self->getBigid ) ) {
		$tmpstr = "<bigid xsi:type=\"xsd:string\">" . $self->getBigid . "</bigid>";
	} else {
		$tmpstr = "<bigid xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
	}
	$result .= $tmpstr;

	# id;
	if( defined( $self->getId ) ) {
		$tmpstr = "<id xsi:type=\"xsd:long\">" . $self->getId . "</id>";
	} else {
		$tmpstr = "<id xsi:type=\"xsd:long\" xsi:nil=\"true\" />";
	}
	$result .= $tmpstr;

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

	return @obj_list;
}

# parse a given xml node, construct one OrganOntologyRelationship object
# param: xml node
# returns: one OrganOntologyRelationship object
sub fromWSXMLNode {
	my $OrganOntologyRelationshipNode = $_[1];
	
	## begin ELEMENT_NODE children ##
		my $bigid;
		my $id;
		my $type;
	## end ELEMENT_NODE children ##

	# get all children for this node
	for my $childrenNode ($OrganOntologyRelationshipNode->getChildNodes) {
	    if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
		if( ! defined($childrenNode->getFirstChild) ){ next; };
		my $textNode = $childrenNode->getFirstChild;
		## begin iterate ELEMENT_NODE ##
		if (0) {
			# do nothing, just a place holder for "if" component
		}
			elsif ($childrenNode->getNodeName eq "bigid") {
				$bigid=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "id") {
				$id=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "type") {
				$type=$textNode->getNodeValue;
			}
		## end iterate ELEMENT_NODE ##
	    }
	}
	my $newobj = new CaCORE::CaBIO::OrganOntologyRelationship;
	## begin set attr ##
		$newobj->setBigid($bigid);
		$newobj->setId($id);
		$newobj->setType($type);
	## end set attr ##
	
	return $newobj;
}

## begin getters and setters ##

sub getBigid {
	my $self = shift;
	return $self->{bigid};
}

sub setBigid {
	my $self = shift;
	$self->{bigid} = shift;
}

sub getId {
	my $self = shift;
	return $self->{id};
}

sub setId {
	my $self = shift;
	$self->{id} = shift;

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

	my $current_id = shift;
	my $l = shift;
	my %worklist = %$l;
	
	# prefix portion of the xml
	$result .= "<multiRef id=\"id" . $assigned_id ."\" soapenc:root=\"0\" soapenv:encodingStyle=\"http://schemas.xmlsoap.org/soap/encoding/\" xsi:type=\"ns" . $current_id . ":Anomaly\" xmlns:soapenc=\"http://schemas.xmlsoap.org/soap/encoding/\" xmlns:ns...
	my $tmpstr = "";
	$current_id ++;
	
	## begin attribute to XML ##
	# bigid;
	if( defined( $self->getBigid ) ) {
		$tmpstr = "<bigid xsi:type=\"xsd:string\">" . $self->getBigid . "</bigid>";
	} else {
		$tmpstr = "<bigid xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
	}
	$result .= $tmpstr;

	# description;
	if( defined( $self->getDescription ) ) {
		$tmpstr = "<description xsi:type=\"xsd:string\">" . $self->getDescription . "</description>";
	} else {
		$tmpstr = "<description xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
	}
	$result .= $tmpstr;

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

	return @obj_list;
}

# parse a given xml node, construct one Anomaly object
# param: xml node
# returns: one Anomaly object
sub fromWSXMLNode {
	my $AnomalyNode = $_[1];
	
	## begin ELEMENT_NODE children ##
		my $bigid;
		my $description;
		my $id;
	## end ELEMENT_NODE children ##

	# get all children for this node
	for my $childrenNode ($AnomalyNode->getChildNodes) {
	    if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
		if( ! defined($childrenNode->getFirstChild) ){ next; };
		my $textNode = $childrenNode->getFirstChild;
		## begin iterate ELEMENT_NODE ##
		if (0) {
			# do nothing, just a place holder for "if" component
		}
			elsif ($childrenNode->getNodeName eq "bigid") {
				$bigid=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "description") {
				$description=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "id") {
				$id=$textNode->getNodeValue;
			}
		## end iterate ELEMENT_NODE ##
	    }
	}
	my $newobj = new CaCORE::CaBIO::Anomaly;
	## begin set attr ##
		$newobj->setBigid($bigid);
		$newobj->setDescription($description);
		$newobj->setId($id);
	## end set attr ##
	
	return $newobj;
}

## begin getters and setters ##

sub getBigid {
	my $self = shift;
	return $self->{bigid};
}

sub setBigid {
	my $self = shift;
	$self->{bigid} = shift;
}

sub getDescription {
	my $self = shift;
	return $self->{description};
}

sub setDescription {
	my $self = shift;
	$self->{description} = shift;

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

	$result .= $tmpstr;

	# NSCNumber;
	if( defined( $self->getNSCNumber ) ) {
		$tmpstr = "<NSCNumber xsi:type=\"xsd:long\">" . $self->getNSCNumber . "</NSCNumber>";
	} else {
		$tmpstr = "<NSCNumber xsi:type=\"xsd:long\" xsi:nil=\"true\" />";
	}
	$result .= $tmpstr;

	# bigid;
	if( defined( $self->getBigid ) ) {
		$tmpstr = "<bigid xsi:type=\"xsd:string\">" . $self->getBigid . "</bigid>";
	} else {
		$tmpstr = "<bigid xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
	}
	$result .= $tmpstr;

	# comment;
	if( defined( $self->getComment ) ) {
		$tmpstr = "<comment xsi:type=\"xsd:string\">" . $self->getComment . "</comment>";
	} else {
		$tmpstr = "<comment xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
	}
	$result .= $tmpstr;

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

# parse a given xml node, construct one Agent object
# param: xml node
# returns: one Agent object
sub fromWSXMLNode {
	my $AgentNode = $_[1];
	
	## begin ELEMENT_NODE children ##
		my $EVSId;
		my $NSCNumber;
		my $bigid;
		my $comment;
		my $id;
		my $isCMAPAgent;
		my $name;
		my $source;
	## end ELEMENT_NODE children ##

	# get all children for this node
	for my $childrenNode ($AgentNode->getChildNodes) {
	    if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

		## begin iterate ELEMENT_NODE ##
		if (0) {
			# do nothing, just a place holder for "if" component
		}
			elsif ($childrenNode->getNodeName eq "EVSId") {
				$EVSId=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "NSCNumber") {
				$NSCNumber=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "bigid") {
				$bigid=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "comment") {
				$comment=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "id") {
				$id=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "isCMAPAgent") {
				$isCMAPAgent=$textNode->getNodeValue;
			}

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

			elsif ($childrenNode->getNodeName eq "source") {
				$source=$textNode->getNodeValue;
			}
		## end iterate ELEMENT_NODE ##
	    }
	}
	my $newobj = new CaCORE::CaBIO::Agent;
	## begin set attr ##
		$newobj->setEVSId($EVSId);
		$newobj->setNSCNumber($NSCNumber);
		$newobj->setBigid($bigid);
		$newobj->setComment($comment);
		$newobj->setId($id);
		$newobj->setIsCMAPAgent($isCMAPAgent);
		$newobj->setName($name);
		$newobj->setSource($source);
	## end set attr ##
	
	return $newobj;
}

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

sub getNSCNumber {
	my $self = shift;
	return $self->{NSCNumber};
}

sub setNSCNumber {
	my $self = shift;
	$self->{NSCNumber} = shift;
}

sub getBigid {
	my $self = shift;
	return $self->{bigid};
}

sub setBigid {
	my $self = shift;
	$self->{bigid} = shift;
}

sub getComment {
	my $self = shift;
	return $self->{comment};
}

sub setComment {
	my $self = shift;
	$self->{comment} = shift;

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

	$result .= $tmpstr;

	# PIName;
	if( defined( $self->getPIName ) ) {
		$tmpstr = "<PIName xsi:type=\"xsd:string\">" . $self->getPIName . "</PIName>";
	} else {
		$tmpstr = "<PIName xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
	}
	$result .= $tmpstr;

	# bigid;
	if( defined( $self->getBigid ) ) {
		$tmpstr = "<bigid xsi:type=\"xsd:string\">" . $self->getBigid . "</bigid>";
	} else {
		$tmpstr = "<bigid xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
	}
	$result .= $tmpstr;

	# currentStatus;
	if( defined( $self->getCurrentStatus ) ) {
		$tmpstr = "<currentStatus xsi:type=\"xsd:string\">" . $self->getCurrentStatus . "</currentStatus>";
	} else {
		$tmpstr = "<currentStatus xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
	}
	$result .= $tmpstr;

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

# parse a given xml node, construct one ClinicalTrialProtocol object
# param: xml node
# returns: one ClinicalTrialProtocol object
sub fromWSXMLNode {
	my $ClinicalTrialProtocolNode = $_[1];
	
	## begin ELEMENT_NODE children ##
		my $NIHAdminCode;
		my $PDQIdentifier;
		my $PIName;
		my $bigid;
		my $currentStatus;
		my $currentStatusDate;
		my $documentNumber;
		my $id;
		my $leadOrganizationId;
		my $leadOrganizationName;
		my $participationType;
		my $phase;
		my $title;
		my $treatmentFlag;

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

		}
			elsif ($childrenNode->getNodeName eq "NIHAdminCode") {
				$NIHAdminCode=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "PDQIdentifier") {
				$PDQIdentifier=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "PIName") {
				$PIName=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "bigid") {
				$bigid=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "currentStatus") {
				$currentStatus=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "currentStatusDate") {
				$currentStatusDate=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "documentNumber") {
				$documentNumber=$textNode->getNodeValue;
			}

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

				$treatmentFlag=$textNode->getNodeValue;
			}
		## end iterate ELEMENT_NODE ##
	    }
	}
	my $newobj = new CaCORE::CaBIO::ClinicalTrialProtocol;
	## begin set attr ##
		$newobj->setNIHAdminCode($NIHAdminCode);
		$newobj->setPDQIdentifier($PDQIdentifier);
		$newobj->setPIName($PIName);
		$newobj->setBigid($bigid);
		$newobj->setCurrentStatus($currentStatus);
		$newobj->setCurrentStatusDate($currentStatusDate);
		$newobj->setDocumentNumber($documentNumber);
		$newobj->setId($id);
		$newobj->setLeadOrganizationId($leadOrganizationId);
		$newobj->setLeadOrganizationName($leadOrganizationName);
		$newobj->setParticipationType($participationType);
		$newobj->setPhase($phase);
		$newobj->setTitle($title);
		$newobj->setTreatmentFlag($treatmentFlag);

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

sub getPIName {
	my $self = shift;
	return $self->{PIName};
}

sub setPIName {
	my $self = shift;
	$self->{PIName} = shift;
}

sub getBigid {
	my $self = shift;
	return $self->{bigid};
}

sub setBigid {
	my $self = shift;
	$self->{bigid} = shift;
}

sub getCurrentStatus {
	my $self = shift;
	return $self->{currentStatus};
}

sub setCurrentStatus {
	my $self = shift;
	$self->{currentStatus} = shift;

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

	$result .= $tmpstr;

	# IMTCODE;
	if( defined( $self->getIMTCODE ) ) {
		$tmpstr = "<IMTCODE xsi:type=\"xsd:long\">" . $self->getIMTCODE . "</IMTCODE>";
	} else {
		$tmpstr = "<IMTCODE xsi:type=\"xsd:long\" xsi:nil=\"true\" />";
	}
	$result .= $tmpstr;

	# bigid;
	if( defined( $self->getBigid ) ) {
		$tmpstr = "<bigid xsi:type=\"xsd:string\">" . $self->getBigid . "</bigid>";
	} else {
		$tmpstr = "<bigid xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
	}
	$result .= $tmpstr;

	# diseaseCategory;
	if( defined( $self->getDiseaseCategory ) ) {
		$tmpstr = "<diseaseCategory xsi:type=\"xsd:string\">" . $self->getDiseaseCategory . "</diseaseCategory>";
	} else {
		$tmpstr = "<diseaseCategory xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
	}
	$result .= $tmpstr;

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

# parse a given xml node, construct one ProtocolAssociation object
# param: xml node
# returns: one ProtocolAssociation object
sub fromWSXMLNode {
	my $ProtocolAssociationNode = $_[1];
	
	## begin ELEMENT_NODE children ##
		my $CTEPNAME;
		my $IMTCODE;
		my $bigid;
		my $diseaseCategory;
		my $diseaseSubCategory;
		my $id;
	## end ELEMENT_NODE children ##

	# get all children for this node
	for my $childrenNode ($ProtocolAssociationNode->getChildNodes) {
	    if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
		if( ! defined($childrenNode->getFirstChild) ){ next; };
		my $textNode = $childrenNode->getFirstChild;
		## begin iterate ELEMENT_NODE ##
		if (0) {
			# do nothing, just a place holder for "if" component
		}
			elsif ($childrenNode->getNodeName eq "CTEPNAME") {
				$CTEPNAME=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "IMTCODE") {
				$IMTCODE=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "bigid") {
				$bigid=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "diseaseCategory") {
				$diseaseCategory=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "diseaseSubCategory") {
				$diseaseSubCategory=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "id") {
				$id=$textNode->getNodeValue;
			}
		## end iterate ELEMENT_NODE ##
	    }
	}
	my $newobj = new CaCORE::CaBIO::ProtocolAssociation;
	## begin set attr ##
		$newobj->setCTEPNAME($CTEPNAME);
		$newobj->setIMTCODE($IMTCODE);
		$newobj->setBigid($bigid);
		$newobj->setDiseaseCategory($diseaseCategory);
		$newobj->setDiseaseSubCategory($diseaseSubCategory);
		$newobj->setId($id);
	## end set attr ##
	
	return $newobj;
}

## begin getters and setters ##

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

sub getIMTCODE {
	my $self = shift;
	return $self->{IMTCODE};
}

sub setIMTCODE {
	my $self = shift;
	$self->{IMTCODE} = shift;
}

sub getBigid {
	my $self = shift;
	return $self->{bigid};
}

sub setBigid {
	my $self = shift;
	$self->{bigid} = shift;
}

sub getDiseaseCategory {
	my $self = shift;
	return $self->{diseaseCategory};
}

sub setDiseaseCategory {
	my $self = shift;
	$self->{diseaseCategory} = shift;

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

	my $current_id = shift;
	my $l = shift;
	my %worklist = %$l;
	
	# prefix portion of the xml
	$result .= "<multiRef id=\"id" . $assigned_id ."\" soapenc:root=\"0\" soapenv:encodingStyle=\"http://schemas.xmlsoap.org/soap/encoding/\" xsi:type=\"ns" . $current_id . ":GeneOntologyRelationship\" xmlns:soapenc=\"http://schemas.xmlsoap.org/soap/enc...
	my $tmpstr = "";
	$current_id ++;
	
	## begin attribute to XML ##
	# bigid;
	if( defined( $self->getBigid ) ) {
		$tmpstr = "<bigid xsi:type=\"xsd:string\">" . $self->getBigid . "</bigid>";
	} else {
		$tmpstr = "<bigid xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
	}
	$result .= $tmpstr;

	# id;
	if( defined( $self->getId ) ) {
		$tmpstr = "<id xsi:type=\"xsd:long\">" . $self->getId . "</id>";
	} else {
		$tmpstr = "<id xsi:type=\"xsd:long\" xsi:nil=\"true\" />";
	}
	$result .= $tmpstr;

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

	return @obj_list;
}

# parse a given xml node, construct one GeneOntologyRelationship object
# param: xml node
# returns: one GeneOntologyRelationship object
sub fromWSXMLNode {
	my $GeneOntologyRelationshipNode = $_[1];
	
	## begin ELEMENT_NODE children ##
		my $bigid;
		my $id;
		my $relationshipType;
	## end ELEMENT_NODE children ##

	# get all children for this node
	for my $childrenNode ($GeneOntologyRelationshipNode->getChildNodes) {
	    if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
		if( ! defined($childrenNode->getFirstChild) ){ next; };
		my $textNode = $childrenNode->getFirstChild;
		## begin iterate ELEMENT_NODE ##
		if (0) {
			# do nothing, just a place holder for "if" component
		}
			elsif ($childrenNode->getNodeName eq "bigid") {
				$bigid=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "id") {
				$id=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "relationshipType") {
				$relationshipType=$textNode->getNodeValue;
			}
		## end iterate ELEMENT_NODE ##
	    }
	}
	my $newobj = new CaCORE::CaBIO::GeneOntologyRelationship;
	## begin set attr ##
		$newobj->setBigid($bigid);
		$newobj->setId($id);
		$newobj->setRelationshipType($relationshipType);
	## end set attr ##
	
	return $newobj;
}

## begin getters and setters ##

sub getBigid {
	my $self = shift;
	return $self->{bigid};
}

sub setBigid {
	my $self = shift;
	$self->{bigid} = shift;
}

sub getId {
	my $self = shift;
	return $self->{id};
}

sub setId {
	my $self = shift;
	$self->{id} = shift;

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

	my $current_id = shift;
	my $l = shift;
	my %worklist = %$l;
	
	# prefix portion of the xml
	$result .= "<multiRef id=\"id" . $assigned_id ."\" soapenc:root=\"0\" soapenv:encodingStyle=\"http://schemas.xmlsoap.org/soap/encoding/\" xsi:type=\"ns" . $current_id . ":GenericReporter\" xmlns:soapenc=\"http://schemas.xmlsoap.org/soap/encoding/\" ...
	my $tmpstr = "";
	$current_id ++;
	
	## begin attribute to XML ##
	# bigid;
	if( defined( $self->getBigid ) ) {
		$tmpstr = "<bigid xsi:type=\"xsd:string\">" . $self->getBigid . "</bigid>";
	} else {
		$tmpstr = "<bigid xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
	}
	$result .= $tmpstr;

	# id;
	if( defined( $self->getId ) ) {
		$tmpstr = "<id xsi:type=\"xsd:long\">" . $self->getId . "</id>";
	} else {
		$tmpstr = "<id xsi:type=\"xsd:long\" xsi:nil=\"true\" />";
	}
	$result .= $tmpstr;

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

	return @obj_list;
}

# parse a given xml node, construct one GenericReporter object
# param: xml node
# returns: one GenericReporter object
sub fromWSXMLNode {
	my $GenericReporterNode = $_[1];
	
	## begin ELEMENT_NODE children ##
		my $bigid;
		my $id;
		my $name;
		my $type;
	## end ELEMENT_NODE children ##

	# get all children for this node
	for my $childrenNode ($GenericReporterNode->getChildNodes) {
	    if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
		if( ! defined($childrenNode->getFirstChild) ){ next; };
		my $textNode = $childrenNode->getFirstChild;
		## begin iterate ELEMENT_NODE ##
		if (0) {
			# do nothing, just a place holder for "if" component
		}
			elsif ($childrenNode->getNodeName eq "bigid") {
				$bigid=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "id") {
				$id=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "name") {
				$name=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "type") {
				$type=$textNode->getNodeValue;
			}
		## end iterate ELEMENT_NODE ##
	    }
	}
	my $newobj = new CaCORE::CaBIO::GenericReporter;
	## begin set attr ##
		$newobj->setBigid($bigid);
		$newobj->setId($id);
		$newobj->setName($name);
		$newobj->setType($type);
	## end set attr ##
	
	return $newobj;
}

## begin getters and setters ##

sub getBigid {
	my $self = shift;
	return $self->{bigid};
}

sub setBigid {
	my $self = shift;
	$self->{bigid} = shift;
}

sub getId {
	my $self = shift;
	return $self->{id};
}

sub setId {
	my $self = shift;
	$self->{id} = shift;

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

	my $current_id = shift;
	my $l = shift;
	my %worklist = %$l;
	
	# prefix portion of the xml
	$result .= "<multiRef id=\"id" . $assigned_id ."\" soapenc:root=\"0\" soapenv:encodingStyle=\"http://schemas.xmlsoap.org/soap/encoding/\" xsi:type=\"ns" . $current_id . ":Pathway\" xmlns:soapenc=\"http://schemas.xmlsoap.org/soap/encoding/\" xmlns:ns...
	my $tmpstr = "";
	$current_id ++;
	
	## begin attribute to XML ##
	# bigid;
	if( defined( $self->getBigid ) ) {
		$tmpstr = "<bigid xsi:type=\"xsd:string\">" . $self->getBigid . "</bigid>";
	} else {
		$tmpstr = "<bigid xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
	}
	$result .= $tmpstr;

	# description;
	if( defined( $self->getDescription ) ) {
		$tmpstr = "<description xsi:type=\"xsd:string\">" . $self->getDescription . "</description>";
	} else {
		$tmpstr = "<description xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
	}
	$result .= $tmpstr;

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

	return @obj_list;
}

# parse a given xml node, construct one Pathway object
# param: xml node
# returns: one Pathway object
sub fromWSXMLNode {
	my $PathwayNode = $_[1];
	
	## begin ELEMENT_NODE children ##
		my $bigid;
		my $description;
		my $diagram;
		my $displayValue;
		my $id;
		my $name;
	## end ELEMENT_NODE children ##

	# get all children for this node
	for my $childrenNode ($PathwayNode->getChildNodes) {
	    if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
		if( ! defined($childrenNode->getFirstChild) ){ next; };
		my $textNode = $childrenNode->getFirstChild;
		## begin iterate ELEMENT_NODE ##
		if (0) {
			# do nothing, just a place holder for "if" component
		}
			elsif ($childrenNode->getNodeName eq "bigid") {
				$bigid=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "description") {
				$description=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "diagram") {
				$diagram=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "displayValue") {
				$displayValue=$textNode->getNodeValue;
			}

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

				$id=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "name") {
				$name=$textNode->getNodeValue;
			}
		## end iterate ELEMENT_NODE ##
	    }
	}
	my $newobj = new CaCORE::CaBIO::Pathway;
	## begin set attr ##
		$newobj->setBigid($bigid);
		$newobj->setDescription($description);
		$newobj->setDiagram($diagram);
		$newobj->setDisplayValue($displayValue);
		$newobj->setId($id);
		$newobj->setName($name);
	## end set attr ##
	
	return $newobj;
}

## begin getters and setters ##

sub getBigid {
	my $self = shift;
	return $self->{bigid};
}

sub setBigid {
	my $self = shift;
	$self->{bigid} = shift;
}

sub getDescription {
	my $self = shift;
	return $self->{description};
}

sub setDescription {
	my $self = shift;
	$self->{description} = shift;

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

	my $current_id = shift;
	my $l = shift;
	my %worklist = %$l;
	
	# prefix portion of the xml
	$result .= "<multiRef id=\"id" . $assigned_id ."\" soapenc:root=\"0\" soapenv:encodingStyle=\"http://schemas.xmlsoap.org/soap/encoding/\" xsi:type=\"ns" . $current_id . ":DiseaseOntologyRelationship\" xmlns:soapenc=\"http://schemas.xmlsoap.org/soap/...
	my $tmpstr = "";
	$current_id ++;
	
	## begin attribute to XML ##
	# bigid;
	if( defined( $self->getBigid ) ) {
		$tmpstr = "<bigid xsi:type=\"xsd:string\">" . $self->getBigid . "</bigid>";
	} else {
		$tmpstr = "<bigid xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
	}
	$result .= $tmpstr;

	# id;
	if( defined( $self->getId ) ) {
		$tmpstr = "<id xsi:type=\"xsd:long\">" . $self->getId . "</id>";
	} else {
		$tmpstr = "<id xsi:type=\"xsd:long\" xsi:nil=\"true\" />";
	}
	$result .= $tmpstr;

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

	return @obj_list;
}

# parse a given xml node, construct one DiseaseOntologyRelationship object
# param: xml node
# returns: one DiseaseOntologyRelationship object
sub fromWSXMLNode {
	my $DiseaseOntologyRelationshipNode = $_[1];
	
	## begin ELEMENT_NODE children ##
		my $bigid;
		my $id;
		my $type;
	## end ELEMENT_NODE children ##

	# get all children for this node
	for my $childrenNode ($DiseaseOntologyRelationshipNode->getChildNodes) {
	    if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
		if( ! defined($childrenNode->getFirstChild) ){ next; };
		my $textNode = $childrenNode->getFirstChild;
		## begin iterate ELEMENT_NODE ##
		if (0) {
			# do nothing, just a place holder for "if" component
		}
			elsif ($childrenNode->getNodeName eq "bigid") {
				$bigid=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "id") {
				$id=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "type") {
				$type=$textNode->getNodeValue;
			}
		## end iterate ELEMENT_NODE ##
	    }
	}
	my $newobj = new CaCORE::CaBIO::DiseaseOntologyRelationship;
	## begin set attr ##
		$newobj->setBigid($bigid);
		$newobj->setId($id);
		$newobj->setType($type);
	## end set attr ##
	
	return $newobj;
}

## begin getters and setters ##

sub getBigid {
	my $self = shift;
	return $self->{bigid};
}

sub setBigid {
	my $self = shift;
	$self->{bigid} = shift;
}

sub getId {
	my $self = shift;
	return $self->{id};
}

sub setId {
	my $self = shift;
	$self->{id} = shift;

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

	my $current_id = shift;
	my $l = shift;
	my %worklist = %$l;
	
	# prefix portion of the xml
	$result .= "<multiRef id=\"id" . $assigned_id ."\" soapenc:root=\"0\" soapenv:encodingStyle=\"http://schemas.xmlsoap.org/soap/encoding/\" xsi:type=\"ns" . $current_id . ":CytogeneticLocation\" xmlns:soapenc=\"http://schemas.xmlsoap.org/soap/encoding...
	my $tmpstr = "";
	$current_id ++;
	
	## begin attribute to XML ##
	# bigid;
	if( defined( $self->getBigid ) ) {
		$tmpstr = "<bigid xsi:type=\"xsd:string\">" . $self->getBigid . "</bigid>";
	} else {
		$tmpstr = "<bigid xsi:type=\"xsd:string\" xsi:nil=\"true\" />";
	}
	$result .= $tmpstr;

	# endCytobandLocId;
	if( defined( $self->getEndCytobandLocId ) ) {
		$tmpstr = "<endCytobandLocId xsi:type=\"xsd:long\">" . $self->getEndCytobandLocId . "</endCytobandLocId>";
	} else {
		$tmpstr = "<endCytobandLocId xsi:type=\"xsd:long\" xsi:nil=\"true\" />";
	}
	$result .= $tmpstr;

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

	return @obj_list;
}

# parse a given xml node, construct one CytogeneticLocation object
# param: xml node
# returns: one CytogeneticLocation object
sub fromWSXMLNode {
	my $CytogeneticLocationNode = $_[1];
	
	## begin ELEMENT_NODE children ##
		my $bigid;
		my $endCytobandLocId;
		my $startCytobandLocId;
		my $id;
	## end ELEMENT_NODE children ##

	# get all children for this node
	for my $childrenNode ($CytogeneticLocationNode->getChildNodes) {
	    if ($childrenNode->getNodeType == XML::DOM::ELEMENT_NODE()) {
		if( ! defined($childrenNode->getFirstChild) ){ next; };
		my $textNode = $childrenNode->getFirstChild;
		## begin iterate ELEMENT_NODE ##
		if (0) {
			# do nothing, just a place holder for "if" component
		}
			elsif ($childrenNode->getNodeName eq "bigid") {
				$bigid=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "endCytobandLocId") {
				$endCytobandLocId=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "startCytobandLocId") {
				$startCytobandLocId=$textNode->getNodeValue;
			}
			elsif ($childrenNode->getNodeName eq "id") {
				$id=$textNode->getNodeValue;
			}
		## end iterate ELEMENT_NODE ##
	    }
	}
	my $newobj = new CaCORE::CaBIO::CytogeneticLocation;
	## begin set attr ##
		$newobj->setBigid($bigid);
		$newobj->setEndCytobandLocId($endCytobandLocId);
		$newobj->setStartCytobandLocId($startCytobandLocId);
		$newobj->setId($id);
	## end set attr ##
	
	return $newobj;
}

## begin getters and setters ##

sub getBigid {
	my $self = shift;
	return $self->{bigid};
}

sub setBigid {
	my $self = shift;
	$self->{bigid} = shift;
}

sub getEndCytobandLocId {
	my $self = shift;
	return $self->{endCytobandLocId};
}

sub setEndCytobandLocId {
	my $self = shift;
	$self->{endCytobandLocId} = shift;

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

=over 4

=item EVSId

data type: C<string>

=item NSCNumber

data type: C<long>

=item bigid

data type: C<string>

=item comment

data type: C<string>

=item id

data type: C<long>

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

=head2 DESCRIPTION



=head2 ATTRIBUTES of Anomaly

The following are all the attributes of the Anomaly object and their data types:

=over 4

=item bigid

data type: C<string>

=item description

data type: C<string>

=item id

data type: C<long>

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

=head2 DESCRIPTION



=head2 ATTRIBUTES of Chromosome

The following are all the attributes of the Chromosome object and their data types:

=over 4

=item bigid

data type: C<string>

=item id

data type: C<long>

=item number

data type: C<string>

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

data type: C<string>

=item PDQIdentifier

data type: C<string>

=item PIName

data type: C<string>

=item bigid

data type: C<string>

=item currentStatus

data type: C<string>

=item currentStatusDate

data type: C<dateTime>

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

=head2 DESCRIPTION



=head2 ATTRIBUTES of Clone

The following are all the attributes of the Clone object and their data types:

=over 4

=item bigid

data type: C<string>

=item id

data type: C<long>

=item insertSize

data type: C<long>

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

=head2 DESCRIPTION



=head2 ATTRIBUTES of CloneRelativeLocation

The following are all the attributes of the CloneRelativeLocation object and their data types:

=over 4

=item bigid

data type: C<string>

=item id

data type: C<long>

=item type

data type: C<string>

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

=head2 DESCRIPTION



=head2 ATTRIBUTES of Cytoband

The following are all the attributes of the Cytoband object and their data types:

=over 4

=item bigid

data type: C<string>

=item id

data type: C<long>

=item name

data type: C<string>

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

=head2 DESCRIPTION



=head2 ATTRIBUTES of CytogeneticLocation

The following are all the attributes of the CytogeneticLocation object and their data types:

=over 4

=item bigid

data type: C<string>

=item endCytobandLocId

data type: C<long>

=item startCytobandLocId

data type: C<long>

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

=head2 DESCRIPTION



=head2 ATTRIBUTES of DiseaseOntology

The following are all the attributes of the DiseaseOntology object and their data types:

=over 4

=item bigid

data type: C<string>

=item id

data type: C<long>

=item name

data type: C<string>

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

=head2 DESCRIPTION



=head2 ATTRIBUTES of DiseaseOntologyRelationship

The following are all the attributes of the DiseaseOntologyRelationship object and their data types:

=over 4

=item bigid

data type: C<string>

=item id

data type: C<long>

=item type

data type: C<string>

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

=head2 DESCRIPTION



=head2 ATTRIBUTES of Gene

The following are all the attributes of the Gene object and their data types:

=over 4

=item bigid

data type: C<string>

=item clusterId

data type: C<long>

=item fullName

data type: C<string>

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

=head2 DESCRIPTION



=head2 ATTRIBUTES of GeneAlias

The following are all the attributes of the GeneAlias object and their data types:

=over 4

=item bigid

data type: C<string>

=item id

data type: C<long>

=item name

data type: C<string>

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

=head2 DESCRIPTION



=head2 ATTRIBUTES of GeneOntology

The following are all the attributes of the GeneOntology object and their data types:

=over 4

=item bigid

data type: C<string>

=item id

data type: C<long>

=item name

data type: C<string>

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

=head2 DESCRIPTION



=head2 ATTRIBUTES of GeneOntologyRelationship

The following are all the attributes of the GeneOntologyRelationship object and their data types:

=over 4

=item bigid

data type: C<string>

=item id

data type: C<long>

=item relationshipType

data type: C<string>

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

=head2 DESCRIPTION



=head2 ATTRIBUTES of GeneRelativeLocation

The following are all the attributes of the GeneRelativeLocation object and their data types:

=over 4

=item bigid

data type: C<string>

=item id

data type: C<long>

=item type

data type: C<string>

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

=head2 ATTRIBUTES of GenericArray

The following are all the attributes of the GenericArray object and their data types:

=over 4

=item arrayName

data type: C<string>

=item bigid

data type: C<string>

=item id

data type: C<long>

=item platform

data type: C<string>

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

=head2 DESCRIPTION



=head2 ATTRIBUTES of GenericReporter

The following are all the attributes of the GenericReporter object and their data types:

=over 4

=item bigid

data type: C<string>

=item id

data type: C<long>

=item name

data type: C<string>

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

=head2 DESCRIPTION



=head2 ATTRIBUTES of HomologousAssociation

The following are all the attributes of the HomologousAssociation object and their data types:

=over 4

=item bigid

data type: C<string>

=item homologousId

data type: C<long>

=item id

data type: C<long>

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

=head2 DESCRIPTION



=head2 ATTRIBUTES of Library

The following are all the attributes of the Library object and their data types:

=over 4

=item bigid

data type: C<string>

=item cloneProducer

data type: C<string>

=item cloneVector

data type: C<string>

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

=over 4

=item accessionNumber

data type: C<string>

=item accessionNumberVersion

data type: C<string>

=item bigid

data type: C<string>

=item id

data type: C<long>

=item length

data type: C<long>

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

=head2 DESCRIPTION



=head2 ATTRIBUTES of OrganOntology

The following are all the attributes of the OrganOntology object and their data types:

=over 4

=item bigid

data type: C<string>

=item id

data type: C<long>

=item name

data type: C<string>

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

=head2 DESCRIPTION



=head2 ATTRIBUTES of OrganOntologyRelationship

The following are all the attributes of the OrganOntologyRelationship object and their data types:

=over 4

=item bigid

data type: C<string>

=item id

data type: C<long>

=item type

data type: C<string>

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

=head2 DESCRIPTION



=head2 ATTRIBUTES of Pathway

The following are all the attributes of the Pathway object and their data types:

=over 4

=item bigid

data type: C<string>

=item description

data type: C<string>

=item diagram

data type: C<string>

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

=head2 DESCRIPTION



=head2 ATTRIBUTES of PopulationFrequency

The following are all the attributes of the PopulationFrequency object and their data types:

=over 4

=item bigid

data type: C<string>

=item ethnicity

data type: C<string>

=item id

data type: C<long>

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

=head2 DESCRIPTION



=head2 ATTRIBUTES of Protein

The following are all the attributes of the Protein object and their data types:

=over 4

=item bigid

data type: C<string>

=item copyrightStatement

data type: C<string>

=item id

data type: C<long>

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

=head2 DESCRIPTION



=head2 ATTRIBUTES of ProteinAlias

The following are all the attributes of the ProteinAlias object and their data types:

=over 4

=item bigid

data type: C<string>

=item id

data type: C<long>

=item name

data type: C<string>

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

=head2 DESCRIPTION



=head2 ATTRIBUTES of ProteinSequence

The following are all the attributes of the ProteinSequence object and their data types:

=over 4

=item bigid

data type: C<string>

=item checkSum

data type: C<string>

=item id

data type: C<long>

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

=head2 DESCRIPTION



=head2 ATTRIBUTES of Protocol

The following are all the attributes of the Protocol object and their data types:

=over 4

=item bigid

data type: C<string>

=item description

data type: C<string>

=item id

data type: C<long>

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

=over 4

=item CTEPNAME

data type: C<string>

=item IMTCODE

data type: C<long>

=item bigid

data type: C<string>

=item diseaseCategory

data type: C<string>

=item diseaseSubCategory

data type: C<string>

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

data type: C<string>

=item alleleA

data type: C<string>

=item alleleB

data type: C<string>

=item bigid

data type: C<string>

=item id

data type: C<long>

=item validationStatus

data type: C<string>

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

=head2 DESCRIPTION



=head2 ATTRIBUTES of Target

The following are all the attributes of the Target object and their data types:

=over 4

=item bigid

data type: C<string>

=item id

data type: C<long>

=item name

data type: C<string>

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

=head2 ATTRIBUTES of Taxon

The following are all the attributes of the Taxon object and their data types:

=over 4

=item abbreviation

data type: C<string>

=item bigid

data type: C<string>

=item commonName

data type: C<string>

=item ethnicityStrain

data type: C<string>

lib/CaCORE/CaBIO.pm  view on Meta::CPAN

=head2 DESCRIPTION



=head2 ATTRIBUTES of Vocabulary

The following are all the attributes of the Vocabulary object and their data types:

=over 4

=item bigid

data type: C<string>

=item coreTerm

data type: C<string>

=item generalTerm

data type: C<string>