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Revision 1.1 - (download) (as text) (annotate)
Tue Jan 17 18:49:46 2006 UTC (13 years, 10 months ago) by mkubal
Branch: MAIN
CVS Tags: mgrast_dev_08112011, rast_rel_2009_05_18, mgrast_dev_08022011, rast_rel_2014_0912, rast_rel_2008_06_18, myrast_rel40, rast_rel_2008_06_16, mgrast_dev_05262011, rast_rel_2008_12_18, mgrast_dev_04082011, rast_rel_2008_07_21, rast_rel_2010_0928, rast_2008_0924, mgrast_version_3_2, mgrast_dev_12152011, rast_rel_2008_04_23, mgrast_dev_06072011, rast_rel_2008_09_30, rast_rel_2009_0925, rast_rel_2010_0526, rast_rel_2014_0729, mgrast_dev_02212011, rast_rel_2010_1206, caBIG-05Apr06-00, mgrast_release_3_0, mgrast_dev_03252011, rast_rel_2010_0118, mgrast_rel_2008_0924, mgrast_rel_2008_1110_v2, rast_rel_2009_02_05, rast_rel_2011_0119, mgrast_rel_2008_0625, mgrast_release_3_0_4, mgrast_release_3_0_2, mgrast_release_3_0_3, mgrast_release_3_0_1, mgrast_dev_03312011, mgrast_release_3_1_2, mgrast_release_3_1_1, mgrast_release_3_1_0, mgrast_dev_04132011, rast_rel_2008_10_09, mgrast_dev_04012011, rast_release_2008_09_29, mgrast_rel_2008_0806, mgrast_rel_2008_0923, mgrast_rel_2008_0919, rast_rel_2009_07_09, rast_rel_2010_0827, mgrast_rel_2008_1110, myrast_33, rast_rel_2011_0928, rast_rel_2008_09_29, mgrast_rel_2008_0917, rast_rel_2008_10_29, mgrast_dev_04052011, mgrast_dev_02222011, caBIG-13Feb06-00, rast_rel_2009_03_26, mgrast_dev_10262011, rast_rel_2008_11_24, rast_rel_2008_08_07, HEAD
added Organism class

package GeneImpl;

sub new {
    #$proteinCollection is a ref to an array
    my ($class, $id, $name, $proteinCollection) = @_;
    $self = { id => $id,
	      name => $name,
	      proteinCollection => $proteinCollection
	      };
    return bless($self, $class);
}

package OrganismImpl;

sub new {
    my ($class, $id, $ncbi, $s_name, $c_name,$org_collection) = @_;
    $self = { id => $id,
	      ncbiTaxonomyID => $ncbi,
              scientificName => $s_name,
	      commonName => $c_name,
	      organismCollection => $org_collection
	    };
    return bless($self, $class);
}

package ProteinImpl;

sub new {
    my ($class, $id, $uniprotkbPrimaryAccession, $uniprotkbEntryName ) = @_;
    $self = {
	componentNameCollection  => undef,
	databaseCrossReferenceCollection  => undef,
	domainNameCollection  => undef,
	featureCollection  => undef,
	geneCollection  => undef,
	id  => $id,
	keywordCollection  => undef,
	organelleCollection  => undef,
	organismCollection  => undef,
	proteinNameCollection  => undef,
	proteinSequence  => undef,
	proteinType  => undef,
	uniprotkbAccessionCollection  => undef,
	uniprotkbEntryName  => $uniprotkbEntryName,
	uniprotkbPrimaryAccession  => $uniprotkbPrimaryAccession
	};
    return bless($self, $class);
}

package ProteinNameImpl;

sub new {
    #$proteinCollection is a ref to an array
    my ($class, $id, $proteinCollection, $value) = @_;
    $self = { id => $id,
	      proteinCollection => $proteinCollection,
	      value => $value
	      };
    return bless($self, $class);
}


##
# queryObjectRequest does not do what we want because of rpc encoding
# i think.  just here for historical record
##

package queryObjectRequest;

sub new {
    my ($class, $orgTargetObjectName, $orgCriteriaObj) = @_;
    $self = { orgTargetObjectName => $orgTargetObjectName,
	      OrgCriteriaObject => $orgCriteriaObj
	      };
    return bless($self, $class);
}



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