Genetics
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<UL>
<LI><A HREF="#name">NAME</A></LI>
<LI><A HREF="#synopsis">SYNOPSIS</A></LI>
<LI><A HREF="#description">DESCRIPTION</A></LI>
<LI><A HREF="#license">LICENSE</A></LI>
<LI><A HREF="#feedback">FEEDBACK</A></LI>
<LI><A HREF="#author steve mathias">AUTHOR - Steve Mathias</A></LI>
<LI><A HREF="#details">DETAILS</A></LI>
<LI><A HREF="#imported packages">Imported Packages</A></LI>
<LI><A HREF="#inheritance">Inheritance</A></LI>
<LI><A HREF="#public methods">Public Methods</A></LI>
<UL>
<LI><A HREF="#getcluster">getCluster</A></LI>
<LI><A HREF="#getminicluster">getMiniCluster</A></LI>
<LI><A HREF="#getsubject">getSubject</A></LI>
<LI><A HREF="#getminisubject">getMiniSubject</A></LI>
<LI><A HREF="#getkindred">getKindred</A></LI>
<LI><A HREF="#getminikindred">getMiniKindred</A></LI>
<LI><A HREF="#getmarker">getMarker</A></LI>
<LI><A HREF="#getminimarker">getMiniMarker</A></LI>
<LI><A HREF="#getminimarkerbyname">getMiniMarkerByName</A></LI>
<LI><A HREF="#getsnp">getSNP</A></LI>
<LI><A HREF="#getminisnp">getMiniSNP</A></LI>
<LI><A HREF="#getgenotype">getGenotype</A></LI>
<LI><A HREF="#getminigenotype">getMiniGenotype</A></LI>
<LI><A HREF="#getstudyvariable">getStudyVariable</A></LI>
<LI><A HREF="#getministudyvariable">getMiniStudyVariable</A></LI>
<LI><A HREF="#getphenotype">getPhenotype</A></LI>
<LI><A HREF="#getminiphenotype">getMiniPhenotype</A></LI>
<LI><A HREF="#getfrequencysource">getFrequencySource</A></LI>
<LI><A HREF="#getminifrequencysource">getMiniFrequencySource</A></LI>
<LI><A HREF="#gethtmarkercollection">getHtMarkerCollection</A></LI>
<LI><A HREF="#gethaplotype">getHaplotype</A></LI>
<LI><A HREF="#getminihaplotype">getMiniHaplotype</A></LI>
<LI><A HREF="#getdnasample">getDNASample</A></LI>
<LI><A HREF="#gettissuesample">getTissueSample</A></LI>
<LI><A HREF="#getmap">getMap</A></LI>
<LI><A HREF="#getminimap">getMiniMap</A></LI>
</UL>
<LI><A HREF="#private methods">Private methods</A></LI>
<UL>
<LI><A HREF="#_getobjassocdata">_getObjAssocData</A></LI>
</UL>
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<HR>
<P>
<H1><A NAME="name">NAME</A></H1>
<P>Genetics::API::DB::Read</P>
<P>
<HR>
<H1><A NAME="synopsis">SYNOPSIS</A></H1>
<PRE>
use Genetics::API ;</PRE>
<PRE>
$api = new Genetics::API(DSN => {driver => "mysql",
host => $Host,
database => $Database},
user => $UserName,
password => $Password) ;</PRE>
<PRE>
$id = 123456 ;
$subject = $api->getSubject($id) ;</PRE>
<P>
<HR>
<H1><A NAME="description">DESCRIPTION</A></H1>
<P>The Genetics::API::DB packages provide an interface for the manipulation of
Genperl objects in a relationa; database. This package contains the methods
for retrieving objects from a database by id. To retrieve objects using more
complex criteria, see Genetics::API::DB::Query.</P>
<P>Two versions of get methods are provided for most object types. One returns
``full'' objects containing all the data in the database associated with an
object id; the other returns ``mini'' objects containing only a subset of the
data associated with an object. Generally, the getMini methods do not return
any of the general object annotation fields (ie. things like Keywords,
DBXReferences, etc. are not returned with ``mini'' objects). In some cases,
certain class-specific data is also left out of ``mini'' objects. See the
individual getMini method descriptions for details on this.</P>
<P>
<HR>
<H1><A NAME="license">LICENSE</A></H1>
<P>This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.</P>
<P>This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.</P>
<P>You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA</P>
<P>
<HR>
<H1><A NAME="feedback">FEEDBACK</A></H1>
<P>Currently, all feedback should be sent directly to the author.</P>
<P>
<HR>
<H1><A NAME="author steve mathias">AUTHOR - Steve Mathias</A></H1>
<P>Email: <A HREF="mailto:mathias@genomica.com">mathias@genomica.com</A></P>
doc/Read.html view on Meta::CPAN
<PRE>
Function : Get (read) a Genetics::Object::HtMarkerCollection object from the database.
Argument : The Object ID of the HtMarkerCollection to be returned.
Returns : A Genetics::Object::HtMarkerCollection object.
Scope : Public</PRE>
<P>
<H2><A NAME="gethaplotype">getHaplotype</A></H2>
<PRE>
Function : Get (read) a Genetics::Object::Haplotype object from the database.
Argument : The Object ID of the Haplotype to be returned.
Returns : A Genetics::Object::Haplotype object.
Scope : Public</PRE>
<P>
<H2><A NAME="getminihaplotype">getMiniHaplotype</A></H2>
<PRE>
Function : Get a "light" version of a Genetics::Object::Haplotype object
from the database.
Argument : The Object ID of the Haplotype to be returned.
Returns : A Genetics::Object::Haplotype object.
Scope : Public
Comments : "Light" version means that the object has only the name and id
fields from Object, and it does not contain any associated NameAlias,
Contact, DBXReference or Keyword data.</PRE>
<P>
<H2><A NAME="getdnasample">getDNASample</A></H2>
<PRE>
Function : Get (read) a Genetics::Object::DNASample object from the database.
Argument : The Object ID of the DNASample to be returned.
Returns : A Genetics::Object::DNASample object.
Scope : Public</PRE>
<P>
<H2><A NAME="gettissuesample">getTissueSample</A></H2>
<PRE>
Function : Get (read) a Genetics::Object::TissueSample object from the database.
Argument : The Object ID of the TissueSample to be returned.
Returns : A Genetics::Object::TissueSample object.
Scope : Public</PRE>
<P>
<H2><A NAME="getmap">getMap</A></H2>
<PRE>
Function : Get (read) a Genetics::Object::Map object from the database.
Argument : The Object ID of the Map to be returned.
Returns : A Genetics::Object::Map object.
Scope : Public</PRE>
<P>
<H2><A NAME="getminimap">getMiniMap</A></H2>
<PRE>
Function : Get "light" version of a Genetics::Object::Map object from
the database.
Argument : The Object ID of the Map to be returned.
Returns : A Genetics::Object::Map object.
Scope : Public
Comments : "Light" version means that the object has only the name and id
fields from Object, and it does not contain any associated NameAlias,
Contact, DBXReference or Keyword data. It also has a sub-set of
Map-specific fields.</PRE>
<P>
<HR>
<H1><A NAME="private methods">Private methods</A></H1>
<P>
<H2><A NAME="_getobjassocdata">_getObjAssocData</A></H2>
<PRE>
Function : get (read) data from and associated with the Object table/object.
Arguments : Scalar containing an Object.id and a reference to a hash which
will be populated with the data.
Returns : N/A
Scope : Private
Called by : The various getObjectSubClass methods.
Comments : The format of the data structure created by this method is
identical to that passed to Object::new().</PRE>
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