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Genetics

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<TITLE>Update.pm</TITLE>
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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="#updatecluster">updateCluster</A></LI>
		<LI><A HREF="#updatesubject">updateSubject</A></LI>
		<LI><A HREF="#updatekindred">updateKindred</A></LI>
		<LI><A HREF="#updatemarker">updateMarker</A></LI>
		<LI><A HREF="#updatesnp">updateSNP</A></LI>
		<LI><A HREF="#updategenotype">updateGenotype</A></LI>
		<LI><A HREF="#updatestudyvariable">updateStudyVariable</A></LI>
		<LI><A HREF="#updatephenotype">updatePhenotype</A></LI>
		<LI><A HREF="#updatefrequencysource">updateFrequencySource</A></LI>
		<LI><A HREF="#updatehtmarkercollection">updateHtMarkerCollection</A></LI>
		<LI><A HREF="#updatehaplotype">updateHaplotype</A></LI>
		<LI><A HREF="#updatednasample">updateDNASample</A></LI>
		<LI><A HREF="#updatetissuesample">updateTissueSample</A></LI>
		<LI><A HREF="#updatemap">updateMap</A></LI>
	</UL>

	<LI><A HREF="#private methods">Private methods</A></LI>
	<UL>

		<LI><A HREF="#_updateobjassocdata">_updateObjAssocData</A></LI>
		<LI><A HREF="#_updatesubjectkindredrefs">_updateSubjectKindredRefs</A></LI>
		<LI><A HREF="#_updatekindredsubjectrefs">_updateKindredSubjectRefs</A></LI>
		<LI><A HREF="#_updateassayattrs">_updateAssayAttrs</A></LI>
	</UL>

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<HR>
<P>
<H1><A NAME="name">NAME</A></H1>
<P>Genetics::API::DB::Update</P>
<P>
<HR>
<H1><A NAME="synopsis">SYNOPSIS</A></H1>
<PRE>
  use Genetics::API ;</PRE>
<PRE>
  $api = new Genetics::API(DSN =&gt; {driver =&gt; &quot;mysql&quot;,
                                   host =&gt; $Host,
                                   database =&gt; $Database},
                           user =&gt; $UserName,
                           password =&gt; $Password) ;</PRE>
<PRE>
  $subject = $api-&gt;getSubject(3) ;
  $subject-&gt;name(&quot;Elvis&quot;) ;
  $api-&gt;updateSubject($subject) ;</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 relational database.  This package contains the methods
for updating objects that have previously been saved to the database.  To save
new objects, see Genetics::API::DB::Create.</P>
<P>The following describes the update behavior implemented by the methods in 
this package:
  - The data in each object field will completely replace the data in the 
    database for that field.
  - Data for fields not present in an object will not be affected.
  - In order to delete data for a particular field, the value of that field 
    should be set to ``DELETE''.
  - In order to add to existing data for a particular field, use an appropriate 
    method in Genetics::API or handle it manually.</P>
<P>Examples:</P>
<PRE>
  To completely replace a SNPs set of Alleles:
     @alleles = ( {name =&gt; &quot;A&quot;, type =&gt; &quot;Nucleotide&quot;},
                   name =&gt; &quot;C&quot;, type =&gt; &quot;Nucleotide&quot;} ) ;
     $snp = $api-&gt;getSNP(11) ;
     $snp-&gt;Alleles(\@alleles) ;
     $api-&gt;updateSNP($snp) ;</PRE>
<PRE>
  To add an Allele to a SNP:
     $snp = $api-&gt;getSNP(11) ;
     $alleleListptr = $snp-&gt;Alleles ;
     push( @$alleleListptr, {name =&gt; &quot;A&quot;, type =&gt; &quot;Nucleotide&quot;} ) ;
     $snp-&gt;Alleles($alleleListptr) ;
     $api-&gt;updateSNP($snp) ;</PRE>
<P>
<HR>

doc/Update.html view on Meta::CPAN

                         where ptID = ?&quot; ) ;
  $sth-&gt;execute($pt-&gt;field(&quot;value&quot;), $id) ;
  $sth-&gt;finish() ;
  # Phenotype AssayAttributes
  if ( defined ($aaListPtr = $pt-&gt;field(&quot;AssayAttrs&quot;)) ) {
    $self-&gt;_updateAssayAttrs($aaListPtr, &quot;Phenotype&quot;, $id) ;
  }
</PRE>
<PRE>

  $DEBUG and carp &quot; -&gt;[updatePhenotype] End.&quot; ;</PRE>
<PRE>
  return(1) ;
}</PRE>
<P>
<H2><A NAME="updatefrequencysource">updateFrequencySource</A></H2>
<PRE>
  Function  : Update a Genetics::Object::FrequencySource object in the database.
  Argument  : The Genetics::Object::FrequencySource object to be updated.
  Returns   : 1 on success, undef otherwise.
  Scope     : Public</PRE>
<P>
<H2><A NAME="updatehtmarkercollection">updateHtMarkerCollection</A></H2>
<PRE>
  Function  : Update a Genetics::Object::HtMarkerCollection object in the database.
  Argument  : The Genetics::Object::HtMarkerCollection object to be updated.
  Returns   : 1 on success, undef otherwise.
  Scope     : Public</PRE>
<P>
<H2><A NAME="updatehaplotype">updateHaplotype</A></H2>
<PRE>
  Function  : Update a Genetics::Object::Haplotype object in the database.
  Argument  : The Genetics::Object::Haplotype object to be updated.
  Returns   : 1 on success, undef otherwise.
  Scope     : Public</PRE>
<P>
<H2><A NAME="updatednasample">updateDNASample</A></H2>
<PRE>
  Function  : Update a Genetics::Object::DNASample object in the database.
  Argument  : The Genetics::Object::DNASample object to be updated.
  Returns   : 1 on success, undef otherwise.
  Scope     : Public</PRE>
<P>
<H2><A NAME="updatetissuesample">updateTissueSample</A></H2>
<PRE>
  Function  : Update a Genetics::Object::TissueSample object in the database.
  Argument  : The Genetics::Object::TissueSample object to be updated.
  Returns   : 1 on success, undef otherwise.
  Scope     : Public</PRE>
<P>
<H2><A NAME="updatemap">updateMap</A></H2>
<PRE>
  Function  : Update a Genetics::Object::Map object in the database.
  Argument  : The Genetics::Object::Map object to be updated.
  Returns   : 1 on success, undef otherwise.
  Scope     : Public</PRE>
<P>
<HR>
<H1><A NAME="private methods">Private methods</A></H1>
<P>
<H2><A NAME="_updateobjassocdata">_updateObjAssocData</A></H2>
<PRE>
  Function  : Update data in, and associated with, the Object table/object.
  Argument  : The Genetics::Object object to be updated.
  Returns   : 1 on success, undef otherwise.
  Scope     : Private
  Called by : The various updateObjectSubClass methods.
  Comments  : The following Object fields cannot be modified: id, objType, 
              dateModified.</PRE>
<P>
<H2><A NAME="_updatesubjectkindredrefs">_updateSubjectKindredRefs</A></H2>
<PRE>
  Function  : Updates references between Subjects and Kindreds.
  Argument  : A Subject ID and a Kindred ID (can be undef).
  Returns   : N/A
  Scope     : Private
  Called By : updateSubject() when Subject.kindredID is modified.
  Comments  : This method updates the KindredSubject table based on 
              a change to a Subject.kindredID field.</PRE>
<P>
<H2><A NAME="_updatekindredsubjectrefs">_updateKindredSubjectRefs</A></H2>
<PRE>
  Function  : Updates references between Kindreds and Subjects.
  Argument  : A Kindred ID and an array reference to a list of Subject IDs.
  Returns   : N/A
  Scope     : Private
  Called By : updateSubject() and updateKindred().
  Comments  : This method updates the KindredSubject table based on a changes 
              made to a Kindred-&gt;Subjects field.
              This method also updates the Subject.kindredID field of each of 
              the relevant Subjects.</PRE>
<P>
<H2><A NAME="_updateassayattrs">_updateAssayAttrs</A></H2>
<PRE>
  Function  : Update AssayAttributes associated with a Genotype, AlleleCall 
              or Phenotype.
  Arguments : Array reference to the list of AssayAttributes, scalar 
              containing the type of object with which the AssayAttributes 
              are associated, and another scalar containing the id of that 
              object.
  Returns   : N/A
  Scope     : Private
  Called by : updateGenotype(), updatePhenotype().
  Comments  :</PRE>

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