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SKIPPY / Bio-Affymetrix-0.1 / pdoc / Affymetrix / CDF / Probeset.html 
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Probeset documentation.
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<HR><H4>Bio::Affymetrix::CDF</H4>
<H3>Probeset</H3>
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<TABLE BORDER="1" WIDTH="100%"><TR>
<TD><A HREF="#SUMMARY">Summary</A></TD>
<TD><A HREF="#vardefs">Package variables</A></TD>
<TD><A HREF="#SYNOPSIS">Synopsis</A></TD>
<TD><A HREF="#DESCRIPTION">Description</A></TD>
<TD><A HREF="#General">General documentation</A></TD>
<TD><A HREF="#Methods">Methods</A></TD>
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<TABLE BORDER="0" WIDTH="100%" CELLSPACING="0"><TR><TD BGCOLOR="#ffae84"><B>Summary</B></TD></TR>
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<TABLE BORDER="0" WIDTH="100%"><TR><TD><pre><B>Bio::Affymetrix::CDF::Probeset</B>- an Affymetrix probeset in an CDF file<BR></pre></TD></TR>
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<A NAME="vardefs"></A>
<TABLE BORDER="0" WIDTH="100%" CELLSPACING="0"><TR BGCOLOR="#ffae84"><TD><B>Package variables</B></TD>
<TD ALIGN="RIGHT"><A HREF="#TOP">top</A></TD></TR></TABLE><TABLE BORDER="0" WIDTH="100%"><TR><TD COLSPAN="2">No package variables defined.</TD></TR>
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<TABLE BORDER="0" WIDTH="100%" CELLSPACING="0"><TR BGCOLOR="#ffae84"><TD WIDTH="150"><B>Included modules</B></TD><TD ALIGN="RIGHT"><A HREF="#TOP">top</A></TD></TR></TABLE><TABLE BORDER="0"><TR><TD COLSPAN="2"><b><font color="#0000ff"><a href="Probe.html">Bio::Affymetrix::CDF::Probe</a></font></b> </TD></TR>
<TR><TD COLSPAN="2"><b><font color="#0000ff">strict</font></b></TD></TR>
<TR><TD COLSPAN="2"><b><font color="#0000ff">warnings</font></b></TD></TR>
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<A NAME="SYNOPSIS"></A>
<TABLE BORDER="0" WIDTH="100%" CELLSPACING="0"><TR BGCOLOR="#ffae84"><TD><B>Synopsis</B></TD><TD ALIGN="RIGHT"><A HREF="#TOP">top</A></TD></TR></TABLE><TABLE BORDER="0"><TR><TD COLSPAN="2"><pre>use Bio::Affymetrix::CDF;<BR><BR># Parse the CDF file<BR><BR>my $cdf=new CDF();<BR><BR>$cdf-&gt;parse_from_file(&quot;foo.cdf&quot;);<BR><BR># Print out all of the probeset names on this chip type<BR><BR>my $probeset=$chp-&gt;probesets()-&gt;[0];<BR><BR>FINISH ME HERE<BR></pre>
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<A NAME="DESCRIPTION"></A>
<TABLE BORDER="0" WIDTH="100%" CELLSPACING="0"><TR BGCOLOR="#ffae84"><TD><B>Description</B></TD><TD ALIGN="RIGHT"><A HREF="#TOP">top</A></TD></TR></TABLE><TABLE BORDER="0"><TR><TD COLSPAN="2"><pre>The Affymetrix microarray system produces files in a variety of<BR>formats. If this means nothing to you, these modules are probably not<BR>for you :). After these modules have parsed a CDF file, the resulting<BR>Bio::Affymetrix::CDF file contains a list of<BR>Bio::Affmetrix::CDF::Probeset objects. This allows you look at the<BR>details of the probeset.<BR></pre>
<pre>You can only get probe-level information if you have parsed the CDF<BR>object with probe-level parsing turned on.<BR></pre>
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<A NAME="Methods"></A>
<TABLE BORDER="0" WIDTH="100%" CELLSPACING="0"><TR BGCOLOR="#ffae84"><TD><B>Methods</B></TD><TD ALIGN="RIGHT"><A HREF="#TOP">top</A></TD></TR></TABLE>
<TABLE BORDER="1" CELLSPACING="5"><TR><TD><B>CDF</B></TD><TD><A HREF="#POD1">Description</A></TD><TD><A HREF="#CODE1">Code</A></TD></TR>
<TR><TD><B>_parse_from_filehandle</B></TD><TD><FONT COLOR="RED"><B>No description</B></FONT></TD><TD><A HREF="#CODE2">Code</A></TD></TR>
<TR><TD><B>is_sense</B></TD><TD><A HREF="#POD2">Description</A></TD><TD><A HREF="#CODE3">Code</A></TD></TR>
<TR><TD><B>mutation_type</B></TD><TD><A HREF="#POD3">Description</A></TD><TD><A HREF="#CODE4">Code</A></TD></TR>
<TR><TD><B>name</B></TD><TD><A HREF="#POD4">Description</A></TD><TD><A HREF="#CODE5">Code</A></TD></TR>
<TR><TD><B>new</B></TD><TD><A HREF="#POD5">Description</A></TD><TD><A HREF="#CODE6">Code</A></TD></TR>
<TR><TD><B>original_num_probepairs</B></TD><TD><A HREF="#POD6">Description</A></TD><TD><A HREF="#CODE7">Code</A></TD></TR>
<TR><TD><B>original_num_probes</B></TD><TD><A HREF="#POD7">Description</A></TD><TD><A HREF="#CODE8">Code</A></TD></TR>
<TR><TD><B>original_number_blocks</B></TD><TD><FONT COLOR="RED"><B>No description</B></FONT></TD><TD><A HREF="#CODE9">Code</A></TD></TR>
<TR><TD><B>probes</B></TD><TD><A HREF="#POD8">Description</A></TD><TD><A HREF="#CODE10">Code</A></TD></TR>
<TR><TD><B>unit_name</B></TD><TD><A HREF="#POD9">Description</A></TD><TD><A HREF="#CODE11">Code</A></TD></TR>
<TR><TD><B>unit_number</B></TD><TD><A HREF="#POD10">Description</A></TD><TD><A HREF="#CODE12">Code</A></TD></TR>
<TR><TD><B>unit_type</B></TD><TD><FONT COLOR="RED"><B>No description</B></FONT></TD><TD><A HREF="#CODE13">Code</A></TD></TR>
</TABLE>
<A NAME="MethDesc"></A>
<HR><H2>Methods description</H2>
<TABLE BORDER="0" WIDTH="100%" CELLSPACING="0" CELLSPACING="0">
<TR BGCOLOR="#4492df"><TD WIDTH="200"><A NAME="_pod_CDF"></A><A NAME="POD1"></A><B>CDF</B></TD><TD><A HREF="#CODE1">code</A></TD><TD><A HREF="#TOP">top</A></TD><TD>prev</TD><TD><A HREF="#POD2">next</A></TD></TR></TABLE>
<pre>  Arg [1]    : Bio::Affymetrix::CDF object $probelist<BR>  Example    : my $cdf=$ps-&gt;probes()<BR>  Description: Get/set CDF object this probeset belongs to.<BR>  Returntype : Bio::Affymetrix::CDF object<BR>  Exceptions : none<BR>  Caller     : general<BR></pre>
<TABLE BORDER="0" WIDTH="100%" CELLSPACING="0" CELLSPACING="0">
<TR BGCOLOR="#4492df"><TD WIDTH="200"><A NAME="_pod_is_sense"></A><A NAME="POD2"></A><B>is_sense</B></TD><TD><A HREF="#CODE3">code</A></TD><TD><A HREF="#TOP">top</A></TD><TD><A HREF="#POD1">prev</A></TD><TD><A HREF="#POD3">next</A></TD></TR></TABLE>
<pre>  Arg [1]    : 	boolean $sense (optional)<BR>  Example    : 	if ($ps-&gt;is_sense()) { .... }<BR>  Description: 	Returns true when this is a sense (rather than<BR>anti-sense) probeset<BR>  Returntype : boolean<BR>  Exceptions : none<BR>  Caller     : general<BR></pre>
<TABLE BORDER="0" WIDTH="100%" CELLSPACING="0" CELLSPACING="0">
<TR BGCOLOR="#4492df"><TD WIDTH="200"><A NAME="_pod_mutation_type"></A><A NAME="POD3"></A><B>mutation_type</B></TD><TD><A HREF="#CODE4">code</A></TD><TD><A HREF="#TOP">top</A></TD><TD><A HREF="#POD2">prev</A></TD><TD><A HREF="#POD4">next</A></TD></TR></TABLE>
<pre>  Arg [0]    : 	integer<BR>  Example    : none<BR>  Description: Get/set mutation_type. If this is a genotyping probe<BR>set, 0=substitution, 1=insertion, 2=deletion<BR>  Returntype : integer<BR>  Exceptions : none<BR>  Caller     : general<BR></pre>
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<TR BGCOLOR="#4492df"><TD WIDTH="200"><A NAME="_pod_name"></A><A NAME="POD4"></A><B>name</B></TD><TD><A HREF="#CODE5">code</A></TD><TD><A HREF="#TOP">top</A></TD><TD><A HREF="#POD3">prev</A></TD><TD><A HREF="#POD5">next</A></TD></TR></TABLE>
<pre>  Arg [1]    : string<BR>  Example    : my $name=$ps-&gt;name()<BR>  Description: Get/set name of probeset<BR>  Returntype : string<BR>  Exceptions : none<BR>  Caller     : general<BR></pre>
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<TR BGCOLOR="#4492df"><TD WIDTH="200"><A NAME="_pod_new"></A><A NAME="POD5"></A><B>new</B></TD><TD><A HREF="#CODE6">code</A></TD><TD><A HREF="#TOP">top</A></TD><TD><A HREF="#POD4">prev</A></TD><TD><A HREF="#POD6">next</A></TD></TR></TABLE>
<pre>  Arg [0]    : none<BR>  Example    : my $cdf=new <B>Bio::Affymetrix::CDF::Probeset</B>();<BR>  Description: constructor for Bio::Affymetrix::CDF::Probeset<BR>object. You probably do not want to make these objects yourself yet, however.<BR>  Returntype : new Bio::Affmetrix::CDF object<BR>  Exceptions : none<BR>  Caller     : general<BR></pre>
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<TR BGCOLOR="#4492df"><TD WIDTH="200"><A NAME="_pod_original_num_probepairs"></A><A NAME="POD6"></A><B>original_num_probepairs</B></TD><TD><A HREF="#CODE7">code</A></TD><TD><A HREF="#TOP">top</A></TD><TD><A HREF="#POD5">prev</A></TD><TD><A HREF="#POD7">next</A></TD></TR></TABLE>
<pre>  Arg [0]    : 	none<BR>  Example    : 	my $probepairs=$ps-&gt;original_num_probepairs()<BR>  Description: 	Get the number of probepairs in this probeset<BR>  Returntype : integer<BR>  Exceptions : none<BR>  Caller     : general<BR></pre>
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<TR BGCOLOR="#4492df"><TD WIDTH="200"><A NAME="_pod_original_num_probes"></A><A NAME="POD7"></A><B>original_num_probes</B></TD><TD><A HREF="#CODE8">code</A></TD><TD><A HREF="#TOP">top</A></TD><TD><A HREF="#POD6">prev</A></TD><TD><A HREF="#POD8">next</A></TD></TR></TABLE>
<pre>  Arg [0]    : 	none<BR>  Example    : 	my $probepairs=$ps-&gt;original_num_probes()<BR>  Description: 	Get the number of probes in this probeset<BR>  Returntype : integer<BR>  Exceptions : none<BR>  Caller     : general<BR></pre>
<TABLE BORDER="0" WIDTH="100%" CELLSPACING="0" CELLSPACING="0">
<TR BGCOLOR="#4492df"><TD WIDTH="200"><A NAME="_pod_probes"></A><A NAME="POD8"></A><B>probes</B></TD><TD><A HREF="#CODE10">code</A></TD><TD><A HREF="#TOP">top</A></TD><TD><A HREF="#POD7">prev</A></TD><TD><A HREF="#POD9">next</A></TD></TR></TABLE>
<pre>  Arg [1]    : arrayref $probelist<BR>  Example    : my @probes=$ps-&gt;probes()<BR>  Description: Get/set list of probes making up this array. Only available if<BR>with probes mode is used.<BR>  Returntype : reference to array of Bio::Affymetrix::CDF::Probe objects<BR>  Exceptions : none<BR>  Caller     : general<BR></pre>
<TABLE BORDER="0" WIDTH="100%" CELLSPACING="0" CELLSPACING="0">
<TR BGCOLOR="#4492df"><TD WIDTH="200"><A NAME="_pod_unit_name"></A><A NAME="POD9"></A><B>unit_name</B></TD><TD><A HREF="#CODE11">code</A></TD><TD><A HREF="#TOP">top</A></TD><TD><A HREF="#POD8">prev</A></TD><TD><A HREF="#POD10">next</A></TD></TR></TABLE>
<pre>  Arg [1]    : 	string $unit_name (optional)<BR>  Example    : 	my $unit_name=$ps-&gt;unit_name()<BR>  Description: 	Always NONE for expression arrays<BR>  Returntype : string<BR>  Exceptions : none<BR>  Caller     : general<BR></pre>
<TABLE BORDER="0" WIDTH="100%" CELLSPACING="0" CELLSPACING="0">
<TR BGCOLOR="#4492df"><TD WIDTH="200"><A NAME="_pod_unit_number"></A><A NAME="POD10"></A><B>unit_number</B></TD><TD><A HREF="#CODE12">code</A></TD><TD><A HREF="#TOP">top</A></TD><TD><A HREF="#POD9">prev</A></TD><TD><A HREF="#POD11">next</A></TD></TR></TABLE>
<pre>  Arg [0]    : 	none<BR>  Example    : 	my $probepairs=$ps-&gt;unit_number()<BR>  Description: 	Get the unit number of this probeset (a unique number<BR>assigned to each probe in the CDF file but otherwise meaningless)<BR>  Returntype : integer<BR>  Exceptions : none<BR>  Caller     : general<BR></pre>
<A NAME="MethCode"></A>
<HR><H2>Methods code</H2>
<TABLE BORDER="0" WIDTH="100%" CELLSPACING="0">
<TR BGCOLOR="#dcab68"><TD WIDTH="200"><A NAME="CODE1"></A><B>CDF</B></TD><TD><A HREF="#POD1">description</A></TD><TD WIDTH="30"><A HREF="#TOP">top</A></TD><TD WIDTH="30">prev</TD><TD WIDTH="30"><A HREF="#CODE2">next</A></TD></TR></TABLE>
<font color="#0000ff"><b>sub</b></font> <font color="#ff0000"><b>CDF</b></font>
 {<pre>    <font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$self</font>=<font color="#4169e1"><b>shift</b></font>;

    <font color="#0000ff"><b>if</b></font> <font color="#0000ff"><b>(</b></font><font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$q</font>=<font color="#4169e1"><b>shift</b></font><font color="#0000ff"><b>)</b></font> <font color="#0000ff"><b>{</b></font>
	<font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"CDF"</font><font color="#0000ff"><b>}</b></font>=<font color="#1f32ff">$q</font>;
    <font color="#0000ff"><b>}</b></font>
    <font color="#0000ff"><b>return</b></font> <font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"CDF"</font><font color="#0000ff"><b>}</b></font>;</pre>}<BR>
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<TR BGCOLOR="#dcab68"><TD WIDTH="200"><A NAME="CODE2"></A><B>_parse_from_filehandle</B></TD><TD>description</TD><TD WIDTH="30"><A HREF="#TOP">top</A></TD><TD WIDTH="30"><A HREF="#CODE1">prev</A></TD><TD WIDTH="30"><A HREF="#CODE3">next</A></TD></TR></TABLE>
<font color="#0000ff"><b>sub</b></font> <font color="#ff00ff"><b>_parse_from_filehandle</b></font>
 {<pre>    <font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$self</font>=<font color="#4169e1"><b>shift</b></font>;
    <font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$fh</font>=<font color="#4169e1"><b>shift</b></font>;

    <font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"FH"</font><font color="#0000ff"><b>}</b></font>=<font color="#1f32ff">$fh</font>;

    <font color="#ff0000">## Handle trivia from unit header</font><BR>    <font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$i</font>;

    <font color="#0000ff"><b>while</b></font> <font color="#0000ff"><b>(</b></font><font color="#4169e1"><b>defined</b></font><font color="#0000ff"><b>(</b></font><font color="#1f32ff">$i</font>=&lt;<font color="#1f32ff">$fh</font>&gt;<font color="#0000ff"><b>)</b></font> &amp;&amp; <font color="#0000ff"><b>(</b></font>!<font color="#0000ff"><b>(</b></font><font color="#1f32ff">$i</font>=~<font color="#006400"><b>/^\[.*\]$/o</b></font><font color="#0000ff"><b>)</b></font><font color="#0000ff"><b>)</b></font><font color="#0000ff"><b>)</b></font> <font color="#0000ff"><b>{</b></font>
	<font color="#0000ff"><b>if</b></font> <font color="#0000ff"><b>(</b></font><font color="#1f32ff">$i</font>=~<font color="#006400"><b>/^([^=]+)=(.*)$/o</b></font><font color="#0000ff"><b>)</b></font> <font color="#0000ff"><b>{</b></font> 
	    <font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$name</font>=<font color="#1f32ff">$1</font>;
	    <font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$value</font>=<font color="#1f32ff">$2</font>;
	    <font color="#0000ff"><b>if</b></font> <font color="#0000ff"><b>(</b></font><font color="#4169e1"><b>uc</b></font> <font color="#1f32ff">$name</font> <font color="#0000ff"><b>eq</b></font> <font color="#007400">"NAME"</font><font color="#0000ff"><b>)</b></font> <font color="#0000ff"><b>{</b></font>
		<font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"UNITNAME"</font><font color="#0000ff"><b>}</b></font>=<font color="#1f32ff">$value</font>;
	    <font color="#0000ff"><b>}</b></font> <font color="#0000ff"><b>elsif</b></font> <font color="#0000ff"><b>(</b></font><font color="#4169e1"><b>uc</b></font> <font color="#1f32ff">$name</font> <font color="#0000ff"><b>eq</b></font> <font color="#007400">"DIRECTION"</font><font color="#0000ff"><b>)</b></font> <font color="#0000ff"><b>{</b></font>
		<font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"SENSE"</font><font color="#0000ff"><b>}</b></font>=<font color="#0000ff"><b>(</b></font><font color="#1f32ff">$value</font>==1<font color="#0000ff"><b>)</b></font>;
	    <font color="#0000ff"><b>}</b></font> <font color="#0000ff"><b>else</b></font> <font color="#0000ff"><b>{</b></font>
		<font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#4169e1"><b>uc</b></font> <font color="#1f32ff">$name</font><font color="#0000ff"><b>}</b></font>=<font color="#1f32ff">$value</font>;
	    <font color="#0000ff"><b>}</b></font>
	<font color="#0000ff"><b>}</b></font>
    <font color="#0000ff"><b>}</b></font>

    <font color="#ff0000">## Block section</font><BR>    <font color="#0000ff"><b>while</b></font> <font color="#0000ff"><b>(</b></font><font color="#4169e1"><b>defined</b></font><font color="#0000ff"><b>(</b></font><font color="#1f32ff">$i</font>=&lt;<font color="#1f32ff">$fh</font>&gt;<font color="#0000ff"><b>)</b></font> &amp;&amp; <font color="#0000ff"><b>(</b></font>!<font color="#0000ff"><b>(</b></font><font color="#1f32ff">$i</font>=~<font color="#006400"><b>/^\[.*\]$/o</b></font><font color="#0000ff"><b>)</b></font><font color="#0000ff"><b>)</b></font><font color="#0000ff"><b>)</b></font> <font color="#0000ff"><b>{</b></font>
	<font color="#0000ff"><b>if</b></font> <font color="#0000ff"><b>(</b></font><font color="#1f32ff">$i</font>=~<font color="#006400"><b>/^([^=]+)=(.*)$/o</b></font><font color="#0000ff"><b>)</b></font> <font color="#0000ff"><b>{</b></font> 
	    <font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$name</font>=<font color="#1f32ff">$1</font>;
	    <font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$value</font>=<font color="#1f32ff">$2</font>;
	    <font color="#0000ff"><b>if</b></font> <font color="#0000ff"><b>(</b></font><font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"probemode"</font><font color="#0000ff"><b>}</b></font>&amp;&amp;<font color="#1f32ff">$name</font>=~<font color="#006400"><b>/Cell\d+/o</b></font><font color="#0000ff"><b>)</b></font> <font color="#0000ff"><b>{</b></font>
		<font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$h</font>= <font color="#0000ff"><b>new</b></font> <A HREF="../CDF.html"><font color="#8000ff"><b>Bio::Affymetrix::CDF</b></font></A>::<font color="#ff8204">Probe</font><font color="#0000ff"><b>(</b></font><font color="#0000ff"><b>)</b></font>;
		<font color="#0000ff"><b>my</b></font> <font color="#1f32ff">@s</font>=<font color="#4169e1"><b>split</b></font> <font color="#006400"><b>/\t/</b></font>,<font color="#1f32ff">$value</font>;
		<font color="#1f32ff">$h</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"NAME"</font><font color="#0000ff"><b>}</b></font>=<font color="#1f32ff">$name</font>;
		<font color="#1f32ff">$h</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"X"</font><font color="#0000ff"><b>}</b></font>=<font color="#1f32ff">$s</font><font color="#0000ff"><b>[</b></font>0<font color="#0000ff"><b>]</b></font>;
		<font color="#1f32ff">$h</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"Y"</font><font color="#0000ff"><b>}</b></font>=<font color="#1f32ff">$s</font><font color="#0000ff"><b>[</b></font>1<font color="#0000ff"><b>]</b></font>;
		<font color="#1f32ff">$h</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"PROBE"</font><font color="#0000ff"><b>}</b></font>=<font color="#1f32ff">$s</font><font color="#0000ff"><b>[</b></font>2<font color="#0000ff"><b>]</b></font>;
		<font color="#1f32ff">$h</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"EXPOS"</font><font color="#0000ff"><b>}</b></font>=<font color="#1f32ff">$s</font><font color="#0000ff"><b>[</b></font>5<font color="#0000ff"><b>]</b></font>;
		<font color="#1f32ff">$h</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"POS"</font><font color="#0000ff"><b>}</b></font>=<font color="#1f32ff">$s</font><font color="#0000ff"><b>[</b></font>6<font color="#0000ff"><b>]</b></font>;
		<font color="#1f32ff">$h</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"PBASE"</font><font color="#0000ff"><b>}</b></font>=<font color="#1f32ff">$s</font><font color="#0000ff"><b>[</b></font>8<font color="#0000ff"><b>]</b></font>;
		<font color="#1f32ff">$h</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"ATOM"</font><font color="#0000ff"><b>}</b></font>=<font color="#1f32ff">$s</font><font color="#0000ff"><b>[</b></font>9<font color="#0000ff"><b>]</b></font>;
		<font color="#1f32ff">$h</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"INDEX"</font><font color="#0000ff"><b>}</b></font>=<font color="#1f32ff">$s</font><font color="#0000ff"><b>[</b></font>10<font color="#0000ff"><b>]</b></font>;
		
		<font color="#4169e1"><b>push</b></font> @<font color="#0000ff"><b>{</b></font><font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"PROBES"</font><font color="#0000ff"><b>}</b></font><font color="#0000ff"><b>}</b></font>,<font color="#1f32ff">$h</font>;
	    <font color="#0000ff"><b>}</b></font> <font color="#0000ff"><b>elsif</b></font> <font color="#0000ff"><b>(</b></font><font color="#4169e1"><b>uc</b></font> <font color="#1f32ff">$name</font> <font color="#0000ff"><b>eq</b></font> <font color="#007400">"NAME"</font><font color="#0000ff"><b>)</b></font> <font color="#0000ff"><b>{</b></font>
		<font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"NAME"</font><font color="#0000ff"><b>}</b></font>=<font color="#1f32ff">$value</font>;
	    <font color="#0000ff"><b>}</b></font>
	<font color="#0000ff"><b>}</b></font>
    <font color="#0000ff"><b>}</b></font>

    <font color="#0000ff"><b>return</b></font> <font color="#1f32ff">$i</font>;</pre>}<BR>
<TABLE BORDER="0" WIDTH="100%" CELLSPACING="0">
<TR BGCOLOR="#dcab68"><TD WIDTH="200"><A NAME="CODE3"></A><B>is_sense</B></TD><TD><A HREF="#POD2">description</A></TD><TD WIDTH="30"><A HREF="#TOP">top</A></TD><TD WIDTH="30"><A HREF="#CODE2">prev</A></TD><TD WIDTH="30"><A HREF="#CODE4">next</A></TD></TR></TABLE>
<font color="#0000ff"><b>sub</b></font> <font color="#ff0000"><b>is_sense</b></font>
 {<pre>    <font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$self</font>=<font color="#4169e1"><b>shift</b></font>;

    <font color="#0000ff"><b>if</b></font> <font color="#0000ff"><b>(</b></font><font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$q</font>=<font color="#4169e1"><b>shift</b></font><font color="#0000ff"><b>)</b></font> <font color="#0000ff"><b>{</b></font>
	<font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"SENSE"</font><font color="#0000ff"><b>}</b></font>=<font color="#1f32ff">$q</font>;
    <font color="#0000ff"><b>}</b></font>
    <font color="#0000ff"><b>return</b></font> <font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"SENSE"</font><font color="#0000ff"><b>}</b></font>;</pre>}<BR>
<TABLE BORDER="0" WIDTH="100%" CELLSPACING="0">
<TR BGCOLOR="#dcab68"><TD WIDTH="200"><A NAME="CODE4"></A><B>mutation_type</B></TD><TD><A HREF="#POD3">description</A></TD><TD WIDTH="30"><A HREF="#TOP">top</A></TD><TD WIDTH="30"><A HREF="#CODE3">prev</A></TD><TD WIDTH="30"><A HREF="#CODE5">next</A></TD></TR></TABLE>
<font color="#0000ff"><b>sub</b></font> <font color="#ff0000"><b>mutation_type</b></font>
 {<pre>    <font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$self</font>=<font color="#4169e1"><b>shift</b></font>;

    <font color="#0000ff"><b>if</b></font> <font color="#0000ff"><b>(</b></font><font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$q</font>=<font color="#4169e1"><b>shift</b></font><font color="#0000ff"><b>)</b></font> <font color="#0000ff"><b>{</b></font>
	<font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"MUTATIONTYPE"</font><font color="#0000ff"><b>}</b></font>=<font color="#1f32ff">$q</font>;
    <font color="#0000ff"><b>}</b></font>
    <font color="#0000ff"><b>return</b></font> <font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"MUTATIONTYPE"</font><font color="#0000ff"><b>}</b></font>;</pre>}<BR>
<TABLE BORDER="0" WIDTH="100%" CELLSPACING="0">
<TR BGCOLOR="#dcab68"><TD WIDTH="200"><A NAME="CODE5"></A><B>name</B></TD><TD><A HREF="#POD4">description</A></TD><TD WIDTH="30"><A HREF="#TOP">top</A></TD><TD WIDTH="30"><A HREF="#CODE4">prev</A></TD><TD WIDTH="30"><A HREF="#CODE6">next</A></TD></TR></TABLE>
<font color="#0000ff"><b>sub</b></font> <font color="#ff0000"><b>name</b></font>
 {<pre>    <font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$self</font>=<font color="#4169e1"><b>shift</b></font>;

    <font color="#0000ff"><b>if</b></font> <font color="#0000ff"><b>(</b></font><font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$q</font>=<font color="#4169e1"><b>shift</b></font><font color="#0000ff"><b>)</b></font> <font color="#0000ff"><b>{</b></font>
	<font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"NAME"</font><font color="#0000ff"><b>}</b></font>=<font color="#1f32ff">$q</font>;
    <font color="#0000ff"><b>}</b></font>
    <font color="#0000ff"><b>return</b></font> <font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"NAME"</font><font color="#0000ff"><b>}</b></font>;</pre>}<BR>
<TABLE BORDER="0" WIDTH="100%" CELLSPACING="0">
<TR BGCOLOR="#dcab68"><TD WIDTH="200"><A NAME="CODE6"></A><B>new</B></TD><TD><A HREF="#POD5">description</A></TD><TD WIDTH="30"><A HREF="#TOP">top</A></TD><TD WIDTH="30"><A HREF="#CODE5">prev</A></TD><TD WIDTH="30"><A HREF="#CODE7">next</A></TD></TR></TABLE>
<font color="#0000ff"><b>sub</b></font> <font color="#ff0000"><b>new</b></font>
 {<pre>    <font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$class</font>=<font color="#4169e1"><b>shift</b></font>;
    <font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$q</font>=<font color="#4169e1"><b>shift</b></font>;
    <font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$self</font>=<font color="#0000ff"><b>{</b></font><font color="#0000ff"><b>}</b></font>;
    <font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"probemode"</font><font color="#0000ff"><b>}</b></font>=0;

    <font color="#4169e1"><b>bless</b></font> <font color="#1f32ff">$self</font>,<font color="#1f32ff">$class</font>;


    <font color="#0000ff"><b>return</b></font> <font color="#1f32ff">$self</font>;</pre>}<BR>
<TABLE BORDER="0" WIDTH="100%" CELLSPACING="0">
<TR BGCOLOR="#dcab68"><TD WIDTH="200"><A NAME="CODE7"></A><B>original_num_probepairs</B></TD><TD><A HREF="#POD6">description</A></TD><TD WIDTH="30"><A HREF="#TOP">top</A></TD><TD WIDTH="30"><A HREF="#CODE6">prev</A></TD><TD WIDTH="30"><A HREF="#CODE8">next</A></TD></TR></TABLE>
<font color="#0000ff"><b>sub</b></font> <font color="#ff0000"><b>original_num_probepairs</b></font>
 {<pre>    <font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$self</font>=<font color="#4169e1"><b>shift</b></font>;
    <font color="#0000ff"><b>return</b></font> <font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"NUMATOMS"</font><font color="#0000ff"><b>}</b></font>;</pre>}<BR>
<TABLE BORDER="0" WIDTH="100%" CELLSPACING="0">
<TR BGCOLOR="#dcab68"><TD WIDTH="200"><A NAME="CODE8"></A><B>original_num_probes</B></TD><TD><A HREF="#POD7">description</A></TD><TD WIDTH="30"><A HREF="#TOP">top</A></TD><TD WIDTH="30"><A HREF="#CODE7">prev</A></TD><TD WIDTH="30"><A HREF="#CODE9">next</A></TD></TR></TABLE>
<font color="#0000ff"><b>sub</b></font> <font color="#ff0000"><b>original_num_probes</b></font>
 {<pre>    <font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$self</font>=<font color="#4169e1"><b>shift</b></font>;
    <font color="#0000ff"><b>return</b></font> <font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"NUMCELLS"</font><font color="#0000ff"><b>}</b></font>;</pre>}<BR>
<TABLE BORDER="0" WIDTH="100%" CELLSPACING="0">
<TR BGCOLOR="#dcab68"><TD WIDTH="200"><A NAME="CODE9"></A><B>original_number_blocks</B></TD><TD>description</TD><TD WIDTH="30"><A HREF="#TOP">top</A></TD><TD WIDTH="30"><A HREF="#CODE8">prev</A></TD><TD WIDTH="30"><A HREF="#CODE10">next</A></TD></TR></TABLE>
<font color="#0000ff"><b>sub</b></font> <font color="#ff0000"><b>original_number_blocks</b></font>
 {<pre>    <font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$self</font>=<font color="#4169e1"><b>shift</b></font>;
    <font color="#0000ff"><b>return</b></font> <font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"NUMBERBLOCKS"</font><font color="#0000ff"><b>}</b></font>;</pre>}<BR>
<TABLE BORDER="0" WIDTH="100%" CELLSPACING="0">
<TR BGCOLOR="#dcab68"><TD WIDTH="200"><A NAME="CODE10"></A><B>probes</B></TD><TD><A HREF="#POD8">description</A></TD><TD WIDTH="30"><A HREF="#TOP">top</A></TD><TD WIDTH="30"><A HREF="#CODE9">prev</A></TD><TD WIDTH="30"><A HREF="#CODE11">next</A></TD></TR></TABLE>
<font color="#0000ff"><b>sub</b></font> <font color="#ff0000"><b>probes</b></font>
 {<pre>    <font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$self</font>=<font color="#4169e1"><b>shift</b></font>;
    <font color="#0000ff"><b>if</b></font> <font color="#0000ff"><b>(</b></font>!<font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"probemode"</font><font color="#0000ff"><b>}</b></font><font color="#0000ff"><b>)</b></font> <font color="#0000ff"><b>{</b></font>
	<font color="#4169e1"><b>die</b></font> <font color="#007400">"Probes is not available when not in probemode"</font>;
    <font color="#0000ff"><b>}</b></font>

    <font color="#0000ff"><b>if</b></font> <font color="#0000ff"><b>(</b></font><font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$q</font>=<font color="#4169e1"><b>shift</b></font><font color="#0000ff"><b>)</b></font> <font color="#0000ff"><b>{</b></font>
	<font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"PROBES"</font><font color="#0000ff"><b>}</b></font>=<font color="#1f32ff">$q</font>;
    <font color="#0000ff"><b>}</b></font>
    <font color="#0000ff"><b>return</b></font> <font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"PROBES"</font><font color="#0000ff"><b>}</b></font>;</pre>}<BR>
<TABLE BORDER="0" WIDTH="100%" CELLSPACING="0">
<TR BGCOLOR="#dcab68"><TD WIDTH="200"><A NAME="CODE11"></A><B>unit_name</B></TD><TD><A HREF="#POD9">description</A></TD><TD WIDTH="30"><A HREF="#TOP">top</A></TD><TD WIDTH="30"><A HREF="#CODE10">prev</A></TD><TD WIDTH="30"><A HREF="#CODE12">next</A></TD></TR></TABLE>
<font color="#0000ff"><b>sub</b></font> <font color="#ff0000"><b>unit_name</b></font>
 {<pre>    <font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$self</font>=<font color="#4169e1"><b>shift</b></font>;
    
    <font color="#0000ff"><b>if</b></font> <font color="#0000ff"><b>(</b></font><font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$q</font>=<font color="#4169e1"><b>shift</b></font><font color="#0000ff"><b>)</b></font> <font color="#0000ff"><b>{</b></font>
	<font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"UNITNAME"</font><font color="#0000ff"><b>}</b></font>=<font color="#1f32ff">$q</font>;
    <font color="#0000ff"><b>}</b></font>
    
    <font color="#0000ff"><b>return</b></font> <font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"UNITNAME"</font><font color="#0000ff"><b>}</b></font>;</pre>}<BR>
<TABLE BORDER="0" WIDTH="100%" CELLSPACING="0">
<TR BGCOLOR="#dcab68"><TD WIDTH="200"><A NAME="CODE12"></A><B>unit_number</B></TD><TD><A HREF="#POD10">description</A></TD><TD WIDTH="30"><A HREF="#TOP">top</A></TD><TD WIDTH="30"><A HREF="#CODE11">prev</A></TD><TD WIDTH="30"><A HREF="#CODE13">next</A></TD></TR></TABLE>
<font color="#0000ff"><b>sub</b></font> <font color="#ff0000"><b>unit_number</b></font>
 {<pre>    <font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$self</font>=<font color="#4169e1"><b>shift</b></font>;
    <font color="#0000ff"><b>return</b></font> <font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"UNITNUMBER"</font><font color="#0000ff"><b>}</b></font>;</pre>}<BR>
<TABLE BORDER="0" WIDTH="100%" CELLSPACING="0">
<TR BGCOLOR="#dcab68"><TD WIDTH="200"><A NAME="CODE13"></A><B>unit_type</B></TD><TD>description</TD><TD WIDTH="30"><A HREF="#TOP">top</A></TD><TD WIDTH="30"><A HREF="#CODE12">prev</A></TD><TD WIDTH="30">next</TD></TR></TABLE>
<font color="#0000ff"><b>sub</b></font> <font color="#ff0000"><b>unit_type</b></font>
 {<pre>    <font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$self</font>=<font color="#4169e1"><b>shift</b></font>;

    <font color="#0000ff"><b>if</b></font> <font color="#0000ff"><b>(</b></font><font color="#0000ff"><b>my</b></font> <font color="#1f32ff">$q</font>=<font color="#4169e1"><b>shift</b></font><font color="#0000ff"><b>)</b></font> <font color="#0000ff"><b>{</b></font>
	<font color="#0000ff"><b>if</b></font> <font color="#0000ff"><b>(</b></font><font color="#1f32ff">$q</font> <font color="#0000ff"><b>eq</b></font> <font color="#007400">"CustomSeq"</font><font color="#0000ff"><b>)</b></font> <font color="#0000ff"><b>{</b></font>
	    <font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"UNITTYPE"</font><font color="#0000ff"><b>}</b></font>=1;
	<font color="#0000ff"><b>}</b></font> <font color="#0000ff"><b>elsif</b></font> <font color="#0000ff"><b>(</b></font><font color="#1f32ff">$q</font> <font color="#0000ff"><b>eq</b></font> <font color="#007400">"genotyping"</font><font color="#0000ff"><b>)</b></font> <font color="#0000ff"><b>{</b></font>
	    <font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"UNITTYPE"</font><font color="#0000ff"><b>}</b></font>=2;
	<font color="#0000ff"><b>}</b></font> <font color="#0000ff"><b>elsif</b></font> <font color="#0000ff"><b>(</b></font><font color="#1f32ff">$q</font> <font color="#0000ff"><b>eq</b></font> <font color="#007400">"expression"</font><font color="#0000ff"><b>)</b></font> <font color="#0000ff"><b>{</b></font>
	    <font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"UNITTYPE"</font><font color="#0000ff"><b>}</b></font>=3;
	<font color="#0000ff"><b>}</b></font> <font color="#0000ff"><b>elsif</b></font> <font color="#0000ff"><b>(</b></font><font color="#1f32ff">$q</font> <font color="#0000ff"><b>eq</b></font> <font color="#007400">"tag/GenFlex"</font><font color="#0000ff"><b>)</b></font> <font color="#0000ff"><b>{</b></font>
	    <font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"UNITTYPE"</font><font color="#0000ff"><b>}</b></font>=7;
	<font color="#0000ff"><b>}</b></font> <font color="#0000ff"><b>else</b></font> <font color="#0000ff"><b>{</b></font>
	    <font color="#4169e1"><b>die</b></font> <font color="#007400">"Not a valid unit type"</font>;
	<font color="#0000ff"><b>}</b></font>
    <font color="#0000ff"><b>}</b></font>

    <font color="#0000ff"><b>if</b></font> <font color="#0000ff"><b>(</b></font><font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"UNITTYPE"</font><font color="#0000ff"><b>}</b></font>==1<font color="#0000ff"><b>)</b></font> <font color="#0000ff"><b>{</b></font>
	<font color="#0000ff"><b>return</b></font> <font color="#007400">"CustomSeq"</font>;
    <font color="#0000ff"><b>}</b></font> <font color="#0000ff"><b>elsif</b></font> <font color="#0000ff"><b>(</b></font><font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"UNITTYPE"</font><font color="#0000ff"><b>}</b></font>==2<font color="#0000ff"><b>)</b></font> <font color="#0000ff"><b>{</b></font>
	<font color="#0000ff"><b>return</b></font> <font color="#007400">"genotyping"</font>;
    <font color="#0000ff"><b>}</b></font> <font color="#0000ff"><b>elsif</b></font> <font color="#0000ff"><b>(</b></font><font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"UNITTYPE"</font><font color="#0000ff"><b>}</b></font>==3<font color="#0000ff"><b>)</b></font> <font color="#0000ff"><b>{</b></font>
	<font color="#0000ff"><b>return</b></font> <font color="#007400">"expression"</font>;
    <font color="#0000ff"><b>}</b></font> <font color="#0000ff"><b>elsif</b></font> <font color="#0000ff"><b>(</b></font><font color="#1f32ff">$self</font>-&gt;<font color="#0000ff"><b>{</b></font><font color="#007400">"UNITTYPE"</font><font color="#0000ff"><b>}</b></font>==7<font color="#0000ff"><b>)</b></font> <font color="#0000ff"><b>{</b></font>
	<font color="#0000ff"><b>return</b></font> <font color="#007400">"tag/GenFlex"</font>;
    <font color="#0000ff"><b>}</b></font></pre>}<BR>
<A NAME="General"></A>
<HR><H2>General documentation</H2>
<TABLE BORDER="0" WIDTH="100%" CELLSPACING="0">
<TR BGCOLOR="#4492df"><TD><A NAME="_pod_COPYRIGHT"><B>COPYRIGHT</A></B></TD>
<TD><A HREF="#TOP">top</A></TD></TR><TR><TD COLSPAN="2"><pre>This module is free software. You can copy or redistribute it under the same terms as Perl itself.<BR></pre>
</TD></TR>
<TR BGCOLOR="#4492df"><TD><A NAME="_pod_AUTHORS"><B>AUTHORS</A></B></TD>
<TD><A HREF="#TOP">top</A></TD></TR><TR><TD COLSPAN="2"><pre>    <BR>Nick James (nick at arabidopsis.info)<BR><BR>David J Craigon (david at arabidopsis.info)<BR><BR>Nottingham Arabidopsis Stock Centre, University of Nottingham.<BR></pre>
</TD></TR>
</TABLE>
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