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<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
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<head><title>NEXUS CLASS LIBRARY: NxsAssumptionsBlock Class</title>
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<td align="left"><span class="classy">NEXUS CLASS LIBRARY</span></td>
<td align="right"><span class="classy"><a href="v2.0index.html">home</a> | <a href="classes.html">classes</a> | <a href="functions.html">functions</a></span></td>
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</td></tr>
</table>
<h1>Class NxsAssumptionsBlock</h1>
<h2>Data Members</h2>
<a href="#charBlockPtr"><span class="quickref">charBlockPtr</span></a>, <a href="#charsets"><span class="quickref">charsets</span></a>, <a href="#def_charset"><span class="quickref">def_charset</span></a>, <a href="#def_exset"><span class="quickref">def_exset</span></a>, <a href="#def_taxset"><span class="quickref">def_taxset</span></a>, <a href="#exsets"><span class="quickref">exsets</span></a>, <a href="#taxa"><span class="quickref">taxa</span></a>, <a href="#taxsets"><span class="quickref">taxsets</span></a>
<h2>Member Functions</h2>
<a href="#ApplyExSet170"><span class="quickref">ApplyExSet</span></a><a href="#GetCharSet74"><span class="quickref">, GetCharSet</span></a><a href="#GetCharSetNames62"><span class="quickref">, GetCharSetNames</span></a><a href="#GetDefCharSetName84"><span class="quickref">, GetDefCharSetName</span></a><a href="#GetDefExSetName160"><span class="quickref">, GetDefExSetName</span></a><a href="#GetDefTaxSetName122"><span class="quickref">, GetDefTaxSetName</span></a><a href="#GetExSet150"><span class="quickref">, GetExSet</span></a><a href="#GetExSetNames138"><span class="quickref">, GetExSetNames</span></a><a href="#GetNumCharSets54"><span class="quickref">, GetNumCharSets</span></a><a href="#GetNumExSets130"><span class="quickref">, GetNumExSets</span></a><a href="#GetNumTaxSets92"><span class="quickref">, GetNumTaxSets</span></a><a href="#GetTaxSet112"><span class="quickref">, GetTaxSet</span></a><a href="#GetTaxSetNames100"><span class="quickref">, GetTaxSetNames</span></a><a href="#HandleCharset180"><span class="quickref">, HandleCharset</span></a><a href="#HandleEndblock226"><span class="quickref">, HandleEndblock</span></a><a href="#HandleExset247"><span class="quickref">, HandleExset</span></a><a href="#HandleTaxset295"><span class="quickref">, HandleTaxset</span></a><a href="#NxsAssumptionsBlock25"><span class="quickref">, NxsAssumptionsBlock</span></a><a href="#NxsAssumptionsBlock37"><span class="quickref">, ~NxsAssumptionsBlock</span></a><a href="#Read340"><span class="quickref">, Read</span></a><a href="#ReplaceTaxaBlockPtr44"><span class="quickref">, ReplaceTaxaBlockPtr</span></a><a href="#Report423"><span class="quickref">, Report</span></a><a href="#Reset405"><span class="quickref">, Reset</span></a><a href="#SetCallback510"><span class="quickref">, SetCallback</span></a><a href="#TaxonLabelToNumber521"><span class="quickref">, TaxonLabelToNumber</span></a>
<h2>Class Description</h2>
<p>
This class handles reading and storage for the <a href="NxsReader.html">NxsReader</a> block ASSUMPTIONS. It overrides the member functions Read and Reset, which are abstract virtual functions in the base class <a href="NxsBlock.html">NxsBlock</a> . Adding a new data member? Don't forget to:<ul> <li>Describe it in the class declaration using a C-style comment.</li> <li>Initialize it (unless it is self-initializing) in the constructor and re-initialize it in the Reset function.</li> <li>Describe the initial state in the constructor documentation.</li> <li>Delete memory allocated to it in both the destructor and Reset function.</li> <li>Report it in some way in the Report function.</li></ul>
<h3>Key to symbols and colors</h3>
<p><span class="public">public</span>, <span class="protected">protected</span>, <span class="private">private</span>, <code>A</code> = abstract, <code>C</code> = constructor, <code>D</code> = destructor, <code>I</code> = inline, <code>S</code> = static, <code>V</code> = virtual, <code>F</code> = friend</p>
<p> </p>
<center>
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<td><span class="groupheading">Data Members</span></td>
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<td> </td>
<td> </td>
<td align="right" valign="top" width="15%"><code> <a href="NxsCharactersBlock.html">NxsCharactersBlock</a></code></td>
<td> </td>
<td align="left" valign="top" width="82%"><code class="private"><a name="charBlockPtr">*charBlockPtr</a></code></td>
</tr>
<tr>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>pointer to the NxsCharactersBlock-derived object to be notified in the event of exset changes</dd></td>
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</td></tr>
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<td> </td>
<td> </td>
<td align="right" valign="top" width="15%"><code> NxsUnsignedSetMap</code></td>
<td> </td>
<td align="left" valign="top" width="82%"><code class="protected"><a name="charsets">charsets</a></code></td>
</tr>
<tr>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>the variable storing charsets</dd></td>
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<td> </td>
<td> </td>
<td align="right" valign="top" width="15%"><code> <a href="NxsString.html">NxsString</a></code></td>
<td> </td>
<td align="left" valign="top" width="82%"><code class="protected"><a name="def_charset">def_charset</a></code></td>
</tr>
<tr>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>the default charset</dd></td>
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<td> </td>
<td> </td>
<td align="right" valign="top" width="15%"><code> <a href="NxsString.html">NxsString</a></code></td>
<td> </td>
<td align="left" valign="top" width="82%"><code class="protected"><a name="def_exset">def_exset</a></code></td>
</tr>
<tr>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>the default exset</dd></td>
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<td> </td>
<td> </td>
<td align="right" valign="top" width="15%"><code> <a href="NxsString.html">NxsString</a></code></td>
<td> </td>
<td align="left" valign="top" width="82%"><code class="protected"><a name="def_taxset">def_taxset</a></code></td>
</tr>
<tr>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>the default taxset</dd></td>
</tr>
</table>
</td></tr>
<tr><td>
<table width="100%" border="0" cellpadding="1">
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<td> </td>
<td> </td>
<td align="right" valign="top" width="15%"><code> NxsUnsignedSetMap</code></td>
<td> </td>
<td align="left" valign="top" width="82%"><code class="protected"><a name="exsets">exsets</a></code></td>
</tr>
<tr>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>the variable storing exsets</dd></td>
</tr>
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</td></tr>
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<td> </td>
<td> </td>
<td align="right" valign="top" width="15%"><code> <a href="NxsTaxaBlock.html">NxsTaxaBlock</a></code></td>
<td> </td>
<td align="left" valign="top" width="82%"><code class="private"><a name="taxa">*taxa</a></code></td>
</tr>
<tr>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>pointer to the NxsTaxaBlock object</dd></td>
</tr>
</table>
</td></tr>
<tr><td>
<table width="100%" border="0" cellpadding="1">
<tr>
<td> </td>
<td> </td>
<td align="right" valign="top" width="15%"><code> NxsUnsignedSetMap</code></td>
<td> </td>
<td align="left" valign="top" width="82%"><code class="protected"><a name="taxsets">taxsets</a></code></td>
</tr>
<tr>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>the variable storing taxsets</dd></td>
</tr>
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</td></tr>
</table>
</center>
<p> </p>
<center>
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<td><span class="groupheading">Member Functions</span></td>
</table>
<table border="1" cellpadding="3" cellspacing="0" width="95%">
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<td> </td>
<td> </td>
<td align="right" valign="top" width="15%"><code>void</code></td>
<td> </td>
<td align="left" valign="top" width="82%"><code class="public"><a name="ApplyExSet170">ApplyExSet</a></code><code>(NxsString nm)</code></td>
</tr>
<tr>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>Applies exclusion set having name 'nm' by calling the ApplyExset method of the <a href="NxsCharactersBlock.html">NxsCharactersBlock</a> or <a href="NxsCharactersBlock.html">NxsCharactersBlock</a>-derived object stored in the charBlockPtr pointer (which will be whichever block last called the NxsAssumptionsBlock::SetCallback method).</dd></td>
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<td> </td>
<td> </td>
<td align="right" valign="top" width="15%"><code>NxsUnsignedSet</code></td>
<td> </td>
<td align="left" valign="top" width="82%"><code class="public"><a name="GetCharSet74">&GetCharSet</a></code><code>(NxsString nm)</code></td>
</tr>
<tr>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>Returns reference to character set having name 'nm'.</dd></td>
</tr>
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</td></tr>
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<td> </td>
<td> </td>
<td align="right" valign="top" width="15%"><code>void</code></td>
<td> </td>
<td align="left" valign="top" width="82%"><code class="public"><a name="GetCharSetNames62">GetCharSetNames</a></code><code>(NxsStringVector &names)</code></td>
</tr>
<tr>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>Erases 'names' vector, then fills 'names' with the names of all stored character sets.</dd></td>
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<td> </td>
<td> </td>
<td align="right" valign="top" width="15%"><code><a href="NxsString.html">NxsString</a></code></td>
<td> </td>
<td align="left" valign="top" width="82%"><code class="public"><a name="GetDefCharSetName84">GetDefCharSetName</a></code><code>()</code></td>
</tr>
<tr>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>Returns name of default character set. If returned string has zero length, then no default character set was defined in the data set.</dd></td>
</tr>
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</td></tr>
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<td> </td>
<td> </td>
<td align="right" valign="top" width="15%"><code><a href="NxsString.html">NxsString</a></code></td>
<td> </td>
<td align="left" valign="top" width="82%"><code class="public"><a name="GetDefExSetName160">GetDefExSetName</a></code><code>()</code></td>
</tr>
<tr>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>Returns name of default exclusion set. If returned string has zero length, then no default exclusion set was defined in the data set.</dd></td>
</tr>
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</td></tr>
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<td> </td>
<td> </td>
<td align="right" valign="top" width="15%"><code><a href="NxsString.html">NxsString</a></code></td>
<td> </td>
<td align="left" valign="top" width="82%"><code class="public"><a name="GetDefTaxSetName122">GetDefTaxSetName</a></code><code>()</code></td>
</tr>
<tr>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>Returns name of default taxon set. If returned string has zero length, then no default taxon set was defined in the data set.</dd></td>
</tr>
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</td></tr>
<tr><td>
<table width="100%" border="0" cellpadding="1">
<tr>
<td> </td>
<td> </td>
<td align="right" valign="top" width="15%"><code>NxsUnsignedSet</code></td>
<td> </td>
<td align="left" valign="top" width="82%"><code class="public"><a name="GetExSet150">&GetExSet</a></code><code>(NxsString nm)</code></td>
</tr>
<tr>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>Returns reference to exclusion set having name 'nm'.</dd></td>
</tr>
</table>
</td></tr>
<tr><td>
<table width="100%" border="0" cellpadding="1">
<tr>
<td> </td>
<td> </td>
<td align="right" valign="top" width="15%"><code>void</code></td>
<td> </td>
<td align="left" valign="top" width="82%"><code class="public"><a name="GetExSetNames138">GetExSetNames</a></code><code>(NxsStringVector &names)</code></td>
</tr>
<tr>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>Erases names, then fills names with the names of all stored exclusion sets.</dd></td>
</tr>
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</td></tr>
<tr><td>
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<td> </td>
<td> </td>
<td align="right" valign="top" width="15%"><code>int</code></td>
<td> </td>
<td align="left" valign="top" width="82%"><code class="public"><a name="GetNumCharSets54">GetNumCharSets</a></code><code>()</code></td>
</tr>
<tr>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>Returns the number of character sets stored.</dd></td>
</tr>
</table>
</td></tr>
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<tr>
<td> </td>
<td> </td>
<td align="right" valign="top" width="15%"><code>int</code></td>
<td> </td>
<td align="left" valign="top" width="82%"><code class="public"><a name="GetNumExSets130">GetNumExSets</a></code><code>()</code></td>
</tr>
<tr>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>Returns the number of exclusion sets stored.</dd></td>
</tr>
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<table width="100%" border="0" cellpadding="1">
<tr>
<td> </td>
<td> </td>
<td align="right" valign="top" width="15%"><code>int</code></td>
<td> </td>
<td align="left" valign="top" width="82%"><code class="public"><a name="GetNumTaxSets92">GetNumTaxSets</a></code><code>()</code></td>
</tr>
<tr>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>Returns the number of taxon sets stored.</dd></td>
</tr>
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<td> </td>
<td> </td>
<td align="right" valign="top" width="15%"><code>NxsUnsignedSet</code></td>
<td> </td>
<td align="left" valign="top" width="82%"><code class="public"><a name="GetTaxSet112">&GetTaxSet</a></code><code>(NxsString nm)</code></td>
</tr>
<tr>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>Returns reference to taxon set having name 'nm'.</dd></td>
</tr>
</table>
</td></tr>
<tr><td>
<table width="100%" border="0" cellpadding="1">
<tr>
<td> </td>
<td> </td>
<td align="right" valign="top" width="15%"><code>void</code></td>
<td> </td>
<td align="left" valign="top" width="82%"><code class="public"><a name="GetTaxSetNames100">GetTaxSetNames</a></code><code>(NxsStringVector &names)</code></td>
</tr>
<tr>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>Erases 'names' vector, then fills 'names' with the names of all stored taxon sets.</dd></td>
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</td></tr>
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<td> </td>
<td> </td>
<td align="right" valign="top" width="15%"><code>void</code></td>
<td> </td>
<td align="left" valign="top" width="82%"><code class="public"><a name="HandleCharset180">HandleCharset</a></code><code>(NxsToken &token)</code></td>
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<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>Reads and stores information contained in the command CHARSET within an ASSUMPTIONS block.</dd></td>
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<td> </td>
<td> </td>
<td align="right" valign="top" width="15%"><code>void</code></td>
<td> </td>
<td align="left" valign="top" width="82%"><code class="public"><a name="HandleEndblock226">HandleEndblock</a></code><code>(NxsToken &token)</code></td>
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<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>Called when the END or ENDBLOCK command needs to be parsed from within the ASSUMPTIONS block. Basically just checks to make sure the next token in the data file is a semicolon.</dd></td>
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<td> </td>
<td> </td>
<td align="right" valign="top" width="15%"><code>void</code></td>
<td> </td>
<td align="left" valign="top" width="82%"><code class="public"><a name="HandleExset247">HandleExset</a></code><code>(NxsToken &token)</code></td>
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<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>Reads and stores information contained in the command EXSET within an ASSUMPTIONS block. If EXSET keyword is followed by an asterisk, last read <a href="NxsCharactersBlock.html">NxsCharactersBlock</a> or <a href="NxsCharactersBlock.html">NxsCharactersBlock</a>-derived object is notified of the characters to be excluded (its ApplyExset function is called).</dd></td>
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<td> </td>
<td> </td>
<td align="right" valign="top" width="15%"><code>void</code></td>
<td> </td>
<td align="left" valign="top" width="82%"><code class="public"><a name="HandleTaxset295">HandleTaxset</a></code><code>(NxsToken &token)</code></td>
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<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>Reads and stores information contained in the command TAXSET within an ASSUMPTIONS block.</dd></td>
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</td></tr>
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<td>C</td>
<td> </td>
<td align="right" valign="top" width="15%"><code></code></td>
<td> </td>
<td align="left" valign="top" width="82%"><code class="public"><a name="NxsAssumptionsBlock25">NxsAssumptionsBlock</a></code><code>(NxsTaxaBlock *t)</code></td>
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<tr>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>Sets id = "ASSUMPTIONS", charBlockPtr = NULL, and taxa = t. Assumes taxa is non-NULL.</dd></td>
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</td></tr>
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<tr>
<td>D</td>
<td> </td>
<td align="right" valign="top" width="15%"><code></code></td>
<td> </td>
<td align="left" valign="top" width="82%"><code class="public"><a name="NxsAssumptionsBlock37">~NxsAssumptionsBlock</a></code><code>()</code></td>
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<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>Nothing needs to be done in the destructor.</dd></td>
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</td></tr>
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<tr>
<td>V</td>
<td> </td>
<td align="right" valign="top" width="15%"><code>void</code></td>
<td> </td>
<td align="left" valign="top" width="82%"><code class="public"><a name="Read340">Read</a></code><code>(NxsToken &token)</code></td>
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<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>This function provides the ability to read everything following the block name (which is read by the <a href="NxsReader.html">NxsReader</a> object) to the end or ENDBLOCK statement. Characters are read from the input stream in. Overrides the pure virtual function in the base class.</dd></td>
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</td></tr>
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<tr>
<td> </td>
<td> </td>
<td align="right" valign="top" width="15%"><code>void</code></td>
<td> </td>
<td align="left" valign="top" width="82%"><code class="public"><a name="ReplaceTaxaBlockPtr44">ReplaceTaxaBlockPtr</a></code><code>(NxsTaxaBlock *tb)</code></td>
</tr>
<tr>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>Makes data member taxa point to 'tb'. Assumes tb is non-NULL.</dd></td>
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</td></tr>
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<tr>
<td>V</td>
<td> </td>
<td align="right" valign="top" width="15%"><code>void</code></td>
<td> </td>
<td align="left" valign="top" width="82%"><code class="public"><a name="Report423">Report</a></code><code>(ostream &out)</code></td>
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<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>This function outputs a brief report of the contents of this ASSUMPTIONS block. Overrides the pure virtual function in the base class.</dd></td>
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<tr>
<td>V</td>
<td> </td>
<td align="right" valign="top" width="15%"><code>void</code></td>
<td> </td>
<td align="left" valign="top" width="82%"><code class="public"><a name="Reset405">Reset</a></code><code>()</code></td>
</tr>
<tr>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>Prepares for reading a new ASSUMPTIONS block. Overrides the pure virtual function in the base class.</dd></td>
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</td></tr>
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<tr>
<td> </td>
<td> </td>
<td align="right" valign="top" width="15%"><code>void</code></td>
<td> </td>
<td align="left" valign="top" width="82%"><code class="public"><a name="SetCallback510">SetCallback</a></code><code>(NxsCharactersBlock *p)</code></td>
</tr>
<tr>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>A CHARACTERS, DATA, or ALLELES block can call this function to specify that it is to receive notification when the current taxon or character set changes (e.g., an "EXSET *" command is read or a program requests that one of the predefined taxon sets, character sets, or exsets be applied). Normally, a <a href="NxsCharactersBlock.html">NxsCharactersBlock</a>-derived object calls this function upon entering its MATRIX command, since when that happens it becomes the primary data-containing block.</dd></td>
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</table>
</td></tr>
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<tr>
<td>V</td>
<td> </td>
<td align="right" valign="top" width="15%"><code>unsigned</code></td>
<td> </td>
<td align="left" valign="top" width="82%"><code class="public"><a name="TaxonLabelToNumber521">TaxonLabelToNumber</a></code><code>(NxsString s)</code></td>
</tr>
<tr>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>Converts a taxon label to a number corresponding to the taxon's position within the list maintained by the <a href="NxsTaxaBlock.html">NxsTaxaBlock</a> object. This method overrides the virtual function of the same name in the <a href="NxsBlock.html">NxsBlock</a> base class. If s is not a valid taxon label, returns the value 0.</dd></td>
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</td></tr>
</table>
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