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<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
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<head><title>NEXUS CLASS LIBRARY: NxsReader 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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</table>
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<h1>Class NxsReader</h1>
<h2>Enums</h2>
<a href="#NxsTolerateFlags"><span class="quickref">NxsTolerateFlags</span></a>
<h2>Data Members</h2>
<a href="#blockList"><span class="quickref">blockList</span></a>, <a href="#currBlock"><span class="quickref">currBlock</span></a>
<h2>Member Functions</h2>
<a href="#Add44"><span class="quickref">Add</span></a><a href="#BlockListEmpty125"><span class="quickref">, BlockListEmpty</span></a><a href="#DebugReportBlock142"><span class="quickref">, DebugReportBlock</span></a><a href="#Detach158"><span class="quickref">, Detach</span></a><a href="#EnteringBlock204"><span class="quickref">, EnteringBlock</span></a><a href="#Execute237"><span class="quickref">, Execute</span></a><a href="#ExecuteStarting425"><span class="quickref">, ExecuteStarting</span></a><a href="#ExecuteStopping436"><span class="quickref">, ExecuteStopping</span></a><a href="#ExitingBlock217"><span class="quickref">, ExitingBlock</span></a><a href="#NCLCopyrightNotice396"><span class="quickref">, NCLCopyrightNotice</span></a><a href="#NCLHomePageURL404"><span class="quickref">, NCLHomePageURL</span></a><a href="#NCLNameAndVersion413"><span class="quickref">, NCLNameAndVersion</span></a><a href="#NexusError444"><span class="quickref">, NexusError</span></a><a href="#NxsReader24"><span class="quickref">, NxsReader</span></a><a href="#NxsReader33"><span class="quickref">, ~NxsReader</span></a><a href="#OutputComment460"><span class="quickref">, OutputComment</span></a><a href="#PositionInBlockList69"><span class="quickref">, PositionInBlockList</span></a><a href="#Reassign94"><span class="quickref">, Reassign</span></a><a href="#SkippingBlock472"><span class="quickref">, SkippingBlock</span></a><a href="#SkippingDisabledBlock485"><span class="quickref">, SkippingDisabledBlock</span></a>
<h2>Class Description</h2>
<p>
This is the class that orchestrates the reading of a NEXUS data file. An object of this class should be created, and objects of any block classes that are expected to be needed should be added to <span class="variablename">blockList</span> using the Add member function. The Execute member function is then called, which reads the data file until encountering a block name, at which point the correct block is looked up in <span class="variablename">blockList</span> and that object's Read method called.
<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>
<table border="5" cellpadding="1" cellspacing="0" width="95%">
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<td><span class="groupheading">Enums</span></td>
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<td align="left" width="25%"><code class="public"><a name="NxsTolerateFlags">enum NxsTolerateFlags</a></code></td>
<td></td>
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<td width="15%"> </td>
<td align="left" colspan="2"><code>allowMissingInEquate = 0x0001</code></td>
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<td width="15%"> </td>
<td width="10%"> </td>
<td>if set, equate symbols are allowed for missing data symbol</td>
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<td width="15%"> </td>
<td align="left" colspan="2"><code>allowPunctuationInNames = 0x0002</code></td>
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<td width="15%"> </td>
<td width="10%"> </td>
<td>if set, some punctuation is allowed within tokens representing labels for taxa, characters, and sets</td>
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<p> </p>
<center>
<table border="5" cellpadding="1" cellspacing="0" width="95%">
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<td><span class="groupheading">Data Members</span></td>
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<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> <a href="NxsBlock.html">NxsBlock</a></code></td>
<td> </td>
<td align="left" valign="top" width="82%"><code class="protected"><a name="blockList">*blockList</a></code></td>
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<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>pointer to first block in list of blocks</dd></td>
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</td></tr>
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<table width="100%" border="0" cellpadding="1">
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<td> </td>
<td> </td>
<td align="right" valign="top" width="15%"><code> <a href="NxsBlock.html">NxsBlock</a></code></td>
<td> </td>
<td align="left" valign="top" width="82%"><code class="protected"><a name="currBlock">*currBlock</a></code></td>
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<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>pointer to current block in list of blocks</dd></td>
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<p> </p>
<center>
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<td><span class="groupheading">Member Functions</span></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="Add44">Add</a></code><code>(NxsBlock *newBlock)</code></td>
</tr>
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<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>Adds <span class="variablename">newBlock</span> to the end of the list of <a href="NxsBlock.html">NxsBlock</a> objects growing from <span class="variablename">blockList</span>. If <span class="variablename">blockList</span> points to NULL, this function sets <span class="variablename">blockList</span> to point to <span class="variablename">newBlock</span>. Calls SetNexus method of <span class="variablename">newBlock</span> to inform <span class="variablename">newBlock</span> of the NxsReader object that now owns it. This is useful when the <span class="variablename">newBlock</span> object needs to communicate with the outside world through the NxsReader object, such as when it issues progress reports as it is reading the contents of its block.</dd></td>
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<td> </td>
<td> </td>
<td align="right" valign="top" width="15%"><code>bool</code></td>
<td> </td>
<td align="left" valign="top" width="82%"><code class="public"><a name="BlockListEmpty125">BlockListEmpty</a></code><code>()</code></td>
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<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>If <span class="variablename">blockList</span> data member still equals NULL, returns true; otherwise, returns false. <span class="variablename">blockList</span> will not be equal to NULL if the Add function has been called to add a block object to the list.</dd></td>
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</td></tr>
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<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="DebugReportBlock142">DebugReportBlock</a></code><code>(NxsBlock &nexusBlock)</code></td>
</tr>
<tr>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>This function was created for purposes of debugging a new <a href="NxsBlock.html">NxsBlock</a>. This version does nothing; to create an active DebugReportBlock function, override this version in the derived class and call the Report function of <span class="variablename">nexusBlock</span>. This function is called whenever the main NxsReader Execute function encounters the [&spillall] command comment between blocks in the data file. The Execute function goes through all blocks and passes them, in turn, to this DebugReportBlock function so that their contents are displayed. Placing the [&spillall] command comment between different versions of a block allows multiple blocks of the same type to be tested using one long data file. Say you are interested in testing whether the normal, transpose, and interleave format of a matrix can all be read correctly. If you put three versions of the block in the data file one after the other, the second one will wipe out the first, and the third one will wipe out the second, unless you have a way to report on each one before the next one is read. This function provides that ability.</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="Detach158">Detach</a></code><code>(NxsBlock *oldBlock)</code></td>
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<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>Detaches <span class="variablename">oldBlock</span> from the list of <a href="NxsBlock.html">NxsBlock</a> objects growing from <span class="variablename">blockList</span>. If <span class="variablename">blockList</span> itself points to <span class="variablename">oldBlock</span>, this function sets <span class="variablename">blockList</span> to point to `oldBlock->next'. Note: the object pointed to by <span class="variablename">oldBlock</span> is not deleted, it is simply detached from the linked list. No harm is done in Detaching a block pointer that has already been detached previously; if <span class="variablename">oldBlock</span> is not found in the block list, Detach simply returns quietly. If <span class="variablename">oldBlock</span> is found, its SetNexus object is called to set the NxsReader pointer to NULL, indicating that it is no longer owned by (i.e., attached to) a NxsReader object.</dd></td>
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<td>V</td>
<td> </td>
<td align="right" valign="top" width="15%"><code>bool</code></td>
<td> </td>
<td align="left" valign="top" width="82%"><code class="public"><a name="EnteringBlock204">EnteringBlock</a></code><code>(NxsString blockName)</code></td>
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<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>Called by the NxsReader object when a block named <span class="variablename">blockName</span> is entered. Allows derived class overriding this function to notify user of progress in parsing the NEXUS file. Also gives program the opportunity to ask user if it is ok to purge data currently contained in this block. If user is asked whether existing data should be deleted, and the answer comes back no, then then the overrided function should return false, otherwise it should return true. This (base class) version always returns true.</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="Execute237">Execute</a></code><code>(NxsToken &token, bool notifyStartStop)</code></td>
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<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>Reads the NxsReader data file from the input stream provided by <span class="variablename">token</span>. This function is responsible for reading through the name of a each block. Once it has read a block name, it searches <span class="variablename">blockList</span> for a block object to handle reading the remainder of the block's contents. The block object is responsible for reading the END or ENDBLOCK command as well as the trailing semicolon. This function also handles reading comments that are outside of blocks, as well as the initial "#NEXUS" keyword. The <span class="variablename">notifyStartStop</span> argument is provided in case you do not wish the ExecuteStart and ExecuteStop functions to be called. These functions are primarily used for creating and destroying a dialog box to show progress, and nested Execute calls can thus cause problems (e.g., a dialog box is destroyed when the inner Execute calls ExecuteStop and the outer Execute still expects the dialog box to be available). Specifying <span class="variablename">notifyStartStop</span> false for all the nested Execute calls thus allows the outermost Execute call to control creation and destruction of the dialog box.</dd></td>
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<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="ExecuteStarting425">ExecuteStarting</a></code><code>()</code></td>
</tr>
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<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>Called just after Execute member function reads the opening "#NEXUS" token in a NEXUS data file. Override this virtual base class function if your application needs to do anything at this point in the execution of a NEXUS data file (e.g. good opportunity to pop up a dialog box showing progress). Be sure to call the Execute function with the <span class="variablename">notifyStartStop</span> argument set to true, otherwise ExecuteStarting will not be called.</dd></td>
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<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="ExecuteStopping436">ExecuteStopping</a></code><code>()</code></td>
</tr>
<tr>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>Called when Execute member function encounters the end of the NEXUS data file, or the special comment [&LEAVE] is found between NEXUS blocks. Override this virtual base class function if your application needs to do anything at this point in the execution of a NEXUS data file (e.g. good opportunity to hide or destroy a dialog box showing progress). Be sure to call the Execute function with the <span class="variablename">notifyStartStop</span> argument set to true, otherwise ExecuteStopping will not be called.</dd></td>
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</td></tr>
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<table width="100%" border="0" cellpadding="1">
<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="ExitingBlock217">ExitingBlock</a></code><code>(NxsString blockName)</code></td>
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<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>Called by the NxsReader object when a block named <span class="variablename">blockName</span> is being exited. Allows derived class overriding this function to notify user of progress in parsing the NEXUS file.</dd></td>
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<table width="100%" border="0" cellpadding="1">
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<td> </td>
<td> </td>
<td align="right" valign="top" width="15%"><code>char</code></td>
<td> </td>
<td align="left" valign="top" width="82%"><code class="public"><a name="NCLCopyrightNotice396">*NCLCopyrightNotice</a></code><code>()</code></td>
</tr>
<tr>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>Returns a string containing the copyright notice for the NxsReader Class Library, useful for reporting the use of this library by programs that interact with the user.</dd></td>
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<table width="100%" border="0" cellpadding="1">
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<td> </td>
<td> </td>
<td align="right" valign="top" width="15%"><code>char</code></td>
<td> </td>
<td align="left" valign="top" width="82%"><code class="public"><a name="NCLHomePageURL404">*NCLHomePageURL</a></code><code>()</code></td>
</tr>
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<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>Returns a string containing the URL for the NxsReader Class Library internet home page.</dd></td>
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<table width="100%" border="0" cellpadding="1">
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<td> </td>
<td> </td>
<td align="right" valign="top" width="15%"><code>char</code></td>
<td> </td>
<td align="left" valign="top" width="82%"><code class="public"><a name="NCLNameAndVersion413">*NCLNameAndVersion</a></code><code>()</code></td>
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<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>Returns a string containing the name and current version of the NxsReader Class Library, useful for reporting the use of this library by programs that interact with the user.</dd></td>
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<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="NexusError444">NexusError</a></code><code>(NxsString msg, file_pos pos, long line, long col)</code></td>
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<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>Called when an error is encountered in a NEXUS file. Allows program to give user details of the error as well as the precise location of the error.</dd></td>
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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="NxsReader24">NxsReader</a></code><code>()</code></td>
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<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>Initializes both <span class="variablename">blockList</span> and <span class="variablename">currBlock</span> to NULL.</dd></td>
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<tr><td>
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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="NxsReader33">~NxsReader</a></code><code>()</code></td>
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<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>Nothing to be done.</dd></td>
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</td></tr>
<tr><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="OutputComment460">OutputComment</a></code><code>(const NxsString &comment)</code></td>
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<tr>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>This function may be used to report progess while reading through a file. For example, the NxsAllelesBlock class uses this function to report the name of the population it is currently reading so the user doesn't think the program has hung on large data sets.</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>unsigned</code></td>
<td> </td>
<td align="left" valign="top" width="82%"><code class="public"><a name="PositionInBlockList69">PositionInBlockList</a></code><code>(NxsBlock *b)</code></td>
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<tr>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>Returns position (first block has position 0) of block <span class="variablename">b</span> in <span class="variablename">blockList</span>. Returns UINT_MAX if <span class="variablename">b</span> cannot be found in <span class="variablename">blockList</span>.</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="Reassign94">Reassign</a></code><code>(NxsBlock *oldb, NxsBlock *newb)</code></td>
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<tr>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>Reassign should be called if a block (<span class="variablename">oldb</span>) is about to be deleted (perhaps to make way for new data). Create the new block (<span class="variablename">newb</span>) before deleting <span class="variablename">oldb</span>, then call Reassign to replace <span class="variablename">oldb</span> in <span class="variablename">blockList</span> with <span class="variablename">newb</span>. Assumes <span class="variablename">oldb</span> exists and is in <span class="variablename">blockList</span>.</dd></td>
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</td></tr>
<tr><td>
<table width="100%" border="0" cellpadding="1">
<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="SkippingBlock472">SkippingBlock</a></code><code>(NxsString blockName)</code></td>
</tr>
<tr>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>This function is called when an unknown block named <span class="variablename">blockName</span> is about to be skipped. Override this pure virtual function to provide an indication of progress as the NEXUS file is being read.</dd></td>
</tr>
</table>
</td></tr>
<tr><td>
<table width="100%" border="0" cellpadding="1">
<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="SkippingDisabledBlock485">SkippingDisabledBlock</a></code><code>(NxsString blockName)</code></td>
</tr>
<tr>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>This function is called when a disabled block named <span class="variablename">blockName</span> is encountered in a NEXUS data file being executed. Override this pure virtual function to handle this event in an appropriate manner. For example, the program may wish to inform the user that a data block was encountered in what is supposed to be a tree file.</dd></td>
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</table>
</td></tr>
</table>
</center>
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