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<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head><title>NEXUS CLASS LIBRARY: NxsDistancesBlock Class</title>
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<table border="1" width="100%">
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<table border="0" width="100%">
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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>
</td></tr>
</table>
<h1>Class NxsDistancesBlock</h1>
<h2>Enums</h2>
<a href="#NxsDistancesBlockEnum"><span class="quickref">NxsDistancesBlockEnum</span></a>
<h2>Data Members</h2>
<a href="#diagonal"><span class="quickref">diagonal</span></a>, <a href="#interleave"><span class="quickref">interleave</span></a>, <a href="#labels"><span class="quickref">labels</span></a>, <a href="#matrix"><span class="quickref">matrix</span></a>, <a href="#missing"><span class="quickref">missing</span></a>, <a href="#nchar"><span class="quickref">nchar</span></a>, <a href="#newtaxa"><span class="quickref">newtaxa</span></a>, <a href="#ntax"><span class="quickref">ntax</span></a>, <a href="#taxa"><span class="quickref">taxa</span></a>, <a href="#taxonPos"><span class="quickref">taxonPos</span></a>, <a href="#triangle"><span class="quickref">triangle</span></a>
<h2>Member Functions</h2>
<a href="#GetDistance758"><span class="quickref">GetDistance</span></a><a href="#GetMissingSymbol774"><span class="quickref">, GetMissingSymbol</span></a><a href="#GetNchar749"><span class="quickref">, GetNchar</span></a><a href="#GetNtax741"><span class="quickref">, GetNtax</span></a><a href="#GetTriangle782"><span class="quickref">, GetTriangle</span></a><a href="#HandleDimensionsCommand61"><span class="quickref">, HandleDimensionsCommand</span></a><a href="#HandleFormatCommand134"><span class="quickref">, HandleFormatCommand</span></a><a href="#HandleMatrixCommand404"><span class="quickref">, HandleMatrixCommand</span></a><a href="#HandleNextPass253"><span class="quickref">, HandleNextPass</span></a><a href="#HandleTaxlabelsCommand478"><span class="quickref">, HandleTaxlabelsCommand</span></a><a href="#IsDiagonal814"><span class="quickref">, IsDiagonal</span></a><a href="#IsInterleave822"><span class="quickref">, IsInterleave</span></a><a href="#IsLabels830"><span class="quickref">, IsLabels</span></a><a href="#IsLowerTriangular806"><span class="quickref">, IsLowerTriangular</span></a><a href="#IsMissing839"><span class="quickref">, IsMissing</span></a><a href="#IsRectangular790"><span class="quickref">, IsRectangular</span></a><a href="#IsUpperTriangular798"><span class="quickref">, IsUpperTriangular</span></a><a href="#NxsDistancesBlock27"><span class="quickref">, NxsDistancesBlock</span></a><a href="#NxsDistancesBlock49"><span class="quickref">, ~NxsDistancesBlock</span></a><a href="#Read528"><span class="quickref">, Read</span></a><a href="#Report627"><span class="quickref">, Report</span></a><a href="#Reset707"><span class="quickref">, Reset</span></a><a href="#SetDistance856"><span class="quickref">, SetDistance</span></a><a href="#SetMissing875"><span class="quickref">, SetMissing</span></a><a href="#SetNchar892"><span class="quickref">, SetNchar</span></a>
<h2>Class Description</h2>
<p>
This class handles reading and storage for the NEXUS block DISTANCES. It overrides the member functions Read and Reset, which are abstract virtual functions in the base class <a href="NxsBlock.html">NxsBlock</a> . Below is a table showing the correspondence between the elements of a DISTANCES block and the variables and member functions that can be used to access each piece of information stored.<pre> NEXUS command Command attribute Data Members Member Functions
------------------------------------------------------------------------
DIMENSIONS NEWTAXA newtaxa
NTAX ntax GetNtax
NCHAR nchar GetNchar
FORMAT TRIANGLE triangle GetTriangle
IsUpperTriangular
IsLowerTriangular
IsRectangular
[NO]DIAGONAL diagonal IsDiagonal
[NO]LABELS labels IsLabels
MISSING missing GetMissingSymbol
INTERLEAVE interleave IsInterleave
TAXLABELS (stored in the (access through
<a href="NxsTaxaBlock.html">NxsTaxaBlock</a> data member taxa)
object)
MATRIX matrix GetDistance
IsMissing
SetMissing
SetDistance
------------------------------------------------------------------------
</pre>
<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">Enums</span></td>
</tr>
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<td align="left" width="25%"><code class="public"><a name="NxsDistancesBlockEnum">enum NxsDistancesBlockEnum</a></code></td>
<td></td>
</tr>
</table>
</td></tr>
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<td width="15%"> </td>
<td align="left" colspan="2"><code>upper = 1</code></td>
</tr>
<tr>
<td width="15%"> </td>
<td width="10%"> </td>
<td>matrix is upper-triangular</td>
</tr>
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</td></tr>
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<td width="15%"> </td>
<td align="left" colspan="2"><code>lower = 2</code></td>
</tr>
<tr>
<td width="15%"> </td>
<td width="10%"> </td>
<td>matrix is lower-triangular</td>
</tr>
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<td width="15%"> </td>
<td align="left" colspan="2"><code>both = 3</code></td>
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<td width="15%"> </td>
<td width="10%"> </td>
<td>matrix is rectangular</td>
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</td></tr>
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</td></tr>
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</center>
<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> bool</code></td>
<td> </td>
<td align="left" valign="top" width="82%"><code class="private"><a name="diagonal">diagonal</a></code></td>
</tr>
<tr>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>true if diagonal elements provided when reading in DISTANCES block</dd></td>
</tr>
</table>
</td></tr>
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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="private"><a name="interleave">interleave</a></code></td>
</tr>
<tr>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>true if interleave format used when reading in DISTANCES block</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> bool</code></td>
<td> </td>
<td align="left" valign="top" width="82%"><code class="private"><a name="labels">labels</a></code></td>
</tr>
<tr>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>true if taxon labels were provided when reading in DISTANCES block</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> <a href="NxsDistanceDatum.html">NxsDistanceDatum</a></code></td>
<td> </td>
<td align="left" valign="top" width="82%"><code class="private"><a name="matrix">**matrix</a></code></td>
</tr>
<tr>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>the structure used for storing the pairwise distance matrix</dd></td>
</tr>
</table>
</td></tr>
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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="private"><a name="missing">missing</a></code></td>
</tr>
<tr>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>the symbol used to represent missing data (e.g. '?')</dd></td>
</tr>
</table>
</td></tr>
<tr><td>
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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="private"><a name="nchar">nchar</a></code></td>
</tr>
<tr>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>the number of characters used in generating the pairwise distances</dd></td>
</tr>
</table>
</td></tr>
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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="private"><a name="newtaxa">newtaxa</a></code></td>
</tr>
<tr>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>true if new taxa were named in this DISTANCES block</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> unsigned</code></td>
<td> </td>
<td align="left" valign="top" width="82%"><code class="private"><a name="ntax">ntax</a></code></td>
</tr>
<tr>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>number of taxa (determines dimensions of the matrix)</dd></td>
</tr>
</table>
</td></tr>
<tr><td>
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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 NxsTaxaBlock object that stores the taxon labels</dd></td>
</tr>
</table>
</td></tr>
<tr><td>
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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="private"><a name="taxonPos">*taxonPos</a></code></td>
</tr>
<tr>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>array holding 0-offset index into the NxsTaxaBlock list of taxon labels (used to ensure that order of taxa is same for each interleaved block)</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> int</code></td>
<td> </td>
<td align="left" valign="top" width="82%"><code class="private"><a name="triangle">triangle</a></code></td>
</tr>
<tr>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>indicates whether matrix is upper triangular, lower triangular, or rectangular, taking on one of the elements of the NxsDistancesBlockEnum enumeration</dd></td>
</tr>
</table>
</td></tr>
</table>
</center>
<p> </p>
<center>
<table border="5" cellpadding="1" cellspacing="0" width="95%">
<tr bgcolor="#CCCCFF">
<td><span class="groupheading">Member Functions</span></td>
</table>
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<td> </td>
<td> </td>
<td align="right" valign="top" width="15%"><code>double</code></td>
<td> </td>
<td align="left" valign="top" width="82%"><code class="public"><a name="GetDistance758">GetDistance</a></code><code>(unsigned i, unsigned j)</code></td>
</tr>
<tr>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>Returns the value of the (<span class="variablename">i</span>, <span class="variablename">j</span>)th element of <span class="variablename">matrix</span>. Assumes <span class="variablename">i</span> and <span class="variablename">j</span> are both in the range [0..<span class="variablename">ntax</span>) and the distance stored at `matrix[i][j]' is not missing. Also assumes <span class="variablename">matrix</span> is not NULL.</dd></td>
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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="GetMissingSymbol774">GetMissingSymbol</a></code><code>()</code></td>
</tr>
<tr>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>Returns the value of <span class="variablename">missing</span>.</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>unsigned</code></td>
<td> </td>
<td align="left" valign="top" width="82%"><code class="public"><a name="GetNchar749">GetNchar</a></code><code>()</code></td>
</tr>
<tr>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>Returns the value of nchar.</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>unsigned</code></td>
<td> </td>
<td align="left" valign="top" width="82%"><code class="public"><a name="GetNtax741">GetNtax</a></code><code>()</code></td>
</tr>
<tr>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>Returns the value of ntax.</dd></td>
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</td></tr>
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<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="GetTriangle782">GetTriangle</a></code><code>()</code></td>
</tr>
<tr>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>Returns the value of <span class="variablename">triangle</span>.</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="HandleDimensionsCommand61">HandleDimensionsCommand</a></code><code>(NxsToken &token)</code></td>
</tr>
<tr>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>Called when DIMENSIONS command needs to be parsed from within the DISTANCES block. Deals with everything after the token DIMENSIONS up to and including the semicolon that terminates the DIMENSIONS command.</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="HandleFormatCommand134">HandleFormatCommand</a></code><code>(NxsToken &token)</code></td>
</tr>
<tr>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>Called when FORMAT command needs to be parsed from within the DISTANCES block. Deals with everything after the token FORMAT up to and including the semicolon that terminates the FORMAT command.</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="HandleMatrixCommand404">HandleMatrixCommand</a></code><code>(NxsToken &token)</code></td>
</tr>
<tr>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>Called when MATRIX command needs to be parsed from within the DISTANCES block. Deals with everything after the token MATRIX up to and including the semicolon that terminates the MATRIX command.</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>bool</code></td>
<td> </td>
<td align="left" valign="top" width="82%"><code class="public"><a name="HandleNextPass253">HandleNextPass</a></code><code>(NxsToken &token, unsigned &offset)</code></td>
</tr>
<tr>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>Called from within HandleMatrix, this function is used to deal with interleaved matrices. It is called once for each pass through the taxa. The local variable <span class="variablename">jmax</span> records the number of columns read in the current interleaved page and is used to determine the offset used for j in subsequent pages.</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="HandleTaxlabelsCommand478">HandleTaxlabelsCommand</a></code><code>(NxsToken &token)</code></td>
</tr>
<tr>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>Called when TAXLABELS command needs to be parsed from within the DISTANCES block. Deals with everything after the token TAXLABELS up to and including the semicolon that terminates the TAXLABELS command.</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>bool</code></td>
<td> </td>
<td align="left" valign="top" width="82%"><code class="public"><a name="IsDiagonal814">IsDiagonal</a></code><code>()</code></td>
</tr>
<tr>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>Returns the value of diagonal.</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>bool</code></td>
<td> </td>
<td align="left" valign="top" width="82%"><code class="public"><a name="IsInterleave822">IsInterleave</a></code><code>()</code></td>
</tr>
<tr>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>Returns the value of interleave.</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>bool</code></td>
<td> </td>
<td align="left" valign="top" width="82%"><code class="public"><a name="IsLabels830">IsLabels</a></code><code>()</code></td>
</tr>
<tr>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>Returns the value of labels.</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>bool</code></td>
<td> </td>
<td align="left" valign="top" width="82%"><code class="public"><a name="IsLowerTriangular806">IsLowerTriangular</a></code><code>()</code></td>
</tr>
<tr>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>Returns true if the value of triangle is NxsDistancesBlockEnum(lower), false otherwise.</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>bool</code></td>
<td> </td>
<td align="left" valign="top" width="82%"><code class="public"><a name="IsMissing839">IsMissing</a></code><code>(unsigned i, unsigned j)</code></td>
</tr>
<tr>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>Returns true if the (<span class="variablename">i</span>,<span class="variablename">j</span>)th distance is missing. Assumes <span class="variablename">i</span> and <span class="variablename">j</span> are both in the range [0..<span class="variablename">ntax</span>) and <span class="variablename">matrix</span> is not NULL.</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>bool</code></td>
<td> </td>
<td align="left" valign="top" width="82%"><code class="public"><a name="IsRectangular790">IsRectangular</a></code><code>()</code></td>
</tr>
<tr>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>Returns true if the value of <span class="variablename">triangle</span> is NxsDistancesBlockEnum(both), false otherwise.</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>bool</code></td>
<td> </td>
<td align="left" valign="top" width="82%"><code class="public"><a name="IsUpperTriangular798">IsUpperTriangular</a></code><code>()</code></td>
</tr>
<tr>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>Returns true if the value of triangle is NxsDistancesBlockEnum(upper), false otherwise.</dd></td>
</tr>
</table>
</td></tr>
<tr><td>
<table width="100%" border="0" cellpadding="1">
<tr>
<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="NxsDistancesBlock27">NxsDistancesBlock</a></code><code>(NxsTaxaBlock *t)</code></td>
</tr>
<tr>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>Sets <span class="variablename">id</span> to "DISTANCES", <span class="variablename">taxa</span> to <span class="variablename">t</span>, <span class="variablename">triangle</span> to `NxsDistancesBlockEnum::lower', <span class="variablename">missing</span> to '?', <span class="variablename">matrix</span> and <span class="variablename">taxonPos</span> to NULL, <span class="variablename">labels</span> and <span class="variablename">diagonal</span> to true, <span class="variablename">newtaxa</span> and <span class="variablename">interleave</span> to false, and <span class="variablename">ntax</span> and <span class="variablename">nchar</span> to 0. Assumes <span class="variablename">t</span> is non-NULL.</dd></td>
</tr>
</table>
</td></tr>
<tr><td>
<table width="100%" border="0" cellpadding="1">
<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="NxsDistancesBlock49">~NxsDistancesBlock</a></code><code>()</code></td>
</tr>
<tr>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>Deletes <span class="variablename">matrix</span> and <span class="variablename">taxonPos</span> arrays.</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="Read528">Read</a></code><code>(NxsToken &token)</code></td>
</tr>
<tr>
<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 NEXUS object) to the end or endblock statement. Characters are read from the input stream in. Overrides the abstract virtual function in the base class.</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="Report627">Report</a></code><code>(ostream &out)</code></td>
</tr>
<tr>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>This function outputs a brief report of the contents of this taxa block. Overrides the abstract virtual function in the base class.</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="Reset707">Reset</a></code><code>()</code></td>
</tr>
<tr>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>Flushes taxonLabels and sets ntax to 0 in preparation for reading a new TAXA block.</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="SetDistance856">SetDistance</a></code><code>(unsigned i, unsigned j, double d)</code></td>
</tr>
<tr>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>Sets the value of the (<span class="variablename">i</span>,<span class="variablename">j</span>)th matrix element to <span class="variablename">d</span> and <span class="variablename">missing</span> to false . Assumes <span class="variablename">i</span> and <span class="variablename">j</span> are both in the range [0..<span class="variablename">ntax</span>) and <span class="variablename">matrix</span> is not NULL.</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="SetMissing875">SetMissing</a></code><code>(unsigned i, unsigned j)</code></td>
</tr>
<tr>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>Sets the value of the (<span class="variablename">i</span>, <span class="variablename">j</span>)th <span class="variablename">matrix</span> element to missing. Assumes <span class="variablename">i</span> and <span class="variablename">j</span> are both in the range [0..<span class="variablename">ntax</span>) and <span class="variablename">matrix</span> is not NULL.</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="SetNchar892">SetNchar</a></code><code>(unsigned n)</code></td>
</tr>
<tr>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td><dd>Sets <span class="variablename">nchar</span> to <span class="variablename">n</span>.</dd></td>
</tr>
</table>
</td></tr>
</table>
</center>
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