<?xml version='1.0' encoding='UTF-8' standalone='no'?>
<section xmlns="http://docbook.org/ns/docbook" version="5.0" xmlns:xlink="http://www.w3.org/1999/xlink" xml:id="_rw_phylip_8cpp">
<title>/Users/bernard/b20/bsoft/src/rwmol/rwPhylip.cpp File Reference</title>
<indexterm><primary>/Users/bernard/b20/bsoft/src/rwmol/rwPhylip.cpp</primary></indexterm>
<para>

<para>Library routines to read and write Phylip sequence files. </para>
 
</para>
<programlisting>#include &quot;rwPhylip.h&quot;
#include &quot;utilities.h&quot;
#include &lt;fstream&gt;
</programlisting><simplesect>
    <title>Functions    </title>
        <itemizedlist>
            <listitem><para>int <link linkend="_rw_phylip_8cpp_1afe84bb68ef61afc85636271090bc7b4b">readPhylip</link> (<link linkend="_class_bstring">Bstring</link> &amp;filename, <link linkend="_struct_bmolgroup">Bmolgroup</link> *molgroup)</para>

<para>Reads Phylip format sequence files. </para>
</listitem>
            <listitem><para>int <link linkend="_rw_phylip_8cpp_1aa08aecbd34e2a039e43c1cc39d2ae280">writePhylip</link> (<link linkend="_class_bstring">Bstring</link> &amp;filename, <link linkend="_struct_bmolgroup">Bmolgroup</link> *molgroup)</para>

<para>Writes Phylip format sequence files. </para>
</listitem>
        </itemizedlist>
</simplesect>
<simplesect>
    <title>Variables    </title>
        <itemizedlist>
            <listitem><para>int <link linkend="_rw_phylip_8cpp_1a0b2caeb4b6f130be43e5a2f0267dd453">verbose</link></para>
</listitem>
        </itemizedlist>
</simplesect>
<section>
<title>Detailed Description</title>

<para>Library routines to read and write Phylip sequence files. </para>

<para><formalpara><title>Author: </title>

<para>Bernard Heymann </para>
</formalpara>
<formalpara><title>Date: </title>

<para>Created: 20030308 </para>

<para>Modified: 20110805 </para>
</formalpara>
</para>
</section>
<section>
<title>Function Documentation</title>
<anchor xml:id="_rw_phylip_8cpp_1afe84bb68ef61afc85636271090bc7b4b"/>    <section>
    <title>readPhylip()</title>
<indexterm><primary>readPhylip</primary><secondary>rwPhylip.cpp</secondary></indexterm>
<indexterm><primary>rwPhylip.cpp</primary><secondary>readPhylip</secondary></indexterm>
<para><computeroutput>int readPhylip (<link linkend="_class_bstring">Bstring</link> &amp; filename, <link linkend="_struct_bmolgroup">Bmolgroup</link> * molgroup)</computeroutput></para><para>

<para>Reads Phylip format sequence files. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>&amp;filename</entry>
                                <entry>
<para>sequence file name. </para>
</entry>
                            </row>
                            <row>
                                <entry>*molgroup</entry>
                                <entry>
<para>molecule group. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>int number of molecules read (&lt;0 if reading failed). <literallayout><computeroutput>Phylip format:
21   1419
WMBEX6    MT------------------------------------------------
P89429    MA------------------------------------------------
P09302    MAEITSLFNNSS--------------------------------------
</computeroutput></literallayout> </para>
</formalpara>
</para>
<para>
Definition at line 29 of file rwPhylip.cpp.</para>
    </section><anchor xml:id="_rw_phylip_8cpp_1aa08aecbd34e2a039e43c1cc39d2ae280"/>    <section>
    <title>writePhylip()</title>
<indexterm><primary>writePhylip</primary><secondary>rwPhylip.cpp</secondary></indexterm>
<indexterm><primary>rwPhylip.cpp</primary><secondary>writePhylip</secondary></indexterm>
<para><computeroutput>int writePhylip (<link linkend="_class_bstring">Bstring</link> &amp; filename, <link linkend="_struct_bmolgroup">Bmolgroup</link> * molgroup)</computeroutput></para><para>

<para>Writes Phylip format sequence files. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>&amp;filename</entry>
                                <entry>
<para>sequence file name. </para>
</entry>
                            </row>
                            <row>
                                <entry>*molgroup</entry>
                                <entry>
<para>molecule group. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>int number of molecules written (&lt;0 if writing failed). </para>
</formalpara>
</para>
<para>
Definition at line 94 of file rwPhylip.cpp.</para>
</section>
</section>
<section>
<title>Variable Documentation</title>
<anchor xml:id="_rw_phylip_8cpp_1a0b2caeb4b6f130be43e5a2f0267dd453"/>    <section>
    <title>verbose</title>
<indexterm><primary>verbose</primary><secondary>rwPhylip.cpp</secondary></indexterm>
<indexterm><primary>rwPhylip.cpp</primary><secondary>verbose</secondary></indexterm>
<para><computeroutput>int verbose</computeroutput></para></section>
</section>
</section>
