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<section xmlns="http://docbook.org/ns/docbook" version="5.0" xmlns:xlink="http://www.w3.org/1999/xlink" xml:id="_bseq_8cpp">
<title>/Users/bernard/b20/bsoft/src/bseq.cpp File Reference</title>
<indexterm><primary>/Users/bernard/b20/bsoft/src/bseq.cpp</primary></indexterm>
<para>

<para>A program to manipulate DNA and protein sequences. </para>
 
</para>
<programlisting>#include &quot;rwmolecule.h&quot;
#include &quot;rwgencode.h&quot;
#include &quot;seq_util.h&quot;
#include &quot;utilities.h&quot;
#include &quot;options.h&quot;
#include &quot;timer.h&quot;
</programlisting><simplesect>
    <title>Functions    </title>
        <itemizedlist>
            <listitem><para>int <link linkend="_bseq_8cpp_1a3c04138a5bfe5d72780bb7e82a18e627">main</link> (int argc, char **argv)</para>
</listitem>
        </itemizedlist>
</simplesect>
<simplesect>
    <title>Variables    </title>
        <itemizedlist>
            <listitem><para>int <link linkend="_bseq_8cpp_1a0b2caeb4b6f130be43e5a2f0267dd453">verbose</link></para>
</listitem>
            <listitem><para>const char * <link linkend="_bseq_8cpp_1a4de0ad4c7190962494815c0fa7f948df">use</link> []</para>
</listitem>
        </itemizedlist>
</simplesect>
<section>
<title>Detailed Description</title>

<para>A program to manipulate DNA and protein sequences. </para>

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

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

<para>Created: 20000808 </para>

<para>Modified: 20190613 </para>
</formalpara>
</para>
</section>
<section>
<title>Function Documentation</title>
<anchor xml:id="_bseq_8cpp_1a3c04138a5bfe5d72780bb7e82a18e627"/>    <section>
    <title>main()</title>
<indexterm><primary>main</primary><secondary>bseq.cpp</secondary></indexterm>
<indexterm><primary>bseq.cpp</primary><secondary>main</secondary></indexterm>
<para><computeroutput>int main (int argc, char ** argv)</computeroutput></para><para>
Definition at line 50 of file bseq.cpp.</para>
</section>
</section>
<section>
<title>Variable Documentation</title>
<anchor xml:id="_bseq_8cpp_1a4de0ad4c7190962494815c0fa7f948df"/>    <section>
    <title>use</title>
<indexterm><primary>use</primary><secondary>bseq.cpp</secondary></indexterm>
<indexterm><primary>bseq.cpp</primary><secondary>use</secondary></indexterm>
<para><computeroutput>const char* use[]</computeroutput></para><emphasis role="strong">Initial value:</emphasis><programlisting>=&#32;{
<emphasis role="stringliteral">&quot;&#32;&quot;</emphasis>,
<emphasis role="stringliteral">&quot;Usage:&#32;bseq&#32;[options]&#32;input.seq&#32;output.seq&quot;</emphasis>,
<emphasis role="stringliteral">&quot;------------------------------------------&quot;</emphasis>,
<emphasis role="stringliteral">&quot;Manipulates&#32;DNA&#32;and&#32;protein&#32;sequences.&quot;</emphasis>,
<emphasis role="stringliteral">&quot;&#32;&quot;</emphasis>,
<emphasis role="stringliteral">&quot;Actions:&quot;</emphasis>,
<emphasis role="stringliteral">&quot;-show&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;Show&#32;all&#32;DNA&#32;and&#32;protein&#32;sequences&#32;after&#32;other&#32;operations.&quot;</emphasis>,
<emphasis role="stringliteral">&quot;-Mass&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;Show&#32;the&#32;calculated&#32;mass&#32;for&#32;each&#32;sequence.&quot;</emphasis>,
<emphasis role="stringliteral">&quot;-complement&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;Complement&#32;all&#32;DNA&#32;sequences&#32;before&#32;other&#32;operations.&quot;</emphasis>,
<emphasis role="stringliteral">&quot;-translate&#32;1&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;Translate&#32;all&#32;DNA&#32;sequences&#32;with&#32;this&#32;frame&#32;(0,1,2).&quot;</emphasis>,
<emphasis role="stringliteral">&quot;-finddna&#32;ggattcga&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;DNA&#32;sequence&#32;to&#32;look&#32;for&#32;in&#32;DNA&#32;sequences.&quot;</emphasis>,
<emphasis role="stringliteral">&quot;-findprotein&#32;fghwereaas&#32;&#32;Protein&#32;sequence&#32;to&#32;look&#32;for&#32;in&#32;protein&#32;sequences.&quot;</emphasis>,
<emphasis role="stringliteral">&quot;-findcoding&#32;aklsdrtv&#32;&#32;&#32;&#32;&#32;Coding&#32;sequence&#32;to&#32;look&#32;for&#32;in&#32;DNA&#32;sequences.&quot;</emphasis>,
<emphasis role="stringliteral">&quot;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;Can&#32;be&#32;a&#32;file&#32;name&#32;with&#32;a&#32;protein&#32;sequence.&quot;</emphasis>,
<emphasis role="stringliteral">&quot;&#32;&quot;</emphasis>,
<emphasis role="stringliteral">&quot;Parameters:&quot;</emphasis>,
<emphasis role="stringliteral">&quot;-verbose&#32;7&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;Verbosity&#32;of&#32;output.&quot;</emphasis>,
<emphasis role="stringliteral">&quot;-nogaps&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;Strip&#32;gaps&#32;from&#32;input&#32;sequences.&quot;</emphasis>,
<emphasis role="stringliteral">&quot;-length&#32;1100,1500&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;Sequence&#32;length&#32;range&#32;to&#32;select&#32;for.&quot;</emphasis>,
<emphasis role="stringliteral">&quot;-number&#32;10,14&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;Number&#32;of&#32;residues&#32;on&#32;either&#32;side&#32;to&#32;include&#32;in&#32;output.&quot;</emphasis>,
<emphasis role="stringliteral">&quot;-threshold&#32;50&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;Threshold&#32;percentage&#32;to&#32;report&#32;hits&#32;(default&#32;only&#32;best&#32;hit).&quot;</emphasis>,
<emphasis role="stringliteral">&quot;&#32;&quot;</emphasis>,
<emphasis role="stringliteral">&quot;Input:&quot;</emphasis>,
<emphasis role="stringliteral">&quot;-geneticcode&#32;file.star&#32;&#32;&#32;Genetic&#32;code&#32;file&#32;(default&#32;=&#32;internal&#32;values).&quot;</emphasis>,
<emphasis role="stringliteral">&quot;-elements&#32;prop.star&#32;&#32;&#32;&#32;&#32;&#32;Calculate&#32;elemental&#32;composition.&quot;</emphasis>,
<emphasis role="stringliteral">&quot;&#32;&quot;</emphasis>,
NULL
}
</programlisting><para>
Definition at line 20 of file bseq.cpp.</para>
    </section><anchor xml:id="_bseq_8cpp_1a0b2caeb4b6f130be43e5a2f0267dd453"/>    <section>
    <title>verbose</title>
<indexterm><primary>verbose</primary><secondary>bseq.cpp</secondary></indexterm>
<indexterm><primary>bseq.cpp</primary><secondary>verbose</secondary></indexterm>
<para><computeroutput>int verbose</computeroutput></para></section>
</section>
</section>
