<?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="_ps__sequence_8h">
<title>/Users/bernard/b20/bsoft/include/ps_sequence.h File Reference</title>
<indexterm><primary>/Users/bernard/b20/bsoft/include/ps_sequence.h</primary></indexterm>
<para>

<para>Header file for postscript output for sequence analysis functions. </para>
 
</para>
<programlisting>#include &quot;Complex.h&quot;
#include &quot;utilities.h&quot;
</programlisting><simplesect>
    <title>Functions    </title>
        <itemizedlist>
            <listitem><para>int <link linkend="_ps__sequence_8h_1a8d2df2ead28a189400c5fdc86e75a693">ps_seq_info</link> (<link linkend="_class_bstring">Bstring</link> &amp;filename, <link linkend="_class_bstring">Bstring</link> &amp;title, int nres, int <link linkend="__vector3_8h_1a7baf5ed670fcf9bcca9a3a400820e292">length</link>, double *info, double *nseq, <link linkend="_class_complex">Complex</link>&lt; float &gt; *per, double *freq, char *pattern)</para>

<para>Generates a postscript plot from an information content analysis of a protein sequence alignment. </para>
</listitem>
            <listitem><para>int <link linkend="_ps__sequence_8h_1a3d15669460e9b16c937a359cd8985dcd">ps_seq_hydrophob</link> (<link linkend="_class_bstring">Bstring</link> &amp;filename, <link linkend="_class_bstring">Bstring</link> &amp;title, int <link linkend="__vector3_8h_1a7baf5ed670fcf9bcca9a3a400820e292">length</link>, double *Hphob, int *HPseg, double *nseq, <link linkend="_class_complex">Complex</link>&lt; float &gt; *per)</para>

<para>Generates a postscript plot from a hydrophobicity analysis of a protein sequence alignment. </para>
</listitem>
        </itemizedlist>
</simplesect>
<section>
<title>Detailed Description</title>

<para>Header file for postscript output for sequence analysis functions. </para>

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

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

<para>Created: 20010515 </para>

<para>Modified: 20060722 </para>
</formalpara>
</para>
</section>
<section>
<title>Function Documentation</title>
<anchor xml:id="_ps__sequence_8h_1a3d15669460e9b16c937a359cd8985dcd"/>    <section>
    <title>ps_seq_hydrophob()</title>
<indexterm><primary>ps_seq_hydrophob</primary><secondary>ps_sequence.h</secondary></indexterm>
<indexterm><primary>ps_sequence.h</primary><secondary>ps_seq_hydrophob</secondary></indexterm>
<para><computeroutput>int ps_seq_hydrophob (<link linkend="_class_bstring">Bstring</link> &amp; filename, <link linkend="_class_bstring">Bstring</link> &amp; title, int length, double * Hphob, int * HPseg, double * nseq, <link linkend="_class_complex">Complex</link>&lt; float &gt; * per)</computeroutput></para><para>

<para>Generates a postscript plot from a hydrophobicity analysis of a protein sequence alignment. </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>postscript file name. </para>
</entry>
                            </row>
                            <row>
                                <entry>&amp;title</entry>
                                <entry>
<para>title. </para>
</entry>
                            </row>
                            <row>
                                <entry>length</entry>
                                <entry>
<para>number of alignment positions. </para>
</entry>
                            </row>
                            <row>
                                <entry>*Hphob</entry>
                                <entry>
<para>moving average of average hydrophobicity at each position. </para>
</entry>
                            </row>
                            <row>
                                <entry>*HPseg</entry>
                                <entry>
<para>assignment of hydrophobic segments. </para>
</entry>
                            </row>
                            <row>
                                <entry>*nseq</entry>
                                <entry>
<para>number of sequences represented at each position. </para>
</entry>
                            </row>
                            <row>
                                <entry>*per</entry>
                                <entry>
<para>periodicity analysis. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>int 0. </para>
</formalpara>
</para>
<para>
Definition at line 194 of file ps_sequence.cpp.</para>
    </section><anchor xml:id="_ps__sequence_8h_1a8d2df2ead28a189400c5fdc86e75a693"/>    <section>
    <title>ps_seq_info()</title>
<indexterm><primary>ps_seq_info</primary><secondary>ps_sequence.h</secondary></indexterm>
<indexterm><primary>ps_sequence.h</primary><secondary>ps_seq_info</secondary></indexterm>
<para><computeroutput>int ps_seq_info (<link linkend="_class_bstring">Bstring</link> &amp; filename, <link linkend="_class_bstring">Bstring</link> &amp; title, int nres, int length, double * info, double * nseq, <link linkend="_class_complex">Complex</link>&lt; float &gt; * per, double * freq, char * pattern)</computeroutput></para><para>

<para>Generates a postscript plot from an information content analysis of a protein sequence alignment. </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>postscript file name. </para>
</entry>
                            </row>
                            <row>
                                <entry>&amp;title</entry>
                                <entry>
<para>title. </para>
</entry>
                            </row>
                            <row>
                                <entry>nres</entry>
                                <entry>
<para>number of residue types. </para>
</entry>
                            </row>
                            <row>
                                <entry>length</entry>
                                <entry>
<para>number of alignment positions. </para>
</entry>
                            </row>
                            <row>
                                <entry>*info</entry>
                                <entry>
<para>moving average of information content. </para>
</entry>
                            </row>
                            <row>
                                <entry>*nseq</entry>
                                <entry>
<para>number of sequences represented at each position. </para>
</entry>
                            </row>
                            <row>
                                <entry>*per</entry>
                                <entry>
<para>periodicity analysis. </para>
</entry>
                            </row>
                            <row>
                                <entry>*freq</entry>
                                <entry>
<para>frequence of each residue type at each position. </para>
</entry>
                            </row>
                            <row>
                                <entry>*pattern</entry>
                                <entry>
<para>residue types at each position, in frequency order. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>int 0. </para>
</formalpara>
</para>
<para>
Definition at line 33 of file ps_sequence.cpp.</para>
</section>
</section>
</section>
