<!DOCTYPE article PUBLIC "-//OASIS//DTD DocBook V3.1//EN" [
<!ENTITY intro SYSTEM "intro.sgml">
<!ENTITY requirements SYSTEM "requirements.sgml">
<!ENTITY elementandtype SYSTEM "elementandtype.sgml">
<!ENTITY seqimpl SYSTEM "seqimpl.sgml">
<!ENTITY alignment SYSTEM "alignment.sgml">
<!ENTITY conclusions SYSTEM "conclusions.sgml">
<!ENTITY seqapi "Sequence API for Java">
<!ENTITY % draft "INCLUDE">
]>


<article>
  <title>An API for describing biological sequences written in the
    Java language</title>
  <artheader>
    <author>
      <honorific>Dr</honorific>
      <firstname>Phillip</firstname>
      <surname>Lord</surname>
      <affiliation>
	<orgname>The University of Manchester</orgname>
	<orgdiv>Department of Biological Sciences</orgdiv>
	<address>
	  <otheraddr>2.18, Stopford Buildings</otheraddr>
	  <street>Oxford Road</street>
	  <city>Manchester</city>
	  <postcode>M13 9PT</postcode>
	</address>
      </affiliation>
    </author>
    <pubdate>$Revision: 1.1 $, $Date: 2000/11/22 16:27:00 $</pubdate>
  </artheader>
  
  <abstract>
    <title>Abstract</title>
    
      <para>This document contains a description of the design and
      implementation of the &seqapi;. It is a series of Java classes
      and interfaces which can be used to enable the representation
      and manipulation of biological sequences in the Java
      language. The API has been designed to be as lightweight as
      possible, whilst still allowing considerable
      flexibility. </para>
    <![%draft;[
    <para>
      <emphasis>This documentation is a work in progress at the
	moment. And although the &seqapi; is much more stable it is
	still changing occasionally. Please bear this in mind when you
	read it. </emphasis>
    </para>
    ]]>
  </abstract>
  
  <!-- The introduction -->
  &intro;
  <!-- The requirements -->
  &requirements;
  <!-- The implementation of elements and types-->
  &elementandtype;
  <!-- And of sequences themselves-->
  &seqimpl;
  <!-- Sequence Alignments -->
  &alignment;
  <!-- Conclusions -->
  &conclusions;
</article>
     

  




