BioDASGenomicSequence.java

/*
The MIT License (MIT)

Copyright (c) 2016 Pierre Lindenbaum

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.

*/
package com.github.lindenb.jvarkit.util.bio;

import java.io.ByteArrayOutputStream;
import java.io.InputStream;
import java.io.StringReader;
import java.net.URL;
import java.net.URLEncoder;
import java.util.logging.Logger;

import javax.xml.parsers.SAXParser;
import javax.xml.parsers.SAXParserFactory;
import org.xml.sax.Attributes;
import org.xml.sax.InputSource;
import org.xml.sax.SAXException;
import org.xml.sax.helpers.DefaultHandler;

import com.github.lindenb.jvarkit.lang.AbstractCharSequence;

public class BioDASGenomicSequence extends AbstractCharSequence implements
		ChromosomeSequence
	{
	private static final Logger LOG=Logger.getLogger("jvarkit");
	private boolean _length_searched=false;
	private SAXParser parser;
	private String chrom=null;
	private Integer _length=null;
	private byte buffer[]=null;
	private int buffer_pos=-1;
	private int half_buffer_capacity=1000000;
	
	public BioDASGenomicSequence(String chrom)
		{
		this.chrom=chrom;
		SAXParserFactory f=SAXParserFactory.newInstance();
		f.setSchema(null);
		f.setNamespaceAware(false);
		f.setValidating(false);
		try
			{
			this.parser=f.newSAXParser();
			}
		catch(Exception err)
			{
			throw new RuntimeException(err.getMessage());
			}
	
		}
	
	@Override
	public char charAt(int index0)
		{
		if(index0 >= length())
			{
			throw new IndexOutOfBoundsException("index:"+index0);
			}
		if(buffer!=null && index0>=buffer_pos && index0-buffer_pos < buffer.length)
			{
			return (char)buffer[index0-buffer_pos];
			}
		int minStart=Math.max(0, index0-half_buffer_capacity);
		int maxEnd=Math.min(minStart+2*half_buffer_capacity,this.length());
		try
			{
			
			String uri= "http://genome.ucsc.edu/cgi-bin/das/hg19/dna?segment="+
					URLEncoder.encode(getChrom()+":"+(minStart+1)+","+(maxEnd),
					"UTF-8");
			DasHandler handler=new DasHandler();
			LOG.info("getting "+uri);
			InputStream in=new URL(uri).openStream();
			this.parser.parse(in, handler);
			in.close();
			this.buffer=handler.baos.toByteArray();
			this.buffer_pos=minStart;
			}
		catch (Exception err)
			{
			throw new RuntimeException("BioDas::get",err);
			}
		return (char)buffer[index0-minStart];
		}

	@Override
	public int length()
		{
		if(_length==null && _length_searched==false)
			{
			_length_searched=true;
			LOG.info("getting length");
			try
				{
				DasHandler handler=new DasHandler();
				String uri="http://genome.ucsc.edu/cgi-bin/das/hg19/entry_points";
				LOG.info("getting length "+uri);
				InputStream in=new URL(uri).openStream();
				this.parser.parse(in, handler);
				in.close();
				this._length=handler.length;
				LOG.info("length("+getChrom()+")="+this._length);
				}
			catch (Exception err)
				{
				throw new RuntimeException("BioDas::length",err);
				}
			
			}
		return _length==null?Integer.MAX_VALUE-1:_length;
		}

	@Override
	public String getChrom()
		{
		return this.chrom;
		}
	

	
	private class DasHandler
		extends DefaultHandler
		{
		private ByteArrayOutputStream baos=null;
		int reserve=100000;
		Integer length=null;
		public DasHandler()
			{
			}
		
		 @Override
		public void startDocument() throws SAXException
			{
			baos=null;
			}
		
		 public InputSource resolveEntity (String publicId, String systemId)
	         {
	         return new InputSource(new StringReader(""));
	         }
		
		@Override
	    public void startElement(String uri, String localName, String name,
	            Attributes attributes) throws SAXException
	        {
	        if(name.equals("DNA"))
	            {
	            this.baos=new ByteArrayOutputStream(this.reserve);
	            }
	        else if(name.equals("SEGMENT") )
	        	{
	        	String c=attributes.getValue("id");
	        	if(c==null) return;
	        	if(!(getChrom().equals(c) || getChrom().equals("chr"+c))) return;
	        	c=attributes.getValue("stop");
	        	if(c==null) return;
	        	this.length=Integer.parseInt(c);
	        	}
	        }
		
	    @Override
	    public void characters(char[] ch, int start, int length)
	            throws SAXException
	        {
	        if(this.baos==null) return;
	        for(int i=0;i< length;++i)
	            {
	            char c= Character.toUpperCase(ch[start+i]);
	            if(Character.isWhitespace(c)) continue;
	            this.baos.write((byte)c);
	            }
	        }
	
	
		
		
		}
	public static void main(String[] args)
		{
		BioDASGenomicSequence seq=new BioDASGenomicSequence("chrM");
		for(int i=0;i< seq.length() ;++i) System.out.println(""+i+" : "+seq.charAt(i)+" "+seq.length());
		}

	}