Team:Freiburg software/Code/BlastSearch.java

From 2009.igem.org

BlastSearch

 /*
*    Copyright: synbiowave
*     
*    License: GPL
*     
*    Authors: Paul Staab
*     
*    Version: 0.1 
*    
*    DESCRIPTION:
*    	This class helps handles blastsearches
*/


package blastRobot;

import java.io.BufferedReader;

public class BlastSearch 
{
	//Variables
	private SymbolList sequence;
	private String database="";
	private String program="";
	private String rid="";
	private String numberOfResults="10";
	private List results = new ArrayList();
	
	
	//Constructors
  	public BlastSearch()
  	{
  		  		
  	}
  	
  	public BlastSearch(SymbolList sequence) throws Exception
  	{
  		  	this.sequence = sequence;	
  	}  	

  	public BlastSearch(SymbolList sequence, String database, String program) throws Exception
  	{
  		  	this.sequence = sequence;	
  		  	this.database = database;
  		  	this.program = program;
  	}
  	
  	
  	//Getters and Setters
	public SymbolList getSequence() {
		return sequence;
	}

	public void setSequence(SymbolList sequence) {
		this.sequence = sequence;
	}

	public String getDatabase() {
		return database;
	}

	public void setDatabase(String database) {
		this.database = database;
	}

	public String getProgram() {
		return program;
	}

	public void setProgram(String program) {
		this.program = program;
	}

	public String getRID() {
		return rid;
	}

	public void setRID(String rid) {
		this.rid = rid;
	}
  	
	
	//Methods
  	public void search() throws Exception
  	{
  		
  		//manual create a blast-query...
  		//Should be done as POST, as URLs are limited to 255 chars afaik.
   		URL searchurl = new URL("" +
  				"http://www.ncbi.nlm.nih.gov/blast/Blast.cgi" +
  				"?CMD=Put" +
  				"&DATABASE=" + this.database +
  				"&PROGRAM=" + this.program +
  				"&HITLIST_SIZE=" + this.numberOfResults +
  				"&QUERY=" + this.sequence.seqString() );
  		
  		//Query it
  		BufferedReader reader = new BufferedReader
  		(
  				new InputStreamReader( searchurl.openStream(), "UTF-8"  ) 
  		);
  		
  		//Receive the RID
  		String line = "";
  		while ((line = reader.readLine()) != null)
  		{
  			//BAD method to get the RID of the Request;
  			if ( line.contains("Request ID") ) this.rid += line.substring(70, 81);
  		}
  		reader.close();

  	}
  	
  	public void parseResult() throws Exception
  	{
   		URL searchurl = new URL("" +
  				"http://www.ncbi.nlm.nih.gov/blast/Blast.cgi" +
  				"?CMD=Get" +
  				"&FORMAT_TYPE=XML" +
  				"&RID=" + this.rid );

   		//do the parsing, the biojava-cookbook for documentation
        BlastXMLParserFacade blast = new BlastXMLParserFacade();
        SeqSimilarityAdapter adapter = new SeqSimilarityAdapter();
        blast.setContentHandler(adapter);        
        SearchContentHandler builder = new BlastLikeSearchBuilder(results, new DummySequenceDB("queries"), new DummySequenceDBInstallation() );
        adapter.setSearchContentHandler(builder);
        blast.parse( new InputSource( searchurl.openStream() ) );
  	}   
     
  	public String waveOutput() throws Exception
  	{
  		String waveOutput = "\nBlast-Search\n";
        
        for (Iterator i = results.iterator(); i.hasNext(); ) 
        {
        	SeqSimilaritySearchResult result = (SeqSimilaritySearchResult)i.next();
        	Annotation anno = result.getAnnotation();
   
        	for (Iterator j = anno.keys().iterator(); j.hasNext(); ) 
        	{
        		Object key = j.next();
        		Object property = anno.getProperty(key);
        		waveOutput += (key+" : "+property) + "\n";
        	}
        	waveOutput += ("Hits: \n");
   
        	//list the hits

        	for (Iterator k = result.getHits().iterator(); k.hasNext(); ) 
        	{
        		SeqSimilaritySearchHit hit = (SeqSimilaritySearchHit)k.next();
        		waveOutput += ("\t match: "+ hit.getSubjectID() );
        		waveOutput += ("\t\t\t"+ hit.getEValue() ) + "\n";
        	}
        }
   
        return waveOutput;

  	}
}