"
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;
}
}
