package jet.external;

public class PsiBlast extends jet.external.Command 
{
	/** Classe permettant d'executer une commande psi-blast */	
	
	public PsiBlast(String command, String database, String matrix, String queryFile, String outputFile, int maxResults, double eValue, double psithreshold, int gap_exist,int gap_ext,int maxIteration, String GI, String format, String methods)
	{
	    command=command+" -d "+database;
	    command=command+" -I "+GI;
	    command=command+" -e "+eValue;
	    command=command+" -G "+gap_exist;
	    command=command+" -E "+gap_ext;
	    command=command+" -v "+maxResults;
	    command=command+" -b "+maxResults;
	    command=command+" -M "+matrix;
	    command=command+" -i "+queryFile;
	    command=command+" -h "+psithreshold;
	    command=command+" -j "+maxIteration;
	    command=command+" -o "+outputFile;
	    command=command+" -T "+format;
	    command=command+" -t "+methods;
	    System.out.println(command);
	    setCommand(command);
	    setDirectory(".");
	    sendCommand();
	}
	
	
}
