/* Copyright (c) 2011 Peter Troshin
 *  
 *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0     
 * 
 *  This library is free software; you can redistribute it and/or modify it under the terms of the
 *  Apache License version 2 as published by the Apache Software Foundation
 * 
 *  This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without
 *  even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache 
 *  License for more details.
 * 
 *  A copy of the license is in apache_license.txt. It is also available here:
 * @see: http://www.apache.org/licenses/LICENSE-2.0.txt
 * 
 * Any republication or derived work distributed in source code form
 * must include this copyright and license notice.
 */
package compbio.runner._impl;

import static compbio.runner._impl.BlastParameters.parAlView;
import static compbio.runner._impl.BlastParameters.parDatabase;
import static compbio.runner._impl.BlastParameters.parDel;
import static compbio.runner._impl.BlastParameters.parEvalue;
import static compbio.runner._impl.BlastParameters.parInput;
import static compbio.runner._impl.BlastParameters.parOutput;

import java.io.File;
import java.util.Arrays;
import java.util.List;

import compbio.runner._SkeletalCommandBuilder;

/*
 * TODO look at how a command can be build with an argument list
 */
public class PSIBlast extends _SkeletalCommandBuilder {

	private static final String command = "blastpgp";

	enum blastType {
		blastp, tbastn, blastn
	}

	enum dataBase {
		pdb
	}

	static double default_evalue = 0.001d;
	static final String parBlastType = "-p";

	private final String workDirectory;

	public PSIBlast(String workDirectory) {
		this.workDirectory = workDirectory;
	}

	// Resulting command:
	// TODO lease note that the location seem to be different for 64 bit nodes
	// fc_gpfs/gjb_lab/www-refine/bin/blast_32bit/blast-2.2.17/bin/blastpgp -i
	// $input -d $dbnam -o $output_dir/$outfile.psiblastout.$clus -j $iterations
	// -Q $output_dir/$outfile.PSImatrix.$clus -m $mo

	// BlastAll
	// //fc_gpfs/gjb_lab/www-refine/bin/blast_32bit/blast-2.2.17/bin/blastall -p
	// blastp -i $input -d $dbnam -e $evalue -m 9 -o $outfile

	String getCommand(blastType btype, dataBase database, String input,
			String output) {
		return Environment.getBlastBinDir() + command + parDel + parBlastType
				+ blastType.blastp + parDel + parInput + input + parDel
				+ parDatabase + Environment.getBlastDatabasesDir() + database
				+ parDel + parEvalue + default_evalue + parAlView + parOutput
				+ output;
	}

	String getFullTestCommand(String test_input, String test_outfile) {
		return Environment.getBlastBinDir() + command + parDel + parBlastType
				+ blastType.blastp + parDel + parInput + test_input + parDel
				+ parDatabase + Environment.getBlastDatabasesDir()
				+ dataBase.pdb + parDel + parEvalue + default_evalue
				+ parAlView + parOutput + test_outfile;
	}

	static String getTestCommand() {
		return Environment.getBlastBinDir() + command;
	}

	static List<String> getTestArgs() {
		return Arrays
				.asList(new String[] {
						parBlastType + blastType.blastp,
						parDatabase + Environment.getBlastDatabasesDir()
								+ dataBase.pdb, parEvalue + default_evalue,
						parAlView });
	}

	public boolean removeOutput(String outfile) {
		File out = new File(outfile);
		if (out.exists()) {
			if (out.canWrite()) {
				return out.delete();
			}
		}
		return false;
	}

	public String getCommand(ExecProvider provider) {
		return Environment.getBlastBinDir() + command;
	}

	public String getCommandName() {
		return command;
	}

	@Override
	public List<String> getCreatedFiles() {
		// TODO Auto-generated method stub
		return null;
	}

	@Override
	public String getInput() {
		// TODO Auto-generated method stub
		return null;
	}

}