package compbio.cassandra.readers;

import java.util.ArrayList;
import java.util.List;

import com.datastax.driver.core.ResultSet;
import com.datastax.driver.core.Row;

import compbio.beans.ProteinBean;

/**
 * Reader class for making requests on protein sequences to cassandra.
 * 
 * @author Alexander Sherstnev
 * @author Natasha Sherstneva
 * 
 * @since 0.5
 * @version 1.0 
 * @since December 2013
 */
public class SequenceReader extends CassandraReader {

	public SequenceReader() {
		super();
	}

	/**
	 * query: protein sequence
	 * 
	 * @param sequence
	 *            protein sequence or partial of protein sequence
	 * @param searchtype
	 *            "whole" or "partial" of protein sequence
	 * 
	 * @return List<ProteinBean> to the controller SequenceController
	 * 
	 **/
	public List<ProteinBean> readProteins(String sequence, String searchtype) {
		List<ProteinBean> query = new ArrayList<ProteinBean>();
		if (searchtype.equals("whole")) {
			ResultSet results = CassandraQuery("SELECT JobID, Predictions FROM ProteinRow WHERE Protein = '" + sequence + "';");
			if (results.isExhausted())
				return null;
			List<Row> rows = results.all();
			ProteinBean structure = new ProteinBean(sequence, rows.get(0).getMap("Predictions", String.class, String.class));
			for (Row r : rows) {
				structure.setJobid(r.getString("JobID"));
			}
			query.add(structure);
		} else {
			ResultSet results = CassandraQuery("SELECT * FROM ProteinRow;");
			if (results.isExhausted())
				return null;
			List<Row> rows = results.all();
			for (Row r : rows) {
				String protein = r.getString("Protein");
				if (protein.matches("(.*)" + sequence + "(.*)")) {
					ProteinBean foundsequence = new ProteinBean(protein, r.getMap("Predictions", String.class, String.class));
					foundsequence.setJobid(r.getString("JobID"));
					query.add(foundsequence);
				}
			}
			for (ProteinBean entry : query) {
				entry.setSubProt(CreateSubprotein(entry.getSequence(), sequence));
			}
		}
		return query;
	}

	/**
	 * create a list of parts of protein sequence for highlighting current value
	 * in report;
	 * 
	 * @param protein
	 *            protein sequence
	 * @param subprot
	 *            partial of protein sequence
	 * 
	 * @return List<String>
	 * 
	 **/
	private static List<String> CreateSubprotein(String protein, String subprot) {
		List<String> sub = new ArrayList<String>();
		String subStr = protein;
		while (subStr.length() > 0 && subStr.contains(subprot)) {
			String first = subStr.substring(0, subStr.indexOf(subprot));
			if (first.length() > 0)
				sub.add(first);
			sub.add(subprot);
			subStr = subStr.substring(subStr.indexOf(subprot) + subprot.length(), subStr.length());
		}
		if (subStr.length() > 0)
			sub.add(subStr);
		return sub;
	}
}