package compbio.controllers;

import java.util.List;
import java.util.Map;
import java.util.regex.Pattern;

import org.springframework.stereotype.Controller;
import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RequestMethod;
import org.springframework.web.bind.annotation.RequestParam;

import compbio.beans.ProteinBean;
import compbio.beans.TotalByCounterBean;
import compbio.cassandra.readers.ReaderByCounter;
import compbio.cassandra.readers.SequenceReader;
import compbio.statistic.CassandraRequester;

/**
 * Spring controller for sequence queries. This version works in the servlet
 * style.
 * 
 * @author Alexander Sherstnev
 * @author Natasha Sherstneva
 * 
 * @since 0.5
 * @version 1.0 December 2013
 */
@Controller
@RequestMapping("/sequence")
public class SequenceController extends BasicController {

	/**
	 * pattern for NON-protein alphabet symbols
	 */
	private final Pattern NONPROTEIN = Pattern.compile("[^ARNDCQEGHILKMFPSTWYV]+", Pattern.CASE_INSENSITIVE);

	/**
	 * form a query page for search protein sequence. The servlet should be
	 * available for users and admins only. 
	 * 
	 * @param model
	 *            MVC model
	 * @return link to the JSP query page
	 */
	@RequestMapping(value = "query", method = RequestMethod.GET)
	public String formSequenceQuery(Map<String, Object> model) {
		model.put("username", getPrincipalName());
		model.put("value", "AAAAA");
		return "query/Sequence";
	}

	/**
	 * form a query page for statistics: Protein by job count. The servlet should be
	 * available for users and admins only. 
	 * 
	 * @param model
	 *            MVC model
	 * @return link to the JSP query page
	 */
	@RequestMapping(value = "counts/query", method = RequestMethod.GET)
	public String formCounterQuery(Map<String, Object> model) {
		model.put("username", getPrincipalName());
		model.put("value", 5);
		return "query/SequenceCounts";
	}

	/**
	 * form a report page for search protein sequence.
	 * 
	 * @param model
	 *            MVC model object
	 * @param sequence
	 *            protein sequence or part of sequence
	 * @param searchtype
	 *            defined whether the whole sequence or part of sequence would be searched
	 * @return link to the report JSP page
	 */
	@RequestMapping(value = "sequence/results", method = RequestMethod.GET)
	public String findSequence(@RequestParam("sequence") String sequence, @RequestParam("searchtype") String searchtype,
			Map<String, Object> model) {
		model.put("username", getPrincipalName());
		final long startTime = System.currentTimeMillis();

		// input checks
		String trimmedsequence = sequence.replaceAll("\\s", "");
		if (trimmedsequence.equalsIgnoreCase("")) {
			model.put("error", "The sequence cann't be empty");
			model.put("value", sequence);
			return "query/Sequence";
		}
		if (NONPROTEIN.matcher(trimmedsequence).find()) {
			model.put("error", "The sequence contains symbols not from the standard protein alphabet");
			model.put("value", sequence);
			return "query/Sequence";
		}

		model.put("njobs", 0);
		model.put("prot", trimmedsequence);
		model.put("searchtype", searchtype);

		if (0 < trimmedsequence.length()) {
			SequenceReader reader = new SequenceReader();
			List<ProteinBean> result = reader.readProteins(trimmedsequence, searchtype);
			model.put("results", result);
			if (null != result) {
				if (searchtype.equals("whole"))
					model.put("njobs", result.get(0).getJobid().size());
				else
					model.put("njobs", result.size());
			}
		}
		final long endTime = System.currentTimeMillis();
		model.put("timeExecution", (endTime - startTime));
		return "reportProteinSequences";
	}

	/**
	 * form a report page for statistics: Protein by job count.
	 * 
	 * @param model
	 *            MVC model object
	 * @param counter
	 *           
	 * @return link to the report JSP page
	 */
	@RequestMapping(value = "counts/results", method = RequestMethod.GET)
	public String countSequences(@RequestParam("counterJob") String counter, Map<String, Object> model) {
		model.put("username", getPrincipalName());
		final long startTime = System.currentTimeMillis();

		if (counter.equals("")) {
			model.put("error", "The value must not be empty");
			model.put("value", counter);
			return "query/SequenceCounts";
		}

		int realcounter;
		try {
			realcounter = Integer.parseInt(counter.trim());
		} catch (NumberFormatException e) {
			model.put("error", "The value must be an integer number");
			model.put("value", counter);
			return "query/SequenceCounts";
		}

		if (realcounter < 1) {
			model.put("error", "The value must be greater than 0");
			model.put("value", counter);
			return "query/SequenceCounts";
		}

		ReaderByCounter reader = new ReaderByCounter();

		List<TotalByCounterBean> r = reader.readProteinByCounter(realcounter);
		model.put("results", r);
		model.put("njobs", 0);
		if (null != r) {
			model.put("njobs", r.size());
		}
		final long endTime = System.currentTimeMillis();
		model.put("timeExecution", (endTime - startTime));
		model.put("counter", realcounter);
		return "reportProteinSequencesCounter";
	}

}