/*
 * Copyright (C) 2009-2010 Institute for Computational Biomedicine,
 *                    Weill Medical College of Cornell University
 *
 *  This program is free software; you can redistribute it and/or modify
 *  it under the terms of the GNU General Public License as published by
 *  the Free Software Foundation; either version 3 of the License, or
 *  (at your option) any later version.
 *
 *  This program 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
 *  GNU General Public License for more details.
 *
 *  You should have received a copy of the GNU General Public License
 *  along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */

package edu.cornell.med.icb.goby.modes;

import com.martiansoftware.jsap.JSAPException;
import com.martiansoftware.jsap.JSAPResult;
import edu.cornell.med.icb.goby.alignments.Merge;
import edu.cornell.med.icb.goby.alignments.AlignmentReaderImpl;

import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;

/**
 * Merge several compact alignment files to an alignment file.   Merge is used
 * when assembling results after searching by chromosome or by transcripts.  It
 * is especially useful if the reference does not fit into memory of a computer
 * used for alignment, for example, when searching against transcripts.
 *
 * Each input file must have been generated by searching the same set of
 * reads against different subset of reference sequences. Merging consists of
 * putting back the results as if the set of reads had been searched against
 * the combined reference.
 *
 * Several merging strategies are supported by this class. For instance, one
 * strategy assumes that each set of reads provided as input was searched
 * against a different chromosome (or contig). Another strategy assumes that
 * the reads were aligned to cDNA/transcript individual reference sequences.
 *
 * @author Kevin Dorff
 * @author Fabien Campagne
 */
public class MergeCompactAlignmentsMode extends AbstractGobyMode {
    /**
     * The mode name.
     */
    private static final String MODE_NAME = "merge-compact-alignments";

     /**
      * The mode description help text.
      */
    private static final String MODE_DESCRIPTION = "Merge several compact alignment files to an "
             + "alignment file.   Merge is used when assembling results after searching by "
             + "chromosome or by transcripts.  It is especially useful if the reference does not "
             + "fit into memory of a computer used for alignment, for example, when searching "
             + "against transcripts.  Each input file must have been generated by searching "
             + "the same set of reads against different subset of reference sequences. Merging "
             + "consists of putting back the results as if the set of reads had been searched "
             + "against the combined reference.  Several merging strategies are supported by "
             + "this class. For instance, one strategy assumes that each set of reads provided "
             + "as input was searched against a different chromosome (or contig). Another "
             + "strategy assumes that the reads were aligned to cDNA/transcript individual "
             + "reference sequences.";

    /**
     * Max number of duplicates allowed for the top quality score when there are dupes.
     */
    private static final int K_NUM_OF_BEST_QUAL_TO_KEEP = 2;

    /**
     * The input file.
     */
    private List<File> inputFiles;

    private String geneTranscriptMapFile;

    /**
     * The output file.
     */
    private String outputFile;

    /**
     * Max number of duplicates allowed for the top quality score when there are dupes.
     */
    private int k;

    /**
     * Map to override help / default values.
     */
    private static final Map<String, String> HELP_VALUES;

    static {
        HELP_VALUES = new HashMap<String, String>();
        HELP_VALUES.put("[K_VALUE]", Integer.toString(K_NUM_OF_BEST_QUAL_TO_KEEP));
    }

    @Override
    public String getModeName() {
        return MODE_NAME;
    }

    @Override
    public String getModeDescription() {
        return MODE_DESCRIPTION;
    }

    /**
     * Configure the mode via command line arguments.
     *
     * @param args command line arguments
     * @return this object for chaining
     * @throws IOException error configuring
     * @throws JSAPException error configuring
     */
    @Override
    public AbstractCommandLineMode configure(final String[] args) throws IOException, JSAPException {
        final JSAPResult jsapResult = parseJsapArguments(args, HELP_VALUES);

        final String[] inputFilesAr = jsapResult.getStringArray("input");

        inputFiles = new ArrayList<File>(inputFilesAr.length);
        for (final String file : inputFilesAr) {
            final String basename = AlignmentReaderImpl.getBasename(file);
            inputFiles.add(new File(basename));
        }
        outputFile = jsapResult.getString("output");
        k = jsapResult.getInt("k");
        geneTranscriptMapFile = jsapResult.getString("gene-transcript-map-file");
        System.out.println("Configured with k=" + k);
        return this;
    }

    /**
     * Run the merge mode.
     *
     * @throws java.io.IOException error reading / writing
     */
    @Override
    public void execute() throws IOException {
        final Merge merger = new Merge(geneTranscriptMapFile, k);
        merger.setSilent(false);
        merger.merge(inputFiles, outputFile);
    }

    /**
     * Main method.
     *
     * @param args command line args.
     * @throws com.martiansoftware.jsap.JSAPException
     *                             error parsing
     * @throws java.io.IOException error parsing or executing.
     */
    public static void main(final String[] args) throws JSAPException, IOException {
        new MergeCompactAlignmentsMode().configure(args).execute();
    }
}
