// $Id:
// FORESTER -- software libraries and applications
// for evolutionary biology research and applications.
//
// Copyright (C) 2008-2009 Christian M. Zmasek
// Copyright (C) 2008-2009 Burnham Institute for Medical Research
// All rights reserved
//
// This library is free software; you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Public
// License as published by the Free Software Foundation; either
// version 2.1 of the License, or (at your option) any later version.
//
// 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 GNU
// Lesser General Public License for more details.
//
// You should have received a copy of the GNU Lesser General Public
// License along with this library; if not, write to the Free Software
// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
//
// Contact: phylosoft @ gmail . com
// WWW: www.phylosoft.org/forester

package org.forester.application;

import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Date;
import java.util.List;

import org.forester.io.parsers.PhylogenyParser;
import org.forester.io.parsers.nhx.NHXParser;
import org.forester.io.parsers.phyloxml.PhyloXmlParser;
import org.forester.io.parsers.util.ParserUtils;
import org.forester.io.writers.PhylogenyWriter;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyMethods;
import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
import org.forester.phylogeny.factories.PhylogenyFactory;
import org.forester.sdi.GSDI;
import org.forester.sdi.SDI;
import org.forester.sdi.SDIse;
import org.forester.util.CommandLineArguments;
import org.forester.util.ForesterUtil;

public final class gsdi {

    final static public boolean REPLACE_UNDERSCORES_IN_NH_SPECIES_TREE = true;
    final static private String STRIP_OPTION                           = "s";
    final static private String ALLOW_STRIPPING_OF_GENE_TREE_OPTION       = "g";
    
    final static private String SDI_OPTION                             = "b";
    final static private String MOST_PARSIMONIOUS_OPTION               = "m";
    final static private String GUESS_FORMAT_OF_SPECIES_TREE           = "q";
    final static private String HELP_OPTION_1                          = "help";
    final static private String HELP_OPTION_2                          = "h";
    final static private String DEFAULT_OUTFILE_SUFFIX                 = "_gsdi_out.phylo.xml";
    final static private String SUFFIX_FOR_LIST_OF_STIPPED_GENE_TREE_NODES = "_stripped_gene_tree_nodes.txt";
    final static private String SUFFIX_FOR_LOG_FILE                    = "_gsdi_log.txt";    
    final static private String PRG_NAME                               = "gsdi";
    final static private String PRG_VERSION                            = "0.901";
    final static private String PRG_DATE                               = "120608";
    final static private String PRG_DESC                               = "general speciation duplication inference";
    final static private String E_MAIL                                 = "phylosoft@gmail.com";
    final static private String WWW                                    = "www.phylosoft.org/forester";

    public static void main( final String args[] ) {
        ForesterUtil.printProgramInformation( PRG_NAME,
                                              PRG_DESC,
                                              PRG_VERSION,
                                              PRG_DATE,
                                              E_MAIL,
                                              WWW,
                                              ForesterUtil.getForesterLibraryInformation() );
        CommandLineArguments cla = null;
        try {
            cla = new CommandLineArguments( args );
        }
        catch ( final Exception e ) {
            ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
        }
        if ( cla.isOptionSet( gsdi.HELP_OPTION_1 ) || cla.isOptionSet( gsdi.HELP_OPTION_2 ) ) {
            System.out.println();
            gsdi.print_help();
            System.exit( 0 );
        }
        else if ( ( args.length < 2 ) || ( cla.getNumberOfNames() < 2 ) || ( cla.getNumberOfNames() > 3 ) ) {
            System.out.println();
            System.out.println( "Wrong number of arguments." );
            System.out.println();
            gsdi.print_help();
            System.exit( -1 );
        }
        final List<String> allowed_options = new ArrayList<String>();
        allowed_options.add( gsdi.STRIP_OPTION );
        allowed_options.add( gsdi.SDI_OPTION );
        allowed_options.add( gsdi.GUESS_FORMAT_OF_SPECIES_TREE );
        allowed_options.add( gsdi.MOST_PARSIMONIOUS_OPTION );
        allowed_options.add( gsdi.ALLOW_STRIPPING_OF_GENE_TREE_OPTION );
        
        final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options );
        if ( dissallowed_options.length() > 0 ) {
            ForesterUtil.fatalError( gsdi.PRG_NAME, "unknown option(s): " + dissallowed_options );
        }
        boolean use_sdise = false;
        boolean strip = false;
        boolean most_parsimonous_duplication_model = false;
        boolean species_tree_in_phyloxml = true;
        boolean allow_stripping_of_gene_tree = false;
        if ( cla.isOptionSet( gsdi.STRIP_OPTION ) ) {
            strip = true;
        }
        if ( cla.isOptionSet( gsdi.SDI_OPTION ) ) {
            use_sdise = true;
        }
        if ( cla.isOptionSet( gsdi.MOST_PARSIMONIOUS_OPTION ) ) {
            if ( use_sdise ) {
                ForesterUtil.fatalError( gsdi.PRG_NAME, "Can only use most parsimonious duplication mode with GSDI" );
            }
            most_parsimonous_duplication_model = true;
        }
        if ( cla.isOptionSet( gsdi.GUESS_FORMAT_OF_SPECIES_TREE ) ) {
            species_tree_in_phyloxml = false;
        }
        if ( cla.isOptionSet( gsdi.ALLOW_STRIPPING_OF_GENE_TREE_OPTION ) ) {
            if ( use_sdise ) {
                ForesterUtil.fatalError( gsdi.PRG_NAME, "Can only allow stripping of gene tree with GSDI" );
            }
            allow_stripping_of_gene_tree = true;
        }
       
        
        
        Phylogeny species_tree = null;
        Phylogeny gene_tree = null;
        File gene_tree_file = null;
        File species_tree_file = null;
        File out_file = null;
        try {
            gene_tree_file = cla.getFile( 0 );
            species_tree_file = cla.getFile( 1 );
            if ( cla.getNumberOfNames() == 3 ) {
                out_file = cla.getFile( 2 );
            }
            else {
                out_file = new File( ForesterUtil.removeSuffix( gene_tree_file.toString() ) + DEFAULT_OUTFILE_SUFFIX );
                //out_file = new File( gsdi.DEFAULT_OUTFILE );
            }
        }
        catch ( final IllegalArgumentException e ) {
            ForesterUtil.fatalError( gsdi.PRG_NAME, "error in command line: " + e.getMessage() );
        }
        if ( ForesterUtil.isReadableFile( gene_tree_file ) != null ) {
            ForesterUtil.fatalError( gsdi.PRG_NAME, ForesterUtil.isReadableFile( gene_tree_file ) );
        }
        if ( ForesterUtil.isReadableFile( species_tree_file ) != null ) {
            ForesterUtil.fatalError( gsdi.PRG_NAME, ForesterUtil.isReadableFile( species_tree_file ) );
        }
        if ( ForesterUtil.isWritableFile( out_file ) != null ) {
            ForesterUtil.fatalError( gsdi.PRG_NAME, ForesterUtil.isWritableFile( out_file ) );
        }
        try {
            final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
            if ( species_tree_in_phyloxml ) {
                species_tree = factory.create( species_tree_file, new PhyloXmlParser() )[ 0 ];
            }
            else {
                final PhylogenyParser p = ParserUtils.createParserDependingOnFileType( species_tree_file, true );
                if ( REPLACE_UNDERSCORES_IN_NH_SPECIES_TREE && ( p instanceof NHXParser ) ) {
                    ( ( NHXParser ) p ).setReplaceUnderscores( true );
                }
                species_tree = factory.create( species_tree_file, p )[ 0 ];
                PhylogenyMethods.transferNodeNameToField( species_tree,
                                                          PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME );
            }
        }
        catch ( final IOException e ) {
            ForesterUtil.fatalError( gsdi.PRG_NAME,
                                     "Failed to read species tree from [" + gene_tree_file + "]: " + e.getMessage() );
        }
        try {
            final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
            gene_tree = factory.create( gene_tree_file, new PhyloXmlParser() )[ 0 ];
        }
        catch ( final IOException e ) {
            ForesterUtil.fatalError( gsdi.PRG_NAME,
                                     "Failed to read gene tree from [" + gene_tree_file + "]: " + e.getMessage() );
        }
        gene_tree.setRooted( true );
        species_tree.setRooted( true );
        if ( !gene_tree.isCompletelyBinary() ) {
            ForesterUtil.fatalError( gsdi.PRG_NAME, "gene tree (\"" + gene_tree_file + "\") is not completely binary" );
        }
        if ( use_sdise ) {
            if ( !species_tree.isCompletelyBinary() ) {
                ForesterUtil.fatalError( gsdi.PRG_NAME, "species tree (\"" + species_tree_file
                        + "\") is not completely binary" );
            }
        }
        // For timing.
        // gene_tree = Helper.createBalancedTree( 10 );
        // species_tree = Helper.createBalancedTree( 13 );
        // species_tree = Helper.createUnbalancedTree( 1024 );
        // gene_tree = Helper.createUnbalancedTree( 8192 );
        // species_tree = gene_tree.copyTree();
        // gene_tree = species_tree.copyTree();
        // Helper.numberSpeciesInOrder( species_tree );
        // Helper.numberSpeciesInOrder( gene_tree );
        // Helper.randomizeSpecies( 1, 8192, gene_tree );
        // Helper.intervalNumberSpecies( gene_tree, 4096 );
        // Helper.numberSpeciesInDescOrder( gene_tree );
        System.out.println();
        System.out.println( "Strip species tree: " + strip );
        SDI sdi = null;
        final long start_time = new Date().getTime();
        try {
            if ( use_sdise ) {
                System.out.println();
                System.out.println( "Using SDIse algorithm" );
                sdi = new SDIse( gene_tree, species_tree );
            }
            else {
                System.out.println();
                System.out.println( "Using GSDI algorithm" );
                System.out.println();
                System.out.println( "Use most parsimonous duplication model: " + most_parsimonous_duplication_model );
                System.out.println( "Allow stripping of gene tree nodes    : " + allow_stripping_of_gene_tree );
                sdi = new GSDI( gene_tree, species_tree, most_parsimonous_duplication_model, allow_stripping_of_gene_tree );
              
            }
        }
        catch ( final Exception e ) {
            ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() );
        }
        System.out.println();
        System.out.println( "Running time (excluding I/O): " + ( new Date().getTime() - start_time ) + "ms" );
        try {
            final PhylogenyWriter writer = new PhylogenyWriter();
            writer.toPhyloXML( out_file, gene_tree, 0 );
        }
        catch ( final IOException e ) {
            ForesterUtil.fatalError( PRG_NAME, "Failed to write to [" + out_file + "]: " + e.getMessage() );
        }
        System.out.println();
        System.out.println( "Successfully wrote resulting gene tree to: " + out_file );
        System.out.println();
        if ( use_sdise ) {
            sdi.computeMappingCostL();
            System.out.println( "Mapping cost                    : " + sdi.computeMappingCostL() );
        }
        System.out.println( "Number of duplications          : " + sdi.getDuplicationsSum() );
        if ( !use_sdise && !most_parsimonous_duplication_model ) {
            System.out.println( "Number of potential duplications: "
                    + ( ( GSDI ) sdi ).getSpeciationOrDuplicationEventsSum() );
        }
        if ( !use_sdise ) {
            System.out.println( "Number of speciations            : " + ( ( GSDI ) sdi ).getSpeciationsSum() );
        }
        System.out.println();
        some stat on gene tree:
            filename, name
            number of external nodes, strppided nodes
        some stats on sepcies tree, external nodes,
        filename, name
        internal nodes
        how many of which are polytomies
        //wrote log file to
        if ( allow_stripping_of_gene_tree ) {
            stripped x nodes, y external nodes remain
            
            
        }
    }

    private static void print_help() {
        System.out.println( "Usage: " + gsdi.PRG_NAME
                + " [-options] <gene tree in phyloXML format> <species tree in phyloXML format> [outfile]" );
        System.out.println();
        System.out.println( "Options:" );
        System.out.println( " -" + gsdi.ALLOW_STRIPPING_OF_GENE_TREE_OPTION + ": to allow stripping of gene tree nodes without a matching species in the species tree (writes list of stripped nodes to " + );
        System.out.println( " -" + gsdi.STRIP_OPTION + ": to strip the species tree of unneeded species prior to duplication inference" );
        System.out.println( " -" + gsdi.SDI_OPTION + ": to use SDI algorithm instead of GSDI algorithm" );//TODO gsdi.ALLOW_STRIPPING_OF_GENE_TREE_OPTION not allowed
        System.out.println( " -" + gsdi.MOST_PARSIMONIOUS_OPTION
                + ": use most parimonious duplication model for GSDI: " );
        System.out.println( "     assign nodes as speciations which would otherwise be assiged" );
        System.out.println( "     as unknown because of polytomies in the species tree" );
        System.out.println( " -" + gsdi.GUESS_FORMAT_OF_SPECIES_TREE + ": to allow species tree in other formats than" );
        System.out.println( "     phyloXML (Newick, NHX, Nexus)" );
        
        
        System.out.println();
        System.out.println( "Species tree:" );
        System.out.println( " In phyloXML format (unless option -" + gsdi.GUESS_FORMAT_OF_SPECIES_TREE
                + " is used, in which case the species matching between gene tree and species tree must be via scientific name), with taxonomy data in appropriate fields" );
        System.out.println();
        System.out.println( "Gene tree:" );
        System.out.println( " In phyloXM format, with taxonomy and sequence data in appropriate fields" );
        System.out.println();
        System.out.println( "Example:" );
        System.out.println( "gsdi 
        System.out.println();
        System.out.println( "Note -- GSDI algorithm is under development" );
        System.out.println();
    }
}