// $Id:
// FORESTER -- software libraries and applications
// for evolutionary biology research and applications.
//
// Copyright (C) 2017 Christian M. Zmasek
// Copyright (C) 2017 J. Craig Venter Institute
// 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: phyloxml @ gmail . com
// WWW: https://sites.google.com/site/cmzmasek/home/software/forester

package org.forester.application;

import java.io.File;
import java.io.IOException;
import java.text.DecimalFormat;
import java.util.ArrayList;
import java.util.List;
import java.util.regex.Pattern;
import java.util.regex.PatternSyntaxException;

import org.forester.clade_analysis.AnalysisMulti;
import org.forester.clade_analysis.Prefix;
import org.forester.clade_analysis.ResultMulti;
import org.forester.io.parsers.PhylogenyParser;
import org.forester.io.parsers.util.ParserUtils;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
import org.forester.phylogeny.factories.PhylogenyFactory;
import org.forester.util.CommandLineArguments;
import org.forester.util.EasyWriter;
import org.forester.util.ForesterUtil;

public final class cladinator {

    final static private String        PRG_NAME                 = "cladinator";
    final static private String        PRG_VERSION              = "1.00";
    final static private String        PRG_DATE                 = "170902";
    final static private String        PRG_DESC                 = "clades within clades of annotated labels -- analysis of pplacer-type outputs";
    final static private String        E_MAIL                   = "phyloxml@gmail.com";
    final static private String        WWW                      = "https://sites.google.com/site/cmzmasek/home/software/forester";
    final static private String        HELP_OPTION_1            = "help";
    final static private String        HELP_OPTION_2            = "h";
    final static private String        SEP_OPTION               = "s";
    final static private String        QUERY_PATTERN_OPTION     = "q";
    final static private String        SPECIFICS_CUTOFF_OPTION  = "c";
    final static private double        SPECIFICS_CUTOFF_DEFAULT = 0.8;
    final static private String        SEP_DEFAULT              = ".";
    final static private Pattern       QUERY_PATTERN_DEFAULT    = AnalysisMulti.DEFAULT_QUERY_PATTERN_FOR_PPLACER_TYPE;
    private final static DecimalFormat df                       = new DecimalFormat( "0.0#######" );

    public static void main( final String args[] ) {
        try {
            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( HELP_OPTION_1 ) || cla.isOptionSet( HELP_OPTION_2 ) ) {
                System.out.println();
                print_help();
                System.exit( 0 );
            }
            if ( ( cla.getNumberOfNames() != 1 ) && ( cla.getNumberOfNames() != 2 ) ) {
                print_help();
                System.exit( -1 );
            }
            final List<String> allowed_options = new ArrayList<>();
            allowed_options.add( SEP_OPTION );
            allowed_options.add( QUERY_PATTERN_OPTION );
            allowed_options.add( SPECIFICS_CUTOFF_OPTION );
            final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options );
            if ( dissallowed_options.length() > 0 ) {
                ForesterUtil.fatalError( PRG_NAME, "unknown option(s): " + dissallowed_options );
            }
            double cutoff_specifics = SPECIFICS_CUTOFF_DEFAULT;
            if ( cla.isOptionSet( SPECIFICS_CUTOFF_OPTION ) ) {
                if ( cla.isOptionValueSet( SPECIFICS_CUTOFF_OPTION ) ) {
                    cutoff_specifics = cla.getOptionValueAsDouble( SPECIFICS_CUTOFF_OPTION );
                    if ( cutoff_specifics < 0 ) {
                        ForesterUtil.fatalError( PRG_NAME, "cutoff cannot be negative" );
                    }
                }
                else {
                    ForesterUtil.fatalError( PRG_NAME, "no value for cutoff for specifics" );
                }
            }
            String separator = SEP_DEFAULT;
            if ( cla.isOptionSet( SEP_OPTION ) ) {
                if ( cla.isOptionValueSet( SEP_OPTION ) ) {
                    separator = cla.getOptionValue( SEP_OPTION );
                }
                else {
                    ForesterUtil.fatalError( PRG_NAME, "no value for separator option" );
                }
            }
            Pattern compiled_query_str = null;
            if ( cla.isOptionSet( QUERY_PATTERN_OPTION ) ) {
                if ( cla.isOptionValueSet( QUERY_PATTERN_OPTION ) ) {
                    final String query_str = cla.getOptionValue( QUERY_PATTERN_OPTION );
                    try {
                        compiled_query_str = Pattern.compile( query_str );
                    }
                    catch ( final PatternSyntaxException e ) {
                        ForesterUtil.fatalError( PRG_NAME, "error in regular expression: " + e.getMessage() );
                    }
                }
                else {
                    ForesterUtil.fatalError( PRG_NAME, "no value for query pattern option" );
                }
            }
            final Pattern pattern = ( compiled_query_str != null ) ? compiled_query_str : QUERY_PATTERN_DEFAULT;
            final File intreefile = cla.getFile( 0 );
            final String error_intreefile = ForesterUtil.isReadableFile( intreefile );
            if ( !ForesterUtil.isEmpty( error_intreefile ) ) {
                ForesterUtil.fatalError( PRG_NAME, error_intreefile );
            }
            final File outtablefile;
            if ( cla.getNumberOfNames() > 1 ) {
                outtablefile = cla.getFile( 1 );
                final String error_outtablefile = ForesterUtil.isWritableFile( outtablefile );
                if ( !ForesterUtil.isEmpty( error_outtablefile ) ) {
                    ForesterUtil.fatalError( PRG_NAME, error_outtablefile );
                }
            }
            else {
                outtablefile = null;
            }
            System.out.println( "Input tree                 : " + intreefile );
            System.out.println( "Specific-hit support cutoff: " + cutoff_specifics );
            System.out.println( "Annotation-separator       : " + separator );
            System.out.println( "Query pattern              : " + pattern );
            if ( outtablefile != null ) {
                System.out.println( "Output table               : " + outtablefile );
            }
            Phylogeny p = null;
            try {
                final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
                final PhylogenyParser pp = ParserUtils.createParserDependingOnFileType( intreefile, true );
                p = factory.create( intreefile, pp )[ 0 ];
            }
            catch ( final IOException e ) {
                ForesterUtil.fatalError( PRG_NAME, "Could not read \"" + intreefile + "\" [" + e.getMessage() + "]" );
                System.exit( -1 );
            }
            System.out.println( "Ext. nodes in input tree   : " + p.getNumberOfExternalNodes() );
            final ResultMulti res = AnalysisMulti.execute( p, pattern, separator, cutoff_specifics );
            printResult( res );
            if ( outtablefile != null ) {
                writeResultToTable( res, outtablefile );
            }
        }
        catch ( final IllegalArgumentException e ) {
            ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
        }
        catch ( final IOException e ) {
            ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
        }
        catch ( final Exception e ) {
            e.printStackTrace();
            ForesterUtil.fatalError( PRG_NAME, "Unexpected errror!" );
        }
    }

    private final static void printResult( final ResultMulti res ) {
        System.out.println();
        System.out.println( "Result:" );
        System.out.println();
        if ( ( res.getAllMultiHitPrefixes() == null ) | ( res.getAllMultiHitPrefixes().size() < 1 ) ) {
            System.out.println( "No match to query pattern!" );
        }
        else {
            System.out.println( "Matching Clade(s):" );
            for( final Prefix prefix : res.getCollapsedMultiHitPrefixes() ) {
                System.out.println( prefix );
            }
            if ( res.isHasSpecificMultiHitsPrefixes() ) {
                System.out.println();
                System.out.println( "Specific-hit(s):" );
                for( final Prefix prefix : res.getSpecificMultiHitPrefixes() ) {
                    System.out.println( prefix );
                }
                System.out.println();
                System.out.println( "Matching Clade(s) with Specific-hit(s):" );
                for( final Prefix prefix : res.getCollapsedMultiHitPrefixes() ) {
                    System.out.println( prefix );
                    for( final Prefix spec : res.getSpecificMultiHitPrefixes() ) {
                        if ( spec.getPrefix().startsWith( prefix.getPrefix() ) ) {
                            System.out.println( "    " + spec );
                        }
                    }
                }
            }
            if ( !ForesterUtil.isEmpty( res.getAllMultiHitPrefixesDown() ) ) {
                System.out.println();
                System.out.println( "Matching Down-tree Bracketing Clade(s):" );
                for( final Prefix prefix : res.getCollapsedMultiHitPrefixesDown() ) {
                    System.out.println( prefix );
                }
            }
            if ( !ForesterUtil.isEmpty( res.getAllMultiHitPrefixesUp() ) ) {
                System.out.println();
                System.out.println( "Matching Up-tree Bracketing Clade(s):" );
                for( final Prefix prefix : res.getCollapsedMultiHitPrefixesUp() ) {
                    System.out.println( prefix );
                }
            }
        }
        System.out.println();
    }

    private final static void writeResultToTable( final ResultMulti res, final File outtablefile ) throws IOException {
        final EasyWriter w = ForesterUtil.createEasyWriter( outtablefile );
        if ( ( res.getAllMultiHitPrefixes() == null ) | ( res.getAllMultiHitPrefixes().size() < 1 ) ) {
            w.println( "No match to query pattern!" );
        }
        else {
            for( final Prefix prefix : res.getCollapsedMultiHitPrefixes() ) {
                w.print( "Matching Clades" );
                w.print( "\t" );
                w.print( prefix.getPrefix() );
                w.print( "\t" );
                w.print( df.format( prefix.getConfidence() ) );
                w.println();
            }
            if ( res.isHasSpecificMultiHitsPrefixes() ) {
                for( final Prefix prefix : res.getSpecificMultiHitPrefixes() ) {
                    w.print( "Specific-hits" );
                    w.print( "\t" );
                    w.print( prefix.getPrefix() );
                    w.print( "\t" );
                    w.print( df.format( prefix.getConfidence() ) );
                    w.println();
                }
            }
            if ( !ForesterUtil.isEmpty( res.getAllMultiHitPrefixesDown() ) ) {
                for( final Prefix prefix : res.getCollapsedMultiHitPrefixesDown() ) {
                    w.print( "Matching Down-tree Bracketing Clades" );
                    w.print( "\t" );
                    w.print( prefix.getPrefix() );
                    w.print( "\t" );
                    w.print( df.format( prefix.getConfidence() ) );
                    w.println();
                }
            }
            if ( !ForesterUtil.isEmpty( res.getAllMultiHitPrefixesUp() ) ) {
                for( final Prefix prefix : res.getCollapsedMultiHitPrefixesUp() ) {
                    w.print( "Matching Up-tree Bracketing Clades" );
                    w.print( "\t" );
                    w.print( prefix.getPrefix() );
                    w.print( "\t" );
                    w.print( df.format( prefix.getConfidence() ) );
                    w.println();
                }
            }
        }
        w.flush();
        w.close();
    }

    private final static void print_help() {
        System.out.println( "Usage:" );
        System.out.println();
        System.out.println( PRG_NAME + " [options] <input tree file> [output table file]" );
        System.out.println();
        System.out.println( " options:" );
        System.out.println( "  -" + SPECIFICS_CUTOFF_OPTION
                + "=<double>: the cutoff for \"specific-hit\" support values (default: " + SPECIFICS_CUTOFF_DEFAULT
                + ")" );
        System.out.println( "  -" + SEP_OPTION + "=<separator>: the annotation-separator to be used (default: "
                + SEP_DEFAULT + ")" );
        System.out.println( "  -" + QUERY_PATTERN_OPTION
                + "=<query pattern>: the regular expression for the query (default: \"" + QUERY_PATTERN_DEFAULT
                + "\" for pplacer output)" );
        System.out.println();
        System.out.println( "Example:" );
        System.out.println();
        System.out.println( " " + PRG_NAME + " -c=0.5 -s=. my_tree.nh result.tsv" );
        System.out.println();
    }
}