// $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: https://sites.google.com/site/cmzmasek/home/software/forester

package org.forester.protein;

import java.util.ArrayList;
import java.util.Collections;
import java.util.Comparator;
import java.util.List;
import java.util.SortedSet;
import java.util.TreeSet;

import org.forester.species.BasicSpecies;
import org.forester.species.Species;
import org.forester.util.ForesterUtil;

// Note: when implementing any "equals" method need to keep in mind that
// proteins could have the same name and/or id!
public class BasicProtein implements Protein {

    private final ProteinId          _id;
    private final int                _length;
    private final Species            _species;
    private String                   _name;
    private String                   _desc;
    private String                   _accession;
    private final List<Domain>       _protein_domains;
    public static Comparator<Domain> DomainMidPositionComparator = new Comparator<Domain>() {

        @Override
        public int compare( final Domain d1,
                            final Domain d2 ) {
            final int m1 = ( d1.getTo() + d1.getFrom() );
            final int m2 = ( d2.getTo() + d2.getFrom() );
            return m1 < m2 ? -1 : m1 > m2 ? 1 : d1
                    .getDomainId()
                    .compareTo( d2.getDomainId() );
        }
    };

    public BasicProtein( final String id_str, final String species_str, final int length ) {
        if ( length < 0 ) {
            throw new IllegalArgumentException( "attempt to create protein of length " + length );
        }
        if ( ForesterUtil.isEmpty( id_str ) ) {
            throw new IllegalArgumentException( "attempt to create protein with null or empty identifier" );
        }
        if ( ForesterUtil.isEmpty( species_str ) ) {
            throw new IllegalArgumentException( "attempt to create protein with null or empty species" );
        }
        _id = new ProteinId( id_str );
        _species = new BasicSpecies( species_str );
        _length = length;
        _protein_domains = new ArrayList<Domain>();
        init();
    }

    @Override
    public void addProteinDomain( final Domain protein_domain ) {
        getProteinDomains().add( protein_domain );
    }

    @Override
    /**
     * If in_nc_order is set to true, this returns true only and only if
     * the order in List 'domains' and this protein (as determined by the start positions
     * of the domains of this proteins, _not_ by their index) are the same
     * (interspersing, 'other', domains in this are ignored).
     * If in_nc_order is set to false, this returns true only and only if
     * this contains all domains listed in 'domains' (order and count do not matter).
     *
     * @param domains a list of domain ids in a certain order.
     * @param in_nc_order to consider order
     * @return
     */
    public boolean contains( final List<String> query_domain_ids, final boolean in_nc_order ) {
        if ( !in_nc_order ) {
            for( final String query_domain_id : query_domain_ids ) {
                if ( !getProteinDomainIds().contains( query_domain_id ) ) {
                    return false;
                }
            }
            return true;
        }
        else {
            int current_start_position = -1;
            I: for( final String query_domain_id : query_domain_ids ) {
                if ( getProteinDomainIds().contains( query_domain_id ) ) {
                    final List<Domain> found_domains = getProteinDomains( query_domain_id );
                    final SortedSet<Integer> ordered_start_positions = new TreeSet<Integer>();
                    for( final Domain found_domain : found_domains ) {
                        ordered_start_positions.add( found_domain.getFrom() );
                    }
                    for( final int start_position : ordered_start_positions ) {
                        if ( start_position > current_start_position ) {
                            current_start_position = start_position;
                            continue I;
                        }
                    }
                    return false;
                }
                else {
                    return false;
                }
            }
            return true;
        }
    }

    @Override
    public String getAccession() {
        return _accession;
    }

    @Override
    public String getDescription() {
        return _desc;
    }

    @Override
    public List<Domain> getDomainsSortedByPosition() {
        final List<Domain> domains = new ArrayList<Domain>( getProteinDomains().size() );
        for( final Domain domain : getProteinDomains() ) {
            domains.add( domain );
        }
        Collections.sort( domains, DomainMidPositionComparator );
        return domains;
    }

    @Override
    public int getLength() {
        return _length;
    }

    @Override
    public String getName() {
        return _name;
    }

    @Override
    public int getNumberOfProteinDomains() {
        return getProteinDomains().size();
    }

    @Override
    public Domain getProteinDomain( final int index ) {
        return _protein_domains.get( index );
    }

    @Override
    public int getProteinDomainCount( final String domain_id ) {
        return getProteinDomains( domain_id ).size();
    }

    @Override
    public List<Domain> getProteinDomains() {
        return _protein_domains;
    }

    @Override
    public List<Domain> getProteinDomains( final String domain_id ) {
        final List<Domain> domains = new ArrayList<Domain>();
        for( final Domain domain : getProteinDomains() ) {
            if ( domain.getDomainId().equals( domain_id ) ) {
                domains.add( domain );
            }
        }
        return domains;
    }

    @Override
    public ProteinId getProteinId() {
        return _id;
    }

    @Override
    public Species getSpecies() {
        return _species;
    }

    public void setAccession( final String accession ) {
        _accession = accession;
    }

    public void setDescription( final String description ) {
        _desc = description;
    }

    public void setName( final String name ) {
        _name = name;
    }

    public String toDomainArchitectureString( final String separator ) {
        final StringBuilder sb = new StringBuilder();
        boolean first = true;
        for( final Domain d : getDomainsSortedByPosition() ) {
            if ( first ) {
                first = false;
            }
            else {
                sb.append( separator );
            }
            sb.append( d.getDomainId() );
        }
        return sb.toString();
    }

    public String toDomainArchitectureString( final String separator,
                                              final int repeats_limit,
                                              final String repeat_separator ) {
        if ( repeats_limit < 3 ) {
            throw new IllegalArgumentException( "repeats limit cannot be smaller than 3" );
        }
        final StringBuilder sb = new StringBuilder();
        StringBuilder buffer = new StringBuilder();
        String prev_id = "";
        int counter = 1;
        for( final Domain d : getDomainsSortedByPosition() ) {
            final String id = d.getDomainId();
            if ( prev_id.equals( id ) ) {
                counter++;
            }
            else {
                counter = 1;
                sb.append( buffer );
                buffer = new StringBuilder();
            }
            if ( counter < repeats_limit ) {
                buffer.append( id );
                buffer.append( separator );
            }
            else if ( counter == repeats_limit ) {
                buffer = new StringBuilder();
                buffer.append( id );
                buffer.append( repeat_separator );
                buffer.append( id );
                buffer.append( repeat_separator );
                buffer.append( id );
                buffer.append( separator );
            }
            prev_id = id;
        }
        sb.append( buffer.substring( 0, buffer.length() - 1 ) );
        return sb.toString();
    }

    @Override
    public String toString() {
        return toDomainArchitectureString( "~" );
    }

    private List<String> getProteinDomainIds() {
        final List<String> ids = new ArrayList<String>( getProteinDomains().size() );
        for( final Domain domain : getProteinDomains() ) {
            ids.add( domain.getDomainId() );
        }
        return ids;
    }

    private void init() {
        _desc = "";
        _accession = "";
        _name = "";
    }
}