/*
 *                    BioJava development code
 *
 * This code may be freely distributed and modified under the
 * terms of the GNU Lesser General Public Licence.  This should
 * be distributed with the code.  If you do not have a copy,
 * see:
 *
 *      http://www.gnu.org/copyleft/lesser.html
 *
 * Copyright for this code is held jointly by the individual
 * authors.  These should be listed in @author doc comments.
 *
 * For more information on the BioJava project and its aims,
 * or to join the biojava-l mailing list, visit the home page
 * at:
 *
 *      http://www.biojava.org/
 *
 */
package org.biojava.nbio.aaproperties.xml;

import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
import org.biojava.nbio.core.sequence.template.CompoundSet;
import org.biojava.nbio.core.sequence.template.Sequence;

import java.util.*;

public class ModifiedAminoAcidCompoundSet implements CompoundSet<AminoAcidCompound> {

    private final Map<String, AminoAcidCompound> aminoAcidCompoundCache = new HashMap<String, AminoAcidCompound>();

    public ModifiedAminoAcidCompoundSet(List<AminoAcidComposition> aaList, Map<Character, Double> aaSymbol2MolecularWeight) {
        this.aminoAcidCompoundCache.put("-", new AminoAcidCompound(null, "-", "", "", 0.0f));
        for (AminoAcidComposition aa : aaList) {
            this.aminoAcidCompoundCache.put(aa.getSymbol(),
                    new AminoAcidCompound(null, aa.getSymbol(), aa.getShorName(), aa.getName(),
                            aaSymbol2MolecularWeight.get(aa.getSymbol().charAt(0)).floatValue()));
        }
    }

    @Override
    public int getMaxSingleCompoundStringLength() {
        return 1;
    }

    @Override
    public boolean isCompoundStringLengthEqual() {
        return true;
    }

    @Override
    public AminoAcidCompound getCompoundForString(String string) {
        if (string.length() == 0) {
            return null;
        }
        if (string.length() > this.getMaxSingleCompoundStringLength()) {
            throw new IllegalArgumentException("String supplied (" + string + ") is too long. Max is " + getMaxSingleCompoundStringLength());
        }
        return this.aminoAcidCompoundCache.get(string);
    }

    @Override
    public String getStringForCompound(AminoAcidCompound compound) {
        return compound.toString();
    }

    @Override
    public boolean compoundsEquivalent(AminoAcidCompound compoundOne, AminoAcidCompound compoundTwo) {
        // TODO Auto-generated method stub
        return false;
    }

    @Override
    public Set<AminoAcidCompound> getEquivalentCompounds(AminoAcidCompound compound) {
        // TODO Auto-generated method stub
        return null;
    }

    @Override
    public boolean hasCompound(AminoAcidCompound compound) {
        return aminoAcidCompoundCache.containsValue(compound);
    }

    @Override
    public List<AminoAcidCompound> getAllCompounds() {
        return new ArrayList<AminoAcidCompound>(aminoAcidCompoundCache.values());
    }

    @Override
    public boolean isComplementable() {
        return false;
    }

    @Override
    public boolean isValidSequence(Sequence<AminoAcidCompound> sequence) {
        for (AminoAcidCompound c : sequence) {
            if (!hasCompound(c)) {
                return false;
            }
        }
        return true;
    }

}
