/*
 *                    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/
 *
 * Created on 01-21-2010
 *
 * @author Richard Holland
 *
 *
 */
package org.biojava.nbio.core.sequence.template;

import org.biojava.nbio.core.sequence.AccessionID;

import java.util.Iterator;
import java.util.List;

public class SequenceProxyView<C extends Compound> implements SequenceView<C> {

        private Integer bioStart;
        private Integer bioEnd;
        private Sequence<C> sequence;

        public SequenceProxyView() {
        }

        public SequenceProxyView(Sequence<C> sequence) {
                this(sequence, 1, sequence.getLength());
        }

        /**
         * Main constructor for working with SequenceProxyViews
         *
         * @param sequence Sequence to proxy
         * @param bioStart Start; cannot be less than 1
         * @param bioEnd End; cannot be greater than the sequence length
         */
        public SequenceProxyView(Sequence<C> sequence, Integer bioStart, Integer bioEnd) {
                this.sequence = sequence;
                setBioStart(bioStart);
                setBioEnd(bioEnd);
        }

        @Override
        public Sequence<C> getViewedSequence() {
                return sequence;
        }

        @Override
        public String getSequenceAsString() {
                return SequenceMixin.toString(this);
        }

        @Override
        public List<C> getAsList() {
                return SequenceMixin.toList(this);
        }

        @Override
        public C getCompoundAt(int position) {
                return getViewedSequence().getCompoundAt((getBioStart() + position) - 1);
        }

        @Override
        public int getIndexOf(C compound) {
                return SequenceMixin.indexOf(this, compound);
        }

        @Override
        public int getLastIndexOf(C compound) {
                return SequenceMixin.lastIndexOf(this, compound);
        }

        @Override
        public int getLength() {
                return (getBioEnd() - getBioStart()) + 1;
        }

        @Override
        public CompoundSet<C> getCompoundSet() {
                return getViewedSequence().getCompoundSet();
        }

        @Override
        public SequenceView<C> getSubSequence(final Integer bioStart, final Integer bioEnd) {
                return new SequenceProxyView<C>(this, bioStart, bioEnd);
        }

        @Override
        public Iterator<C> iterator() {
                return new SequenceMixin.SequenceIterator<C>(this);
        }

        @Override
        public AccessionID getAccession() {
                return getViewedSequence().getAccession();
        }

        /**
         * @return the bioStart
         */
        @Override
        public Integer getBioStart() {
                return bioStart;
        }

        /**
         * @param bioStart the bioStart to set
         */
        public void setBioStart(Integer bioStart) {
                if (bioStart < 1) {
                        throw new IllegalArgumentException("The given start "
                                        + bioStart + " is less than 1; cannot index less than 1");
                }
                this.bioStart = bioStart;
        }

        /**
         * @return the bioEnd
         */
        @Override
        public Integer getBioEnd() {
                return bioEnd;
        }

        /**
         * @param bioEnd the bioEnd to set
         */
        public void setBioEnd(Integer bioEnd) {
                if(sequence == null) {
                        throw new NullPointerException("No sequence given before setting the end coordinate; cannot be done");
                }
                // had a bug in the code that allowed this to work. The length of a any exon or cds sequence was always the length of the
                //parent sequence. Sequence class doesn't have bioStart and bioEnd exposed to do a proper comparison of getting
                // a subsequence. Januar-20=2011 Scooter
         //   if (bioEnd > sequence.getLength()) {
         //       throw new IllegalArgumentException("The given end "
         //               + bioEnd + " is greater than sequence length"
         //               + sequence.getLength());
         //   }
                this.bioEnd = bioEnd;
        }

        @Override
        public int countCompounds(C... compounds) {
                return SequenceMixin.countCompounds(this, compounds);
        }

        @Override
        public SequenceView<C> getInverse() {
                return SequenceMixin.inverse(this);
        }
}