/*
 * Copyright (c) 2007-2012 The Broad Institute, Inc.
 * SOFTWARE COPYRIGHT NOTICE
 * This software and its documentation are the copyright of the Broad Institute, Inc. All rights are reserved.
 *
 * This software is supplied without any warranty or guaranteed support whatsoever. The Broad Institute is not responsible for its use, misuse, or functionality.
 *
 * This software is licensed under the terms of the GNU Lesser General Public License (LGPL),
 * Version 2.1 which is available at http://www.opensource.org/licenses/lgpl-2.1.php.
 */

package org.broad.igv.feature;


import org.broad.igv.feature.genome.Genome;
import org.broad.igv.track.WindowFunction;

import java.util.Random;

//~--- JDK imports ------------------------------------------------------------


/**
 * A sub region of a feature.  For example,  a Gene exon
 *
 * @author jrobinso
 */
public class Exon extends AbstractFeature {

    /**
     * The index of the exon relative to the start codon.  The exon with the start
     * codon is number "1".
     */
    private int number;
    private int readingFrame = -1;

    /**
     * Coding start position.  This is the leftmost position of the coding region, not neccessarily the 5'utr end
     */
    private int codingStart;
    private int codingEnd;
    private AminoAcidSequence aminoAcidSequence;
    boolean utr = false;

    // The position of the first base of this exon relative to the start of the mRNA.  This will correspond
    // to either the beginning or end of the exon, depending on the strand
    private int mrnaBase = -1;

    //private Equalizer equalizer = new DefaultEqualizer();
    private int hashCode = 0;


    public void setMrnaBase(int base) {
        this.mrnaBase = base;
    }

    public int getAminoAcidNumber(int genomeCoordinate) {
        if (mrnaBase < 0) {
            return -1;
        }
        if (genomeCoordinate < getStart() || genomeCoordinate > getEnd()) {
            throw new IndexOutOfBoundsException();
        }
        if (getStrand() == Strand.POSITIVE) {
            int mrnaCoord = mrnaBase + (genomeCoordinate - codingStart) - 1;
            return mrnaCoord < 0 ? -1 : mrnaCoord / 3 + 1;

        } else if (getStrand() == Strand.NEGATIVE) {
            int mrnaCoord = mrnaBase + (codingEnd - genomeCoordinate);
            return mrnaCoord < 0 ? -1 : mrnaCoord / 3 + 1;

        } else {
            return 0;
        }
    }


    public Exon(String chr, int start, int end, Strand strand) {
        super(chr, start, end, strand);

        // By default the entre exon is a coding region
        this.codingStart = start;
        this.codingEnd = end;
    }

    /**
     * Flag indicating that the entire exon is the UTR.
     *
     * @param utr
     */
    public void setUTR(boolean utr) {
        this.utr = utr;
        if (utr) {
            if (getStrand() == Strand.POSITIVE) {
                codingStart = codingEnd = getEnd();
            } else {
                codingStart = codingEnd = getStart();
            }
        }
    }

    public boolean isUTR() {
        return utr;
    }


    public boolean isUTR(int position) {
        return utr || (position < codingStart || position > codingEnd);
    }

    public void setCodingStart(int codingStart) {
        this.codingStart = Math.max(getStart(), codingStart);
        hashCode = 0;  // Invalidate hashCode
    }


    public void setCodingEnd(int codingEnd) {
        this.codingEnd = Math.min(getEnd(), codingEnd);
        hashCode = 0;     // Invalidate hashCode
    }


    public void setReadingFrame(int offset) {
        this.readingFrame = offset;
    }


    public void setPhase(int phase) {
        if (getStrand() == Strand.POSITIVE) {
            readingFrame = phase;
        } else if (getStrand() == Strand.NEGATIVE) {
            int modLen = (getCodingLength() - phase) % 3;
            readingFrame = modLen;
        }
    }


    public int getCdStart() {
        return codingStart;
    }


    public int getCdEnd() {
        return this.codingEnd;
    }


    public int getCodingLength() {
        return utr ? 0 : Math.max(0, codingEnd - codingStart);
    }


    public int getReadingShift() {
        return readingFrame;
    }

    public AminoAcidSequence getAminoAcidSequence(Genome genome) {
        if (aminoAcidSequence == null) {
            computeAminoAcidSequence(genome);
        }
        return aminoAcidSequence;
    }

    private void computeAminoAcidSequence(Genome genome) {
        if (utr) {
            return;
        }
        int start = getStart();
        int end = getEnd();
        String chr = getChr();
        if (readingFrame >= 0) {
            int readStart = (codingStart > start) ? codingStart : start + readingFrame;
            int readEnd = Math.min(end, codingEnd);
            if (readEnd > readStart + 3) {
                byte[] seqBytes = genome.getSequence(chr, readStart, readEnd);
                if (seqBytes != null) {
                    aminoAcidSequence = AminoAcidManager.getAminoAcidSequence(seqBytes, readStart, getStrand());
                }
            }
        }
    }


    public LocusScore copy() {
        Exon copy = new Exon(getChr(), getStart(), getEnd(), getStrand());
        copy.aminoAcidSequence = this.aminoAcidSequence;
        copy.codingEnd = this.codingEnd;
        copy.codingStart = this.codingStart;
        return copy;
    }

    public String getValueString(double position, WindowFunction windowFunction) {
        String msg = number > 0 ? "Exon number: " + number : "";
        int aaNumber = this.getAminoAcidNumber((int) position);
        if (aaNumber > 0) {
            msg += "<br>Amino acid number: " + aaNumber;
        }
        msg += "<br>" + getLocusString();
        if (description != null) msg += description;
        return msg;
    }

    public void setNumber(int number) {
        this.number = number;
    }

    public String getURL() {
        return null;  //To change body of implemented methods use File | Settings | File Templates.
    }

    @Override
    public boolean equals(Object object) {
        //return equalizer.equals(this, object);
        if (object == null || !(object instanceof Exon)) {
            return false;
        }
        Exon other = (Exon) object;
        boolean eq = getChr().equals(other.getChr());
        eq &= getStart() == other.getStart();
        eq &= getEnd() == other.getEnd();
        eq &= getCdStart() == other.getCdStart();
        eq &= getCdEnd() == other.getCdEnd();
        eq &= getStrand() == other.getStrand();
        return eq;
    }

    @Override
    public int hashCode() {
        if (hashCode != 0) {
            return hashCode;
        }

        int hc = getChr().hashCode() + getStrand().hashCode();
        Random rand = new Random(hc);
        hc = rand.nextInt();
        rand.setSeed(getStart());
        hc += rand.nextInt();
        rand.setSeed(getEnd());
        hc += rand.nextInt();
        rand.setSeed(getCdStart());
        hc += rand.nextInt();
        rand.setSeed(getCdEnd());
        hc += rand.nextInt();

        if (hc == 0) {
            hc = 1;
        }
        hashCode = hc;
        return hc;
    }

}

@@ -6044,1155 +6044,7 @@
  %7D%0A%0A
-    @Override%0A    public boolean equals(Object object) %7B%0A        //return equalizer.equals(this, object);%0A        if (object == null %7C%7C !(object instanceof Exon)) %7B%0A            return false;%0A        %7D%0A        Exon other = (Exon) object;%0A        boolean eq = getChr().equals(other.getChr());%0A        eq &= getStart() == other.getStart();%0A        eq &= getEnd() == other.getEnd();%0A        eq &= getCdStart() == other.getCdStart();%0A        eq &= getCdEnd() == other.getCdEnd();%0A        eq &= getStrand() == other.getStrand();%0A        return eq;%0A    %7D%0A%0A    @Override%0A    public int hashCode() %7B%0A        if (hashCode != 0) %7B%0A            return hashCode;%0A        %7D%0A%0A        int hc = getChr().hashCode() + getStrand().hashCode();%0A        Random rand = new Random(hc);%0A        hc = rand.nextInt();%0A        rand.setSeed(getStart());%0A        hc += rand.nextInt();%0A        rand.setSeed(getEnd());%0A        hc += rand.nextInt();%0A        rand.setSeed(getCdStart());%0A        hc += rand.nextInt();%0A        rand.setSeed(getCdEnd());%0A        hc += rand.nextInt();%0A%0A        if (hc == 0) %7B%0A            hc = 1;%0A        %7D%0A        hashCode = hc;%0A        return hc;%0A    %7D%0A
 %0A%7D%0A

Remove hashCode and equals implementations from Exon (performance)