/*
 * Copyright (c) 2007-2010 by The Broad Institute, Inc. and the Massachusetts Institute of Technology.
 * All Rights Reserved.
 *
 * 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.
 *
 * THE SOFTWARE IS PROVIDED "AS IS." THE BROAD AND MIT MAKE NO REPRESENTATIONS OR WARRANTIES OF
 * ANY KIND CONCERNING THE SOFTWARE, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES
 * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT
 * OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE.  IN NO EVENT SHALL THE BROAD OR MIT, OR THEIR
 * RESPECTIVE TRUSTEES, DIRECTORS, OFFICERS, EMPLOYEES, AND AFFILIATES BE LIABLE FOR ANY DAMAGES OF
 * ANY KIND, INCLUDING, WITHOUT LIMITATION, INCIDENTAL OR CONSEQUENTIAL DAMAGES, ECONOMIC
 * DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER THE BROAD OR MIT SHALL
 * BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE
 * FOREGOING.
 */

package org.broad.igv.sam;

import org.broad.igv.feature.BasicFeature;
import org.broad.igv.feature.Exon;
import org.broad.igv.feature.LocusScore;
import org.broad.igv.feature.Strand;
import org.broad.igv.track.WindowFunction;

/**
 * Some alignment formats are parsed as Features.
 * <p/>
 * This is all getting rather ciruclar,  some refactoring is in order.
 *
 * @author jrobinso
 * @date Aug 5, 2010
 */
public class FeatureWrappedAlignment implements Alignment {
    String readName;
    String chr;
    int start;
    int end;
    AlignmentBlock[] blocks;
    Strand strand;

    BasicFeature f;

    public FeatureWrappedAlignment(BasicFeature f) {

        this.readName = f.getName();
        this.chr = f.getChr();
        this.start = f.getStart();
        this.end = f.getEnd();
        strand = f.getStrand();

        if (f.getExonCount() > 0) {
            blocks = new AlignmentBlock[f.getExonCount()];
            int i=0;
            for(Exon exon : f.getExons()) {
                int length = exon.getLength();
                byte [] seq = new byte[length];
                blocks[i] = new AlignmentBlock(exon.getStart(), seq, seq);
                i++;
            }
        }
    }

    public String getReadName() {
        return readName;
    }

    public String getReadSequence() {
        return null;
    }

    public String getChromosome() {
        return chr;
    }

    public String getChr() {
        return chr;
    }

    public int getAlignmentStart() {
        return start;
    }

    public boolean contains(double location) {
        return location >= start && location <= getEnd();
    }

    public AlignmentBlock[] getAlignmentBlocks() {
        return blocks;
    }

    public AlignmentBlock[] getInsertions() {
        return null;
    }

    public String getCigarString() {
        return "*";
    }

    public int getInferredInsertSize() {
        return 0;
    }

    public int getMappingQuality() {
        return 255;
    }

    public ReadMate getMate() {
        return null;
    }

    public boolean isProperPair() {
        return true;
    }

    public boolean isMapped() {
        return true;
    }

    public boolean isPaired() {
        return false;
    }

    public boolean isNegativeStrand() {
        return strand == Strand.NEGATIVE;
    }

    public boolean isDuplicate() {
        return false;
    }

    public float getScore() {
        return 1.0f;
    }

    public void setConfidence(float confidence) {
        // ignore
    }

    public float getConfidence() {
        return 1.0f;
    }

    public LocusScore copy() {
        return this;
    }

    public String getValueString(double position, WindowFunction windowFunction) {
        return readName + "<br>Read length = " + (getEnd() - getStart());
    }

    /**
     * @return the start
     */
    public int getStart() {
        return start;
    }

    /**
     * @param start the start to set
     */
    public void setStart(int start) {
        this.start = start;
    }

    /**
     * @return the end
     */
    public int getEnd() {
        return end;
    }

    public int getAlignmentEnd() {
        return end;
    }

    /**
     * @param end the end to set
     */
    public void setEnd(int end) {
        this.end = end;
    }

    public byte getBase(double position) {
        return 0;
    }

    public byte getPhred(double position) {
        return 0;
    }

    public String getSample() {
        return null;
    }

    public String getReadGroup() {
        return null;
    }

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

    public Strand getFragmentStrand(int readPair) {
        return Strand.NONE;
    }

    public void setMateSequence(String sequence) {
        //To change body of implemented methods use File | Settings | File Templates.
    }

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

    public boolean isSmallInsert() {
        return false;  //To change body of implemented methods use File | Settings | File Templates.
    }

    public boolean isVendorFailedRead() {
        return false;  //To change body of implemented methods use File | Settings | File Templates.
    }

    public char[] getGapTypes() {
        return null;
    }
}
