/*
 * Copyright (c) 2005-2012 The Regents of the University of California.
 * All rights reserved.
 *
 * '$Author: crawl $'
 * '$Date: 2012-04-13 17:49:27 +0000 (Fri, 13 Apr 2012) $' 
 * '$Revision: 29712 $'
 * 
 * Permission is hereby granted, without written agreement and without
 * license or royalty fees, to use, copy, modify, and distribute this
 * software and its documentation for any purpose, provided that the above
 * copyright notice and the following two paragraphs appear in all copies
 * of this software.
 *
 * IN NO EVENT SHALL THE UNIVERSITY OF CALIFORNIA BE LIABLE TO ANY PARTY
 * FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES
 * ARISING OUT OF THE USE OF THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF
 * THE UNIVERSITY OF CALIFORNIA HAS BEEN ADVISED OF THE POSSIBILITY OF
 * SUCH DAMAGE.
 *
 * THE UNIVERSITY OF CALIFORNIA SPECIFICALLY DISCLAIMS ANY WARRANTIES,
 * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
 * MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE SOFTWARE
 * PROVIDED HEREUNDER IS ON AN "AS IS" BASIS, AND THE UNIVERSITY OF
 * CALIFORNIA HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES,
 * ENHANCEMENTS, OR MODIFICATIONS.
 *
 */
package org.kepler.bio.util;

import java.io.BufferedReader;
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.IOException;
import java.math.BigDecimal;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Iterator;
import java.util.List;

//////////////////////////////////////////////////////////////////////////
////BlastTabularResult

/**
* This class is for the lines in blast tabular result. Each line will be one object. 
* They are compared by E-Value and Bit.
* 
* @author Jianwu Wang
* @version $Id: BlastTabularResult.java 29712 2012-04-13 17:49:27Z crawl $
*/
public class BlastTabularResult implements Comparable<BlastTabularResult> {
        
        String queryId, subjectId, eValue;
        float identity, bitScore;
        int alignmentLength, mismatches, gapOpenings, qStart, qEnd, sStart, sEnd;
        BigDecimal eValueDec;
        
        public BlastTabularResult(String result){
                String[] resElements = result.split("\t");
                this.queryId = resElements[0];
                this.subjectId = resElements[1];
                this.identity = new Float(resElements[2]).floatValue();
                this.alignmentLength = new Integer(resElements[3]).intValue();
                this.mismatches = new Integer(resElements[4]).intValue();
                this.gapOpenings = new Integer(resElements[5]).intValue();
                this.qStart = new Integer(resElements[6]).intValue();
                this.qEnd = new Integer(resElements[7]).intValue();
                this.sStart = new Integer(resElements[8]).intValue();
                this.sEnd = new Integer(resElements[9]).intValue();
                this.eValue = resElements[10];
                this.bitScore = new Float(resElements[11]).floatValue();
        }

        public String getQueryId() {
                return queryId;
        }

        public void setQueryId(String queryId) {
                this.queryId = queryId;
        }

        public String getSubjectId() {
                return subjectId;
        }

        public void setSubjectId(String subjectId) {
                this.subjectId = subjectId;
        }

        public String geteValue() {
                return eValue;
        }

        public void seteValue(String eValue) {
                this.eValue = eValue;
        }

        public Float getIdentity() {
                return identity;
        }

        public void setIdentity(Float identity) {
                this.identity = identity;
        }

        public int getAlignmentLength() {
                return alignmentLength;
        }

        public void setAlignmentLength(int alignmentLength) {
                this.alignmentLength = alignmentLength;
        }

        public int getMismatches() {
                return mismatches;
        }

        public void setMismatches(int mismatches) {
                this.mismatches = mismatches;
        }

        public int getGapOpenings() {
                return gapOpenings;
        }

        public void setGapOpenings(int gapOpenings) {
                this.gapOpenings = gapOpenings;
        }

        public int getqStart() {
                return qStart;
        }

        public void setqStart(int qStart) {
                this.qStart = qStart;
        }

        public int getqEnd() {
                return qEnd;
        }

        public void setqEnd(int qEnd) {
                this.qEnd = qEnd;
        }

        public int getsStart() {
                return sStart;
        }

        public void setsStart(int sStart) {
                this.sStart = sStart;
        }

        public int getsEnd() {
                return sEnd;
        }

        public void setsEnd(int sEnd) {
                this.sEnd = sEnd;
        }

        public float getBitScore() {
                return bitScore;
        }

        public void setBitScore(float bitScore) {
                this.bitScore = bitScore;
        }
        
        public String toString(){
                return queryId + "\t" + subjectId + "\t" + identity + "\t" + alignmentLength + "\t" + mismatches +  "\t" + gapOpenings + "\t" +qStart + "\t" +qEnd + "\t" +sStart + "\t" +sEnd + "\t" + eValue + "\t" + bitScore;               
        }

        @Override
        public int compareTo(BlastTabularResult result) {
                result.getQueryId();
                //same query id
                if (this.getQueryId().equals(result.getQueryId())){
                        this.eValueDec = new BigDecimal(this.geteValue());
                        BigDecimal resultEValueDec = new BigDecimal(result.geteValue());
                        int evalueCompare = eValueDec.compareTo(resultEValueDec);
                        // same e value, compare bit
                        if (evalueCompare == 0) {
                                float bitCom = this.getBitScore() - result.getBitScore();
                                if (bitCom == 0)
                                        return 0;
                                else if (bitCom > 0)
                                        return -1;
                                else
                                        return 1;
                        } else{
                                return evalueCompare;
                        }
                } else
                        return this.getQueryId().compareTo(result.getQueryId());
        }
        
        public static void main(String[] args){
                BufferedReader reader;
                StringBuffer lineBuffer = null;
                BlastTabularResult blastResult = null;
                List<BlastTabularResult> blastResList = new ArrayList<BlastTabularResult>();
                try {
                        reader = new BufferedReader(new FileReader("/Users/jianwu/Projects/bioinfo/testQueryFile/testdbOtiny-PACT-cross.out11"));
                lineBuffer = new StringBuffer();
                while (true) {
                    String line = reader.readLine();
                    if (line == null) {
                        break;
                    }
                    blastResult = new BlastTabularResult(line);
                    blastResList.add(blastResult);
                }
                } catch (FileNotFoundException e) {
                        e.printStackTrace();
                } catch (IOException e) {
                        e.printStackTrace();
                }

//              String[] lines = lineBuffer.toString().split("\n");
                Collections.sort(blastResList);
                Iterator blastIt = blastResList.iterator();
                while (blastIt.hasNext()){
                        System.out.println(blastIt.next());
                }
        
        }

}