/*--------------------------------------------------------------------------
    *  Copyright 2008 utgenome.org
    *
    *  Licensed under the Apache License, Version 2.0 (the "License");
    *  you may not use this file except in compliance with the License.
    *  You may obtain a copy of the License at
    *
    *     http://www.apache.org/licenses/LICENSE-2.0
    *
   *  Unless required by applicable law or agreed to in writing, software
   *  distributed under the License is distributed on an "AS IS" BASIS,
   *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
   *  See the License for the specific language governing permissions and
   *  limitations under the License.
   *--------------------------------------------------------------------------*/
  //--------------------------------------
  // utgb-core Project
  //
  // Alignment.java
  // Since: Sep 5, 2008
  //
  // $URL$ 
  // $Author$
  //--------------------------------------
  package org.utgenome.gwt.utgb.client.bio;
  
  import java.util.ArrayList;
  
  import com.google.gwt.user.client.rpc.IsSerializable;
  
  /**
   * Alignment result
   * 
   * @author leo
   * 
   */
  public class Alignment implements IsSerializable {
  
  	private int numMatch;
  	private int numMisMatch;
  	private int numRepMatch;
  	private int numN;
  
  	// query sequence
  	private String queryName;
  	private int querySize;
  	private int queryStart;
  	private int queryEnd;
  
  	// target sequence
  	private String targetName;
  	private int targetSize;
  	private int targetStart;
  	private int targetEnd;
  
  	private String strand; // "+" or "-"
  
  	// alignment blocks
  	private int blockCount = 0;
  	private ArrayList<Integer> blockSizeList = new ArrayList<Integer>();
  	private ArrayList<Integer> queryStartList = new ArrayList<Integer>();
  	private ArrayList<Integer> targetStartList = new ArrayList<Integer>();
  
  	public int getNumMatch() {
  		return numMatch;
  	}
  
  	public int getQueryLen() {
  		return querySize;
  	}
  
  	public void setQueryLen(int querySize) {
  		this.querySize = querySize;
  	}
  
  	public int getTargetSize() {
  		return targetSize;
  	}
  
  	public void setTargetSize(int targetSize) {
  		this.targetSize = targetSize;
  	}
  
  	public void setNumMatch(int numMatch) {
  		this.numMatch = numMatch;
  	}
  
  	public int getNumMisMatch() {
  		return numMisMatch;
  	}
  
  	public void setNumMisMatch(int numMisMatch) {
  		this.numMisMatch = numMisMatch;
  	}
  
  	public int getNumRepMatch() {
  		return numRepMatch;
  	}
  
 	public void setNumRepMatch(int numRepMatch) {
 		this.numRepMatch = numRepMatch;
 	}
 
 	public int getNumN() {
 		return numN;
 	}
 
 	public void setNumN(int numN) {
 		this.numN = numN;
 	}
 
 	public String getQueryName() {
 		return queryName;
 	}
 
 	public void setQueryName(String queryName) {
 		this.queryName = queryName;
 	}
 
 	public long getQueryStart() {
 		return queryStart;
 	}
 
 	public void setQueryStart(int queryStart) {
 		this.queryStart = queryStart;
 	}
 
 	public long getQueryEnd() {
 		return queryEnd;
 	}
 
 	public void setQueryEnd(int queryEnd) {
 		this.queryEnd = queryEnd;
 	}
 
 	public String getTargetName() {
 		return targetName;
 	}
 
 	public void setTargetName(String targetName) {
 		this.targetName = targetName;
 	}
 
 	public int getTargetStart() {
 		return targetStart;
 	}
 
 	public void setTargetStart(int targetStart) {
 		this.targetStart = targetStart;
 	}
 
 	public int getTargetEnd() {
 		return targetEnd;
 	}
 
 	public void setTargetEnd(int targetEnd) {
 		this.targetEnd = targetEnd;
 	}
 
 	public String getStrand() {
 		return strand;
 	}
 
 	public boolean isPlusStrand() {
 		return strand.equals("+");
 	}
 
 	public void setStrand(String strand) {
 		this.strand = strand;
 	}
 
 	public int getBlockCount() {
 		return blockCount;
 	}
 
 	public void setBlockCount(int blockCount) {
 		this.blockCount = blockCount;
 	}
 
 	public ArrayList<Integer> getBlockSizes() {
 		return blockSizeList;
 	}
 
 	public ArrayList<Integer> getQueryStarts() {
 		return queryStartList;
 	}
 
 	public ArrayList<Integer> getTargetStarts() {
 		return targetStartList;
 	}
 
 	public void addBlockSizes(int blockSize) {
 		this.blockSizeList.add(blockSize);
 	}
 
 	public void addQueryStarts(int queryStart) {
 		this.queryStartList.add(queryStart);
 	}
 
 	public void addTargetStarts(int targetStart) {
 		this.targetStartList.add(targetStart);
 	}
 
 }