public class Species {
	public String name;
	public int[][] geneMap = {};
	private int clusterTotal = 0;
	
	public Species() {
		/**
		ArrayList<Integer> tmp = new ArrayList<Integer>();
		tmp.add(-1);
		System.out.println(tmp.get(0));
		geneMap.add(tmp);
		* 
		*/
	}
	
	public void setName(String newName) {
		name = newName;
	}
	
	// adds a cluster, if the cluster already exists in this species' gene map, then it adds a hit to the count
	public void addCluster(int clusterID, int hits) {
		int[][] tmpMap = new int[geneMap.length + 1][2];
		for(int i = 0; i < geneMap.length; i ++) {
			tmpMap[i] = geneMap[i];
		}
		tmpMap[clusterTotal][0] = clusterID;
		tmpMap[clusterTotal][1] = hits;
		clusterTotal ++;
		geneMap = tmpMap;
	}
	
	public int findClusterFrequency(int clusterID) {
		int index = findClusterIndex(clusterID);
		if (index == -1) {
			return 0;
		}
		return geneMap[index][1];
	}
	
	private int findClusterIndex(int clusterID) {
		int index = -1;
		for (int i = 0; i < geneMap.length; i ++) {
			if (geneMap[i][0] == clusterID) {
				index = i;
			}
		}
		return index;
	}
	
}