package compbio.cassandra;

import java.util.ArrayList;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;

public class ProteinBean implements PredictionIndex{
	private String sequence;
	private String jnetpred;
	private List<String> jobid;
	private LinkedHashMap<String,String> predictions;
	private List<String> subProt;		// protein sequence divided by several parts for highlighting the particular part
	private int size;
	
	public ProteinBean (String seq, Map<String,String> pred) {
		this.sequence = seq;
		this.predictions = new LinkedHashMap<String,String>();	
		this.jobid = new ArrayList<String>();
		setPredictions(pred);
	}
	
	public void setSequence (String seq) {
		this.sequence = seq;
	}
	
	public void setPredictions(Map<String,String> pred) {
		if (predictions == null)
			predictions = new LinkedHashMap<String,String>();	
		for (String index : predIndex) {
			this.predictions.put(index, pred.get(index));
		}	
		this.size = predictions.size();
	}
	
	public String getSequence () {
		return sequence;
	}
	
	public String getJnetpred () {
		return jnetpred;
	}
	
	public void setJnetpred (Map<String,String> pred) {
		if (pred != null) {
			if (pred.containsKey("jnetpred")) 
				jnetpred = pred.get("jnetpred");
		}
	}
	
	public List<String> getJobid () {
		return jobid;
	}
	
	public void setJobid (String id) {
		this.jobid.add(id);
	}

	public int getSize () {
		return size;
	}
	
	public LinkedHashMap<String,String> getPredictions () {
		return predictions;
	}
	
	public void setSubProt(List<String> subProt) {
		this.subProt = subProt;
	}

	public List<String> getSubProt() {
		return subProt;
	}

}