package task_3.task_3;
/*
import java.io.BufferedReader;
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.util.Iterator;

//import javax.swing.text.html.HTMLDocument.Iterator;

import org.biojava.bio.BioException;
import org.biojava.bio.seq.Feature;
import org.biojava.bio.seq.FeatureFilter;
import org.biojava.bio.seq.FeatureHolder;
import org.biojavax.Note;
import org.biojavax.RichAnnotation;
import org.biojavax.RichObjectFactory;
import org.biojavax.bio.seq.RichFeature;
import org.biojavax.bio.seq.RichSequence;
import org.biojavax.ontology.ComparableTerm;
*/
//Java libraries
import java.io.*;
import java.util.*;
//BioJava libraries
import org.biojava.bio.*;
import org.biojava.bio.seq.*;
import org.biojava.bio.seq.io.*;
//BioJava extension libraries
import org.biojavax.*;
import org.biojavax.ontology.*;
import org.biojavax.bio.*;
import org.biojavax.bio.seq.*;

public class ExtractInformation {

	//Create the RichSequence object
	RichSequence richSeq;

	//ExtractInformation constructor
	public ExtractInformation(String fileName){
		//fileName = "ACTG1.gb" ;
		//Load the sequence file
		try {
			richSeq = RichSequence.IOTools.readGenbankDNA(new BufferedReader(new FileReader(fileName)),null).nextRichSequence();
		}
		catch(FileNotFoundException fnfe){
			System.out.println("FileNotFoundException: " + fnfe);
		}
		catch(BioException bioe1){
			System.err.println("Not a Genbank sequence trying EMBL");
			try  {
				richSeq = RichSequence.IOTools.readEMBLDNA(new BufferedReader(new FileReader(fileName)),null).nextRichSequence();
			}
			catch(BioException bioe2){
				System.err.println("Not an EMBL sequence either");
			    System.exit(1);
			}
			catch(FileNotFoundException fnfe){
				System.out.println("FileNotFoundException: " + fnfe);
			}
		}
		 //Filter the sequence on CDS features
		FeatureFilter ff = new FeatureFilter.ByType("CDS");
		FeatureHolder fh = richSeq.filter(ff);

		 //Iterate through the CDS features
		for (Iterator i = fh.features(); i.hasNext();){//мб косяк в итераторе будет
			RichFeature rf = (RichFeature)i.next();
			//Get the strand orientation of the feature
			char featureStrand = rf.getStrand().getToken();

		    //Get the location of the feature
		    String featureLocation = rf.getLocation().toString();
		    System.out.println(featureLocation);
		}
	}
	//Main method
	public static void main(String args []) {
		if (args.length != 1){
			System.out.println("Usage: java ExtractInformation ``");
			System.exit(1);
		} else {
			new ExtractInformation(args[0]);
		}
	}
}