import javax.swing.ImageIcon;
import javax.swing.KeyStroke;

import com.algosome.common.event.IndexSelectionModel;
import com.algosome.genecoder.bio.sequence.SequenceData;
import com.algosome.genecoder.bio.sequence.SequenceManager;
import com.algosome.genecoder.bio.sequence.SequenceModel;
import com.algosome.genecoder.bio.sequence.SequenceFactoryBridge;
import com.algosome.genecoder.plugin.DefinedTypes;
import com.algosome.genecoder.plugin.ISequenceActionPlugin;
import com.algosome.genecoder.plugin.PluginListener;
import com.algosome.genecoder.plugin.SequenceCount;
import com.algosome.genecoder.plugin.DefinedTypes.Option;
import com.algosome.genecoder.io.GeneCoderIOBridge;

/**
 * An example implementation of an Action plugin which 
 * @author Greg Cope
 *
 */
class ExamplePlugin implements ISequenceActionPlugin{

	private SequenceData sequenceData = null;
	
	@Override
	public SequenceCount getRequiredSequenceCount() {
		return SequenceCount.ONE;//operates on only one sequence
	}

	@Override
	public void setSequenceData(SequenceData seq) {
		sequenceData = seq;
	}

	@Override
	public void breakDown() {
		//break down anything necessary - nothing with this Plugin
	}

	@Override
	public void doStart() {
		//perform any setup here - nothing with this plugin
	}

	@Override
	public String getDescription() {
		return "An example plugin";
	}

	@Override
	public String getName() {
		return "Example Action";
	}

	@Override
	public Option getType() {
		return DefinedTypes.Option.DNA;
	}

	@Override
	public void doAction(PluginListener listener) throws Exception {
		/*
		 * Given this Plugin is defined with SequenceCount.ONE, only one sequence
		 * should be selected and operated on. The following code operates on this assumption
		 * be retrieving the SelectionModels and getting the selected Sequence.
		 */
		IndexSelectionModel model = sequenceData.getSequenceManagerContainer().getSelectionModel();
		int selection = model.getSelectedIndex();
		assert selection != -1 : "The selection should NOT be -1";
		SequenceManager sequenceManager = sequenceData.getSequenceManagerContainer().getSequenceManagers().get(selection);
		IndexSelectionModel smModel = sequenceManager.getSelectionModel();
		int selectedSequenceIndex = smModel.getSelectedIndex();
		assert selectedSequenceIndex != -1 : "The selection should NOT be -1";
		SequenceModel sequenceModel = sequenceManager.getSequences().get(selectedSequenceIndex);
		System.out.println(sequenceModel.getSequence().getSequenceName());
		/*
		 * Do Manipulation here
		 */
		
		System.out.println("Constructing sequence");
        Sequence seq = SequenceFactoryBridge.getInstance().constructSequence("AGCTAAAAGGGGACCCTA", Sequence.SEQUENCE_TYPE_DNA);//construct a new DNA sequence
		System.out.println(seq.getSequence());
		/*
		List seqs = GeneCoderIOBridge.getGeneCoderIOBridge().readSequence(new File(""));//enter absolute File path to read a File.
		System.out.println(seqs.get(0).getSequence());
		*/
		System.out.println(GeneCoderIOBridge.getGeneCoderIOBridge().convertToGenbank(seq))
        
	}

	@Override
	public ImageIcon getImageIcon() {
		return null;
	}

	@Override
	public KeyStroke getShortcut() {
		return null;
	}

	@Override
	public void stopAction() {
		//do nothing.
	}
	
}