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package com.myorg.myplugin;

import java.util.HashMap;
import java.util.List;

import com.affymetrix.genometryImpl.BioSeq;
import com.affymetrix.genometryImpl.operator.AbstractAnnotationOperator;
import com.affymetrix.genometryImpl.operator.Operator;
import com.affymetrix.genometryImpl.parsers.FileTypeCategory;
import com.affymetrix.genometryImpl.symmetry.SeqSymmetry;
import com.affymetrix.genometryImpl.symmetry.SimpleSymWithProps;
import com.affymetrix.genometryImpl.symmetry.TypeContainerAnnot;

public class MyPlugin extends AbstractAnnotationOperator implements Operator {

	MyPlugin(FileTypeCategory category){
		super(category);
	}
	
	@Override
	public String getName() {
		return this.category.toString().toLowerCase() +"_my_plugin";
	}

	@Override
	public String getDisplay() {
		return "My Operation";
	}

	private boolean overlap(BioSeq aseq, SeqSymmetry s0, SeqSymmetry s1) {
		return s0.getSpan(aseq) != null && s1.getSpan(aseq) != null && s0.getSpan(aseq).getMax() > s1.getSpan(aseq).getMin() && s0.getSpan(aseq).getMin() < s1.getSpan(aseq).getMax();
	}

	@Override
	public SeqSymmetry operate(BioSeq aseq, List<SeqSymmetry> symList) {
		SimpleSymWithProps result = new SimpleSymWithProps();
		result.setProperties(new HashMap<String,Object>());
		TypeContainerAnnot t0 = (TypeContainerAnnot)symList.get(0);
		TypeContainerAnnot t1 = (TypeContainerAnnot)symList.get(1);
		result.setProperty("type", t0.getType() + " " + getName());
		for (int i = 0; i < t0.getChildCount(); i++) {
			SeqSymmetry s0 = t0.getChild(i);
			for (int j = 0; j < t1.getChildCount(); j++) {
				SeqSymmetry s1 = t1.getChild(j);
				if (overlap(aseq, s0, s1)) {
					result.addChild(s0);
					result.addSpan(s0.getSpan(aseq));
					break;
				}
			}
		}
		return result;
	}
}