Page History

public class MyPlugin extends AbstractAnnotationOperator implements Operator {

	// Constructor
	MyPlugin(FileTypeCategory category){
		super(category);
	}

	// Method to determine the internal plugin name
	@Override
	public String getName() {
		return this.category.toString().toLowerCase() +"_my_plugin";
	}


	// Method to determine the display name for the operation
	@Override
	public String getDisplay() {
		return "My Operation";
	}


	// Private method to check if two symmetries are overlapped used by the operate()
	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();
	}


	// Core code for the operation which loops over input symmetries and return the overlapped ones
	@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;
	}