package de.mpiwg.anteater.results.impl;

import java.util.ArrayList;
import java.util.List;

import de.mpiwg.anteater.AnteaterConfiguration;
import de.mpiwg.anteater.results.AResultManager;
import de.mpiwg.anteater.results.AnnotationTag;
import de.mpiwg.anteater.results.SpeciesScientificResult;
import de.mpiwg.anteater.text.TextType;

public class ScientificNameResultManager extends AResultManager<SpeciesScientificResult> {

	public final static String SCIENTIFIC_NAME_TAG_Start = "<species_scientific name=\"";
	public final static String SCIENTIFIC_NAME_ID_ATTR = "\" ncbiID=\"";
	public final static String SCIENTIFIC_NAME_TAG_End = "\" >";
	public final static String SCIENTIFIC_NAME_TAG_CLOSE = "</species_scientific>";
	public final static String TAG_TYPE = "scientific_name";
	
	public ScientificNameResultManager(AnteaterConfiguration configuration) {
		super(configuration);
	}

	@Override
	protected List<AnnotationTag> getSpecificSummaryTags(
			List<SpeciesScientificResult> results, int textIndex) {
		return getTags(results, textIndex, TextType.TYPE_SUMMARY);
	}

	@Override
	protected List<AnnotationTag> getSpecificSuppleInfTags(
			List<SpeciesScientificResult> results, int textIndex) {
		return getTags(results, textIndex, TextType.TYPE_SUPLINF);
	}
	
	protected List<AnnotationTag> getTags(List<SpeciesScientificResult> results, int textIndex, int type) {
		List<AnnotationTag> tags = new ArrayList<AnnotationTag>();

		// get applicants for text
		List<SpeciesScientificResult> namesOfSum = new ArrayList<SpeciesScientificResult>();
		for (SpeciesScientificResult r : results) {
			if (r.getResult().getType() == type
					&& r.getResult().getTextIdx() == textIndex)
				namesOfSum.add(r);
		}


		for (SpeciesScientificResult name : namesOfSum) {
			tags.add(new AnnotationTag(SCIENTIFIC_NAME_TAG_Start + name.getFinding().getScientificName() + SCIENTIFIC_NAME_ID_ATTR + (name.getFinding().getNcbiId() != null ? name.getFinding().getNcbiId() : "") + SCIENTIFIC_NAME_TAG_End, name.getFinding().getStart(), SCIENTIFIC_NAME_TAG_CLOSE, name.getFinding().getStart()
					+ name.getFinding().getLength(), TAG_TYPE));
		}

		return tags;
	}

}