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Variant annotation and effect prediction package.
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package org.snpeff.interval;

import java.io.Serializable;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.HashMap;
import java.util.Iterator;
import java.util.LinkedList;
import java.util.List;

import org.snpeff.snpEffect.Config;
import org.snpeff.util.Timer;

/**
 * A collection of genes (marker intervals)
 * Note: It is assumed that all genes belong to the same genome
 *
 * @author pcingola
 */
public class Genes implements Iterable, Serializable {

	private static final long serialVersionUID = 9022385501946879197L;

	public boolean debug = false;
	Genome genome;
	HashMap genesById;

	public Genes(Genome genome) {
		genesById = new HashMap<>();
		this.genome = genome;
	}

	/**
	 * Add a gene interval to this collection
	 */
	public void add(Gene gene) {
		genesById.put(gene.getId(), gene);
	}

	/**
	 * In a circular genome, a gene can have negative coordinates or crosses
	 * over chromosome end. These genes are mirrored to the opposite end of
	 * the chromosome so that they can be referenced by both circular
	 * coordinates.
	 */
	public void createCircularGenes() {
		List newGenes = new LinkedList<>();

		// Check if any gene spans across chromosome limits
		for (Gene g : genome.getGenes()) {
			if (g.isCircular()) {
				newGenes.add(g.circularClone());
			}
		}

		// Add all newly created genes
		if (!newGenes.isEmpty()) {
			for (Gene g : newGenes)
				genome.getGenes().add(g);
			if (Config.get().isVerbose()) Timer.showStdErr("Total: " + newGenes.size() + " added as circular mirrored genes (appended '" + Gene.CIRCULAR_GENE_ID + "' to IDs).");
		}

	}

	/**
	 * Creates a list of Intergenic regions
	 */
	public List createIntergenic() {
		ArrayList intergenics = new ArrayList<>(genesById.size());

		// Create a list of genes sorted by position
		ArrayList genesSorted = new ArrayList<>(genesById.size());
		genesSorted.addAll(genesById.values());
		Collections.sort(genesSorted);

		// For each gene, transcript
		Gene genePrev = null;
		Chromosome chrPrev = null;
		for (Gene gene : genesSorted) {
			// Chromosome change? Invalidate genePrev
			if (chrPrev != gene.getChromosome()) {
				// Add last intergenic region from previous chromosome
				if (chrPrev != null && genePrev != null) {
					Intergenic intergenic = Intergenic.createIntergenic(genePrev, null);
					if (intergenic != null) intergenics.add(intergenic);
				}
				genePrev = null;
			}

			// Intergenic region's [start, end] interval
			int start = (genePrev != null ? genePrev.getEnd() + 1 : 0);
			int end = gene.getStart() - 1;

			// Valid intergenic region?
			if (start < end) {
				Intergenic intergenic = Intergenic.createIntergenic(genePrev, gene);
				if (intergenic != null) intergenics.add(intergenic);
			}

			// Is it null or ends before this one? update 'genePrev'
			if ((genePrev == null) || (gene.getEnd() > genePrev.getEnd())) genePrev = gene;

			// Update chrPrev
			chrPrev = gene.getChromosome();
		}

		// Add intergenic region for last gene in the list
		if (genePrev != null) {
			Intergenic intergenic = Intergenic.createIntergenic(genePrev, null);
			if (intergenic != null) intergenics.add(intergenic);
		}

		return intergenics;

	}

	/**
	 * Create splice sites.
	 *
	 * @param createIfMissing : If true, create canonical splice sites if they are missing.
	 *
	 * For a definition of splice site, see comments at the beginning of SpliceSite.java
	 */
	public void createSpliceSites(int spliceSiteSize, int spliceRegionExonSize, int spliceRegionIntronMin, int spliceRegionIntronMax) {
		// For each gene, transcript
		for (Gene gene : this)
			for (Transcript tr : gene)
				tr.createSpliceSites(spliceSiteSize, spliceRegionExonSize, spliceRegionIntronMin, spliceRegionIntronMax);
	}

	/**
	 * Creates a list of UP/DOWN stream regions (for each transcript)
	 * Upstream (downstream) stream is defined as upDownLength before (after) transcript
	 *
	 * Note: If upDownLength <=0 no interval is created
	 */
	public List createUpDownStream(int upDownLength) {
		ArrayList list = new ArrayList<>();
		if (upDownLength <= 0) return list;

		// For each gene, transcript
		for (Gene gene : this) {
			for (Transcript tr : gene) {
				tr.createUpDownStream(upDownLength);
				list.add(tr.getUpstream());
				list.add(tr.getDownstream());
			}
		}
		return list;
	}

	/**
	 * Find a transcript by ID
	 */
	public Transcript findTranscript(String trId) {
		for (Gene g : this)
			for (Transcript tr : g)
				if (tr.getId().equals(trId)) return tr;
		return null;
	}

	/**
	 * Obtain a gene interval
	 */
	public Gene get(String geneId) {
		return genesById.get(geneId);
	}

	/**
	 * Obtain a gene by GeneName
	 * WARNING: The first match is returned. If multiple genes share the
	 *          same gene name, no order can be expected for this method.
	 */
	public Gene getGeneByName(String geneName) {
		for (Gene g : this)
			if (g.getGeneName().equals(geneName)) return g;
		return null;
	}

	@Override
	public Iterator iterator() {
		return genesById.values().iterator();
	}

	public int size() {
		return genesById.size();
	}

	public Collection sorted() {
		ArrayList genes = new ArrayList<>();
		genes.addAll(genesById.values());
		Collections.sort(genes, new IntervalComparatorByStart());
		return genes;
	}

	@Override
	public String toString() {
		StringBuilder sb = new StringBuilder();
		for (Gene gint : this)
			sb.append(gint + "\n");
		return sb.toString();
	}

	public Collection values() {
		return genesById.values();
	}

}