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

import org.snpeff.interval.Exon;
import org.snpeff.interval.Transcript;
import org.snpeff.interval.Variant;
import org.snpeff.snpEffect.EffectType;
import org.snpeff.snpEffect.VariantEffect.ErrorWarningType;
import org.snpeff.snpEffect.VariantEffects;

/**
 * Calculate codon changes produced by a SNP
 * @author pcingola
 */
public class CodonChangeSnp extends CodonChange {

	public CodonChangeSnp(Variant variant, Transcript transcript, VariantEffects variantEffects) {
		super(variant, transcript, variantEffects);
		returnNow = true; // A SNP can only affect one exon
	}

	/**
	 * Analyze SNPs in this transcript.
	 * Add changeEffect to 'changeEffect'
	 */
	@Override
	protected boolean codonChange(Exon exon) {
		// Get old and new codons
		codonsRef = codonsRef();
		codonsAlt = codonsAlt();

		// Use a generic low priority variant, this allows 'setCodons' to override it
		effect(exon, EffectType.CODON_CHANGE, true);

		if (codonsRef.isEmpty()) variantEffects.addErrorWarning(variant, ErrorWarningType.ERROR_MISSING_CDS_SEQUENCE);

		return true;
	}

	/**
	 * Get new (modified) codons
	 */
	@Override
	protected String codonsAlt() {
		// Was there a problem getting 'codonsOld'? => We cannot do anything
		if (codonsRef.isEmpty()) return "";

		char codonChars[] = codonsRef.toLowerCase().toCharArray();
		char snpBase = variant.netChange(transcript.isStrandMinus()).charAt(0);
		if (codonStartIndex < codonChars.length) codonChars[codonStartIndex] = Character.toUpperCase(snpBase);

		String codonsNew = new String(codonChars);
		return codonsNew;
	}

	/**
	 * Get original codons in CDS
	 */
	@Override
	protected String codonsRef() {
		int numCodons = 1;

		// Get CDS
		String cdsStr = transcript.cds();
		int cdsLen = cdsStr.length();

		// Calculate minBase (first codon base in the CDS)
		int minBase = codonStartNum * CodonChange.CODON_SIZE;
		if (minBase < 0) minBase = 0;

		// Calculate maxBase (last codon base in the CDS)
		int maxBase = codonStartNum * CodonChange.CODON_SIZE + numCodons * CodonChange.CODON_SIZE;
		if (maxBase > cdsLen) maxBase = cdsLen;

		// Sanity checks
		if (cdsStr.isEmpty() // Empty CDS => Cannot get codon (e.g. one or more exons are missing their sequences
				|| (cdsLen <= minBase) // Codon past CDS sequence => Cannot get codon
		) return "";

		// Create codon sequence
		char codonChars[] = cdsStr.substring(minBase, maxBase).toLowerCase().toCharArray();

		// Capitatlize changed base
		if (codonStartIndex < codonChars.length) codonChars[codonStartIndex] = Character.toUpperCase(codonChars[codonStartIndex]);
		String codon = new String(codonChars);

		return codon;
	}
}