de.charite.compbio.jannovar.reference.TranscriptSequenceDecorator Maven / Gradle / Ivy

package de.charite.compbio.jannovar.reference;

import de.charite.compbio.jannovar.Immutable;
import de.charite.compbio.jannovar.impl.util.StringUtil;

// TODO(holtgrem): Test this class!

/**
 * Decorator for {@link TranscriptModel} that helps with operations on its sequence
 *
 * @author Manuel Holtgrewe
 */
@Immutable
public final class TranscriptSequenceDecorator {

	/**
	 * The wrapped {@link TranscriptModel}.
	 */
	private final TranscriptModel transcript;

	public TranscriptSequenceDecorator(TranscriptModel transcript) {
		this.transcript = transcript;
	}

	/**
	 * @return the wrapped {@link TranscriptModel}
	 */
	public TranscriptModel getTranscript() {
		return transcript;
	}

	/**
	 * Update the base given by frameShift in the given codon string transcriptCodon to
	 * targetNC and return updated codon.
	 *
	 * @param transcriptCodon the wild type codon nucleotide string from the codon
	 * @param frameShift      the frame within the codon
	 * @param targetNC        the target nucleotide
	 * @return variant codon string
	 */
	public static String codonWithUpdatedBase(String transcriptCodon, int frameShift, char targetNC) {
		assert (0 <= frameShift && frameShift <= 2);
		if (frameShift == 0)
			return StringUtil.concatenate(targetNC, transcriptCodon.charAt(1), transcriptCodon.charAt(2));
		else if (frameShift == 1)
			return StringUtil.concatenate(transcriptCodon.charAt(0), targetNC, transcriptCodon.charAt(2));
		else
			return StringUtil.concatenate(transcriptCodon.charAt(0), transcriptCodon.charAt(1), targetNC);
	}

	/**
	 * Insert the string in insertion at the position given by frameShift in the given codon
	 * string transcriptCodon to targetNC and return the updated nucleic string.
	 *
	 * @param transcriptNTs the wild type nucleotide string from the codon
	 * @param frameShift    the frame within the codon
	 * @param insertion     the String with the nucleotides
	 * @return variant codon string
	 */
	public static String nucleotidesWithInsertion(String transcriptNTs, int frameShift, String insertion) {
		assert (0 <= frameShift && frameShift <= 2);
		if (frameShift == 0)
			return StringUtil.concatenate(insertion, transcriptNTs);
		else if (frameShift == 1)
			return StringUtil.concatenate(transcriptNTs.charAt(0), insertion, transcriptNTs.substring(1));
		else
			return StringUtil.concatenate(transcriptNTs.charAt(0), transcriptNTs.charAt(1), insertion,
				transcriptNTs.substring(2));
	}

	/**
	 * Returns the codon (String of length 3) for a change at a given position
	 *
	 * @param txPos  transcript position of the change
	 * @param cdsPos CDS position of the change
	 * @return the codon affected by a change at the given position
	 * @throws InvalidCodonException if the requested codon is not accessible
	 */
	public String getCodonAt(TranscriptPosition txPos, CDSPosition cdsPos) throws InvalidCodonException {
		int frameShift = cdsPos.getPos() % 3;
		int codonStart = txPos.getPos() - frameShift; // codon start in transcript string
		int endPos = codonStart + 3;
		if (transcript.getSequence().length() < endPos)
			throw new InvalidCodonException("Could not access codon " + codonStart + " - " + endPos
				+ ", transcript sequence length is " + transcript.getSequence().length());
		return transcript.getSequence().substring(codonStart, endPos);
	}

	/**
	 * Returns a number of codons (String of length 3 * len) starting from the affected one by the change
	 * at txPos/cdsPos.
	 * 
	 * If there is not a sufficient number of nucleotides in the transcript string then return fewer, only up to the
	 * end.
	 *
	 * @param txPos  transcript position of the change
	 * @param cdsPos CDS position of the change
	 * @param count  number of codons to return
	 * @return the codon affected by a change at the given position
	 */
	public String getCodonsStartingFrom(TranscriptPosition txPos, CDSPosition cdsPos, int count) {
		int frameShift = cdsPos.getPos() % 3;
		int codonStart = txPos.getPos() - frameShift; // codon start in transcript string
		int endPos = codonStart + 3 * count;
		if (endPos > transcript.getSequence().length())
			endPos = transcript.getSequence().length();
		return transcript.getSequence().substring(codonStart, endPos);
	}

	/**
	 * Returns all codons (String of length 3 * len) starting from the affected one by the change at
	 * txPos/cdsPos.
	 *
	 * @param txPos  transcript position of the change
	 * @param cdsPos CDS position of the change
	 * @return the codon affected by a change at the given position
	 */
	public String getCodonsStartingFrom(TranscriptPosition txPos, CDSPosition cdsPos) {
		return getCodonsStartingFrom(txPos, cdsPos, transcript.getSequence().length());
	}

}