net.maizegenetics.dna.map.TOPMInterface Maven / Gradle / Ivy
/*
* TOPMInterface
*/
package net.maizegenetics.dna.map;
import java.io.File;
import net.maizegenetics.dna.tag.Tags;
import net.maizegenetics.dna.map.Chromosome;
/**
* Tags on Physical Map (TOPM) Interface. Define methods for the TOPM classes.
* The TOPM class holds information relating tags to the physical map, variants
* (SNPs) called by the tag, and quality of mapping information.
*
* Physical map information is recorded with chromosome, strand, start and end positions. If a tags maps to multiple
* locations with equal quality it is recorded in multimaps with the count of multi-mapping.
*
* Each SNP call for a tag is record in the variant fields. The position by the variant offset,
* which is added to the startPosition (negative values indicate before the startPosition). Each variant is also
* defined by the SNP call implied by the given tag. The called are stored in a byte using the
* NucleotideAlignmentConstants (A=00, C=01, G=02, T=03).
*
* @author Ed Buckler and Terry Casstevens
*/
public interface TOPMInterface extends Tags {
public final static byte BYTE_MISSING = Byte.MIN_VALUE;
public final static int INT_MISSING = Integer.MIN_VALUE;
/**
* Adds Variant definition.
*
* @param tagIndex tag index
* @param offset offset
* @param base base value one of: NucleotideAlignmentConstants.A_ALLELE,
* NucleotideAlignmentConstants.C_ALLELE,
* NucleotideAlignmentConstants.G_ALLELE,
* NucleotideAlignmentConstants.T_ALLELE,
* NucleotideAlignmentConstants.GAP_ALLELE,
* NucleotideAlignmentConstants.INSERT_ALLELE, Alignment.UNKNOWN_ALLELE
*
* @return variant index or -1 if max number variants reached at this tag.
*/
public int addVariant(int tagIndex, byte offset, byte base);
/**
* Compares tags at given indices.
*
* @param index1 first index
* @param index2 second index
*
* @return -1 if tag at first index less than tag at second index. 1 if tag
* at first index greater. 0 if equal.
*/
public int compare(int index1, int index2);
/**
* Returns chromosome at give tag index.
*
* @param index tag index
*
* @return chromosome
*/
public int getChromosome(int index);
/**
* Returns an array whose values are the distinct chromosomes in this
* file, as stored in the chromosome[] array. The indices are arbitrary.
*
* @return list of distinct chromosomes
*/
public int[] getChromosomes();
/**
* Finds the index in the myChromosomes[] (length = # of chromosomes) corresponding
* to the provided int version of the chromosome name
* @param IntChrName
* @return int index of that chromosome if present (Integer.MIN_VALUE otherwise)
*/
public int getChromosomeIndex(int intChrName);
/**
* Round(Log2(P))
*
* @param index tag index
*
* @return DcoP
*/
public byte getDcoP(int index);
/**
* Returns Divergence
*
* @param index tag index
*
* @return Divergence
*/
public byte getDivergence(int index);
/**
* Returns End Position of Tag
*
* @param index tag index
*
* @return end position of tag
*/
public int getEndPosition(int index);
/**
* Returns Loci created from getChromosomes().
*
* @return Loci
*/
public Chromosome[] getLoci();
/**
* Get Chromosome representing chromosome for given tag.
*
* @param tagIndex tag index
*
* @return Chromosome
*/
public Chromosome getLocus(int tagIndex);
public byte getMapP(int index);
/**
* Returns maximum number of variants stored per tag.
*
* @return maximum number of variants
*/
public int getMaxNumVariants();
public byte getMultiMaps(int index);
/**
* Returns chromosome, strand, and start position for given tag.
*
* @param index tag index
*
* @return index 0 is chromosome, 1 is strand, and 2 is start position
*/
public int[] getPositionArray(int index);
/**
* Consider removing this. -Terry
*/
public int getReadIndexForPositionIndex(int posIndex);
/**
* Returns number of tags.
*
* @return number of tags
*/
public int getSize();
/**
* Returns start position of given tag.
*
* @param index tag index
*
* @return start position
*/
public int getStartPosition(int index);
/**
* Returns Strand for given tag.
*
* @param tagIndex tag index
*
* @return 1 = same sense as reference FASTA file. -1 = opposite sense.
* unknown = Byte.MIN_VALUE
*/
public byte getStrand(int tagIndex);
/**
* Returns variant definition at given tag and variant index.
*
* @param tagIndex tag index
* @param variantIndex variant index
*
* @return variant definition (see addVariant())
*/
public byte getVariantDef(int tagIndex, int variantIndex);
/**
* Returns the set of unique positions for the given chromosome
*
* @param chromosome
* @return unique positions on chromosome
*/
public int[] getUniquePositions(int chromosome);
/**
* Returns an array containing all variant definitions for given tag.
*
* @param tagIndex tag index
*
* @return variant definitions for tag
*/
public byte[] getVariantDefArray(int tagIndex);
/**
* Returns variant position offset from start position at given tag and
* variant index.
*
* @param tagIndex tag index
* @param variantIndex variant index
*
* @return variant position offset
*/
public byte getVariantPosOff(int tagIndex, int variantIndex);
/**
* Returns an array containing all variant position offsets for given tag.
*
* @param tagIndex tag index
*
* @return variant position offsets for tag
*/
public byte[] getVariantPosOffArray(int tagIndex);
/**
* Returns variant position offsets for all tags. First index of result is
* tag and second is variant.
*
* @return all variant position offsets
*/
public byte[][] getVariantOff();
/**
* Returns variant definitions for all tags. First index of result is tag
* and second is variant.
*
* @return all variant definitions
*/
public byte[][] getVariantDef();
/**
* Sets chromosome, strand, start position, and end position for given tag.
*
* @param index tag index
* @param chromosome chromosome
* @param strand strand
* @param positionMin start position
* @param positionMax end position
*/
public void setChromoPosition(int index, int chromosome, byte strand, int positionMin, int positionMax);
/**
* Set Divergence for given tag
*
* @param index tag index
* @param divergence divergence
*/
public void setDivergence(int index, byte divergence);
/**
* Set MapP for given tag
*
* @param index tag index
* @param mapP MapP
*/
public void setMapP(int index, byte mapP);
public void setMapP(int index, double mapP);
/**
* Set variant definition at given tag and variant index.
*
* @param tagIndex tag index
* @param variantIndex variant index
* @param def definition (see addVariant())
*/
public void setVariantDef(int tagIndex, int variantIndex, byte def);
/**
* Set variant position offset at given tag and variant index.
*
* @param tagIndex tag index
* @param variantIndex variant index
* @param offset position offset
*/
public void setVariantPosOff(int tagIndex, int variantIndex, byte offset);
/**
* Clears all variant definitions and position offsets.
*/
public void clearVariants();
public void writeTextFile(File outfile);
}