public class ChromosomeMappingTools
extends java.lang.Object
Modifier and Type | Field | Description |
---|---|---|
static java.lang.String |
CDS |
|
static java.lang.String |
CHROMOSOME |
Constructor | Description |
---|---|
ChromosomeMappingTools() |
Modifier and Type | Method | Description |
---|---|---|
static java.lang.String |
formatExonStructure(GeneChromosomePosition chromosomePosition) |
Pretty print the details of a GeneChromosomePosition to a String
|
static java.util.List<com.google.common.collect.Range<java.lang.Integer>> |
getCDSExonRanges(GeneChromosomePosition chromPos) |
Extracts the exon boundaries in CDS coordinates.
|
static int |
getCDSLength(GeneChromosomePosition chromPos) |
Get the length of the CDS in nucleotides.
|
static int |
getCDSLengthForward(java.util.List<java.lang.Integer> exonStarts,
java.util.List<java.lang.Integer> exonEnds,
int cdsStart,
int cdsEnd) |
Get the length of the coding sequence
|
static int |
getCDSLengthReverse(java.util.List<java.lang.Integer> exonStarts,
java.util.List<java.lang.Integer> exonEnds,
int cdsStart,
int cdsEnd) |
Get the length of the coding sequence
|
static int |
getCDSPosForChromosomeCoordinate(int coordinate,
GeneChromosomePosition chromosomePosition) |
I have a genomic coordinate, where is it on the mRNA
|
static int |
getCDSPosForward(int chromPos,
java.util.List<java.lang.Integer> exonStarts,
java.util.List<java.lang.Integer> exonEnds,
int cdsStart,
int cdsEnd) |
Converts the genetic coordinate to the position of the nucleotide on the mRNA sequence for a gene
living on the forward DNA strand.
|
static int |
getCDSPosReverse(int chromPos,
java.util.List<java.lang.Integer> exonStarts,
java.util.List<java.lang.Integer> exonEnds,
int cdsStart,
int cdsEnd) |
Converts the genetic coordinate to the position of the nucleotide on the mRNA sequence for a gene
living on the reverse DNA strand.
|
static java.util.List<com.google.common.collect.Range<java.lang.Integer>> |
getChromosomalRangesForCDS(GeneChromosomePosition chromPos) |
Extracts the boundaries of the coding regions in chromosomal coordinates
|
static ChromPos |
getChromosomePosForCDScoordinate(int cdsNucleotidePosition,
GeneChromosomePosition chromPos) |
maps the position of a CDS nucleotide back to the genome
|
static ChromPos |
getChromPosForward(int cdsPos,
java.util.List<java.lang.Integer> exonStarts,
java.util.List<java.lang.Integer> exonEnds,
int cdsStart,
int cdsEnd) |
Get the CDS position mapped onto the chromosome position
|
static ChromPos |
getChromPosReverse(int cdsPos,
java.util.List<java.lang.Integer> exonStarts,
java.util.List<java.lang.Integer> exonEnds,
int cdsStart,
int cdsEnd) |
Get the CDS position mapped on the chromosome position
|
public static final java.lang.String CHROMOSOME
public static final java.lang.String CDS
public static java.lang.String formatExonStructure(GeneChromosomePosition chromosomePosition)
chromosomePosition
- public static int getCDSLength(GeneChromosomePosition chromPos)
chromPos
- public static ChromPos getChromosomePosForCDScoordinate(int cdsNucleotidePosition, GeneChromosomePosition chromPos)
cdsNucleotidePosition
- public static ChromPos getChromPosReverse(int cdsPos, java.util.List<java.lang.Integer> exonStarts, java.util.List<java.lang.Integer> exonEnds, int cdsStart, int cdsEnd)
exonStarts
- exonEnds
- cdsStart
- cdsEnd
- public static ChromPos getChromPosForward(int cdsPos, java.util.List<java.lang.Integer> exonStarts, java.util.List<java.lang.Integer> exonEnds, int cdsStart, int cdsEnd)
exonStarts
- exonEnds
- cdsStart
- cdsEnd
- public static int getCDSLengthReverse(java.util.List<java.lang.Integer> exonStarts, java.util.List<java.lang.Integer> exonEnds, int cdsStart, int cdsEnd)
exonStarts
- exonEnds
- cdsStart
- cdsEnd
- public static int getCDSLengthForward(java.util.List<java.lang.Integer> exonStarts, java.util.List<java.lang.Integer> exonEnds, int cdsStart, int cdsEnd)
exonStarts
- exonEnds
- cdsStart
- cdsEnd
- public static java.util.List<com.google.common.collect.Range<java.lang.Integer>> getCDSExonRanges(GeneChromosomePosition chromPos)
chromPos
- public static java.util.List<com.google.common.collect.Range<java.lang.Integer>> getChromosomalRangesForCDS(GeneChromosomePosition chromPos)
chromPos
- public static int getCDSPosForChromosomeCoordinate(int coordinate, GeneChromosomePosition chromosomePosition)
coordinate
- chromosomePosition
- public static int getCDSPosForward(int chromPos, java.util.List<java.lang.Integer> exonStarts, java.util.List<java.lang.Integer> exonEnds, int cdsStart, int cdsEnd)
chromPos
- The genetic coordinate on a chromosomeexonStarts
- The list holding the genetic coordinates pointing to the start positions of the exons (including UTR regions)exonEnds
- The list holding the genetic coordinates pointing to the end positions of the exons (including UTR regions)cdsStart
- The start position of a coding regioncdsEnd
- The end position of a coding regionpublic static int getCDSPosReverse(int chromPos, java.util.List<java.lang.Integer> exonStarts, java.util.List<java.lang.Integer> exonEnds, int cdsStart, int cdsEnd)
chromPos
- The genetic coordinate on a chromosomeexonStarts
- The list holding the genetic coordinates pointing to the start positions of the exons (including UTR regions)exonEnds
- The list holding the genetic coordinates pointing to the end positions of the exons (including UTR regions)cdsStart
- The start position of a coding regioncdsEnd
- The end position of a coding region