Package org.biojava.nbio.genome.util
Class ChromosomeMappingTools
- java.lang.Object
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- org.biojava.nbio.genome.util.ChromosomeMappingTools
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public class ChromosomeMappingTools extends java.lang.Object
A class that can map chromosomal positions to mRNA (coding sequence) positions.- Author:
- Andreas Prlic
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Field Summary
Fields Modifier and Type Field Description static java.lang.String
CDS
static java.lang.String
CHROMOSOME
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Constructor Summary
Constructors Constructor Description ChromosomeMappingTools()
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description static java.lang.String
formatExonStructure(GeneChromosomePosition chromosomePosition)
Pretty print the details of a GeneChromosomePosition to a Stringstatic 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 sequencestatic 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 sequencestatic int
getCDSPosForChromosomeCoordinate(int coordinate, GeneChromosomePosition chromosomePosition)
I have a genomic coordinate, where is it on the mRNAstatic 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 coordinatesstatic ChromPos
getChromosomePosForCDScoordinate(int cdsNucleotidePosition, GeneChromosomePosition chromPos)
maps the position of a CDS nucleotide back to the genomestatic 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 positionstatic 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
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Field Detail
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CHROMOSOME
public static final java.lang.String CHROMOSOME
- See Also:
- Constant Field Values
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CDS
public static final java.lang.String CDS
- See Also:
- Constant Field Values
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Method Detail
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formatExonStructure
public static java.lang.String formatExonStructure(GeneChromosomePosition chromosomePosition)
Pretty print the details of a GeneChromosomePosition to a String- Parameters:
chromosomePosition
-- Returns:
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getCDSLength
public static int getCDSLength(GeneChromosomePosition chromPos)
Get the length of the CDS in nucleotides.- Parameters:
chromPos
-- Returns:
- length of the CDS in nucleotides.
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getChromosomePosForCDScoordinate
public static ChromPos getChromosomePosForCDScoordinate(int cdsNucleotidePosition, GeneChromosomePosition chromPos)
maps the position of a CDS nucleotide back to the genome- Parameters:
cdsNucleotidePosition
-- Returns:
- a ChromPos object
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getChromPosReverse
public 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- Parameters:
exonStarts
-exonEnds
-cdsStart
-cdsEnd
-- Returns:
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getChromPosForward
public 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- Parameters:
exonStarts
-exonEnds
-cdsStart
-cdsEnd
-- Returns:
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getCDSLengthReverse
public 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- Parameters:
exonStarts
-exonEnds
-cdsStart
-cdsEnd
-- Returns:
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getCDSLengthForward
public 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- Parameters:
exonStarts
-exonEnds
-cdsStart
-cdsEnd
-- Returns:
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getCDSExonRanges
public static java.util.List<com.google.common.collect.Range<java.lang.Integer>> getCDSExonRanges(GeneChromosomePosition chromPos)
Extracts the exon boundaries in CDS coordinates. (needs to be divided by 3 to get AA positions)- Parameters:
chromPos
-- Returns:
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getChromosomalRangesForCDS
public 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- Parameters:
chromPos
-- Returns:
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getCDSPosForChromosomeCoordinate
public static int getCDSPosForChromosomeCoordinate(int coordinate, GeneChromosomePosition chromosomePosition)
I have a genomic coordinate, where is it on the mRNA- Parameters:
coordinate
-chromosomePosition
-- Returns:
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getCDSPosForward
public 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.- Parameters:
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- Returns:
- the position of the nucleotide base on the mRNA sequence corresponding to the input genetic coordinate (base 1)
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getCDSPosReverse
public 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.- Parameters:
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- Returns:
- the position of the nucleotide base on the mRNA sequence corresponding to the input genetic coordinate (base 1)
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