Field Detail

• CHROMOSOME

  public static final java.lang.String CHROMOSOME

  See Also:

  Constant Field Values

• CDS

  public static final java.lang.String CDS

  See Also:

  Constant Field Values

Constructor Detail

• ChromosomeMappingTools

  public ChromosomeMappingTools​()

Method Detail

• formatExonStructure

  public static java.lang.String formatExonStructure​(GeneChromosomePosition chromosomePosition)

  Pretty print the details of a GeneChromosomePosition to a String

  Parameters:

  chromosomePosition -

  Returns:

• getCDSLength

  public static int getCDSLength​(GeneChromosomePosition chromPos)

  Get the length of the CDS in nucleotides.

  Parameters:

  chromPos -

  Returns:

  length of the CDS in nucleotides.

• 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

• 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:

• 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:

• 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:

• 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:

• 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:

• 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:

• getCDSPosForChromosomeCoordinate

  public static int getCDSPosForChromosomeCoordinate​(int coordinate,
                                                     GeneChromosomePosition chromosomePosition)

  I have a genomic coordinate, where is it on the mRNA

  Parameters:

  coordinate -

  chromosomePosition -

  Returns:

• 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 chromosome

  exonStarts - 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 region

  cdsEnd - 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)

• 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 chromosome

  exonStarts - 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 region

  cdsEnd - 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)