Package pal.datatype

Class Nucleotides

java.lang.Object
pal.datatype.SimpleDataType
pal.datatype.Nucleotides
All Implemented Interfaces:
Serializable, DataType, MolecularDataType
public class Nucleotides extends SimpleDataType implements MolecularDataType
implements DataType for nucleotides
Version:
$Id: Nucleotides.java,v 1.20 2004/09/13 05:20:47 matt Exp $
Author:
Korbinian Strimmer, Alexei Drummond
See Also:

  • Field Details

  • Constructor Details

    • Nucleotides

      public Nucleotides()

    • Nucleotides

      public Nucleotides(boolean isRNA)
      If isRNA is true than getChar(state) will return a U instead of a T

  • Method Details

    • getNumStates

      public int getNumStates()
      Description copied from interface: DataType
      get number of unique states
      Specified by:
      getNumStates in interface DataType
      Returns:
      number of unique states

    • isUnknownStateImpl

      protected final boolean isUnknownStateImpl(int state)
      Description copied from class: SimpleDataType
      For subclasses to handle, without regard for gaps
      Specified by:
      isUnknownStateImpl in class SimpleDataType
      Returns:
      true if this state is an unknown state

    • getStateImpl

      protected int getStateImpl(char c)
      Get state corresponding to character c
      NOTE: IF YOU CHANGE THIS IT MAY STOP THE NUCLEOTIDE TRANSLATOR FROM WORKING! - It relies on the fact that all the states for 'ACGTU' are between [0, 3]
      Specified by:
      getStateImpl in class SimpleDataType

    • getCharImpl

      protected char getCharImpl(int state)
      Get character corresponding to a given state
      Specified by:
      getCharImpl in class SimpleDataType

    • getDescription

      public String getDescription()
      Description copied from interface: DataType
      description of data type
      Specified by:
      getDescription in interface DataType
      Returns:
      a string describing the data type

    • getTypeID

      public int getTypeID()
      Description copied from interface: DataType
      get numerical code describing the data type
      Specified by:
      getTypeID in interface DataType
      Returns:
      the unique numerical code describing the data type

    • isTransitionByState

      public final boolean isTransitionByState(int firstState, int secondState)
      Returns:
      true if A->G, G->A, C->T, or T->C if firstState equals secondState returns FALSE!

    • isTransitionByChar

      public final boolean isTransitionByChar(char firstChar, char secondChar)
      Returns:
      true if A->G, G->A, C->T, or T->C if firstState equals secondState returns FALSE! (I've renamed things to avoid confusion between java typing of ints and chars)

    • getNucleotideStates

      public int[] getNucleotideStates(int[] residueStates)
      Specified by:
      getNucleotideStates in interface MolecularDataType
      Parameters:
      residueStates - an array of states corresponding to states of this datatype
      Returns:
      a copy of the input

    • getRelavantLength

      public int getRelavantLength(int numberOfStates)
      Returns:
      the input

    • getMolecularStatesFromSimpleNucleotides

      public int[] getMolecularStatesFromSimpleNucleotides(int[] nucleotideStates, int startingIndex)
      Specified by:
      getMolecularStatesFromSimpleNucleotides in interface MolecularDataType
      Returns:
      a copy of the input

    • getMolecularStatesFromIUPACNucleotides

      public int[] getMolecularStatesFromIUPACNucleotides(int[] nucleotideStates, int startingIndex)
      Specified by:
      getMolecularStatesFromIUPACNucleotides in interface MolecularDataType
      Returns:
      a copy of the input

    • isCreatesIUPACNuecleotides

      public boolean isCreatesIUPACNuecleotides()
      Specified by:
      isCreatesIUPACNuecleotides in interface MolecularDataType
      Returns:
      false Nucleotide data will suffice

    • getNucleotideLength

      public final int getNucleotideLength()
      Specified by:
      getNucleotideLength in interface MolecularDataType
      Returns:
      1

    • getComplementState

      public static final int getComplementState(int baseState)
      Obtain the complement state
      Parameters:
      baseState - the base state to complement (may be IUPAC but IUPACness is lost)
      Returns:
      the complement state

    • getSequenceComplement

      public static final int[] getSequenceComplement(int[] sequence)
      Obtain the complement of a sequence of nucleotides (or IUPACNucleotides - but IUPAC ness is lost)
      Parameters:
      sequence - the sequence (of nucleotide states)
      Returns:
      the complement

    • complementSequence

      public static final void complementSequence(int[] sequence)
      Complement of a sequence of nucleotides (or IUPACNucleotides - but IUPAC ness is lost)
      Parameters:
      sequence - the sequence (of nucleotide states) (is modified)