Package pal.datatype

Class DataType.Utils

java.lang.Object
pal.datatype.DataType.Utils
Enclosing interface:
DataType

public static final class DataType.Utils extends Object
Some useful methods for implmenting classes and for DataType users
  • Constructor Summary

    Constructors
    Constructor
    Description
     
  • Method Summary

    Modifier and Type
    Method
    Description
    static final byte[]
    getByteStates(char[] sequence, DataType dt)
    For converting a sequence to an array of bytes where each byte represents the state of the corresponding character in sequence
    static final byte[]
    getByteStates(String sequence, DataType dt)
    For converting a sequence to an array of bytes where each byte represents the state of the corresponding character in sequence
    static final char[][]
    getChars(int[][] sequences, char unknownChar, char gapChar, DataType dt)
    For converting an array of sequence to arrays of ints where each int represents the state of the corresponding character in sequence
    static final char[]
    getChars(int[] sequence, char unknownChar, char gapChar, DataType dt)
    For converting a sequence of ints representing states to an array of chars
    static final char[]
    getChars(int[] sequence, DataType dt)
    For converting a sequence of ints representing states to an array of chars
    static DataType
    getInstance(int typeID)
    create object according to this code
    static final char[]
    getPreferredChars(char[] sequence, DataType dt)
    Converts a sequence of characters to the preferred form for a data type
    static final char[]
    getPreferredChars(char[] sequence, DataType dt, boolean specialDots)
    Converts a sequence of characters to the preferred form for a data type
    static final String
    Converts a sequence of characters to the preferred form for a data type (using Strings)
    static final String
    getPreferredChars(String sequence, DataType dt, boolean specialDots)
    Converts a sequence of characters to the preferred form for a data type (using Strings) * @param specialDots if true then the dot (period) '.' is used even if it is not the prefered character by the data type
    static final int[][]
    getStates(char[][] sequences, int unknownState, int gapState, DataType dt)
    For converting an array of sequence to arrays of ints where each int represents the state of the corresponding character in sequence
    static final int[][]
    getStates(char[][] sequences, DataType dt)
    For converting an array of sequence to arrays of ints where each int represents the state of the corresponding character in sequence
    static final int[]
    getStates(char[] sequence, int unknownState, int gapState, DataType dt)
    For converting a sequence to an array of ints where each int represents the state of the corresponding character in sequence Allows user selection of unknown and gap states
    static final int[]
    getStates(char[] sequence, DataType dt)
    For converting a sequence to an array of ints where each int represents the state of the corresponding character in sequence
    static final boolean
    isGap(DataType d, char c)
    Deprecated.
    use DataType.isGapChar()
    static final boolean
    Useful for implementing classes to check if a character is a suggest gap character Users of datatypes should query the datatype to see if a character is a gap - not use this method.
    static final void
    leftAlignSequence(int[] sequence, DataType dt)
    Realigns a sequence of states so that there are no gaps at the beggining (shifts to the left if necessary)
    static final void
    reverseSequence(int[] sequence)
    Reverses an array of states
    static final String
    toString(DataType dt, int[] states)
    For converting an array of states into a String of characters, based on a DataType

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
  • Constructor Details

    • Utils

      public Utils()
  • Method Details

    • isSuggestedGap

      public static final boolean isSuggestedGap(char c)
      Useful for implementing classes to check if a character is a suggest gap character Users of datatypes should query the datatype to see if a character is a gap - not use this method.
    • getInstance

      public static DataType getInstance(int typeID)
      create object according to this code
      Parameters:
      typeID - selected data type
      Returns:
      DataType object
    • isGap

      public static final boolean isGap(DataType d, char c)
      Deprecated.
      use DataType.isGapChar()
      Returns:
      true if the character represents a gap in the sequence.
    • getPreferredChars

      public static final char[] getPreferredChars(char[] sequence, DataType dt)
      Converts a sequence of characters to the preferred form for a data type
    • getPreferredChars

      public static final char[] getPreferredChars(char[] sequence, DataType dt, boolean specialDots)
      Converts a sequence of characters to the preferred form for a data type
      Parameters:
      specialDots - if true then the dot (period) '.' is used even if it is not the prefered character by the data type
    • getPreferredChars

      public static final String getPreferredChars(String sequence, DataType dt)
      Converts a sequence of characters to the preferred form for a data type (using Strings)
    • getPreferredChars

      public static final String getPreferredChars(String sequence, DataType dt, boolean specialDots)
      Converts a sequence of characters to the preferred form for a data type (using Strings) * @param specialDots if true then the dot (period) '.' is used even if it is not the prefered character by the data type
      Parameters:
      specialDots - if true then the dot (period) '.' is used even if it is not the prefered character by the data type
    • getByteStates

      public static final byte[] getByteStates(String sequence, DataType dt)
      For converting a sequence to an array of bytes where each byte represents the state of the corresponding character in sequence
    • getByteStates

      public static final byte[] getByteStates(char[] sequence, DataType dt)
      For converting a sequence to an array of bytes where each byte represents the state of the corresponding character in sequence
    • getStates

      public static final int[][] getStates(char[][] sequences, int unknownState, int gapState, DataType dt)
      For converting an array of sequence to arrays of ints where each int represents the state of the corresponding character in sequence
      Parameters:
      unknownState - ensures that the state representation is set to this value (like -1)
    • getStates

      public static final int[] getStates(char[] sequence, int unknownState, int gapState, DataType dt)
      For converting a sequence to an array of ints where each int represents the state of the corresponding character in sequence Allows user selection of unknown and gap states
    • getStates

      public static final int[][] getStates(char[][] sequences, DataType dt)
      For converting an array of sequence to arrays of ints where each int represents the state of the corresponding character in sequence
    • getStates

      public static final int[] getStates(char[] sequence, DataType dt)
      For converting a sequence to an array of ints where each int represents the state of the corresponding character in sequence
    • getChars

      public static final char[][] getChars(int[][] sequences, char unknownChar, char gapChar, DataType dt)
      For converting an array of sequence to arrays of ints where each int represents the state of the corresponding character in sequence
      Parameters:
      unknownChar - The character uses for unknown states
      gapChar - the character to use for gap states (may be the same as the unknownChar)
    • getChars

      public static final char[] getChars(int[] sequence, char unknownChar, char gapChar, DataType dt)
      For converting a sequence of ints representing states to an array of chars
      Parameters:
      unknownChar - The character uses for unknown states
      gapChar - the character to use for gap states (may be the same as the unknownChar)
    • getChars

      public static final char[] getChars(int[] sequence, DataType dt)
      For converting a sequence of ints representing states to an array of chars
    • toString

      public static final String toString(DataType dt, int[] states)
      For converting an array of states into a String of characters, based on a DataType
    • reverseSequence

      public static final void reverseSequence(int[] sequence)
      Reverses an array of states
      Parameters:
      sequence - the sequence of states
    • leftAlignSequence

      public static final void leftAlignSequence(int[] sequence, DataType dt)
      Realigns a sequence of states so that there are no gaps at the beggining (shifts to the left if necessary)
      Parameters:
      sequence - the base sequence
      dt - the datatype of the sequence states