Package pal.datatype

Class DataType.Utils

  • Enclosing interface:
    DataType

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

      Constructors 
      Constructor Description
      Utils()  
    • Method Summary

      All Methods Static Methods Concrete Methods Deprecated Methods 
      Modifier and Type Method Description
      static 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 byte[] getByteStates​(java.lang.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 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 char[] getChars​(int[] sequence, char unknownChar, char gapChar, DataType dt)
      For converting a sequence of ints representing states to an array of chars
      static 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 char[] getPreferredChars​(char[] sequence, DataType dt)
      Converts a sequence of characters to the preferred form for a data type
      static char[] getPreferredChars​(char[] sequence, DataType dt, boolean specialDots)
      Converts a sequence of characters to the preferred form for a data type
      static java.lang.String getPreferredChars​(java.lang.String sequence, DataType dt)
      Converts a sequence of characters to the preferred form for a data type (using Strings)
      static java.lang.String getPreferredChars​(java.lang.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 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 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 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 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 boolean isGap​(DataType d, char c)
      Deprecated.
      use DataType.isGapChar()
      static 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.
      static 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 void reverseSequence​(int[] sequence)
      Reverses an array of states
      static java.lang.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 Detail

      • Utils

        public Utils()
    • Method Detail

      • 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 java.lang.String getPreferredChars​(java.lang.String sequence,
                                                               DataType dt)
        Converts a sequence of characters to the preferred form for a data type (using Strings)
      • getPreferredChars

        public static final java.lang.String getPreferredChars​(java.lang.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​(java.lang.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 java.lang.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