Package pl.poznan.put.structure

Class DotBracketSymbol

java.lang.Object
pl.poznan.put.structure.DotBracketSymbol
All Implemented Interfaces:
Serializable, Comparable<DotBracketSymbol>
Direct Known Subclasses:
ImmutableDotBracketSymbol
@Immutable public abstract class DotBracketSymbol extends Object implements Comparable<DotBracketSymbol>, Serializable
A single symbol in a dot-bracket structure.
See Also:

  • Constructor Details

    • DotBracketSymbol

      public DotBracketSymbol()

  • Method Details

    • isPairing

      public static boolean isPairing(char c)
      Checks if the given character is a pairing character in dot-bracket format.
      Parameters:
      c - The character to check.
      Returns:
      True if c is either an opening or closing symbol.

    • isOpening

      public static boolean isOpening(char c)
      Checks if the given character is an opening character in dot-bracket format.
      Parameters:
      c - The character to check
      Returns:
      True if c is one of: ([{<ABCDEFGHIJKLMNOPQRSTUVWXYZ.

    • isClosing

      public static boolean isClosing(char c)
      Checks if the given character is a closing character in dot-bracket format.
      Parameters:
      c - The character to check
      Returns:
      True if c is one of: )]}>abcdefghijklmnopqrstuvwxyz.

    • matchingBracket

      public static char matchingBracket(char c)
      Finds a matching bracket (closing for opening and vice versa) of the same level.
      Parameters:
      c - The character to find a matching bracket for.
      Returns:
      A matching bracket or a dot if the input is also a dot.

    • sequence

      @Parameter(order=1) public abstract char sequence()
      Returns:
      The sequence character.

    • structure

      @Parameter(order=2) public abstract char structure()
      Returns:
      The structure character (dot or bracket).

    • index

      @Parameter(order=3) public abstract int index()
      Returns:
      The index of this symbol.

    • isMissing

      public final boolean isMissing()
      Returns:
      True if this symbol is a minus '-'.

    • isPairing

      public final boolean isPairing()
      Returns:
      True if this symbol is either opening or closing.

    • isOpening

      public final boolean isOpening()
      Returns:
      True if this symbol is opening (see isOpening(char)).

    • isClosing

      public final boolean isClosing()
      Returns:
      True if this symbol is closing (see isClosing(char)).

    • order

      public final int order()
      Returns:
      The pseudoknot order of this symbol.

    • toString

      public final String toString()
      Overrides:
      toString in class Object

    • compareTo

      public final int compareTo(DotBracketSymbol t)
      Specified by:
      compareTo in interface Comparable<DotBracketSymbol>