Class Edit

  • All Implemented Interfaces:
    java.io.Serializable

    public final class Edit
    extends java.lang.Object
    implements java.io.Serializable

    Encapsulates an edit operation on a SymbolList. See SymbolList for a full description.

    Author:
    Matthew Pocock, George Waldon
    See Also:
    Serialized Form
    • Constructor Summary

      Constructors 
      Constructor Description
      Edit​(int pos, int length, SymbolList replacement)
      Create a new Edit.
      Edit​(int pos, int length, SymbolList replacement, java.util.Map<java.lang.String,​java.lang.Object> props)
      Create a new Edit with some properties.
      Edit​(int pos, Alphabet alpha, Symbol replacement)
      Convenience construtor for making single residue changes
    • Method Summary

      • Methods inherited from class java.lang.Object

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

      • Edit

        public Edit​(int pos,
                    int length,
                    SymbolList replacement)
        Create a new Edit.
        Parameters:
        pos - the start of the edit
        length - the length of the edit
        replacement - a SymbolList representing the symbols that replace those from pos to pos + length-1 inclusive
      • Edit

        public Edit​(int pos,
                    int length,
                    SymbolList replacement,
                    java.util.Map<java.lang.String,​java.lang.Object> props)
        Create a new Edit with some properties.
        Parameters:
        pos - the start of the edit
        length - the length of the edit
        replacement - a SymbolList representing the symbols that replace those from pos to pos + length-1 inclusive
        props - a map of String properties and associated objects adding metainformation to this edit; for example a property may describe the fate of features surrounding this edit.
      • Edit

        public Edit​(int pos,
                    Alphabet alpha,
                    Symbol replacement)
             throws IllegalSymbolException
        Convenience construtor for making single residue changes
        Parameters:
        pos - the position of the change
        alpha - the Alphabet of the replacement Symbol
        replacement - the replacement Symbol
        Throws:
        IllegalSymbolException - if the replacement Symbol is not contained in alpha