All Implemented Interfaces:

Serializable

public final class Edit
extends Object
implements Serializable 

Author:

Matthew Pocock, George Waldon

See Also:

Serialized Form

• Field Summary

  Fields

  Modifier and Type	Field and Description
  int	length
  int	pos
  Map<String,Object>	props
  SymbolList	replacement

• Constructor Summary

  Constructors

  Constructor and Description
  Edit (int pos, Alphabet alpha, Symbol replacement) Convenience construtor for making single residue changes
  Edit (int pos, int length, SymbolList replacement) Create a new Edit.
  Edit (int pos, int length, SymbolList replacement, Map<String,Object> props) Create a new Edit with some properties.

• Method Summary

  • Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

• Field Detail

  • pos

    public final int pos 

  • length

    public final int length 

  • replacement

    public final SymbolList replacement 

  • props

    public final Map<String,Object> props 

• 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,
     Map<String,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