org.biojava.bio.symbol

Class Edit

java.lang.Object

org.biojava.bio.symbol.Edit

All Implemented Interfaces:

Serializable

public final class Edit
extends Object
implements Serializable

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

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