Package 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:

  • Field Details

  • Constructor Details

    • 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