## Hierarchy For Package org.biojava.bio.alignment

Package Hierarchies:
  All Packages

## Class Hierarchy

- java.lang.Object
  - org.biojava.utils.AbstractChangeable (implements org.biojava.utils.Changeable)
    - org.biojava.bio.symbol.AbstractSymbolList (implements org.biojava.bio.symbol.SymbolList)
      - org.biojava.bio.alignment.AbstractULAlignment (implements org.biojava.bio.alignment.UnequalLengthAlignment)
        - org.biojava.bio.alignment.FlexibleAlignment (implements org.biojava.bio.alignment.ARAlignment, org.biojava.bio.alignment.EditableAlignment)
      - org.biojava.bio.alignment.AbstractULAlignment.SubULAlignment (implements org.biojava.bio.alignment.UnequalLengthAlignment)
  - org.biojava.bio.alignment.AbstractULAlignment.LeftRightLocationComparator (implements java.util.Comparator<T>)
  - org.biojava.bio.alignment.SequenceAlignment
    - org.biojava.bio.alignment.NeedlemanWunsch
      - org.biojava.bio.alignment.SmithWaterman
  - org.biojava.bio.alignment.SimpleAlignmentElement (implements org.biojava.bio.alignment.AlignmentElement)
  - org.biojava.bio.alignment.SubstitutionMatrix
  - java.lang.Throwable (implements java.io.Serializable)
    - java.lang.Exception
      - java.lang.RuntimeException
        - org.biojava.bio.BioRuntimeException
          - org.biojava.bio.alignment.IllegalAlignmentEditException

## Interface Hierarchy

- org.biojava.bio.alignment.AlignmentElement
- org.biojava.utils.Changeable
  - org.biojava.bio.symbol.SymbolList
    - org.biojava.bio.symbol.Alignment
      - org.biojava.bio.alignment.ARAlignment
      - org.biojava.bio.alignment.UnequalLengthAlignment
- org.biojava.bio.alignment.EditableAlignment
- org.biojava.bio.alignment.QualitativeAlignment