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## Hierarchy For All Packages

Package Hierarchies:
  uk.ac.man.bioinf, uk.ac.man.bioinf.analysis.consensus, uk.ac.man.bioinf.analysis.misc, uk.ac.man.bioinf.analysis.regexp, uk.ac.man.bioinf.apps.cinema, uk.ac.man.bioinf.apps.cinema.color, uk.ac.man.bioinf.apps.cinema.consensus, uk.ac.man.bioinf.apps.cinema.core, uk.ac.man.bioinf.apps.cinema.core.test, uk.ac.man.bioinf.apps.cinema.group, uk.ac.man.bioinf.apps.cinema.io, uk.ac.man.bioinf.apps.cinema.motif, uk.ac.man.bioinf.apps.cinema.resources, uk.ac.man.bioinf.apps.cinema.shared, uk.ac.man.bioinf.apps.cinema.utils, uk.ac.man.bioinf.apps.commandline, uk.ac.man.bioinf.apps.invoker, uk.ac.man.bioinf.apps.optionable, uk.ac.man.bioinf.apps.systemevents, uk.ac.man.bioinf.apps.xml, uk.ac.man.bioinf.apps.xml.test, uk.ac.man.bioinf.database.fetch, uk.ac.man.bioinf.debug, uk.ac.man.bioinf.gui.color, uk.ac.man.bioinf.gui.misc, uk.ac.man.bioinf.gui.optionable, uk.ac.man.bioinf.gui.util, uk.ac.man.bioinf.gui.util.forms, uk.ac.man.bioinf.gui.viewer, uk.ac.man.bioinf.gui.viewer.event, uk.ac.man.bioinf.gui.viewer.plaf, uk.ac.man.bioinf.gui.viewer.test, uk.ac.man.bioinf.io, uk.ac.man.bioinf.io.parsers, uk.ac.man.bioinf.io.test, uk.ac.man.bioinf.module, uk.ac.man.bioinf.sequence, uk.ac.man.bioinf.sequence.alignment, uk.ac.man.bioinf.sequence.alignment.event, uk.ac.man.bioinf.sequence.complex, uk.ac.man.bioinf.sequence.event, uk.ac.man.bioinf.sequence.geom, uk.ac.man.bioinf.sequence.group, uk.ac.man.bioinf.sequence.identifier, uk.ac.man.bioinf.sequence.test, uk.ac.man.bioinf.sequence.types, uk.ac.man.bioinf.util

## Class Hierarchy

- class java.lang.Object
  - class uk.ac.man.bioinf.debug.AbstractDebug (implements uk.ac.man.bioinf.debug.DebugInterface)
    - class uk.ac.man.bioinf.apps.cinema.utils.CinemaDebug.DebugImpl
    - class uk.ac.man.bioinf.apps.cinema.shared.CinemaDebug.DebugImpl
    - class uk.ac.man.bioinf.debug.DefaultDebug
    - class uk.ac.man.bioinf.debug.DefaultFileDebug
    - class uk.ac.man.bioinf.debug.NullDebug
  - class javax.swing.text.AbstractDocument (implements javax.swing.text.Document, java.io.Serializable)
    - class javax.swing.text.PlainDocument
      - class uk.ac.man.bioinf.gui.util.forms.FormattedDocument
      - class uk.ac.man.bioinf.gui.util.forms.IntegerField.IntegerDocument
      - class uk.ac.man.bioinf.gui.util.forms.WholeNumberField.WholeNumberDocument
  - class uk.ac.man.bioinf.util.AbstractEnumeration
    - class uk.ac.man.bioinf.sequence.types.AbstractElement
      - class uk.ac.man.bioinf.sequence.types.AminoAcid (implements uk.ac.man.bioinf.sequence.types.ProteinResidue)
      - class uk.ac.man.bioinf.sequence.types.DNANucleotide (implements uk.ac.man.bioinf.sequence.types.DNAResidue)
      - class uk.ac.man.bioinf.sequence.types.RNANucleotide (implements uk.ac.man.bioinf.sequence.types.RNAResidue)
    - class uk.ac.man.bioinf.module.AbstractEnumeratedModuleIdentifier (implements uk.ac.man.bioinf.module.ModuleIdentifier)
      - class uk.ac.man.bioinf.apps.cinema.CinemaBootIdentifier
      - class uk.ac.man.bioinf.apps.cinema.color.CinemaColorIdentifier
      - class uk.ac.man.bioinf.apps.cinema.io.CinemaCommandLineParserIdentifier
      - class uk.ac.man.bioinf.apps.cinema.consensus.CinemaConsensusIdentifier
      - class uk.ac.man.bioinf.apps.cinema.core.CinemaCoreIdentifier
      - class uk.ac.man.bioinf.apps.cinema.group.CinemaGroupIdentifier
      - class uk.ac.man.bioinf.apps.cinema.core.CinemaModuleCoreIdentifier
      - class uk.ac.man.bioinf.apps.cinema.motif.CinemaMotifIdentifier
      - class uk.ac.man.bioinf.apps.cinema.shared.CinemaSharedIdentifier
      - class uk.ac.man.bioinf.apps.cinema.utils.CinemaUtilityIdentifier
      - class uk.ac.man.bioinf.apps.cinema.io.SequenceInputModuleIdentifier
      - class uk.ac.man.bioinf.apps.cinema.io.SequenceOutputModuleIdentifier
      - class uk.ac.man.bioinf.apps.xml.XMLBootIdentifier
    - class uk.ac.man.bioinf.apps.cinema.CinemaProperties
    - class uk.ac.man.bioinf.util.Direction
    - class uk.ac.man.bioinf.module.ModuleExceptionType
    - class uk.ac.man.bioinf.sequence.event.SequenceEventType
  - class uk.ac.man.bioinf.util.AbstractEnumeration.ElementIterator (implements java.util.Iterator)
  - class uk.ac.man.bioinf.sequence.group.AbstractGappedSequenceGroup (implements uk.ac.man.bioinf.sequence.group.GappedSequenceGroup)
    - class uk.ac.man.bioinf.sequence.group.DefaultGappedSequenceGroup
    - class uk.ac.man.bioinf.sequence.group.GroupSequenceAlignment (implements uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener, uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)
      - class uk.ac.man.bioinf.apps.cinema.group.CinemaGroup
  - class uk.ac.man.bioinf.sequence.identifier.AbstractIdentifier (implements uk.ac.man.bioinf.sequence.identifier.Identifier)
    - class uk.ac.man.bioinf.analysis.consensus.ConsensusIdentifier
    - class uk.ac.man.bioinf.sequence.identifier.DatabaseIdentifier
      - class uk.ac.man.bioinf.sequence.identifier.SwissProtIdentifier
    - class uk.ac.man.bioinf.sequence.identifier.SimpleIdentifier
  - class javax.swing.AbstractListModel (implements javax.swing.ListModel, java.io.Serializable)
    - class uk.ac.man.bioinf.apps.cinema.core.AlignmentToListModel
    - class uk.ac.man.bioinf.gui.misc.ChunkyListModel
  - class uk.ac.man.bioinf.sequence.complex.AbstractModification (implements uk.ac.man.bioinf.sequence.complex.Modification)
    - class uk.ac.man.bioinf.sequence.complex.SingletonModification
      - class uk.ac.man.bioinf.sequence.complex.Methylation
  - class uk.ac.man.bioinf.io.parsers.AbstractProteinAlignmentInputParser (implements uk.ac.man.bioinf.io.AlignmentInputParser)
    - class uk.ac.man.bioinf.io.parsers.PIRProteinAlignmentParser (implements uk.ac.man.bioinf.io.AlignmentOutputParser)
  - class uk.ac.man.bioinf.io.parsers.AbstractProteinSequenceInputParser (implements uk.ac.man.bioinf.io.SequenceInputParser)
    - class uk.ac.man.bioinf.io.parsers.FastaSequenceParser
  - class uk.ac.man.bioinf.sequence.AbstractSequence (implements uk.ac.man.bioinf.sequence.Sequence)
    - class uk.ac.man.bioinf.sequence.AbstractMutableSequence (implements uk.ac.man.bioinf.sequence.MutableSequence)
      - class uk.ac.man.bioinf.sequence.complex.AbstractComplexSequence (implements uk.ac.man.bioinf.sequence.complex.ComplexSequence)
        - class uk.ac.man.bioinf.sequence.complex.DefaultComplexSequence
        - class uk.ac.man.bioinf.sequence.complex.DefaultGappedComplexSequence (implements uk.ac.man.bioinf.sequence.complex.GappedComplexSequence)
      - class uk.ac.man.bioinf.sequence.AbstractEditableSequence (implements uk.ac.man.bioinf.sequence.EditableSequence)
        - class uk.ac.man.bioinf.sequence.DefaultEditableSequence (implements uk.ac.man.bioinf.sequence.EditableSequence)
      - class uk.ac.man.bioinf.sequence.alignment.AbstractGappedSequence (implements uk.ac.man.bioinf.sequence.alignment.GappedSequence)
        - class uk.ac.man.bioinf.analysis.consensus.DefaultConsensusSequence (implements uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener, uk.ac.man.bioinf.analysis.consensus.ConsensusSequence, uk.ac.man.bioinf.sequence.event.SequenceListener)
          - class uk.ac.man.bioinf.analysis.consensus.ThreadedConsensusSequence
        - class uk.ac.man.bioinf.sequence.alignment.DefaultGappedSequence
    - class uk.ac.man.bioinf.sequence.DefaultSequence
  - class uk.ac.man.bioinf.sequence.alignment.AbstractSequenceAlignment (implements uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.sequence.event.VetoableSequenceListener)
    - class uk.ac.man.bioinf.sequence.alignment.DefaultSequenceAlignment
      - class uk.ac.man.bioinf.sequence.alignment.SingleSequenceAlignment
  - class uk.ac.man.bioinf.apps.cinema.io.AbstractSequenceInputParserExceptionHandler (implements uk.ac.man.bioinf.io.ParserExceptionHandler)
    - class uk.ac.man.bioinf.apps.cinema.io.FileSequenceInputParserExceptionHandler
  - class uk.ac.man.bioinf.apps.cinema.io.AbstractSequenceParserExceptionHandler (implements uk.ac.man.bioinf.io.ParserExceptionHandler)
    - class uk.ac.man.bioinf.apps.cinema.io.FileSequenceParserExceptionHandler
  - class uk.ac.man.bioinf.sequence.types.AbstractSequenceType (implements uk.ac.man.bioinf.sequence.SequenceType)
    - class uk.ac.man.bioinf.sequence.complex.AbstractComplexSequenceType (implements uk.ac.man.bioinf.sequence.complex.ComplexSequenceType)
    - class uk.ac.man.bioinf.sequence.types.AbstractEnumeratedSequenceType
      - class uk.ac.man.bioinf.sequence.types.DNASequenceType
      - class uk.ac.man.bioinf.sequence.types.ProteinSequenceType
      - class uk.ac.man.bioinf.sequence.types.RNASequenceType
  - class uk.ac.man.bioinf.sequence.alignment.AlignmentColumn
  - class uk.ac.man.bioinf.sequence.alignment.event.AlignmentEventType
  - class uk.ac.man.bioinf.sequence.alignment.event.AlignmentListenerSupport
  - class uk.ac.man.bioinf.io.test.AlignmentParserInputTest
  - class uk.ac.man.bioinf.io.test.AlignmentParserIOTest
  - class uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionListenerSupport
  - class uk.ac.man.bioinf.apps.cinema.color.AminoAcidColorMapMetaData (implements uk.ac.man.bioinf.apps.cinema.color.ColorMapMetaData)
  - class uk.ac.man.bioinf.util.ArrayManipulation
  - class uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentViewerUI.KeyScroller (implements java.awt.event.ActionListener)
  - class uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentViewerUI.PointListener (implements javax.swing.event.ChangeListener)
  - class uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentViewerUI.SelectionClearer (implements java.awt.event.ActionListener)
  - class uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentViewerUI.SelectionToggler (implements java.awt.event.ActionListener)
  - class javax.swing.plaf.basic.BasicListUI.MouseInputHandler (implements javax.swing.event.MouseInputListener)
    - class uk.ac.man.bioinf.gui.misc.SwappingListBasicUI.SwappingMouseInputHandler
  - class uk.ac.man.bioinf.gui.viewer.BorderFastAlignmentViewerCellRenderer (implements uk.ac.man.bioinf.gui.viewer.FastAlignmentViewerCellRenderer)
  - class uk.ac.man.bioinf.gui.viewer.test.ButtonPanelTest (implements java.awt.event.ItemListener)
  - class uk.ac.man.bioinf.apps.commandline.CalculatePercentageID
  - class uk.ac.man.bioinf.util.ChangeableListenerSupport
    - class uk.ac.man.bioinf.util.SequenceAlignmentToChangeableAdaptor (implements uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener, uk.ac.man.bioinf.util.Changeable, uk.ac.man.bioinf.sequence.event.SequenceListener)
  - class uk.ac.man.bioinf.gui.viewer.event.ChangeListenerSupport
  - class uk.ac.man.bioinf.apps.commandline.CheckMotifLocationAgainstPrints
  - class uk.ac.man.bioinf.apps.cinema.Cinema
  - class uk.ac.man.bioinf.apps.cinema.group.CinemaAnchorManager (implements java.beans.PropertyChangeListener)
  - class uk.ac.man.bioinf.apps.cinema.utils.CinemaFileOptionableExceptionHandler (implements uk.ac.man.bioinf.apps.optionable.OptionableExceptionHandler)
  - class uk.ac.man.bioinf.apps.cinema.group.CinemaGroupManager
  - class uk.ac.man.bioinf.apps.cinema.resources.CinemaResources
  - class uk.ac.man.bioinf.apps.cinema.core.test.CinemaTestLaunch
  - class uk.ac.man.bioinf.apps.cinema.core.test.CinemaTestModuleLaunch
  - class uk.ac.man.bioinf.apps.cinema.CinemaXMLParserFactory (implements uk.ac.man.bioinf.apps.xml.XMLParserFactory)
  - class uk.ac.man.bioinf.util.CollectionPrinter
  - class uk.ac.man.bioinf.gui.viewer.ColorFastAlignmentViewerCellRenderer (implements uk.ac.man.bioinf.gui.viewer.FastAlignmentViewerCellRenderer)
  - class uk.ac.man.bioinf.gui.color.ColorGenerator
  - class uk.ac.man.bioinf.gui.color.ColorList
  - class uk.ac.man.bioinf.apps.cinema.color.ColormapColorMapMetaData (implements uk.ac.man.bioinf.apps.cinema.color.ColorMapMetaData)
  - class uk.ac.man.bioinf.gui.color.ColorStore
  - class uk.ac.man.bioinf.sequence.test.ComplexElementAndModificationTest
  - class uk.ac.man.bioinf.sequence.complex.ComplexElementFactory
  - class uk.ac.man.bioinf.sequence.test.ComplexSequenceTest
  - class java.awt.Component (implements java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable)
    - class java.awt.Container
      - class javax.swing.CellRendererPane (implements javax.accessibility.Accessible)
        - class uk.ac.man.bioinf.gui.viewer.test.CellRendererPaneReplacement
      - class javax.swing.JComponent (implements java.io.Serializable)
        - class uk.ac.man.bioinf.gui.viewer.JAlignmentViewer (implements uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener, uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionListener, uk.ac.man.bioinf.sequence.event.SequenceListener)
          - class uk.ac.man.bioinf.gui.viewer.PrintableJAlignmentViewer (implements java.awt.print.Printable)
        - class javax.swing.JLabel (implements javax.accessibility.Accessible, javax.swing.SwingConstants)
          - class uk.ac.man.bioinf.gui.viewer.DefaultAlignmentViewerCellRenderer (implements uk.ac.man.bioinf.gui.viewer.AlignmentViewerCellRenderer)
          - class javax.swing.DefaultListCellRenderer (implements javax.swing.ListCellRenderer, java.io.Serializable)
            - class uk.ac.man.bioinf.apps.cinema.core.AlignmentToListCellRenderer
        - class javax.swing.JPanel (implements javax.accessibility.Accessible)
          - class uk.ac.man.bioinf.gui.viewer.JAlignmentButtonPanel (implements uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener, java.awt.ItemSelectable)
          - class uk.ac.man.bioinf.gui.viewer.PrintableAlignmentPanel
          - class uk.ac.man.bioinf.gui.viewer.test.SliderExample
          - class uk.ac.man.bioinf.gui.util.TripletPanel
          - class uk.ac.man.bioinf.gui.util.forms.ValidatedForm
        - class javax.swing.JPopupMenu (implements javax.accessibility.Accessible, javax.swing.MenuElement)
          - class uk.ac.man.bioinf.gui.viewer.ButtonViewerPopupMenu (implements java.awt.event.ItemListener)
        - class javax.swing.JScrollPane (implements javax.accessibility.Accessible, javax.swing.ScrollPaneConstants)
          - class uk.ac.man.bioinf.gui.viewer.JChangedScrollPane
          - class uk.ac.man.bioinf.gui.viewer.JLayableScrollPane
        - class javax.swing.JSlider (implements javax.accessibility.Accessible, javax.swing.SwingConstants)
          - class uk.ac.man.bioinf.gui.viewer.JAlignmentRuler
        - class javax.swing.JSplitPane (implements javax.accessibility.Accessible)
          - class uk.ac.man.bioinf.gui.optionable.OptionableJSplitPane (implements uk.ac.man.bioinf.apps.optionable.Optionable)
        - class javax.swing.text.JTextComponent (implements javax.accessibility.Accessible, javax.swing.Scrollable)
          - class javax.swing.JTextField (implements javax.swing.SwingConstants)
            - class uk.ac.man.bioinf.gui.util.forms.DecimalField
            - class uk.ac.man.bioinf.gui.util.forms.IntegerField
            - class uk.ac.man.bioinf.gui.util.forms.WholeNumberField
      - class java.awt.Window (implements javax.accessibility.Accessible)
        - class java.awt.Frame (implements java.awt.MenuContainer)
          - class javax.swing.JFrame (implements javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants)
            - class uk.ac.man.bioinf.gui.viewer.test.AlignmentViewerTest
            - class uk.ac.man.bioinf.gui.util.ApplicationFrame
            - class uk.ac.man.bioinf.apps.cinema.motif.CinemaMotifFrame (implements java.awt.event.ActionListener, uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionListener, javax.swing.event.ListSelectionListener, java.beans.PropertyChangeListener)
            - class uk.ac.man.bioinf.gui.optionable.OptionableJFrame (implements uk.ac.man.bioinf.apps.optionable.Optionable)
              - class uk.ac.man.bioinf.apps.cinema.utils.CinemaAlignmentFrame (implements java.beans.PropertyChangeListener)
              - class uk.ac.man.bioinf.apps.cinema.group.CinemaGroupFrame (implements java.awt.event.ActionListener, uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener, javax.swing.event.ListSelectionListener, java.beans.PropertyChangeListener)
  - class javax.swing.plaf.ComponentUI
    - class uk.ac.man.bioinf.gui.viewer.plaf.AlignmentRulerUI
    - class uk.ac.man.bioinf.gui.viewer.plaf.AlignmentViewerUI
      - class uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentViewerUI (implements javax.swing.event.MouseInputListener, java.beans.PropertyChangeListener)
        - class uk.ac.man.bioinf.gui.viewer.plaf.MetalAlignmentViewerUI
    - class javax.swing.plaf.ListUI
      - class javax.swing.plaf.basic.BasicListUI
        - class uk.ac.man.bioinf.gui.misc.SwappingListBasicUI
    - class javax.swing.plaf.SliderUI
      - class javax.swing.plaf.basic.BasicSliderUI
        - class uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentRulerUI
  - class uk.ac.man.bioinf.apps.xml.ConfigNode
  - class uk.ac.man.bioinf.apps.cinema.utils.ConsensusPercentageIDColorMap (implements uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener, uk.ac.man.bioinf.gui.color.ColorMap, uk.ac.man.bioinf.sequence.event.SequenceListener)
  - class uk.ac.man.bioinf.debug.Debug
  - class uk.ac.man.bioinf.debug.DebugMultiplexer (implements uk.ac.man.bioinf.debug.DebugInterface)
  - class uk.ac.man.bioinf.gui.viewer.DefaultAlignmentSelectionRenderer (implements uk.ac.man.bioinf.gui.viewer.AlignmentSelectionRenderer)
  - class uk.ac.man.bioinf.apps.cinema.color.DefaultColorMapMetaData (implements uk.ac.man.bioinf.apps.cinema.color.ColorMapMetaData)
  - class uk.ac.man.bioinf.sequence.complex.DefaultComplexElement (implements uk.ac.man.bioinf.sequence.complex.ComplexElement)
  - class uk.ac.man.bioinf.sequence.complex.DefaultComplexSequenceType (implements uk.ac.man.bioinf.sequence.complex.ComplexSequenceType)
  - class uk.ac.man.bioinf.gui.viewer.DefaultFastAlignmentViewerCellRenderer (implements uk.ac.man.bioinf.gui.viewer.FastAlignmentViewerCellRenderer)
  - class uk.ac.man.bioinf.module.DefaultModuleFactoryInstance (implements uk.ac.man.bioinf.module.ModuleFactoryInstance)
    - class uk.ac.man.bioinf.apps.cinema.CinemaModuleFactoryInstance
  - class uk.ac.man.bioinf.io.DefaultParserExceptionHandler (implements uk.ac.man.bioinf.io.ParserExceptionHandler)
  - class uk.ac.man.bioinf.gui.viewer.DefaultSequenceCursor (implements uk.ac.man.bioinf.gui.viewer.SequenceCursor)
  - class uk.ac.man.bioinf.apps.xml.DefaultXMLParser (implements uk.ac.man.bioinf.apps.xml.XMLParserFactory)
  - class uk.ac.man.bioinf.gui.color.DoubleArrayColorMap (implements uk.ac.man.bioinf.gui.color.ColorMap)
  - class uk.ac.man.bioinf.sequence.test.EditableSequenceTest
  - class uk.ac.man.bioinf.sequence.alignment.EmptyGappedSequence (implements uk.ac.man.bioinf.sequence.alignment.GappedSequence)
  - class uk.ac.man.bioinf.sequence.EmptySequence (implements uk.ac.man.bioinf.sequence.Sequence)
  - class uk.ac.man.bioinf.sequence.alignment.EmptySequenceAlignment (implements uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)
  - class uk.ac.man.bioinf.sequence.types.EmptySequenceType (implements uk.ac.man.bioinf.sequence.SequenceType)
  - class java.util.EventObject (implements java.io.Serializable)
    - class uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent
      - class uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentEvent
    - class uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionEvent
    - class uk.ac.man.bioinf.util.ChangeableEvent
    - class uk.ac.man.bioinf.sequence.event.SequenceEvent
      - class uk.ac.man.bioinf.sequence.event.VetoableSequenceEvent
    - class uk.ac.man.bioinf.apps.systemevents.SystemEvent
  - class uk.ac.man.bioinf.database.fetch.ExpasySequenceRetriever (implements uk.ac.man.bioinf.database.fetch.SequenceRetriever)
  - class uk.ac.man.bioinf.database.fetch.FetchSequenceBySwissProtID
  - class uk.ac.man.bioinf.sequence.identifier.FileSource (implements uk.ac.man.bioinf.sequence.identifier.Source)
  - class uk.ac.man.bioinf.sequence.alignment.Gap (implements uk.ac.man.bioinf.sequence.Element)
  - class uk.ac.man.bioinf.sequence.test.GappableSequenceTest
  - class uk.ac.man.bioinf.analysis.regexp.GappedSequenceCharacterIterator
  - class uk.ac.man.bioinf.apps.commandline.GappedSequenceSearch
  - class uk.ac.man.bioinf.sequence.test.GappedSequenceTest
  - class uk.ac.man.bioinf.module.GenericModuleIdentifier (implements uk.ac.man.bioinf.module.ModuleIdentifier)
  - class uk.ac.man.bioinf.apps.cinema.color.GrayScaleVariance (implements uk.ac.man.bioinf.apps.cinema.color.ColorMapMetaData)
  - class uk.ac.man.bioinf.sequence.complex.HardModificationSetFactory (implements uk.ac.man.bioinf.sequence.complex.ModificationSetFactoryInterface)
  - class uk.ac.man.bioinf.gui.color.IndividualElementColorMap (implements uk.ac.man.bioinf.gui.color.ColorMap)
  - class java.io.InputStream
    - class uk.ac.man.bioinf.io.NarrowedInputStream
  - class uk.ac.man.bioinf.gui.viewer.Install (implements java.beans.PropertyChangeListener)
  - class uk.ac.man.bioinf.apps.cinema.color.InstancePerAlignmentColorMapMetaData (implements uk.ac.man.bioinf.apps.cinema.color.ColorMapMetaData)
  - class uk.ac.man.bioinf.util.IntArrayList
  - class uk.ac.man.bioinf.apps.cinema.color.IntenseColorMapMetaData (implements uk.ac.man.bioinf.apps.cinema.color.ColorMapMetaData)
  - class uk.ac.man.bioinf.apps.invoker.Invoker (implements java.lang.Runnable)
    - class uk.ac.man.bioinf.apps.invoker.AnonInvoker
  - class uk.ac.man.bioinf.apps.invoker.InvokerInternalQueue (implements java.lang.Runnable, uk.ac.man.bioinf.apps.systemevents.SystemListener)
  - class uk.ac.man.bioinf.apps.invoker.InvokerThreadManager
  - class uk.ac.man.bioinf.apps.cinema.color.Js_TestColorMapMetaData (implements uk.ac.man.bioinf.apps.cinema.color.ColorMapMetaData)
  - class uk.ac.man.bioinf.sequence.complex.ModificationFactory
  - class uk.ac.man.bioinf.module.Module
    - class uk.ac.man.bioinf.apps.cinema.core.CinemaCoreGui (implements uk.ac.man.bioinf.apps.cinema.core.CinemaActionProvider, uk.ac.man.bioinf.apps.systemevents.SystemListener)
    - class uk.ac.man.bioinf.apps.cinema.utils.CinemaDebug (implements java.awt.event.ActionListener)
    - class uk.ac.man.bioinf.apps.cinema.shared.CinemaDebug (implements java.awt.event.ActionListener)
    - class uk.ac.man.bioinf.apps.cinema.utils.CinemaInvoker
    - class uk.ac.man.bioinf.apps.cinema.shared.CinemaSharedQuitExit
    - class uk.ac.man.bioinf.apps.cinema.core.CinemaSystemEvents (implements uk.ac.man.bioinf.apps.systemevents.SystemEventProducer)
    - class uk.ac.man.bioinf.apps.xml.XMLBootModule
      - class uk.ac.man.bioinf.apps.cinema.CinemaBoot
        - class uk.ac.man.bioinf.apps.cinema.CinemaShared
    - class uk.ac.man.bioinf.apps.xml.XMLModule
      - class uk.ac.man.bioinf.apps.cinema.CinemaModule (implements uk.ac.man.bioinf.sequence.alignment.event.AlignmentEventProvider)
        - class uk.ac.man.bioinf.apps.cinema.color.CinemaColorFactory
        - class uk.ac.man.bioinf.apps.cinema.io.CinemaCommandLineParser
        - class uk.ac.man.bioinf.apps.cinema.consensus.CinemaConsensus
        - class uk.ac.man.bioinf.apps.cinema.group.CinemaGroupModule (implements java.awt.event.ActionListener, uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener, uk.ac.man.bioinf.apps.cinema.core.CinemaActionProvider, java.beans.PropertyChangeListener)
        - class uk.ac.man.bioinf.apps.cinema.CinemaGuiModule
          - class uk.ac.man.bioinf.apps.cinema.io.AbstractSequenceInput (implements uk.ac.man.bioinf.apps.cinema.core.CinemaActionProvider)
            - class uk.ac.man.bioinf.apps.cinema.io.FileSequenceInput
          - class uk.ac.man.bioinf.apps.cinema.io.AbstractSequenceOutput (implements uk.ac.man.bioinf.apps.cinema.core.CinemaActionProvider)
            - class uk.ac.man.bioinf.apps.cinema.io.FileSequenceOutput
          - class uk.ac.man.bioinf.apps.cinema.color.CinemaColorSelector (implements uk.ac.man.bioinf.apps.cinema.core.CinemaFramedActionProvider)
          - class uk.ac.man.bioinf.apps.cinema.consensus.CinemaConsensusDisplay (implements uk.ac.man.bioinf.apps.cinema.core.CinemaActionProvider, java.beans.PropertyChangeListener)
          - class uk.ac.man.bioinf.apps.cinema.core.CinemaCoreView (implements uk.ac.man.bioinf.sequence.alignment.event.AlignmentEventProvider, uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)
          - class uk.ac.man.bioinf.apps.cinema.core.CinemaGo
          - class uk.ac.man.bioinf.apps.cinema.core.CinemaMenuSystem
          - class uk.ac.man.bioinf.apps.cinema.core.CinemaSequenceMenu
          - class uk.ac.man.bioinf.apps.cinema.utils.CinemaStatusInformation (implements java.beans.PropertyChangeListener)
        - class uk.ac.man.bioinf.apps.cinema.utils.CinemaMenuBuilder
        - class uk.ac.man.bioinf.apps.cinema.motif.CinemaMotifModule (implements uk.ac.man.bioinf.apps.cinema.core.CinemaActionProvider)
        - class uk.ac.man.bioinf.apps.cinema.utils.CinemaMultipleConsensusViewer (implements java.awt.event.ActionListener, java.beans.PropertyChangeListener)
        - class uk.ac.man.bioinf.apps.cinema.utils.CinemaPersist
          - class uk.ac.man.bioinf.apps.cinema.utils.CinemaFilePersist
        - class uk.ac.man.bioinf.apps.cinema.utils.CinemaRegexp (implements uk.ac.man.bioinf.apps.cinema.core.CinemaFramedActionProvider)
        - class uk.ac.man.bioinf.apps.cinema.utils.CinemaResizeElements (implements uk.ac.man.bioinf.apps.cinema.core.CinemaFramedActionProvider)
        - class uk.ac.man.bioinf.apps.cinema.utils.CinemaSlaveViewerModule
        - class uk.ac.man.bioinf.apps.cinema.shared.CinemaSplash
  - class uk.ac.man.bioinf.module.ModuleContext
    - class uk.ac.man.bioinf.module.DefaultModuleContext
  - class uk.ac.man.bioinf.module.ModuleIdentifierList
  - class uk.ac.man.bioinf.module.ModuleList
  - class uk.ac.man.bioinf.module.ModuleStorageStructure
  - class uk.ac.man.bioinf.io.parsers.MotProteinParser (implements uk.ac.man.bioinf.io.AlignmentOutputParser)
  - class uk.ac.man.bioinf.gui.viewer.MultiplexerFastAlignmentViewerCellRenderer (implements uk.ac.man.bioinf.gui.viewer.FastAlignmentViewerCellRenderer, java.beans.PropertyChangeListener)
    - class uk.ac.man.bioinf.gui.viewer.CursorLessFastAlignmentViewerCellRenderer
  - class uk.ac.man.bioinf.apps.cinema.motif.NamedAlignmentSelectionModel (implements uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionListener, uk.ac.man.bioinf.gui.viewer.AlignmentSelectionModel)
  - class uk.ac.man.bioinf.sequence.identifier.NoIdentifier (implements uk.ac.man.bioinf.sequence.identifier.Identifier)
  - class uk.ac.man.bioinf.sequence.identifier.NoSource (implements uk.ac.man.bioinf.sequence.identifier.Source)
  - class uk.ac.man.bioinf.gui.viewer.NullAlignmentSelectionModel (implements uk.ac.man.bioinf.gui.viewer.AlignmentSelectionModel)
  - class uk.ac.man.bioinf.apps.cinema.color.NullColorMapMetaData (implements uk.ac.man.bioinf.apps.cinema.color.ColorMapMetaData)
  - class uk.ac.man.bioinf.module.NullModuleFactory (implements uk.ac.man.bioinf.module.ModuleFactoryInstance)
    - class uk.ac.man.bioinf.apps.xml.test.XMLLoadingTest
  - class uk.ac.man.bioinf.apps.optionable.NullOptionHandler (implements uk.ac.man.bioinf.apps.optionable.OptionHandler)
  - class uk.ac.man.bioinf.io.NullParserExceptionHandler (implements uk.ac.man.bioinf.io.ParserExceptionHandler)
  - class uk.ac.man.bioinf.gui.util.forms.PasswordDialog
  - class uk.ac.man.bioinf.apps.cinema.color.PedanticColorMapMetaData (implements uk.ac.man.bioinf.apps.cinema.color.ColorMapMetaData)
  - class uk.ac.man.bioinf.analysis.misc.PercentageIDCalculator (implements uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener, uk.ac.man.bioinf.sequence.event.SequenceListener)
  - class uk.ac.man.bioinf.analysis.misc.PercentageIDCalculatorManager
  - class uk.ac.man.bioinf.analysis.consensus.PercentageIDConsensus (implements uk.ac.man.bioinf.analysis.consensus.ConsensusCalculator)
  - class uk.ac.man.bioinf.apps.cinema.consensus.PercentageIDConsensusCalculatorMetaData (implements uk.ac.man.bioinf.apps.cinema.consensus.CinemaConsensusCalculatorMetaData)
    - class uk.ac.man.bioinf.apps.cinema.consensus.ThreadedPercentageIDConsensusCalculatorMetaData
  - class uk.ac.man.bioinf.apps.cinema.color.PercentageIDVarianceColorMapMetaData (implements uk.ac.man.bioinf.apps.cinema.color.ColorMapMetaData)
  - class uk.ac.man.bioinf.gui.color.PercentIDVarianceColorMap (implements uk.ac.man.bioinf.gui.color.ThreadableColorMap)
  - class uk.ac.man.bioinf.gui.util.PopUpHtmlDisplay
  - class uk.ac.man.bioinf.util.ResourceAdapter
    - class uk.ac.man.bioinf.util.PackageResourceAdapter
  - class uk.ac.man.bioinf.apps.optionable.SaveableOptions (implements uk.ac.man.bioinf.apps.optionable.OptionHandler, uk.ac.man.bioinf.apps.systemevents.SystemListener)
    - class uk.ac.man.bioinf.apps.optionable.FileSaveableOptions
  - class javax.swing.ScrollPaneLayout (implements java.awt.LayoutManager, javax.swing.ScrollPaneConstants, java.io.Serializable)
    - class uk.ac.man.bioinf.gui.viewer.InvertedScrollPaneLayout
  - class uk.ac.man.bioinf.sequence.geom.SequenceAlignmentDimension
  - class uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint (implements java.lang.Cloneable, java.lang.Comparable)
  - class uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle (implements java.lang.Comparable, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentShape)
  - class uk.ac.man.bioinf.sequence.test.SequenceAlignmentTest (implements uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener, uk.ac.man.bioinf.sequence.event.SequenceListener, uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentListener, uk.ac.man.bioinf.sequence.event.VetoableSequenceListener)
  - class uk.ac.man.bioinf.analysis.regexp.SequenceCharacterIterator
  - class uk.ac.man.bioinf.sequence.test.SequenceColumnTest
  - class uk.ac.man.bioinf.sequence.SequenceFactory
  - class uk.ac.man.bioinf.sequence.test.SequenceFactoryTest
  - class uk.ac.man.bioinf.sequence.event.SequenceListenerSupport
  - class uk.ac.man.bioinf.sequence.Sequences
  - class uk.ac.man.bioinf.apps.commandline.SequenceSearch
  - class uk.ac.man.bioinf.sequence.test.SequencesTest
  - class uk.ac.man.bioinf.sequence.identifier.SimpleSource (implements uk.ac.man.bioinf.sequence.identifier.Source)
    - class uk.ac.man.bioinf.sequence.identifier.ReaderSource
  - class uk.ac.man.bioinf.gui.viewer.SingleAlignmentSelectionModel (implements uk.ac.man.bioinf.gui.viewer.AlignmentSelectionModel)
  - class uk.ac.man.bioinf.gui.color.SingleColorMap (implements uk.ac.man.bioinf.gui.color.ColorMap)
  - class uk.ac.man.bioinf.gui.viewer.test.SingleSelectionModelTest
  - class uk.ac.man.bioinf.sequence.identifier.StreamSequenceSource (implements uk.ac.man.bioinf.sequence.identifier.SequenceSource)
    - class uk.ac.man.bioinf.sequence.identifier.URLSequenceSource
  - class uk.ac.man.bioinf.apps.systemevents.SystemEventOption
  - class uk.ac.man.bioinf.apps.systemevents.SystemEventSupport (implements uk.ac.man.bioinf.apps.systemevents.SystemEventProducer)
  - class uk.ac.man.bioinf.apps.cinema.color.TaylorColorMapMetaData (implements uk.ac.man.bioinf.apps.cinema.color.ColorMapMetaData)
  - class uk.ac.man.bioinf.gui.viewer.TextFastAlignmentViewerCellRenderer (implements uk.ac.man.bioinf.gui.viewer.FastAlignmentViewerCellRenderer)
  - class uk.ac.man.bioinf.gui.color.ThreadedColorMap (implements uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener, uk.ac.man.bioinf.gui.color.ColorMap, java.beans.PropertyChangeListener, uk.ac.man.bioinf.sequence.event.SequenceListener)
  - class uk.ac.man.bioinf.apps.cinema.color.ThreadedPercentageIDVarianceColorMapMetaData (implements uk.ac.man.bioinf.apps.cinema.color.ColorMapMetaData)
  - class java.lang.Throwable (implements java.io.Serializable)
    - class java.lang.Exception
      - class uk.ac.man.bioinf.sequence.alignment.event.AlignmentVetoException
      - class java.io.IOException
        - class uk.ac.man.bioinf.apps.optionable.OptionableSourceNotFoundException
      - class uk.ac.man.bioinf.module.ModuleException
      - class uk.ac.man.bioinf.apps.optionable.OptionableStateException
      - class java.lang.RuntimeException
        - class uk.ac.man.bioinf.gui.color.ColorMapException
        - class java.lang.IllegalArgumentException
          - class uk.ac.man.bioinf.sequence.identifier.MalformedAccessionException
        - class uk.ac.man.bioinf.sequence.complex.IllegalDuplicateModificationException
        - class uk.ac.man.bioinf.sequence.InvalidSequenceTypeException
        - class uk.ac.man.bioinf.apps.invoker.InvokerInternalEventQueueException
        - class uk.ac.man.bioinf.apps.invoker.InvokerInternalQueueException
        - class uk.ac.man.bioinf.sequence.alignment.NoGapAtThisPositionException
        - class uk.ac.man.bioinf.sequence.complex.NoSuchModificationException
        - class uk.ac.man.bioinf.module.NoSuchRequiredModule
        - class uk.ac.man.bioinf.sequence.NoSuchSequenceElementException
        - class uk.ac.man.bioinf.sequence.alignment.NoSuchSequenceException
        - class uk.ac.man.bioinf.io.ParserException
          - class uk.ac.man.bioinf.io.InvalidSequenceTypeParserException
          - class uk.ac.man.bioinf.io.SequenceWriterException
          - class uk.ac.man.bioinf.io.UnknownElementException
        - class uk.ac.man.bioinf.gui.viewer.ReadonlyException
        - class uk.ac.man.bioinf.sequence.SequenceException
      - class uk.ac.man.bioinf.sequence.event.SequenceVetoException
      - class uk.ac.man.bioinf.apps.systemevents.SystemVetoException
  - class uk.ac.man.bioinf.apps.cinema.color.VariableColorMapMetaData (implements uk.ac.man.bioinf.apps.cinema.color.ColorMapMetaData)
  - class uk.ac.man.bioinf.apps.cinema.color.VariationsColorMapMetaData (implements uk.ac.man.bioinf.apps.cinema.color.ColorMapMetaData)
  - class uk.ac.man.bioinf.apps.cinema.core.VersionInformation
  - class uk.ac.man.bioinf.sequence.complex.WeakModificationSetFactory (implements uk.ac.man.bioinf.sequence.complex.ModificationSetFactoryInterface)
  - class uk.ac.man.bioinf.apps.cinema.color.WhiteColorMapMetaData (implements uk.ac.man.bioinf.apps.cinema.color.ColorMapMetaData)
  - class java.awt.event.WindowAdapter (implements java.awt.event.WindowFocusListener, java.awt.event.WindowListener, java.awt.event.WindowStateListener)
    - class uk.ac.man.bioinf.gui.viewer.test.BasicWindowMonitor
  - class uk.ac.man.bioinf.apps.xml.XMLBootModule.MiniStack
  - class uk.ac.man.bioinf.apps.xml.XMLBootParserListener (implements org.xml.sax.ContentHandler, org.xml.sax.ErrorHandler)
  - class uk.ac.man.bioinf.apps.xml.test.XMLStartTest
  - class uk.ac.man.bioinf.Y
  - class uk.ac.man.bioinf.apps.cinema.color.ZenecaColorMapMetaData (implements uk.ac.man.bioinf.apps.cinema.color.ColorMapMetaData)

## Interface Hierarchy

- interface uk.ac.man.bioinf.sequence.alignment.event.AlignmentEventProvider
  - interface uk.ac.man.bioinf.sequence.alignment.SequenceAlignment (also extends uk.ac.man.bioinf.sequence.identifier.Identifiable, uk.ac.man.bioinf.sequence.event.SequenceEventProvider, uk.ac.man.bioinf.sequence.event.VetoableSequenceListener)
- interface uk.ac.man.bioinf.io.AlignmentInputParser
- interface uk.ac.man.bioinf.io.AlignmentOutputParser
- interface uk.ac.man.bioinf.gui.viewer.AlignmentSelectionModel
- interface uk.ac.man.bioinf.gui.viewer.AlignmentSelectionRenderer
- interface uk.ac.man.bioinf.gui.viewer.AlignmentViewerCellRenderer
- interface uk.ac.man.bioinf.util.Changeable
- interface uk.ac.man.bioinf.util.ChangeableListener
- interface uk.ac.man.bioinf.apps.cinema.core.CinemaActionProvider
- interface uk.ac.man.bioinf.apps.cinema.consensus.CinemaConsensusCalculatorMetaData
- interface uk.ac.man.bioinf.apps.cinema.core.CinemaFramedActionProvider
- interface uk.ac.man.bioinf.gui.color.ColorMap
  - interface uk.ac.man.bioinf.gui.color.ThreadableColorMap
- interface uk.ac.man.bioinf.apps.cinema.color.ColorMapMetaData
- interface uk.ac.man.bioinf.sequence.complex.ComplexElementFactoryInterface
- interface uk.ac.man.bioinf.analysis.consensus.ConsensusCalculator
- interface uk.ac.man.bioinf.debug.DebugInterface
- interface uk.ac.man.bioinf.sequence.Element
  - interface uk.ac.man.bioinf.sequence.complex.ComplexElement
  - interface uk.ac.man.bioinf.sequence.Residue
    - interface uk.ac.man.bioinf.sequence.types.NucleotideResidue
      - interface uk.ac.man.bioinf.sequence.types.DNAResidue
      - interface uk.ac.man.bioinf.sequence.types.RNAResidue
    - interface uk.ac.man.bioinf.sequence.types.ProteinResidue
- interface java.util.EventListener
  - interface uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener
    - interface uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentListener
  - interface uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionListener
  - interface uk.ac.man.bioinf.sequence.event.SequenceListener
    - interface uk.ac.man.bioinf.sequence.event.VetoableSequenceListener
      - interface uk.ac.man.bioinf.sequence.alignment.SequenceAlignment (also extends uk.ac.man.bioinf.sequence.alignment.event.AlignmentEventProvider, uk.ac.man.bioinf.sequence.identifier.Identifiable, uk.ac.man.bioinf.sequence.event.SequenceEventProvider)
  - interface uk.ac.man.bioinf.apps.systemevents.SystemListener
- interface uk.ac.man.bioinf.util.ExceptionHandler
- interface uk.ac.man.bioinf.gui.viewer.FastAlignmentViewerCellRenderer
- interface uk.ac.man.bioinf.sequence.identifier.Identifiable
  - interface uk.ac.man.bioinf.sequence.Sequence
    - interface uk.ac.man.bioinf.sequence.ComplexEditableGappedSequence (also extends uk.ac.man.bioinf.sequence.complex.ComplexSequence, uk.ac.man.bioinf.sequence.EditableSequence, uk.ac.man.bioinf.sequence.alignment.GappedSequence, uk.ac.man.bioinf.sequence.MutableSequence)
    - interface uk.ac.man.bioinf.sequence.complex.ComplexSequence
      - interface uk.ac.man.bioinf.sequence.ComplexEditableGappedSequence (also extends uk.ac.man.bioinf.sequence.EditableSequence, uk.ac.man.bioinf.sequence.alignment.GappedSequence, uk.ac.man.bioinf.sequence.MutableSequence, uk.ac.man.bioinf.sequence.Sequence)
      - interface uk.ac.man.bioinf.sequence.complex.GappedComplexSequence (also extends uk.ac.man.bioinf.sequence.alignment.GappedSequence)
    - interface uk.ac.man.bioinf.sequence.MutableSequence (also extends uk.ac.man.bioinf.sequence.event.SequenceEventProvider)
      - interface uk.ac.man.bioinf.sequence.ComplexEditableGappedSequence (also extends uk.ac.man.bioinf.sequence.complex.ComplexSequence, uk.ac.man.bioinf.sequence.EditableSequence, uk.ac.man.bioinf.sequence.alignment.GappedSequence, uk.ac.man.bioinf.sequence.Sequence)
      - interface uk.ac.man.bioinf.sequence.EditableSequence
        - interface uk.ac.man.bioinf.sequence.ComplexEditableGappedSequence (also extends uk.ac.man.bioinf.sequence.complex.ComplexSequence, uk.ac.man.bioinf.sequence.alignment.GappedSequence, uk.ac.man.bioinf.sequence.MutableSequence, uk.ac.man.bioinf.sequence.Sequence)
      - interface uk.ac.man.bioinf.sequence.alignment.GappedSequence
        - interface uk.ac.man.bioinf.sequence.ComplexEditableGappedSequence (also extends uk.ac.man.bioinf.sequence.complex.ComplexSequence, uk.ac.man.bioinf.sequence.EditableSequence, uk.ac.man.bioinf.sequence.MutableSequence, uk.ac.man.bioinf.sequence.Sequence)
        - interface uk.ac.man.bioinf.analysis.consensus.ConsensusSequence
        - interface uk.ac.man.bioinf.sequence.complex.GappedComplexSequence (also extends uk.ac.man.bioinf.sequence.complex.ComplexSequence)
  - interface uk.ac.man.bioinf.sequence.alignment.SequenceAlignment (also extends uk.ac.man.bioinf.sequence.alignment.event.AlignmentEventProvider, uk.ac.man.bioinf.sequence.event.SequenceEventProvider, uk.ac.man.bioinf.sequence.event.VetoableSequenceListener)
- interface uk.ac.man.bioinf.sequence.identifier.Identifier
- interface uk.ac.man.bioinf.sequence.complex.Modification
- interface uk.ac.man.bioinf.sequence.complex.ModificationSetFactoryInterface
- interface uk.ac.man.bioinf.module.ModuleFactoryInstance
- interface uk.ac.man.bioinf.module.ModuleIdentifier
- interface uk.ac.man.bioinf.apps.optionable.Optionable
- interface uk.ac.man.bioinf.apps.optionable.OptionableExceptionHandler
- interface uk.ac.man.bioinf.apps.optionable.OptionHandler
- interface uk.ac.man.bioinf.io.ParserExceptionHandler
- interface uk.ac.man.bioinf.sequence.geom.SequenceAlignmentShape
- interface uk.ac.man.bioinf.gui.viewer.SequenceCursor
- interface uk.ac.man.bioinf.sequence.event.SequenceEventProvider
  - interface uk.ac.man.bioinf.sequence.MutableSequence (also extends uk.ac.man.bioinf.sequence.Sequence)
    - interface uk.ac.man.bioinf.sequence.ComplexEditableGappedSequence (also extends uk.ac.man.bioinf.sequence.complex.ComplexSequence, uk.ac.man.bioinf.sequence.EditableSequence, uk.ac.man.bioinf.sequence.alignment.GappedSequence, uk.ac.man.bioinf.sequence.Sequence)
    - interface uk.ac.man.bioinf.sequence.EditableSequence
      - interface uk.ac.man.bioinf.sequence.ComplexEditableGappedSequence (also extends uk.ac.man.bioinf.sequence.complex.ComplexSequence, uk.ac.man.bioinf.sequence.alignment.GappedSequence, uk.ac.man.bioinf.sequence.MutableSequence, uk.ac.man.bioinf.sequence.Sequence)
    - interface uk.ac.man.bioinf.sequence.alignment.GappedSequence
      - interface uk.ac.man.bioinf.sequence.ComplexEditableGappedSequence (also extends uk.ac.man.bioinf.sequence.complex.ComplexSequence, uk.ac.man.bioinf.sequence.EditableSequence, uk.ac.man.bioinf.sequence.MutableSequence, uk.ac.man.bioinf.sequence.Sequence)
      - interface uk.ac.man.bioinf.analysis.consensus.ConsensusSequence
      - interface uk.ac.man.bioinf.sequence.complex.GappedComplexSequence (also extends uk.ac.man.bioinf.sequence.complex.ComplexSequence)
  - interface uk.ac.man.bioinf.sequence.alignment.SequenceAlignment (also extends uk.ac.man.bioinf.sequence.alignment.event.AlignmentEventProvider, uk.ac.man.bioinf.sequence.identifier.Identifiable, uk.ac.man.bioinf.sequence.event.VetoableSequenceListener)
- interface uk.ac.man.bioinf.sequence.group.SequenceGroup
  - interface uk.ac.man.bioinf.sequence.group.GappedSequenceGroup
- interface uk.ac.man.bioinf.io.SequenceInputParser
- interface uk.ac.man.bioinf.database.fetch.SequenceRetriever
- interface uk.ac.man.bioinf.sequence.identifier.SequenceSource
- interface uk.ac.man.bioinf.sequence.SequenceType
  - interface uk.ac.man.bioinf.sequence.complex.ComplexSequenceType
- interface uk.ac.man.bioinf.sequence.identifier.Source
- interface uk.ac.man.bioinf.apps.systemevents.SystemEventProducer
- interface uk.ac.man.bioinf.apps.xml.XMLParserFactory

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