Hierarchy For Package pal.alignment

Package Hierarchies:

All Packages

Class Hierarchy

• class java.lang.Object
  • class pal.alignment.AbstractAlignment (implements pal.alignment.Alignment, pal.misc.IdGroup, pal.misc.Report, java.io.Serializable)
    • class pal.alignment.BootstrappedAlignment
    • class pal.alignment.ConcatenatedAlignment
    • class pal.alignment.ConcatenatedAnnotatedAlignment (implements pal.alignment.AnnotationAlignment)
    • class pal.alignment.GapBalancedAlignment (implements java.io.Serializable)
    • class pal.alignment.IndelAlignment
      • class pal.alignment.IndelAnnotatedAlignment (implements pal.alignment.AnnotationAlignment)
    • class pal.alignment.JumbledAlignment
    • class pal.alignment.ReadAlignment
    • class pal.alignment.ReadAlignmentOld
    • class pal.alignment.SimpleAlignment
      • class pal.alignment.MultiLocusAnnotatedAlignment (implements pal.alignment.AnnotationAlignment)
      • class pal.alignment.SimpleAnnotatedAlignment (implements pal.alignment.AnnotationAlignment)
    • class pal.alignment.SitePattern
    • class pal.alignment.StrippedAlignment
      • class pal.alignment.StrippedAnnotatedAlignment (implements pal.alignment.AnnotationAlignment)
  • class pal.alignment.AlignmentBuilder
  • class pal.alignment.AlignmentGenerator.Utils
  • class pal.alignment.AlignmentReaders
  • class pal.alignment.AlignmentReaders.StringAlignment (implements pal.alignment.Alignment)
    • class pal.alignment.AlignmentReaders.PhylipClustalAlignment
    • class pal.alignment.AlignmentReaders.UnalignedAlignment
  • class pal.alignment.AlignmentReceiver.BucketReceiver (implements pal.alignment.AlignmentReceiver)
  • class pal.alignment.AlignmentReceiver.SingleReceiver (implements pal.alignment.AlignmentReceiver)
  • class pal.alignment.AlignmentTool
  • class pal.alignment.AlignmentUtils
  • class pal.alignment.DataTranslator
  • class pal.alignment.Genotype
  • class pal.alignment.SimpleCharacterAlignment (implements pal.alignment.CharacterAlignment, pal.misc.IdGroup, pal.misc.Report, java.io.Serializable)
  • class java.lang.Throwable (implements java.io.Serializable)
    • class java.lang.Exception
      • class pal.alignment.AlignmentParseException

Interface Hierarchy

• interface pal.alignment.AlignmentGenerator
• interface pal.alignment.AlignmentReceiver
• interface pal.misc.Report
  • interface pal.alignment.AnnotationAlignment (also extends pal.alignment.Alignment)
  • interface pal.alignment.CharacterAlignment (also extends pal.misc.IdGroup, java.io.Serializable, pal.misc.TableReport)
• interface java.io.Serializable
  • interface pal.alignment.Alignment (also extends pal.misc.IdGroup)
    • interface pal.alignment.AnnotationAlignment (also extends pal.misc.Report)
  • interface pal.alignment.CharacterAlignment (also extends pal.misc.IdGroup, pal.misc.Report, pal.misc.TableReport)
  • interface pal.misc.IdGroup
    • interface pal.alignment.Alignment (also extends java.io.Serializable)
      • interface pal.alignment.AnnotationAlignment (also extends pal.misc.Report)
    • interface pal.alignment.CharacterAlignment (also extends pal.misc.Report, java.io.Serializable, pal.misc.TableReport)
• interface pal.misc.TableReport
  • interface pal.alignment.CharacterAlignment (also extends pal.misc.IdGroup, pal.misc.Report, java.io.Serializable)