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