Package uk.ac.vamsas.objects.utils

Class Summary
AppDataReference Form, accessors and validation for ApplicationData references in vamsas document.
DocumentStuff various vamsas-client independent helpers for creating and manipulating the vamsasDocument Vobject
Format  
GlyphDictionary dict attribute values for glyph symbol sets found in uk.ac.vamsas.objects.core.AnnotationElement TODO: add validators and multilength symbols.
MapList MapList Simple way of bijectively mapping a non-contiguous linear range to another non-contiguous linear range Use at your own risk! TODO: efficient implementation of private posMap method TODO: test/ensure that sense of from and to ratio start position is conserved (codon start position recovery) TODO: optimize to use int[][] arrays rather than vectors.
Mapping  
Properties  
ProvenanceStuff  
Range Utilities for working with RangeType and MapType objects.
Seq  
SeqAln  
SeqSet  
SymbolDictionary  
Trees