Package fr.orsay.lri.varna.models.templates

Class Summary

RNANodeValue2TemplateDistance	Distance between an RNANodeValue2 and an RNANodeValueTemplate.
RNANodeValueTemplate	An node from an RNA template is either a sequence of non-paired bases, a base pair originally belonging to an helix, or a single base originally belonging to an helix but which was broken in order to remove pseudoknots.
RNANodeValueTemplateBasePair	See RNANodeValueTemplate.
RNANodeValueTemplateBrokenBasePair	See RNANodeValueTemplate.
RNANodeValueTemplateSequence	See RNANodeValueTemplate.
RNATemplate	A model for RNA templates.
RNATemplateAlign	This class is about the alignment between a tree of RNANodeValue2 and a tree of RNANodeValueTemplate.
RNATemplateMapping	A RNATemplateMapping is a mapping between bases in an RNA sequence and elements in a RNA template.

Enum Summary

RNATemplate.EdgeEndPointPosition	Position of an endpoint on an endpoint.
RNATemplate.In1Is	For an helix, tells us whether IN1/OUT1 is the 5' strand (the first strand we meet if we follow the RNA sequence) or the 3' strand (the second we meet if we follow the RNA sequence).

Exception Summary

RNATemplateDrawingAlgorithmException	Exception thrown in case of failure of the template-based RNA drawing algorithm.
RNATemplateMappingException	This exception is thrown when we discover that a template is invalid (it contains impossible connections between elements).