Uses of Class
org.biojava.nbio.core.sequence.template.AbstractCompound

Packages that use AbstractCompound

Package	Description
org.biojava.nbio.alignment.io
org.biojava.nbio.core.sequence.compound

Uses of AbstractCompound in org.biojava.nbio.alignment.io

Methods in org.biojava.nbio.alignment.io that return types with arguments of type AbstractCompound

Modifier and Type	Method and Description
List<AbstractSequence<? extends AbstractCompound>>	StockholmStructure.getBioSequences() used to retrieve sequences from the structure
List<AbstractSequence<? extends AbstractCompound>>	StockholmStructure.getBioSequences(boolean ignoreCase) Because some database files have incorrectly small letters (e.g.
List<AbstractSequence<? extends AbstractCompound>>	StockholmStructure.getBioSequences(boolean ignoreCase, String forcedSequenceType) This function tolerates mixed case letters, and allows for forcing the output biosequence type (PFAM/RFAM).

Uses of AbstractCompound in org.biojava.nbio.core.sequence.compound

Subclasses of AbstractCompound in org.biojava.nbio.core.sequence.compound

Modifier and Type	Class and Description
class	AminoAcidCompound Used to describe an Amino Acid.
class	CodonCompound Define a codon
class	NucleotideCompound