Uses of Interface
info.bioinfweb.commons.bio.biojava3.alignment.template.Alignment

Packages that use Alignment

Package	Description
info.bioinfweb.commons.bio.biojava3.alignment
info.bioinfweb.commons.bio.biojava3.alignment.io
info.bioinfweb.commons.bio.biojava3.alignment.io.fasta
info.bioinfweb.commons.bio.biojava3.alignment.io.hennig86
info.bioinfweb.commons.bio.biojava3.alignment.io.mega
info.bioinfweb.commons.bio.biojava3.alignment.io.nexus
info.bioinfweb.commons.bio.biojava3.alignment.io.phylip
info.bioinfweb.commons.bio.biojava3.alignment.template

Uses of Alignment in info.bioinfweb.commons.bio.biojava3.alignment

Classes in info.bioinfweb.commons.bio.biojava3.alignment that implement Alignment

Modifier and Type	Class and Description
class	SimpleAlignment<S extends org.biojava3.core.sequence.template.Sequence<C>,C extends org.biojava3.core.sequence.template.Compound> Default implementation of Alignment.

Methods in info.bioinfweb.commons.bio.biojava3.alignment with parameters of type Alignment

Modifier and Type	Method and Description
boolean	SimpleAlignment.sequncesEqual(Alignment<?,?> other) Checks if this alignment contains the same sequences (name and sequence) as the specified one.

Uses of Alignment in info.bioinfweb.commons.bio.biojava3.alignment.io

Methods in info.bioinfweb.commons.bio.biojava3.alignment.io that return Alignment

Modifier and Type	Method and Description
Alignment<S,C>	AbstractAlignmentReader.read(java.io.File file)
Alignment<S,C>	AlignmentReader.read(java.io.File file)
Alignment<S,C>	AlignmentReader.read(java.io.InputStream stream)

Methods in info.bioinfweb.commons.bio.biojava3.alignment.io with parameters of type Alignment

Modifier and Type	Method and Description
void	AbstractAlignmentWriter.write(Alignment<S,C> alignment, java.io.File file)
void	AlignmentWriter.write(Alignment<S,C> alignment, java.io.File file)
void	AlignmentWriter.write(Alignment<S,C> alignment, java.io.OutputStream stream)

Uses of Alignment in info.bioinfweb.commons.bio.biojava3.alignment.io.fasta

Methods in info.bioinfweb.commons.bio.biojava3.alignment.io.fasta that return Alignment

Modifier and Type	Method and Description
Alignment<S,C>	FastaReader.read(java.io.InputStream stream)

Methods in info.bioinfweb.commons.bio.biojava3.alignment.io.fasta with parameters of type Alignment

Modifier and Type	Method and Description
void	FastaWriter.write(Alignment<S,C> alignment, java.io.OutputStream stream)

Uses of Alignment in info.bioinfweb.commons.bio.biojava3.alignment.io.hennig86

Methods in info.bioinfweb.commons.bio.biojava3.alignment.io.hennig86 with parameters of type Alignment

Modifier and Type	Method and Description
void	Hennig86Writer.write(Alignment<S,C> alignment, java.io.File file, java.lang.String title)
void	Hennig86Writer.write(Alignment<S,C> alignment, java.io.OutputStream stream)
void	Hennig86Writer.write(Alignment<S,C> alignment, java.io.OutputStream stream, java.lang.String title)

Uses of Alignment in info.bioinfweb.commons.bio.biojava3.alignment.io.mega

Methods in info.bioinfweb.commons.bio.biojava3.alignment.io.mega with parameters of type Alignment

Modifier and Type	Method and Description
void	MEGAWriter.write(Alignment<S,C> alignment, java.io.File file, java.lang.String title)
void	MEGAWriter.write(Alignment<S,C> alignment, java.io.OutputStream stream)
void	MEGAWriter.write(Alignment<S,C> alignment, java.io.OutputStream stream, java.lang.String title)

Uses of Alignment in info.bioinfweb.commons.bio.biojava3.alignment.io.nexus

Methods in info.bioinfweb.commons.bio.biojava3.alignment.io.nexus that return Alignment

Modifier and Type	Method and Description
Alignment<S,C>	NexusReader.read(java.io.InputStream stream)

Methods in info.bioinfweb.commons.bio.biojava3.alignment.io.nexus with parameters of type Alignment

Modifier and Type	Method and Description
void	NexusWriter.write(Alignment<S,C> alignment, java.io.OutputStream stream)

Uses of Alignment in info.bioinfweb.commons.bio.biojava3.alignment.io.phylip

Methods in info.bioinfweb.commons.bio.biojava3.alignment.io.phylip with parameters of type Alignment

Modifier and Type	Method and Description
void	PhylipWriter.write(Alignment<S,C> alignment, java.io.OutputStream stream) Writes the specified alignment in sequential Phylip format.

Uses of Alignment in info.bioinfweb.commons.bio.biojava3.alignment.template

Methods in info.bioinfweb.commons.bio.biojava3.alignment.template with parameters of type Alignment

Modifier and Type	Method and Description
boolean	Alignment.sequncesEqual(Alignment<?,?> other)