Uses of Class
jprotein.data.datatype.Sequence

Packages that use Sequence

jprotein.data.dataformat.info
jprotein.data.dataformat.parser
jprotein.data.datatype
jprotein.io.file
jprotein.io.net
jprotein.tree.data
jprotein.tree.tools

Uses of Sequence in jprotein.data.dataformat.info

Subclasses of Sequence in jprotein.data.dataformat.info

class	BlastPairwiseInfo
class	BlastSequenceInfo

Methods in jprotein.data.dataformat.info that return Sequence

Sequence

BlastPairwiseInfo.getRefSequence()

Methods in jprotein.data.dataformat.info with parameters of type Sequence

void	BlastPairwiseInfo.setRefSequence(Sequence ref)

Uses of Sequence in jprotein.data.dataformat.parser

Methods in jprotein.data.dataformat.parser with parameters of type Sequence

static java.util.Vector

BlastPairwise.getAlignmentComposition(java.util.Vector pAli, Sequence ref)

Uses of Sequence in jprotein.data.datatype

Subclasses of Sequence in jprotein.data.datatype

class	Alignment
class	Sequence3D
class	SequenceInformation

Methods in jprotein.data.datatype that return Sequence

Sequence	MultiAlignment.getAlignment(int index)
Sequence	PairwiseAlignment.getRefSequence()

Methods in jprotein.data.datatype with parameters of type Sequence

void	MultiAlignment.addAlignment(Sequence ali)
java.util.Vector	MultiAlignment.getAlignmentComposition(Sequence ref)
boolean	Sequence.isIdentical(Sequence seq)
void	PairwiseAlignment.setRefSequence(Sequence ref)

Constructors in jprotein.data.datatype with parameters of type Sequence

MultiPairwiseAlignment(Sequence ref)

Uses of Sequence in jprotein.io.file

Constructors in jprotein.io.file with parameters of type Sequence

ETtoHTML(java.lang.String path, Sequence refAli, java.util.Vector sequenceData, java.util.Vector values)

Uses of Sequence in jprotein.io.net

Methods in jprotein.io.net that return Sequence

Sequence	PsiBlastClientOld.getQuerySequence()
Sequence	PsiBlastClient.getQuerySequence()
Sequence	BlastClient.getQuerySequence()

Methods in jprotein.io.net with parameters of type Sequence

void	PsiBlastClientOld.setQuerySequence(Sequence sequence)
void	PsiBlastClient.setQuerySequence(Sequence sequence)
void	BlastClient.setQuerySequence(Sequence sequence)

Uses of Sequence in jprotein.tree.data

Methods in jprotein.tree.data that return Sequence

Sequence

Leaf.getSequence()

Constructors in jprotein.tree.data with parameters of type Sequence

Leaf(Sequence ali, java.util.Vector distances)

Uses of Sequence in jprotein.tree.tools

Methods in jprotein.tree.tools with parameters of type Sequence

java.util.Vector	ET.generateTraceRecord(MultiAlignment ma, Sequence ref)
Leaf	Tree.getLeaf(SimpleNode root, Sequence alignment)
void	DistanceMatrix.setDistantCouple(Sequence seq1, Sequence seq2)