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)