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Packages that use Sequence | |
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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 |
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Subclasses of Sequence in jprotein.data.dataformat.info | |
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class |
BlastPairwiseInfo
|
class |
BlastSequenceInfo
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Methods in jprotein.data.dataformat.info that return Sequence | |
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Sequence |
BlastPairwiseInfo.getRefSequence()
|
Methods in jprotein.data.dataformat.info with parameters of type Sequence | |
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void |
BlastPairwiseInfo.setRefSequence(Sequence ref)
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Uses of Sequence in jprotein.data.dataformat.parser |
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Methods in jprotein.data.dataformat.parser with parameters of type Sequence | |
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static java.util.Vector |
BlastPairwise.getAlignmentComposition(java.util.Vector pAli,
Sequence ref)
|
Uses of Sequence in jprotein.data.datatype |
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Subclasses of Sequence in jprotein.data.datatype | |
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class |
Alignment
|
class |
Sequence3D
|
class |
SequenceInformation
|
Methods in jprotein.data.datatype that return Sequence | |
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Sequence |
MultiAlignment.getAlignment(int index)
|
Sequence |
PairwiseAlignment.getRefSequence()
|
Methods in jprotein.data.datatype with parameters of type Sequence | |
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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 | |
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MultiPairwiseAlignment(Sequence ref)
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Uses of Sequence in jprotein.io.file |
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Constructors in jprotein.io.file with parameters of type Sequence | |
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ETtoHTML(java.lang.String path,
Sequence refAli,
java.util.Vector sequenceData,
java.util.Vector values)
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Uses of Sequence in jprotein.io.net |
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Methods in jprotein.io.net that return Sequence | |
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Sequence |
PsiBlastClientOld.getQuerySequence()
|
Sequence |
PsiBlastClient.getQuerySequence()
|
Sequence |
BlastClient.getQuerySequence()
|
Methods in jprotein.io.net with parameters of type Sequence | |
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void |
PsiBlastClientOld.setQuerySequence(Sequence sequence)
|
void |
PsiBlastClient.setQuerySequence(Sequence sequence)
|
void |
BlastClient.setQuerySequence(Sequence sequence)
|
Uses of Sequence in jprotein.tree.data |
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Methods in jprotein.tree.data that return Sequence | |
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Sequence |
Leaf.getSequence()
|
Constructors in jprotein.tree.data with parameters of type Sequence | |
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Leaf(Sequence ali,
java.util.Vector distances)
|
Uses of Sequence in jprotein.tree.tools |
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Methods in jprotein.tree.tools with parameters of type Sequence | |
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java.util.Vector |
ET.generateTraceRecord(MultiAlignment ma,
Sequence ref)
|
Leaf |
Tree.getLeaf(SimpleNode root,
Sequence alignment)
|
void |
DistanceMatrix.setDistantCouple(Sequence seq1,
Sequence seq2)
|
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