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## 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)`

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