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Packages that use Sequence | |
uk.ac.vamsas.objects | |
uk.ac.vamsas.objects.core | |
uk.ac.vamsas.objects.utils |
Uses of Sequence in uk.ac.vamsas.objects |
Methods in uk.ac.vamsas.objects with parameters of type Sequence | |
void |
EmptyDocumentUpdater.update(Sequence vobj)
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void |
IDocumentUpdater.update(Sequence vobj)
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Uses of Sequence in uk.ac.vamsas.objects.core |
Methods in uk.ac.vamsas.objects.core that return Sequence | |
Sequence |
DataSet.getSequence(int index)
Method getSequence. |
Sequence[] |
DataSet.getSequence()
Method getSequence.Returns the contents of the collection in an Array. |
Sequence |
DataSet.removeSequenceAt(int index)
Method removeSequenceAt. |
Methods in uk.ac.vamsas.objects.core with parameters of type Sequence | |
void |
DataSet.addSequence(Sequence vSequence)
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void |
DataSet.addSequence(int index,
Sequence vSequence)
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boolean |
DataSet.removeSequence(Sequence vSequence)
Method removeSequence. |
void |
DataSet.setSequence(int index,
Sequence vSequence)
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void |
DataSet.setSequence(Sequence[] vSequenceArray)
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Uses of Sequence in uk.ac.vamsas.objects.utils |
Methods in uk.ac.vamsas.objects.utils that return Sequence | |
static Sequence |
Seq.newSequence(java.lang.String Name,
java.lang.String Sequence,
java.lang.String Dictionary,
int start,
int end)
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static Sequence[] |
SeqAln.ReadClustalFile(java.io.InputStream os)
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static Sequence[] |
SeqSet.read_SeqFasta(java.io.InputStream os)
TODO: introduce a dictionary parameter for qualified sequence symbols Reads a sequence set from a stream - will only read prescribed amino acid symbols. |
Methods in uk.ac.vamsas.objects.utils with parameters of type Sequence | |
static AlignmentSequence |
Seq.newAlignmentSequence(java.lang.String name,
java.lang.String alSequence,
Sequence refseq,
long start,
long end)
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static Alignment |
SeqAln.make_Alignment(Entry origin,
Sequence[] seqs)
manufacture an alignment/dataset from an array of sequences |
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