Uses of Class
uk.ac.vamsas.objects.core.Sequence

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)
           
 void IDocumentUpdater.update(Sequence vobj)
           
 

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)
           
 void DataSet.addSequence(int index, Sequence vSequence)
           
 boolean DataSet.removeSequence(Sequence vSequence)
          Method removeSequence.
 void DataSet.setSequence(int index, Sequence vSequence)
           
 void DataSet.setSequence(Sequence[] vSequenceArray)
           
 

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)
           
static Sequence[] SeqAln.ReadClustalFile(java.io.InputStream os)
           
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)
           
static Alignment SeqAln.make_Alignment(Entry origin, Sequence[] seqs)
          manufacture an alignment/dataset from an array of sequences