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

Packages that use Alignment
uk.ac.vamsas.objects   
uk.ac.vamsas.objects.core   
uk.ac.vamsas.objects.utils   
uk.ac.vamsas.test.simpleclient   
 

Uses of Alignment in uk.ac.vamsas.objects
 

Methods in uk.ac.vamsas.objects with parameters of type Alignment
 void EmptyDocumentUpdater.update(Alignment vobj)
           
 void IDocumentUpdater.update(Alignment vobj)
           
 

Uses of Alignment in uk.ac.vamsas.objects.core
 

Methods in uk.ac.vamsas.objects.core that return Alignment
static Alignment Alignment.unmarshal(java.io.Reader reader)
          Method unmarshal.
 Alignment DataSet.getAlignment(int index)
          Method getAlignment.
 Alignment[] DataSet.getAlignment()
          Method getAlignment.Returns the contents of the collection in an Array.
 Alignment DataSet.removeAlignmentAt(int index)
          Method removeAlignmentAt.
 

Methods in uk.ac.vamsas.objects.core with parameters of type Alignment
 void DataSet.addAlignment(Alignment vAlignment)
           
 void DataSet.addAlignment(int index, Alignment vAlignment)
           
 boolean DataSet.removeAlignment(Alignment vAlignment)
          Method removeAlignment.
 void DataSet.setAlignment(int index, Alignment vAlignment)
           
 void DataSet.setAlignment(Alignment[] vAlignmentArray)
           
 

Uses of Alignment in uk.ac.vamsas.objects.utils
 

Subclasses of Alignment in uk.ac.vamsas.objects.utils
 class SeqAln
           
 

Methods in uk.ac.vamsas.objects.utils that return Alignment
static Alignment SeqAln.make_Alignment(Entry origin, Sequence[] seqs)
          manufacture an alignment/dataset from an array of sequences
static Alignment SeqAln.read_FastaAlignment(java.io.InputStream os, Entry entry)
           
static Alignment SeqAln.read_ClustalAlignment(java.io.InputStream os, Entry entry)
           
 

Methods in uk.ac.vamsas.objects.utils with parameters of type Alignment
static void SeqAln.WriteClustalWAlignment(java.io.OutputStream os, Alignment seqAl)
           
 

Uses of Alignment in uk.ac.vamsas.test.simpleclient
 

Methods in uk.ac.vamsas.test.simpleclient with parameters of type Alignment
static boolean ArchiveReports.alignmentReport(Alignment[] al, boolean cascade, java.io.PrintStream outstr)