Deprecated API

Deprecated Methods
uk.ac.vamsas.objects.core.Alignment.setAlignmentAnnotationAsReference(Vector)
            
uk.ac.vamsas.objects.core.DataSet.setAlignmentAsReference(Vector)
            
uk.ac.vamsas.objects.core.AlignmentSequence.setAlignmentSequenceAnnotationAsReference(Vector)
            
uk.ac.vamsas.objects.core.Alignment.setAlignmentSequenceAsReference(Vector)
            
uk.ac.vamsas.objects.core.RangeAnnotation.setAnnotationElementAsReference(Vector)
            
uk.ac.vamsas.objects.core.VamsasDocument.setApplicationDataAsReference(Vector)
            
uk.ac.vamsas.objects.core.VamsasDocument.setAttachmentAsReference(Vector)
            
org.apache.tools.zip.ZipEntry.setComprSize(long)
          since 1.7. Use setCompressedSize directly. 
uk.ac.vamsas.objects.core.DataSet.setDataSetAnnotationsAsReference(Vector)
            
uk.ac.vamsas.objects.core.VAMSAS.setDataSetAsReference(Vector)
            
uk.ac.vamsas.objects.core.Sequence.setDbRefAsReference(Vector)
            
uk.ac.vamsas.objects.core.Provenance.setEntryAsReference(Vector)
            
uk.ac.vamsas.objects.core.AnnotationElement.setGlyphAsReference(Vector)
            
uk.ac.vamsas.objects.core.Entry.setInputAsReference(Vector)
            
uk.ac.vamsas.objects.core.ApplicationData.setInstanceAsReference(Vector)
            
uk.ac.vamsas.objects.core.DbRef.setLinkAsReference(Vector)
            
uk.ac.vamsas.objects.core.RangeAnnotation.setLinkAsReference(Vector)
            
uk.ac.vamsas.objects.core.DbRef.setMapAsReference(Vector)
            
uk.ac.vamsas.objects.core.Tree.setNewickAsReference(Vector)
            
uk.ac.vamsas.objects.core.Input.setObjRefAsReference(Vector)
            
uk.ac.vamsas.objects.core.Entry.setParamAsReference(Vector)
            
uk.ac.vamsas.objects.core.RangeType.setPosAsReference(Vector)
            
uk.ac.vamsas.objects.core.Alignment.setPropertyAsReference(Vector)
            
uk.ac.vamsas.objects.core.DbRef.setPropertyAsReference(Vector)
            
uk.ac.vamsas.objects.core.Entry.setPropertyAsReference(Vector)
            
uk.ac.vamsas.objects.core.NodeType.setPropertyAsReference(Vector)
            
uk.ac.vamsas.objects.core.RangeAnnotation.setPropertyAsReference(Vector)
            
uk.ac.vamsas.objects.core.SequenceType.setPropertyAsReference(Vector)
            
uk.ac.vamsas.objects.core.Tree.setPropertyAsReference(Vector)
            
uk.ac.vamsas.objects.core.ReferenceType.setRefsAsReference(Vector)
            
uk.ac.vamsas.objects.core.RangeAnnotation.setScoreAsReference(Vector)
            
uk.ac.vamsas.objects.core.RangeType.setSegAsReference(Vector)
            
uk.ac.vamsas.objects.core.DataSetAnnotations.setSeqRefAsReference(Vector)
            
uk.ac.vamsas.objects.core.AlignmentAnnotation.setSeqrefsAsReference(Vector)
            
uk.ac.vamsas.objects.core.DataSet.setSequenceAsReference(Vector)
            
uk.ac.vamsas.objects.core.DataSet.setSequenceMappingAsReference(Vector)
            
uk.ac.vamsas.objects.core.Alignment.setTreeAsReference(Vector)
            
uk.ac.vamsas.objects.core.DataSet.setTreeAsReference(Vector)
            
uk.ac.vamsas.objects.core.VAMSAS.setTreeAsReference(Vector)
            
uk.ac.vamsas.objects.core.Treenode.setTreeIdAsReference(Vector)
            
uk.ac.vamsas.objects.core.Tree.setTreenodeAsReference(Vector)
            
uk.ac.vamsas.objects.core.ApplicationData.setUserAsReference(Vector)
            
uk.ac.vamsas.objects.core.AnnotationElement.setValueAsReference(Vector)
            
uk.ac.vamsas.objects.core.VamsasDocument.setVAMSASAsReference(Vector)
            
uk.ac.vamsas.objects.core.NodeType.setVrefAsReference(Vector)
            
uk.ac.vamsas.objects.core.Sequence.setVxrefAsReference(Vector)