Class NextProtXmlAnnotation


  • public class NextProtXmlAnnotation
    extends NextProtXmlNode
    Mimics the 'annotation' tag in a NextProt XML file
    Author:
    Pablo Cingolani
    • Constructor Detail

      • NextProtXmlAnnotation

        public NextProtXmlAnnotation​(NextProtXmlEntry entry,
                                     java.lang.String category)
    • Method Detail

      • addMarkers

        public void addMarkers​(NextProtMarkerFactory markersFactory)
        Create all markers for this annotation
      • description

        public java.lang.String description()
      • getCategory

        public java.lang.String getCategory()
      • getCvTerm

        public CvTerm getCvTerm()
      • setCvTerm

        public void setCvTerm​(CvTerm cvTerm)
      • getDescription

        public java.lang.String getDescription()
      • setDescription

        public void setDescription​(java.lang.String description)
      • getLocations

        public java.util.List<Location> getLocations()
      • hasCvTerm

        public boolean hasCvTerm()
      • isEmpty

        public boolean isEmpty()
      • locationBeginPos

        public void locationBeginPos​(org.xml.sax.Attributes attributes)
      • locationEnd

        public void locationEnd()
        End of location tag
      • locationEndPos

        public void locationEndPos​(org.xml.sax.Attributes attributes)
      • locationIsoformStart

        public void locationIsoformStart​(java.lang.String accession)
      • locationStart

        public void locationStart​(org.xml.sax.Attributes attributes)
      • name

        public java.lang.String name()
        Return an annotation "name" Clean up characters to make them compatible with VCF annotations
      • toString

        public java.lang.String toString()
        Overrides:
        toString in class java.lang.Object
      • toString

        public java.lang.String toString​(java.lang.String prefix)