Package org.snpeff.nextProt

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)