Class XFFTools


  • public class XFFTools
    extends java.lang.Object
    Common functionality for manipulating XFF.
    Author:
    Matthew Pocock
    • Constructor Detail

      • XFFTools

        public XFFTools()
    • Method Detail

      • annotateXFF

        public static void annotateXFF​(java.io.File xffFile,
                                       Sequence sequence)
                                throws java.io.IOException,
                                       org.xml.sax.SAXException,
                                       BioException
        Throws:
        java.io.IOException
        org.xml.sax.SAXException
        BioException
      • annotateXFF

        public static void annotateXFF​(java.io.File xffFile,
                                       Sequence sequence,
                                       Annotation ann)
                                throws java.io.IOException,
                                       org.xml.sax.SAXException,
                                       BioException
        Throws:
        java.io.IOException
        org.xml.sax.SAXException
        BioException
      • readXFF

        public static Sequence readXFF​(java.io.File xffFile,
                                       java.lang.String seqID,
                                       FiniteAlphabet alpha)
                                throws java.io.IOException,
                                       org.xml.sax.SAXException,
                                       BioException
        Throws:
        java.io.IOException
        org.xml.sax.SAXException
        BioException
      • readXFF

        public static Sequence readXFF​(java.io.File xffFile,
                                       java.lang.String seqID)
                                throws java.io.IOException,
                                       org.xml.sax.SAXException,
                                       BioException
        Throws:
        java.io.IOException
        org.xml.sax.SAXException
        BioException
      • writeXFF

        public static void writeXFF​(java.io.File xffFile,
                                    FeatureHolder features)
                             throws java.io.IOException
        Throws:
        java.io.IOException
      • writeXFF

        public static void writeXFF​(java.io.PrintWriter xffPR,
                                    FeatureHolder features)
                             throws java.io.IOException
        Throws:
        java.io.IOException