org.biojava.bio.program.xff
Class XFFTools

java.lang.Object
  org.biojava.bio.program.xff.XFFTools

public class XFFTools

extends Object

Common functionality for manipulating XFF.

Author:

Matthew Pocock

Constructor Summary

XFFTools()

Method Summary

static void	annotateXFF(File xffFile, Sequence sequence)
static void	annotateXFF(File xffFile, Sequence sequence, Annotation ann)
static Sequence	readXFF(File xffFile, String seqID)
static Sequence	readXFF(File xffFile, String seqID, FiniteAlphabet alpha)
static void	writeXFF(File xffFile, FeatureHolder features)
static void	writeXFF(PrintWriter xffPR, FeatureHolder features)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

XFFTools

public XFFTools()

Method Detail

annotateXFF

public static void annotateXFF(File xffFile,
                               Sequence sequence)
                        throws IOException,
                               SAXException,
                               BioException

Throws:

IOException

SAXException

BioException

annotateXFF

public static void annotateXFF(File xffFile,
                               Sequence sequence,
                               Annotation ann)
                        throws IOException,
                               SAXException,
                               BioException

Throws:

IOException

SAXException

BioException

readXFF

public static Sequence readXFF(File xffFile,
                               String seqID,
                               FiniteAlphabet alpha)
                        throws IOException,
                               SAXException,
                               BioException

Throws:

IOException

SAXException

BioException

readXFF

public static Sequence readXFF(File xffFile,
                               String seqID)
                        throws IOException,
                               SAXException,
                               BioException

Throws:

IOException

SAXException

BioException

writeXFF

public static void writeXFF(File xffFile,
                            FeatureHolder features)
                     throws IOException

Throws:

IOException

writeXFF

public static void writeXFF(PrintWriter xffPR,
                            FeatureHolder features)
                     throws IOException

Throws:

IOException