Package org.biojava.bio.program.xff

Class XFFTools

java.lang.Object

org.biojava.bio.program.xff.XFFTools

public class XFFTools
extends java.lang.Object

Common functionality for manipulating XFF.

Author:

Matthew Pocock

Field Summary

Fields

Modifier and Type	Field	Description
static java.lang.String	XFF_BIOJAVA_NS
static java.lang.String	XFF_NS

Constructor Summary

Constructors

Constructor	Description
XFFTools()

Method Summary

Modifier and Type	Method	Description
static void	annotateXFF(java.io.File xffFile, Sequence sequence)
static void	annotateXFF(java.io.File xffFile, Sequence sequence, Annotation ann)
static Sequence	readXFF(java.io.File xffFile, java.lang.String seqID)
static Sequence	readXFF(java.io.File xffFile, java.lang.String seqID, FiniteAlphabet alpha)
static void	writeXFF(java.io.File xffFile, FeatureHolder features)
static void	writeXFF(java.io.PrintWriter xffPR, FeatureHolder features)

Methods inherited from class java.lang.Object

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

Field Detail

XFF_NS

public static final java.lang.String XFF_NS

See Also:

Constant Field Values

XFF_BIOJAVA_NS

public static final java.lang.String XFF_BIOJAVA_NS

See Also:

Constant Field Values

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