org.biojava.bio.program.xff
Class XFFTools

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

public class XFFTools
extends Object

Common functionality for manipulating XFF.

Author:
Matthew Pocock

Field Summary
static String XFF_BIOJAVA_NS
           
static String XFF_NS
           
 
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
 

Field Detail

XFF_NS

public static final String XFF_NS
See Also:
Constant Field Values

XFF_BIOJAVA_NS

public static final String XFF_BIOJAVA_NS
See Also:
Constant Field Values
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