org.biojava.bio.program.gff
Class GFFTools

java.lang.Object
  |
  +--org.biojava.bio.program.gff.GFFTools

public class GFFTools

extends java.lang.Object

Since:

1.2

Author:

Mark Schreiber, Matthew Pocock

Field Summary

static int	NO_FRAME Flag to indicate that there is no frame info.
static double	NO_SCORE Flag to indicate that there is no score info.

Constructor Summary

GFFTools()

Method Summary

static Sequence	annotateSequence(Sequence seq, GFFEntrySet ents) Annotates a sequence with the features from a GFF entry set with sequence name matching this sequence.
static Sequence	annotateSequence(Sequence seq, GFFEntrySet ents, boolean checkSeqName) Annotates a sequence with the features from a GFF entry set.
static SequenceDB	annotateSequences(SequenceDB seqs, GFFEntrySet ents) Annotates all sequences in a sequence DB with features from a GFF entry set.
static GFFEntrySet	gffFromSequence(Sequence seq) Creates a GFFEntrySet containing one entry for each feature on a sequence.
static GFFEntrySet	readGFF(java.io.BufferedReader gffIn)
static GFFEntrySet	readGFF(java.io.BufferedReader gffIn, GFFRecordFilter recFilt)
static GFFEntrySet	readGFF(java.lang.String fileName) Reads a GFFEntrySet from a file with no filtering
static GFFEntrySet	readGFF(java.lang.String fileName, GFFRecordFilter recFilt) Reads a GFFEntrySet from a file with the specified filter
static void	writeGFF(java.io.PrintWriter pw, GFFEntrySet ents) Writes a GFFEntrySet to a PrintWriter
static void	writeGFF(java.lang.String fileName, GFFEntrySet ents) Writes a GFFEntrySet to a file

Methods inherited from class java.lang.Object

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

Field Detail

NO_SCORE

public static double NO_SCORE

Flag to indicate that there is no score info.

NO_FRAME

public static int NO_FRAME

Flag to indicate that there is no frame info.

Constructor Detail

GFFTools

public GFFTools()

Method Detail

readGFF

public static GFFEntrySet readGFF(java.lang.String fileName)
                           throws java.io.FileNotFoundException,
                                  ParserException,
                                  BioException,
                                  java.io.IOException

Reads a GFFEntrySet from a file with no filtering

Parameters:

fileName - the file containing the GFF

Returns:

a GFFEntrySet encapsulating the records read from the file

Throws:

java.io.FileNotFoundException - if file is not found

ParserException - if format is wrong

BioException - if format is wrong

java.io.IOException - if file reading error occurs

readGFF

public static GFFEntrySet readGFF(java.lang.String fileName,
                                  GFFRecordFilter recFilt)
                           throws java.io.FileNotFoundException,
                                  ParserException,
                                  BioException,
                                  java.io.IOException

Reads a GFFEntrySet from a file with the specified filter

Parameters:

fileName - the file containing the GFF

recFilt - the filter to use

Returns:

a GFFEntrySet encapsulating the records read from the file

Throws:

java.io.FileNotFoundException - if file is not found

ParserException - if format is wrong

BioException - if format is wrong

java.io.IOException - if file reading error occurs

readGFF

public static GFFEntrySet readGFF(java.io.BufferedReader gffIn)
                           throws ParserException,
                                  BioException,
                                  java.io.IOException

ParserException

BioException

java.io.IOException

readGFF

public static GFFEntrySet readGFF(java.io.BufferedReader gffIn,
                                  GFFRecordFilter recFilt)
                           throws ParserException,
                                  BioException,
                                  java.io.IOException

ParserException

BioException

java.io.IOException

writeGFF

public static void writeGFF(java.lang.String fileName,
                            GFFEntrySet ents)
                     throws java.io.IOException

Writes a GFFEntrySet to a file

Parameters:

fileName - the file to write to

ents - the entries to write

Throws:

java.io.IOException - if file writing fails

writeGFF

public static void writeGFF(java.io.PrintWriter pw,
                            GFFEntrySet ents)
                     throws java.io.IOException

Writes a GFFEntrySet to a PrintWriter

Parameters:

pw - the PrintWriter to write to

ents - the entries to write

Throws:

java.io.IOException - if file writing fails

annotateSequence

public static Sequence annotateSequence(Sequence seq,
                                        GFFEntrySet ents)

Annotates a sequence with the features from a GFF entry set with sequence name matching this sequence.

Parameters:

seq - the Sequence to annotate.

ents - the the GFF features to annotate it with.

Returns:

a reference to a newly annotated sequence.

annotateSequence

public static Sequence annotateSequence(Sequence seq,
                                        GFFEntrySet ents,
                                        boolean checkSeqName)

Annotates a sequence with the features from a GFF entry set.

Parameters:

seq - the Sequence to annotate.

ents - the the GFF features to annotate it with.

Returns:

a reference to a newly annotated sequence.

annotateSequences

public static SequenceDB annotateSequences(SequenceDB seqs,
                                           GFFEntrySet ents)
                                    throws IllegalIDException,
                                           BioException

Annotates all sequences in a sequence DB with features from a GFF entry set.

Parameters:

seqs - the SequenceDB to annotate

ents - the GFFEntrySet to annote with

Returns:

a SequenceDB with all the annotations on

IllegalIDException

BioException

gffFromSequence

public static GFFEntrySet gffFromSequence(Sequence seq)
                                   throws BioException

Creates a GFFEntrySet containing one entry for each feature on a sequence.

Parameters:

seq - the Sequence to create features for

Returns:

a new GFFEntrySet with gff records for each featre on the sequence

Throws:

BioException - if something went wrong GFF-ifying the sequences features