Package org.biojava.bio.program.gff

Class GFFTools

java.lang.Object

org.biojava.bio.program.gff.GFFTools

public class GFFTools
extends Object

Since:

1.2

Author:

Mark Schreiber, Matthew Pocock

Field Summary

Fields

Modifier and Type	Field	Description
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

Constructors

Constructor	Description
GFFTools()

Method Summary

Modifier and Type	Method	Description
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	gffFromSeqDB(SequenceDB seqDB)	Creates a GFFEntrySet containing one entry for each feature on each sequence of a SequenceDB.
static GFFEntrySet	gffFromSequence(Sequence seq)	Creates a GFFEntrySet containing one entry for each feature on a sequence.
static GFFEntrySet	readGFF(BufferedReader gffIn)	Read all GFF entries from a buffered reader.
static GFFEntrySet	readGFF(BufferedReader gffIn, GFFRecordFilter recFilt)	Read all GFF entries matching a filter from a buffered reader.
static GFFEntrySet	readGFF(File inFile)	Reads a GFFEntrySet from a file with no filtering.
static GFFEntrySet	readGFF(File inFile, GFFRecordFilter recFilt)	Reads a GFFEntrySet from a file with the specified filter.
static GFFEntrySet	readGFF(String fileName)	Deprecated. use: readGff(File)
static GFFEntrySet	readGFF(String fileName, GFFRecordFilter recFilt)	Deprecated. use: readGff(File,GFFRecordFilter)
static void	writeGFF(File outFile, GFFEntrySet ents)	Writes a GFFEntrySet to a file.
static void	writeGFF(PrintWriter pw, GFFEntrySet ents)	Writes a GFFEntrySet to a PrintWriter.
static void	writeGFF(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(String fileName)
                           throws FileNotFoundException,
                                  ParserException,
                                  BioException,
                                  IOException

Deprecated.

use: readGff(File)

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:

FileNotFoundException - if file is not found

ParserException - if format is wrong

BioException - if format is wrong

IOException - if file reading error occurs

readGFF

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

Deprecated.

use: readGff(File,GFFRecordFilter)

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:

FileNotFoundException - if file is not found

ParserException - if format is wrong

BioException - if format is wrong

IOException - if file reading error occurs

readGFF

public static GFFEntrySet readGFF(File inFile)
                           throws FileNotFoundException,
                                  ParserException,
                                  BioException,
                                  IOException

Reads a GFFEntrySet from a file with no filtering.

Parameters:

inFile - the File containing the GFF

Returns:

a GFFEntrySet encapsulating the records read from the file

Throws:

FileNotFoundException - if file is not found

ParserException - if format is wrong

BioException - if format is wrong

IOException - if file reading error occurs

readGFF

public static GFFEntrySet readGFF(File inFile,
                                  GFFRecordFilter recFilt)
                           throws FileNotFoundException,
                                  ParserException,
                                  BioException,
                                  IOException

Reads a GFFEntrySet from a file with the specified filter.

Parameters:

inFile - the File containing the GFF

recFilt - the filter to use

Returns:

a GFFEntrySet encapsulating the records read from the file

Throws:

FileNotFoundException - if file is not found

ParserException - if format is wrong

BioException - if format is wrong

IOException - if file reading error occurs

readGFF

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

Read all GFF entries from a buffered reader. This will read up untill the end of the reader.

Parameters:

gffIn - the BufferedReader to read text from

Returns:

a GFFEntrySet containing all of the GFF that could be read

Throws:

parserException - if the text could not be parsed as GFF

BioException - if there was some error reading the GFF

IOException - if there was an error with the reader

ParserException

readGFF

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

Read all GFF entries matching a filter from a buffered reader. This will read up untill the end of the reader.

Parameters:

gffIn - the BufferedReader to read text from

Returns:

a GFFEntrySet containing all of the GFF that could be read

Throws:

parserException - if the text could not be parsed as GFF

BioException - if there was some error reading the GFF

IOException - if there was an error with the reader

ParserException

writeGFF

public static void writeGFF(String fileName,
                            GFFEntrySet ents)
                     throws IOException

Writes a GFFEntrySet to a file.

Parameters:

fileName - the file to write to

ents - the entries to write

Throws:

IOException - if file writing fails

writeGFF

public static void writeGFF(File outFile,
                            GFFEntrySet ents)
                     throws IOException

Writes a GFFEntrySet to a file.

Parameters:

outFile - the file to write to

ents - the entry set to write

Throws:

IOException - if writing to the file fails

writeGFF

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

Writes a GFFEntrySet to a PrintWriter.

Parameters:

pw - the PrintWriter to write to

ents - the entries to write

Throws:

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.

checkSeqName - boolean flat, if true only annotate sequence with features that have matching sequence names, otherwise annotate all features

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

Throws:

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

gffFromSeqDB

public static GFFEntrySet gffFromSeqDB(SequenceDB seqDB)
                                throws BioException

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

Note: This converts all features in the whole database to in-memorey GFFRecord instances. This will take up considerable memory for large databases.

Parameters:

seqDB - the SequenceDB to create features for

Returns:

a new GFFEntrySet with gff records for each feature on the database

Throws:

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