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

Fields

Modifier and Type	Field and 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 and Description
GFFTools()

Method Summary

Methods

Modifier and Type	Method and 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(java.io.BufferedReader gffIn) Read all GFF entries from a buffered reader.
static GFFEntrySet	readGFF(java.io.BufferedReader gffIn, GFFRecordFilter recFilt) Read all GFF entries matching a filter from a buffered reader.
static GFFEntrySet	readGFF(java.io.File inFile) Reads a GFFEntrySet from a file with no filtering.
static GFFEntrySet	readGFF(java.io.File inFile, GFFRecordFilter recFilt) Reads a GFFEntrySet from a file with the specified filter.
static GFFEntrySet	readGFF(java.lang.String fileName) Deprecated. use: readGff(File)
static GFFEntrySet	readGFF(java.lang.String fileName, GFFRecordFilter recFilt) Deprecated. use: readGff(File,GFFRecordFilter)
static void	writeGFF(java.io.File outFile, GFFEntrySet ents) Writes a GFFEntrySet to a file.
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

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:

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

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:

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.File inFile)
                           throws java.io.FileNotFoundException,
                                  ParserException,
                                  BioException,
                                  java.io.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:

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.File inFile,
                  GFFRecordFilter recFilt)
                           throws java.io.FileNotFoundException,
                                  ParserException,
                                  BioException,
                                  java.io.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:

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

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

java.io.IOException - if there was an error with the reader

ParserException

readGFF

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

java.io.IOException - if there was an error with the reader

ParserException

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.File outFile,
            GFFEntrySet ents)
                     throws java.io.IOException

Writes a GFFEntrySet to a file.

Parameters:

outFile - the file to write to

ents - the entry set to write

Throws:

java.io.IOException - if writing to the file 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.

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