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 Details
- 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 Details
- GFFTools
  
  public GFFTools()
Method Details
- 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

Class GFFTools

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Details

NO_SCORE

NO_FRAME

Constructor Details

GFFTools

Method Details

readGFF

readGFF

readGFF

readGFF

readGFF

readGFF

writeGFF

writeGFF

writeGFF

annotateSequence

annotateSequence

annotateSequences

gffFromSequence

gffFromSeqDB