org.biojava.bio.program.gff
Class GFFTools

java.lang.Object
  extended by org.biojava.bio.program.gff.GFFTools

public class GFFTools
extends 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 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