GFFTools (biojava-legacy 1.9.5 API)

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.

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()

Constructors
Constructor	Description
`GFFTools()`

Method Summary

All Methods Static Methods Concrete Methods Deprecated Methods
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
```
    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
```
    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

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

NO_SCORE

NO_FRAME

Constructor Detail

GFFTools

Method Detail

readGFF

readGFF

readGFF

readGFF

readGFF

readGFF

writeGFF

writeGFF

writeGFF

annotateSequence

annotateSequence

annotateSequences

gffFromSequence

gffFromSeqDB