Uses of Class
org.biojava.bio.program.gff.GFFEntrySet

Packages that use GFFEntrySet

Package	Description
org.biojava.bio.program.gff	GFF manipulation.
org.biojava.bio.seq.distributed	Sequences and SequenceDBs which are composed from data taken from a number of data sources.

Uses of GFFEntrySet in org.biojava.bio.program.gff

Methods in org.biojava.bio.program.gff that return GFFEntrySet

Modifier and Type	Method and Description
GFFEntrySet	GFFEntrySet.filter(GFFRecordFilter filter) Filter this entry set into another set.
static GFFEntrySet	GFFTools.gffFromSeqDB(SequenceDB seqDB) Creates a GFFEntrySet containing one entry for each feature on each sequence of a SequenceDB.
static GFFEntrySet	GFFTools.gffFromSequence(Sequence seq) Creates a GFFEntrySet containing one entry for each feature on a sequence.
static GFFEntrySet	GFFTools.readGFF(BufferedReader gffIn) Read all GFF entries from a buffered reader.
static GFFEntrySet	GFFTools.readGFF(BufferedReader gffIn, GFFRecordFilter recFilt) Read all GFF entries matching a filter from a buffered reader.
static GFFEntrySet	GFFTools.readGFF(File inFile) Reads a GFFEntrySet from a file with no filtering.
static GFFEntrySet	GFFTools.readGFF(File inFile, GFFRecordFilter recFilt) Reads a GFFEntrySet from a file with the specified filter.
static GFFEntrySet	GFFTools.readGFF(String fileName) Deprecated. use: readGff(File)
static GFFEntrySet	GFFTools.readGFF(String fileName, GFFRecordFilter recFilt) Deprecated. use: readGff(File,GFFRecordFilter)

Methods in org.biojava.bio.program.gff with parameters of type GFFEntrySet

Modifier and Type	Method and Description
static Sequence	GFFTools.annotateSequence(Sequence seq, GFFEntrySet ents) Annotates a sequence with the features from a GFF entry set with sequence name matching this sequence.
static Sequence	GFFTools.annotateSequence(Sequence seq, GFFEntrySet ents, boolean checkSeqName) Annotates a sequence with the features from a GFF entry set.
static SequenceDB	GFFTools.annotateSequences(SequenceDB seqs, GFFEntrySet ents) Annotates all sequences in a sequence DB with features from a GFF entry set.
static void	GFFTools.writeGFF(File outFile, GFFEntrySet ents) Writes a GFFEntrySet to a file.
static void	GFFTools.writeGFF(PrintWriter pw, GFFEntrySet ents) Writes a GFFEntrySet to a PrintWriter.
static void	GFFTools.writeGFF(String fileName, GFFEntrySet ents) Writes a GFFEntrySet to a file.

Uses of GFFEntrySet in org.biojava.bio.seq.distributed

Constructors in org.biojava.bio.seq.distributed with parameters of type GFFEntrySet

Constructor and Description
GFFDataSource(GFFEntrySet gffe)