Uses of Class
org.biojava.bio.program.gff.GFFEntrySet
Packages that use GFFEntrySet
Package
Description
GFF manipulation.
Sequences and SequenceDBs which are composed from data taken
from a number of data sources.
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Uses of GFFEntrySet in org.biojava.bio.program.gff
Methods in org.biojava.bio.program.gff that return GFFEntrySetModifier and TypeMethodDescriptionGFFEntrySet.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
Reads aGFFEntrySet
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
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 GFFEntrySetModifier and TypeMethodDescriptionstatic 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