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

Packages that use GFFEntrySet
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
 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(java.io.BufferedReader gffIn)
          Read all GFF entries from a buffered reader.
static GFFEntrySet GFFTools.readGFF(java.io.BufferedReader gffIn, GFFRecordFilter recFilt)
          Read all GFF entries matching a filter from a buffered reader.
static GFFEntrySet GFFTools.readGFF(java.io.File inFile)
          Reads a GFFEntrySet from a file with no filtering.
static GFFEntrySet GFFTools.readGFF(java.io.File inFile, GFFRecordFilter recFilt)
          Reads a GFFEntrySet from a file with the specified filter.
static GFFEntrySet GFFTools.readGFF(java.lang.String fileName)
          Deprecated. use: readGff(File)
static GFFEntrySet GFFTools.readGFF(java.lang.String fileName, GFFRecordFilter recFilt)
          Deprecated. use: readGff(File,GFFRecordFilter)
 

Methods in org.biojava.bio.program.gff with parameters of type GFFEntrySet
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(java.io.File outFile, GFFEntrySet ents)
          Writes a GFFEntrySet to a file.
static void GFFTools.writeGFF(java.io.PrintWriter pw, GFFEntrySet ents)
          Writes a GFFEntrySet to a PrintWriter.
static void GFFTools.writeGFF(java.lang.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
GFFDataSource(GFFEntrySet gffe)