Uses of Class
org.biojava.nbio.genome.parsers.gff.FeatureList

Packages that use FeatureList

Package	Description
org.biojava.nbio.genome
org.biojava.nbio.genome.parsers.gff

Uses of FeatureList in org.biojava.nbio.genome

Methods in org.biojava.nbio.genome with parameters of type FeatureList

Modifier and Type	Method	Description
static void	GeneFeatureHelper.addGeneIDGFF2GeneFeatures(Map<String,ChromosomeSequence> chromosomeSequenceList, FeatureList listGenes)	Load GFF2 feature file generated from the geneid prediction algorithm and map features onto the chromosome sequences
static void	GeneFeatureHelper.addGeneMarkGTFGeneFeatures(Map<String,ChromosomeSequence> chromosomeSequenceList, FeatureList listGenes)
static void	GeneFeatureHelper.addGlimmerGFF3GeneFeatures(Map<String,ChromosomeSequence> chromosomeSequenceList, FeatureList listGenes)
static void	GeneFeatureHelper.addGmodGFF3GeneFeatures(Map<String,ChromosomeSequence> chromosomeSequenceList, FeatureList listGenes)	Load GFF3 file using mRNA as the gene feature as not all GFF3 files are complete

Uses of FeatureList in org.biojava.nbio.genome.parsers.gff

Methods in org.biojava.nbio.genome.parsers.gff that return FeatureList

Modifier and Type	Method	Description
FeatureList	FeatureList.omitOverlapping(String seqname, Location location, boolean useBothStrands)	Create a list of all features that do not overlap the specified location on the specified sequence.
static FeatureList	GeneIDGFF2Reader.read(String filename)	Read a file into a FeatureList.
static FeatureList	GeneMarkGTFReader.read(String filename)	Read a file into a FeatureList.
static FeatureList	GFF3Reader.read(String filename)
static FeatureList	GFF3Reader.read(String filename, List<String> indexes)	Read a file into a FeatureList.
static FeatureList	GFF3Reader.read(Path path)
static FeatureList	GFF3Reader.read(Path path, List<String> indexes)	Read a file into a FeatureList.
FeatureList	FeatureList.selectByAttribute(String key)	Create a list of all features that include the specified attribute key.
FeatureList	FeatureList.selectByAttribute(String key, String value)	Create a list of all features that include the specified attribute key/value pair.
FeatureList	FeatureList.selectByGroup(String groupid)	Create a list of all features that have the specified group id, as defined by the group() method of the features.
FeatureList	FeatureList.selectByType(String type)	Create a list of all features that are of the specified type, as defined by the type() method of the features.
FeatureList	FeatureList.selectByUserData(String key)	Create a list of all features that include the specified key in their userMap().
FeatureList	FeatureList.selectByUserData(String key, Object value)	Create a list of all features that include the specified key/value pair in their userMap().
FeatureList	FeatureList.selectOverlapping(String seqname, Location location, boolean useBothStrands)	Create a list of all features that overlap the specified location on the specified sequence.
FeatureList	FeatureList.sortByStart()	Create a new list that is ordered by the starting index of the features' locations.

Methods in org.biojava.nbio.genome.parsers.gff that return types with arguments of type FeatureList

Modifier and Type	Method	Description
static LinkedHashMap<String,FeatureList>	FeatureHelper.buildFeatureAtrributeIndex(String attribute, FeatureList list)	Build a list of individual features to allow easy indexing and to avoid iterating through large genome gff3 files The index for the returned HashMap is the value of the attribute used to build the index

Methods in org.biojava.nbio.genome.parsers.gff with parameters of type FeatureList

Modifier and Type	Method	Description
static LinkedHashMap<String,FeatureList>	FeatureHelper.buildFeatureAtrributeIndex(String attribute, FeatureList list)	Build a list of individual features to allow easy indexing and to avoid iterating through large genome gff3 files The index for the returned HashMap is the value of the attribute used to build the index
static void	GeneIDGFF2Reader.write(FeatureList features, String filename)	Write features in FeatureList to file.