Uses of Class
org.biojava.nbio.genome.parsers.gff.FeatureList
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Packages that use FeatureList Package Description org.biojava.nbio.genome org.biojava.nbio.genome.parsers.gff -
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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(LinkedHashMap<String,ChromosomeSequence> chromosomeSequenceList, FeatureList listGenes)
Load GFF2 feature file generated from the geneid prediction algorithm and map features onto the chromosome sequencesstatic void
GeneFeatureHelper. addGeneMarkGTFGeneFeatures(LinkedHashMap<String,ChromosomeSequence> chromosomeSequenceList, FeatureList listGenes)
static void
GeneFeatureHelper. addGlimmerGFF3GeneFeatures(LinkedHashMap<String,ChromosomeSequence> chromosomeSequenceList, FeatureList listGenes)
static void
GeneFeatureHelper. addGmodGFF3GeneFeatures(LinkedHashMap<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.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 indexMethods 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 indexstatic void
GeneIDGFF2Reader. write(FeatureList features, String filename)
Write features in FeatureList to file.
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