Uses of Class
org.biojava3.genome.parsers.gff.FeatureList
Packages that use FeatureList
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Uses of FeatureList in org.biojava3.genome
Methods in org.biojava3.genome with parameters of type FeatureListModifier and TypeMethodDescriptionstatic voidGeneFeatureHelper.addGeneIDGFF2GeneFeatures(LinkedHashMap<String, ChromosomeSequence> chromosomeSequenceList, FeatureList listGenes) Load GFF2 feature file generated from the geneid prediction algorithm and map features onto the chromosome sequencesstatic voidGeneFeatureHelper.addGeneMarkGTFGeneFeatures(LinkedHashMap<String, ChromosomeSequence> chromosomeSequenceList, FeatureList listGenes) static voidGeneFeatureHelper.addGlimmerGFF3GeneFeatures(LinkedHashMap<String, ChromosomeSequence> chromosomeSequenceList, FeatureList listGenes) static voidGeneFeatureHelper.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.biojava3.genome.parsers.gff
Methods in org.biojava3.genome.parsers.gff that return FeatureListModifier and TypeMethodDescriptionFeatureList.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 FeatureListRead a file into a FeatureList.static FeatureListRead a file into a FeatureList.static FeatureListRead a file into a FeatureList.FeatureList.selectByAttribute(String key) Create a list of all features that include the specified attribute key.FeatureList.selectByAttribute(String key, String value) Create a list of all features that include the specified attribute key/value pair.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.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.selectByUserData(String key) Create a list of all features that include the specified key in their userMap().FeatureList.selectByUserData(String key, Object value) Create a list of all features that include the specified key/value pair in their userMap().FeatureList.selectOverlapping(String seqname, Location location, boolean useBothStrands) Create a list of all features that overlap the specified location on the specified sequence.FeatureList.sortByStart()Create a new list that is ordered by the starting index of the features' locations.Methods in org.biojava3.genome.parsers.gff that return types with arguments of type FeatureListModifier and TypeMethodDescriptionstatic 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.biojava3.genome.parsers.gff with parameters of type FeatureListModifier and TypeMethodDescriptionstatic 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 voidGeneIDGFF2Reader.write(FeatureList features, String filename) Write features in FeatureList to file.