Index (biojava-genome 4.2.4 API)

A B C D E F G H I L M N O P R S T U V W

A

add(FeatureI) - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList: Add specified feature to the end of the list.
add(Collection<FeatureI>) - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList: Add all features in the specified list or collection to this list.
addGeneIDGFF2GeneFeatures(LinkedHashMap<String, ChromosomeSequence>, FeatureList) - Static method in class org.biojava.nbio.genome.GeneFeatureHelper: Load GFF2 feature file generated from the geneid prediction algorithm and map features onto the chromosome sequences
addGeneMarkGTFGeneFeatures(LinkedHashMap<String, ChromosomeSequence>, FeatureList) - Static method in class org.biojava.nbio.genome.GeneFeatureHelper
addGlimmerGFF3GeneFeatures(LinkedHashMap<String, ChromosomeSequence>, FeatureList) - Static method in class org.biojava.nbio.genome.GeneFeatureHelper
addGmodGFF3GeneFeatures(LinkedHashMap<String, ChromosomeSequence>, FeatureList) - Static method in class org.biojava.nbio.genome.GeneFeatureHelper: Load GFF3 file using mRNA as the gene feature as not all GFF3 files are complete
addIndex(String) - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList: Add an attribute that will be used as index for queries
addIndexes(List<String>) - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList: Add a list of attributes that will be used as indexes for queries
App - Class in org.biojava.nbio.genome: Hello world!
App() - Constructor for class org.biojava.nbio.genome.App
attributes() - Method in class org.biojava.nbio.genome.parsers.gff.Feature: Get the string of key/value attributes.
attributeValues(String) - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList: Create a collection of the unique values for the specified key.
available() - Method in class org.biojava.nbio.genome.parsers.twobit.TwoBitParser

B

bioEnd() - Method in class org.biojava.nbio.genome.parsers.gff.Location: Get end index, in biocoordinates.
bioStart() - Method in class org.biojava.nbio.genome.parsers.gff.Location: Get start index, in biocoordinates.
bioStrand() - Method in class org.biojava.nbio.genome.parsers.gff.Location: Get character representation of strand.
BlastHomologyHits - Class in org.biojava.nbio.genome.homology
BlastHomologyHits() - Constructor for class org.biojava.nbio.genome.homology.BlastHomologyHits
BlastXMLQuery - Class in org.biojava.nbio.genome.query
BlastXMLQuery(String) - Constructor for class org.biojava.nbio.genome.query.BlastXMLQuery
bounds() - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList: The union of all locations of all features in this list, mapped to the positive strand.
buildFeatureAtrributeIndex(String, FeatureList) - Static method in class org.biojava.nbio.genome.parsers.gff.FeatureHelper: 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

C

CDS - Static variable in class org.biojava.nbio.genome.util.ChromosomeMappingTools
CHROMOSOME - Static variable in class org.biojava.nbio.genome.util.ChromosomeMappingTools
ChromosomeMappingTools - Class in org.biojava.nbio.genome.util: A class that take care of the painful mapping
ChromosomeMappingTools() - Constructor for class org.biojava.nbio.genome.util.ChromosomeMappingTools
ChromPos - Class in org.biojava.nbio.genome.parsers.genename: Created by ap3 on 27/10/2014.
ChromPos(int, int) - Constructor for class org.biojava.nbio.genome.parsers.genename.ChromPos
close() - Method in class org.biojava.nbio.genome.parsers.twobit.TwoBitParser: Method closes current sequence and it's necessary to invoke it before setting new current sequence.
closeParser() - Method in class org.biojava.nbio.genome.parsers.twobit.TwoBitParser: Method closes random access file descriptor.
compareTo(Cytoband) - Method in class org.biojava.nbio.genome.parsers.cytoband.Cytoband
compareTo(GeneChromosomePosition) - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
compareTo(GeneName) - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
contains(Location) - Method in class org.biojava.nbio.genome.parsers.gff.Location: Check if this location contains the other.
Cytoband - Class in org.biojava.nbio.genome.parsers.cytoband
Cytoband() - Constructor for class org.biojava.nbio.genome.parsers.cytoband.Cytoband
CytobandParser - Class in org.biojava.nbio.genome.parsers.cytoband: Parses the cytoband (karyotype) file from UCSC.
CytobandParser() - Constructor for class org.biojava.nbio.genome.parsers.cytoband.CytobandParser

D

DEFAULT_BUFFER_SIZE - Variable in class org.biojava.nbio.genome.parsers.twobit.TwoBitParser
DEFAULT_GENENAMES_URL - Static variable in class org.biojava.nbio.genome.parsers.genename.GeneNamesParser
DEFAULT_LOCATION - Static variable in class org.biojava.nbio.genome.parsers.cytoband.CytobandParser
DEFAULT_MAPPING_URL - Static variable in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePositionParser
distance(Location) - Method in class org.biojava.nbio.genome.parsers.gff.Location: Return distance between this location and the other location.
downstream(int) - Method in class org.biojava.nbio.genome.parsers.gff.Location: Return the adjacent location of specified length directly downstream of this location.

E

end() - Method in class org.biojava.nbio.genome.parsers.gff.Location: Get the ending index.
endsAfter(Location) - Method in class org.biojava.nbio.genome.parsers.gff.Location: Check if this location ends after other location ends.
endsBefore(Location) - Method in class org.biojava.nbio.genome.parsers.gff.Location: Check if this location ends before other location ends.
equals(GeneName) - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
equals(Object) - Method in class org.biojava.nbio.genome.parsers.gff.Location

F

Feature - Class in org.biojava.nbio.genome.parsers.gff: A Feature corresponds to a single row in a GFF file.
Feature(Feature) - Constructor for class org.biojava.nbio.genome.parsers.gff.Feature: Make a copy of the specified feature.
Feature(String, String, String, Location, Double, int, String) - Constructor for class org.biojava.nbio.genome.parsers.gff.Feature: Construct a new Feature from raw data (usually a GFF row).
FeatureHelper - Class in org.biojava.nbio.genome.parsers.gff
FeatureHelper() - Constructor for class org.biojava.nbio.genome.parsers.gff.FeatureHelper
FeatureI - Interface in org.biojava.nbio.genome.parsers.gff: A feature on a sequence (for example, an exon or a gene), defined by a location and a set of attributes encoded as key/value pairs.
FeatureList - Class in org.biojava.nbio.genome.parsers.gff: A list of FeatureI objects implemented using a Java ArrayList; corresponds to a GFF file.
FeatureList() - Constructor for class org.biojava.nbio.genome.parsers.gff.FeatureList: Construct an empty list.
FeatureList(Collection<FeatureI>) - Constructor for class org.biojava.nbio.genome.parsers.gff.FeatureList: Construct a new list containing the same features as the specified list.
formatExonStructure(GeneChromosomePosition) - Static method in class org.biojava.nbio.genome.util.ChromosomeMappingTools: Pretty print the details of a GeneChromosomePosition to a String
frame() - Method in class org.biojava.nbio.genome.parsers.gff.Feature: Get frame (aka phase).
fromBio(int, int, char) - Static method in class org.biojava.nbio.genome.parsers.gff.Location: Create location from "biocoordinates", as in GFF file.
fromBioExt(int, int, char, int) - Static method in class org.biojava.nbio.genome.parsers.gff.Location: Create a location from MAF file coordinates, which represent negative strand locations as the distance from the end of the sequence.

G

GCStats - Class in org.biojava.nbio.genome.parsers.gff
GCStats() - Constructor for class org.biojava.nbio.genome.parsers.gff.GCStats
GeneChromosomePosition - Class in org.biojava.nbio.genome.parsers.genename
GeneChromosomePosition() - Constructor for class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
GeneChromosomePositionParser - Class in org.biojava.nbio.genome.parsers.genename: A parser that parses a file from the UCSC genome browser that contains mapping of gene name to chromosome positions
GeneChromosomePositionParser() - Constructor for class org.biojava.nbio.genome.parsers.genename.GeneChromosomePositionParser
GeneFeatureHelper - Class in org.biojava.nbio.genome
GeneFeatureHelper() - Constructor for class org.biojava.nbio.genome.GeneFeatureHelper
GeneIDGFF2Reader - Class in org.biojava.nbio.genome.parsers.gff: http://www.bioperl.org/wiki/GTF Read and write FeatureLists as GFF/GTF formatted files.
GeneIDGFF2Reader() - Constructor for class org.biojava.nbio.genome.parsers.gff.GeneIDGFF2Reader
GeneIDXMLReader - Class in org.biojava.nbio.genome.parsers.geneid
GeneIDXMLReader(String) - Constructor for class org.biojava.nbio.genome.parsers.geneid.GeneIDXMLReader
GeneMarkGTFReader - Class in org.biojava.nbio.genome.parsers.gff: http://www.bioperl.org/wiki/GTF Read and write FeatureLists as GFF/GTF formatted files.
GeneMarkGTFReader() - Constructor for class org.biojava.nbio.genome.parsers.gff.GeneMarkGTFReader
GeneName - Class in org.biojava.nbio.genome.parsers.genename: A simple bean that contains gene name information as available from www.genenames.org
GeneName() - Constructor for class org.biojava.nbio.genome.parsers.genename.GeneName
GeneNamesParser - Class in org.biojava.nbio.genome.parsers.genename: Parses a file from the www.genenames.org website that contains a mapping of human gene names to other databases
GeneNamesParser() - Constructor for class org.biojava.nbio.genome.parsers.genename.GeneNamesParser
getAccessionNr() - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
getAllCytobands(URL) - Method in class org.biojava.nbio.genome.parsers.cytoband.CytobandParser
getAllCytobands(InputStream) - Method in class org.biojava.nbio.genome.parsers.cytoband.CytobandParser
getApprovedName() - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
getApprovedSymbol() - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
getAttribute(String) - Method in class org.biojava.nbio.genome.parsers.gff.Feature: Get value of specified attribute key.
getAttribute(String) - Method in interface org.biojava.nbio.genome.parsers.gff.FeatureI: Get the attribute value for this key.
getAttributeOld(String) - Method in class org.biojava.nbio.genome.parsers.gff.Feature
getAttributes() - Method in class org.biojava.nbio.genome.parsers.gff.Feature
getAttributes() - Method in interface org.biojava.nbio.genome.parsers.gff.FeatureI
getBegin() - Method in class org.biojava.nbio.genome.parsers.gff.Location
getCdsEnd() - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
getCDSExonRanges(GeneChromosomePosition) - Static method in class org.biojava.nbio.genome.util.ChromosomeMappingTools: Extracts the exon boundaries in CDS coordinates.
getCDSLength(GeneChromosomePosition) - Static method in class org.biojava.nbio.genome.util.ChromosomeMappingTools: Get the length of the CDS in nucleotides.
getCDSLengthForward(List<Integer>, List<Integer>, int, int) - Static method in class org.biojava.nbio.genome.util.ChromosomeMappingTools: Get the length of the coding sequence
getCDSLengthReverse(List<Integer>, List<Integer>, int, int) - Static method in class org.biojava.nbio.genome.util.ChromosomeMappingTools: Get the length of the coding sequence
getCDSPosForChromosomeCoordinate(int, GeneChromosomePosition) - Static method in class org.biojava.nbio.genome.util.ChromosomeMappingTools: I have a genomic coordinate, where is it in the Gene?
getCDSPosForward(int, List<Integer>, List<Integer>, int, int) - Static method in class org.biojava.nbio.genome.util.ChromosomeMappingTools: Get the chromosome position mapped onto the mrna CDS transcript position (needs to be divided by 3 to get protein coordinate)
getCDSPosReverse(int, List<Integer>, List<Integer>, int, int) - Static method in class org.biojava.nbio.genome.util.ChromosomeMappingTools
getCdsStart() - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
getChromosomalRangesForCDS(GeneChromosomePosition) - Static method in class org.biojava.nbio.genome.util.ChromosomeMappingTools: Extracts the boundaries of the coding regions in chromosomal coordinates
getChromosome() - Method in class org.biojava.nbio.genome.parsers.cytoband.Cytoband
getChromosome() - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
getChromosome() - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
getChromosomeMappings() - Static method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePositionParser
getChromosomeMappings(InputStream) - Static method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePositionParser
getChromosomePosForCDScoordinate(int, GeneChromosomePosition) - Static method in class org.biojava.nbio.genome.util.ChromosomeMappingTools: maps the position of a CDS nucleotide back to the genome
getChromosomeSequenceFromDNASequence(LinkedHashMap<String, DNASequence>) - Static method in class org.biojava.nbio.genome.GeneFeatureHelper
getChromPosForward(int, List<Integer>, List<Integer>, int, int) - Static method in class org.biojava.nbio.genome.util.ChromosomeMappingTools: Get the CDS position mapped onto the chromosome position
getChromPosReverse(int, List<Integer>, List<Integer>, int, int) - Static method in class org.biojava.nbio.genome.util.ChromosomeMappingTools: Get the CDS position mapped on the chromosome position
getCurrentSequencePosition() - Method in class org.biojava.nbio.genome.parsers.twobit.TwoBitParser
getDNACodingSequences() - Method in class org.biojava.nbio.genome.parsers.geneid.GeneIDXMLReader
getEnd() - Method in class org.biojava.nbio.genome.parsers.cytoband.Cytoband
getEnd() - Method in class org.biojava.nbio.genome.parsers.gff.Location
getEnsemblGeneId() - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
getExonCount() - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
getExonEnds() - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
getExonStarts() - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
getFile() - Method in class org.biojava.nbio.genome.parsers.twobit.TwoBitParser
getGCStats(Collection<DNASequence>) - Static method in class org.biojava.nbio.genome.parsers.gff.GCStats
getGCStatsString(Collection<String>) - Static method in class org.biojava.nbio.genome.parsers.gff.GCStats
getGenebankId() - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
getGeneName() - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
getGeneNames() - Static method in class org.biojava.nbio.genome.parsers.genename.GeneNamesParser
getGeneNames(InputStream) - Static method in class org.biojava.nbio.genome.parsers.genename.GeneNamesParser: Get a list of GeneNames from an input stream.
getGeneSequences(Collection<ChromosomeSequence>) - Static method in class org.biojava.nbio.genome.GeneFeatureHelper
getHgncId() - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
getHitsQueryDef(double) - Method in class org.biojava.nbio.genome.query.BlastXMLQuery
getLocus() - Method in class org.biojava.nbio.genome.parsers.cytoband.Cytoband
getMatches(File, double) - Static method in class org.biojava.nbio.genome.homology.BlastHomologyHits
getOmimId() - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
getOrientation() - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
getPhase() - Method in class org.biojava.nbio.genome.parsers.genename.ChromPos
getPos() - Method in class org.biojava.nbio.genome.parsers.genename.ChromPos
getPreviousNames() - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
getPreviousSymbols() - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
getProteinSequences(Collection<ChromosomeSequence>) - Static method in class org.biojava.nbio.genome.GeneFeatureHelper
getProteinSequences() - Method in class org.biojava.nbio.genome.parsers.geneid.GeneIDXMLReader
getRefseqIds() - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
getSequenceNames() - Method in class org.biojava.nbio.genome.parsers.twobit.TwoBitParser
getStainTypeFromString(String) - Static method in enum org.biojava.nbio.genome.parsers.cytoband.StainType
getStart() - Method in class org.biojava.nbio.genome.parsers.cytoband.Cytoband
getStatus() - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
getSynonyms() - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
getTranscriptionEnd() - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
getTranscriptionStart() - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
getType() - Method in class org.biojava.nbio.genome.parsers.cytoband.Cytoband
getUniprot() - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
GFF3FromUniprotBlastHits - Class in org.biojava.nbio.genome.homology
GFF3FromUniprotBlastHits() - Constructor for class org.biojava.nbio.genome.homology.GFF3FromUniprotBlastHits
GFF3Reader - Class in org.biojava.nbio.genome.parsers.gff: http://www.bioperl.org/wiki/GTF Read and write FeatureLists as GFF/GTF formatted files.
GFF3Reader() - Constructor for class org.biojava.nbio.genome.parsers.gff.GFF3Reader
GFF3Writer - Class in org.biojava.nbio.genome.parsers.gff
GFF3Writer() - Constructor for class org.biojava.nbio.genome.parsers.gff.GFF3Writer
group() - Method in class org.biojava.nbio.genome.parsers.gff.Feature: Get the first item (everything before first semicolon, if it has one) in the attribute field, which is assumed to be a group identifer.
group() - Method in interface org.biojava.nbio.genome.parsers.gff.FeatureI: Get the group id of the feature.
groupValues() - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList: Create a collection of all unique group ids in the list, as defined by the group() method of the features.

H

hasAttribute(String) - Method in class org.biojava.nbio.genome.parsers.gff.Feature
hasAttribute(String, String) - Method in class org.biojava.nbio.genome.parsers.gff.Feature
hasAttribute(String) - Method in interface org.biojava.nbio.genome.parsers.gff.FeatureI: Check if the feature has a value defined for the specified key.
hasAttribute(String, String) - Method in interface org.biojava.nbio.genome.parsers.gff.FeatureI: Check if the feature attributes include the specified key/value pair.
hasAttribute(String) - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList: Check if any feature in list has the specified attribute key.
hasAttribute(String, String) - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList: Check if any feature in list has the specified attribute key/value pair.
hasGaps(int) - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList: Check size of gaps between successive features in list.
hashCode() - Method in class org.biojava.nbio.genome.parsers.gff.Location
hasNext(int, int) - Method in class org.biojava.nbio.genome.parsers.gff.LocIterator: Check if next window of specified size is available.
hasNext() - Method in class org.biojava.nbio.genome.parsers.gff.LocIterator: Check if next window of default size is available.

I

intersection(Location) - Method in class org.biojava.nbio.genome.parsers.gff.Location: Return the intersection, or null if no overlap.
isAfter(Location) - Method in class org.biojava.nbio.genome.parsers.gff.Location: Check if this location is entirely after the other location (no overlap).
isBefore(Location) - Method in class org.biojava.nbio.genome.parsers.gff.Location: Check if this location is entirely before other location (no overlap).
isNegative() - Method in class org.biojava.nbio.genome.parsers.gff.Location: Check if location is on negative strand.
isSameStrand(Location) - Method in class org.biojava.nbio.genome.parsers.gff.Location: Check if this location is on same strand as other location.
iterator() - Method in class org.biojava.nbio.genome.parsers.gff.Location: Create a location iterator over this location with a window size of 1 and an increment of +1 (successive symbols from start to end).
iterator(int, int) - Method in class org.biojava.nbio.genome.parsers.gff.Location: Create a location iterator over this location, using specified window size and increment.

L

length() - Method in class org.biojava.nbio.genome.parsers.gff.Location: Get length of range.
loadFastaAddGeneFeaturesFromGeneIDGFF2(File, File) - Static method in class org.biojava.nbio.genome.GeneFeatureHelper: Loads Fasta file and GFF2 feature file generated from the geneid prediction algorithm
loadFastaAddGeneFeaturesFromGeneMarkGTF(File, File) - Static method in class org.biojava.nbio.genome.GeneFeatureHelper
loadFastaAddGeneFeaturesFromGlimmerGFF3(File, File) - Static method in class org.biojava.nbio.genome.GeneFeatureHelper
loadFastaAddGeneFeaturesFromGmodGFF3(File, File, boolean) - Static method in class org.biojava.nbio.genome.GeneFeatureHelper: Lots of variations in the ontology or descriptors that can be used in GFF3 which requires writing a custom parser to handle a GFF3 generated or used by a specific application.
loadFastaAddGeneFeaturesFromUpperCaseExonFastaFile(File, File, boolean) - Static method in class org.biojava.nbio.genome.GeneFeatureHelper
loadFragment(long, int) - Method in class org.biojava.nbio.genome.parsers.twobit.TwoBitParser
location() - Method in class org.biojava.nbio.genome.parsers.gff.Feature: Get location of feature.
location() - Method in interface org.biojava.nbio.genome.parsers.gff.FeatureI: Get the location of the feature.
Location - Class in org.biojava.nbio.genome.parsers.gff: A location on a sequence.
Location(int, int) - Constructor for class org.biojava.nbio.genome.parsers.gff.Location: Construct new location from coordinates.
Location(Location) - Constructor for class org.biojava.nbio.genome.parsers.gff.Location: Clone other location.
LocIterator - Class in org.biojava.nbio.genome.parsers.gff: Move a sliding window over a Location.
LocIterator(Location, int, int) - Constructor for class org.biojava.nbio.genome.parsers.gff.LocIterator: Construct an iterator that slides a window over a Location.

M

main(String[]) - Static method in class org.biojava.nbio.genome.App
main(String[]) - Static method in class org.biojava.nbio.genome.GeneFeatureHelper
main(String[]) - Static method in class org.biojava.nbio.genome.homology.GFF3FromUniprotBlastHits
main(String[]) - Static method in class org.biojava.nbio.genome.parsers.cytoband.CytobandParser
main(String[]) - Static method in class org.biojava.nbio.genome.parsers.geneid.GeneIDXMLReader
main(String[]) - Static method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePositionParser
main(String[]) - Static method in class org.biojava.nbio.genome.parsers.genename.GeneNamesParser: parses a file from the genenames website
main(String[]) - Static method in class org.biojava.nbio.genome.parsers.gff.Feature: Deprecated.
main(String[]) - Static method in class org.biojava.nbio.genome.parsers.gff.FeatureList: Deprecated.
main(String[]) - Static method in class org.biojava.nbio.genome.parsers.gff.GeneIDGFF2Reader
main(String[]) - Static method in class org.biojava.nbio.genome.parsers.gff.GeneMarkGTFReader
main(String[]) - Static method in class org.biojava.nbio.genome.parsers.gff.GFF3Reader
main(String[]) - Static method in class org.biojava.nbio.genome.parsers.gff.GFF3Writer
main(String[]) - Static method in class org.biojava.nbio.genome.parsers.gff.Location: Deprecated.
main(String[]) - Static method in class org.biojava.nbio.genome.parsers.gff.LocIterator: Deprecated.
main(String[]) - Static method in class org.biojava.nbio.genome.parsers.twobit.TwoBitParser
main(String[]) - Static method in class org.biojava.nbio.genome.query.BlastXMLQuery
main(String[]) - Static method in class org.biojava.nbio.genome.query.OutputHitsGFF
main(String[]) - Static method in class org.biojava.nbio.genome.uniprot.UniprotToFasta
main(String[]) - Static method in class org.biojava.nbio.genome.util.SplitFasta
minus() - Method in class org.biojava.nbio.genome.parsers.gff.Location: Return location that is in same position on negative strand.

N

next() - Method in class org.biojava.nbio.genome.parsers.gff.LocIterator: Get next window of default size, then increment position by default amount.
next(int, int) - Method in class org.biojava.nbio.genome.parsers.gff.LocIterator: Get next window of specified size, then increment position by specified amount.

O

omitOverlapping(String, Location, boolean) - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList: Create a list of all features that do not overlap the specified location on the specified sequence.
opposite() - Method in class org.biojava.nbio.genome.parsers.gff.Location: Return location that is in same position on opposite strand.
org.biojava.nbio.genome - package org.biojava.nbio.genome
org.biojava.nbio.genome.homology - package org.biojava.nbio.genome.homology
org.biojava.nbio.genome.parsers.cytoband - package org.biojava.nbio.genome.parsers.cytoband
org.biojava.nbio.genome.parsers.geneid - package org.biojava.nbio.genome.parsers.geneid
org.biojava.nbio.genome.parsers.genename - package org.biojava.nbio.genome.parsers.genename
org.biojava.nbio.genome.parsers.gff - package org.biojava.nbio.genome.parsers.gff
org.biojava.nbio.genome.parsers.twobit - package org.biojava.nbio.genome.parsers.twobit
org.biojava.nbio.genome.query - package org.biojava.nbio.genome.query
org.biojava.nbio.genome.uniprot - package org.biojava.nbio.genome.uniprot
org.biojava.nbio.genome.util - package org.biojava.nbio.genome.util
outputFastaSequenceLengthGFF3(File, File) - Static method in class org.biojava.nbio.genome.GeneFeatureHelper: Output a gff3 feature file that will give the length of each scaffold/chromosome in the fasta file.
OutputHitsGFF - Class in org.biojava.nbio.genome.query
OutputHitsGFF() - Constructor for class org.biojava.nbio.genome.query.OutputHitsGFF
overlaps(Location) - Method in class org.biojava.nbio.genome.parsers.gff.Location: Check if this location and other location overlap.

P

percentOverlap(Location) - Method in class org.biojava.nbio.genome.parsers.gff.Location: Return percent overlap of two locations.
plus() - Method in class org.biojava.nbio.genome.parsers.gff.Location: Return location that is in same position on plus strand.
prefix(int) - Method in class org.biojava.nbio.genome.parsers.gff.Location: The part of this location before the specified position.
prefix(Location) - Method in class org.biojava.nbio.genome.parsers.gff.Location: The part of this location before the other location (not inclusive).
printFastaSequence() - Method in class org.biojava.nbio.genome.parsers.twobit.TwoBitParser
printFastaSequence(long) - Method in class org.biojava.nbio.genome.parsers.twobit.TwoBitParser
process(File, double, LinkedHashMap<String, GeneSequence>, OutputStream) - Method in class org.biojava.nbio.genome.homology.GFF3FromUniprotBlastHits
process(LinkedHashMap<String, ArrayList<String>>, LinkedHashMap<String, GeneSequence>, OutputStream) - Method in class org.biojava.nbio.genome.homology.GFF3FromUniprotBlastHits
process(File, File, File, double, double, boolean, boolean) - Method in class org.biojava.nbio.genome.query.OutputHitsGFF
process(String, String) - Method in class org.biojava.nbio.genome.uniprot.UniprotToFasta: Convert a Uniprot sequence file to a fasta file.
processNucleotides(File, String, File) - Method in class org.biojava.nbio.genome.util.SplitFasta

R

read(String) - Static method in class org.biojava.nbio.genome.parsers.gff.GeneIDGFF2Reader: Read a file into a FeatureList.
read(String) - Static method in class org.biojava.nbio.genome.parsers.gff.GeneMarkGTFReader: Read a file into a FeatureList.
read(String, List<String>) - Static method in class org.biojava.nbio.genome.parsers.gff.GFF3Reader: Read a file into a FeatureList.
read(String) - Static method in class org.biojava.nbio.genome.parsers.gff.GFF3Reader
read() - Method in class org.biojava.nbio.genome.parsers.twobit.TwoBitParser: Method reads 1 nucleotide from sequence stream.
remainder() - Method in class org.biojava.nbio.genome.parsers.gff.LocIterator: Get portion of bounding location that has not yet been retrieved by next() method.
remove() - Method in class org.biojava.nbio.genome.parsers.gff.LocIterator: Unsupported.
reset() - Method in class org.biojava.nbio.genome.parsers.twobit.TwoBitParser: Method resets current position to the begining of sequence stream.

S

score() - Method in class org.biojava.nbio.genome.parsers.gff.Feature: Get score.
selectByAttribute(String, String) - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList: Create a list of all features that include the specified attribute key/value pair.
selectByAttribute(String) - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList: Create a list of all features that include the specified attribute key.
selectByGroup(String) - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList: Create a list of all features that have the specified group id, as defined by the group() method of the features.
selectByType(String) - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList: Create a list of all features that are of the specified type, as defined by the type() method of the features.
selectByUserData(String, Object) - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList: Create a list of all features that include the specified key/value pair in their userMap().
selectByUserData(String) - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList: Create a list of all features that include the specified key in their userMap().
selectOverlapping(String, Location, boolean) - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList: Create a list of all features that overlap the specified location on the specified sequence.
seqname() - Method in class org.biojava.nbio.genome.parsers.gff.Feature: Get the sequence name.
seqname() - Method in interface org.biojava.nbio.genome.parsers.gff.FeatureI: Get the sequence name.
setAccessionNr(String) - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
setApprovedName(String) - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
setApprovedSymbol(String) - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
setCdsEnd(Integer) - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
setCdsStart(Integer) - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
setChromosome(String) - Method in class org.biojava.nbio.genome.parsers.cytoband.Cytoband
setChromosome(String) - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
setChromosome(String) - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
setCurrentSequence(String) - Method in class org.biojava.nbio.genome.parsers.twobit.TwoBitParser: Method open nucleotide stream for sequence with given name.
setCurrentSequencePosition(long) - Method in class org.biojava.nbio.genome.parsers.twobit.TwoBitParser
setEnd(Integer) - Method in class org.biojava.nbio.genome.parsers.cytoband.Cytoband
setEnsemblGeneId(String) - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
setExonCount(int) - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
setExonEnds(List<Integer>) - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
setExonStarts(List<Integer>) - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
setGenebankId(String) - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
setGeneName(String) - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
setHgncId(String) - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
setLocus(String) - Method in class org.biojava.nbio.genome.parsers.cytoband.Cytoband
setOmimId(String) - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
setOrientation(Character) - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
setPhase(int) - Method in class org.biojava.nbio.genome.parsers.genename.ChromPos
setPos(int) - Method in class org.biojava.nbio.genome.parsers.genename.ChromPos
setPreviousNames(String) - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
setPreviousSymbols(String) - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
setRefseqIds(String) - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
setStart(Integer) - Method in class org.biojava.nbio.genome.parsers.cytoband.Cytoband
setStatus(String) - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
setSynonyms(String) - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
setTranscriptionEnd(Integer) - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
setTranscriptionStart(Integer) - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
setType(StainType) - Method in class org.biojava.nbio.genome.parsers.cytoband.Cytoband
setUniprot(String) - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
skip(long) - Method in class org.biojava.nbio.genome.parsers.twobit.TwoBitParser: Method skips n nucleotides in sequence stream.
sortByStart() - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList: Create a new list that is ordered by the starting index of the features' locations.
source() - Method in class org.biojava.nbio.genome.parsers.gff.Feature: Get source (aka method).
splice(DNASequence) - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList: Concatenate successive portions of the specified sequence using the feature locations in the list.
SplitFasta - Class in org.biojava.nbio.genome.util: Utility to write each Fasta entry to a unique file
SplitFasta() - Constructor for class org.biojava.nbio.genome.util.SplitFasta
StainType - Enum in org.biojava.nbio.genome.parsers.cytoband
start() - Method in class org.biojava.nbio.genome.parsers.gff.Location: Get starting index (origin 0).
startsAfter(Location) - Method in class org.biojava.nbio.genome.parsers.gff.Location: Check if this location starts after the other location starts.
startsBefore(Location) - Method in class org.biojava.nbio.genome.parsers.gff.Location: Check if this location starts before other location starts.
suffix(int) - Method in class org.biojava.nbio.genome.parsers.gff.Location: The part of this location after the specified position.
suffix(Location) - Method in class org.biojava.nbio.genome.parsers.gff.Location: The part of this location after the other location (not inclusive).

T

toString() - Method in class org.biojava.nbio.genome.parsers.cytoband.Cytoband
toString() - Method in class org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition
toString() - Method in class org.biojava.nbio.genome.parsers.genename.GeneName
toString() - Method in class org.biojava.nbio.genome.parsers.gff.Feature
toString() - Method in interface org.biojava.nbio.genome.parsers.gff.FeatureI: A string representation of the feature.
toString() - Method in class org.biojava.nbio.genome.parsers.gff.FeatureList: Return a string representation of all features in this list.
toString() - Method in class org.biojava.nbio.genome.parsers.gff.Location: Return a string representation of location.
toString() - Method in class org.biojava.nbio.genome.parsers.gff.LocIterator: Get string representation of iterator.
TwoBitParser - Class in org.biojava.nbio.genome.parsers.twobit: downloaded from http://storage.bioinf.fbb.msu.ru/~roman/TwoBitParser.java Class is a parser of UCSC Genome Browser file format .2bit used to store nucleotide sequence information.
TwoBitParser(File) - Constructor for class org.biojava.nbio.genome.parsers.twobit.TwoBitParser
type - Variable in enum org.biojava.nbio.genome.parsers.cytoband.StainType
type() - Method in class org.biojava.nbio.genome.parsers.gff.Feature: Get feature type, such as "exon" or "CDS".
type() - Method in interface org.biojava.nbio.genome.parsers.gff.FeatureI: Get the feature type, for example, "exon", "CDS", etc.

U

union(Location) - Method in class org.biojava.nbio.genome.parsers.gff.Location: Return the union.
UniprotToFasta - Class in org.biojava.nbio.genome.uniprot
UniprotToFasta() - Constructor for class org.biojava.nbio.genome.uniprot.UniprotToFasta
upstream(int) - Method in class org.biojava.nbio.genome.parsers.gff.Location: Return the adjacent location of specified length directly upstream of this location.
userData() - Method in class org.biojava.nbio.genome.parsers.gff.Feature: Get HashMap of user data.
userData() - Method in interface org.biojava.nbio.genome.parsers.gff.FeatureI: Get HashMap of user data.

V

valueOf(String) - Static method in enum org.biojava.nbio.genome.parsers.cytoband.StainType: Returns the enum constant of this type with the specified name.
values() - Static method in enum org.biojava.nbio.genome.parsers.cytoband.StainType: Returns an array containing the constants of this enum type, in the order they are declared.

W

window(int, int) - Method in class org.biojava.nbio.genome.parsers.gff.Location: Enable a "sliding window" iteration over a location to use with Java's "for" loop construct.
write(FeatureList, String) - Static method in class org.biojava.nbio.genome.parsers.gff.GeneIDGFF2Reader: Write features in FeatureList to file.
write(OutputStream, LinkedHashMap<String, ChromosomeSequence>) - Method in class org.biojava.nbio.genome.parsers.gff.GFF3Writer: Output gff3 format for a DNA Sequence

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