net.maizegenetics.dna.map

Class GenomeFeatureMap

net.maizegenetics.dna.map.GenomeFeatureMap

public class GenomeFeatureMap

Created by jgw87 on 7/2/14. A map to hold genome features for lookup by name and by location. The features themselves are hierarchical and so can be traced up and down the tree.

As methods are added to return based on different filters, try to unify the results. That is, all filter-like methods should return the same sort of data structure, such as a HashSet of GenomeFeatures. It may be worthwhile to create a custom GenomeFeatureSet class to be able to string such operations together (mygenes = mygenes.ofType("exon").onChrom(1).inRange(1, 10000);), although whether such filters are needed for the bulk of this class's purpose (matching SNPs to genome annotations) is yet to be seen. This class shouldn't be created directly, but should instead use the GenomeFeatureMapBuilder class .build() method

Method Detail

getFeatureFromId

public GenomeFeature getFeatureFromId(java.lang.String id)

getFeaturesInRange

public java.util.HashSet<net.maizegenetics.dna.map.GenomeFeature> getFeaturesInRange(java.lang.String chrom,
                                                                                     int start,
                                                                                     int end)

Get a HashSet of class GenomeFeatures at a specified genome location. Takes chromsome as a String for ones like "Pt", "scaffold487", etc.

Parameters:

chrom - The chromosome name

start - Beginning physical position

end - End physical position

Returns:

org.jetbrains.dokka.NodeRenderContent@5a64461e: A HashSet of GenomeFeatures

See Also:

class GenomeFeature

getFeaturesAtLocation

public java.util.HashSet<net.maizegenetics.dna.map.GenomeFeature> getFeaturesAtLocation(int chrom,
                                                                                        int position)

Get a HashSet of class GenomeFeatures at a specified genome location

Parameters:

chrom - Chromosome number (should be the same as its name)

position - Physical position (base pair)

Returns:

org.jetbrains.dokka.NodeRenderContent@3cf29139: A HashSet of GenomeFeatures

See Also:

class GenomeFeature

getFeaturesAtLocation

public java.util.HashSet<net.maizegenetics.dna.map.GenomeFeature> getFeaturesAtLocation(java.lang.String chrom,
                                                                                        int position)

Get a HashSet of class GenomeFeatures at a specified genome location Takes chromsome as a String for ones like "Pt", "scaffold487", etc.

Parameters:

chrom - Chromosome name

position - Physical position (base pair)

Returns:

org.jetbrains.dokka.NodeRenderContent@11324113: A HashSet of GenomeFeatures

See Also:

class GenomeFeature

getFeaturesInRange

public java.util.HashSet<net.maizegenetics.dna.map.GenomeFeature> getFeaturesInRange(int chrom,
                                                                                     int start,
                                                                                     int end)

Get a HashSet of class GenomeFeatures at a specified genome location. Takes chromsome as a String for ones like "Pt", "scaffold487", etc.

Parameters:

chrom - The chromosome number (should be the same as its name)

start - Beginning physical position

end - End physical position

Returns:

org.jetbrains.dokka.NodeRenderContent@54eba335: A HashSet of GenomeFeatures

See Also:

class GenomeFeature

getFeaturesOfType

public java.util.HashSet<net.maizegenetics.dna.map.GenomeFeature> getFeaturesOfType(java.lang.String type)

Get all class GenomeFeatures of a specified type

Parameters:

type - The type of feature to get

Returns:

org.jetbrains.dokka.NodeRenderContent@2c475b00: A HashSet of GenomeFeatures

See Also:

class GenomeFeature

writeLocationLookupToFile

public void writeLocationLookupToFile(java.lang.String filename)

Write just the location lookup to a tab-delimited file. This is mostly to check that your locations loaded properly, as there is no way to read them back in.

Parameters:

filename - The output file to be written to

writeMapAsJsonFile

public void writeMapAsJsonFile(java.lang.String filename)

Write the map data as a JSON file (which can be read in by class GenomeFeatureMapBuilder). Core attributes (unique ID, chromosome, start, stop, and parent ID) are output to all features. Any additional attributes are output only for those features that have them. Attributes are output in alphabetical order. Since the attribute name has to be output for every feature, this can waste space if all your features have the same attributes. In that case a tab-delimited flat file or precompiled binary file is probably a better choice.

Parameters:

filename - The output file to be written to

See Also:

class GenomeFeatureMapBuilder

writeMapAsFlatFile

public void writeMapAsFlatFile(java.lang.String filename)

Write the map data as a flat, tab-delimited file (which can be read in by class GenomeFeatureMapBuilder). The writer first compiles a set of all attribute types across the map and sets these as the columns (in alphabetical order). Attributes that don't apply to a given feature are output as "NA". This can end up being very wasteful if you have some attributes that only apply to a small percentage of features; in that case, a JSON or binary file is probably a better choice.

Parameters:

filename - The output file to be written to

See Also:

class GenomeFeatureMapBuilder

writeMapAsBinaryFile

public void writeMapAsBinaryFile(java.lang.String filename)

Write the map data as a precompiled binary that can be read back in by class GenomeFeatureMapBuilder). Unlike JSON or flatfile format, this file is not human-readable and is simply a a representation of the Java data structures saved onto a disk. This makes it very compact and fast to read back in. This is the preferred format for long-term storage of a class GenomeFeatureMap since there is (almost) no risk of someone accidentally modifying the file.

Parameters:

filename - The output file to be written to

See Also:

class GenomeFeatureMapBuilder, class GenomeFeatureMap