net.maizegenetics.pangenome.db_loading

Interface PHGData

All Known Subinterfaces:

PHGDataWriter

All Known Implementing Classes:

PHGdbAccess

public interface PHGData

Author:

lcj34

Method Summary

Modifier and Type	Method and Description
List<String>	getChromNamesForHaplotype(String line_name, int hap_number, String version) Method grabs a list of distinct chromosome names for a genome_interval version
int	getGameteGroupIDFromTaxaList(List<String> gametes) Takes a list of taxa and returns the corresponding gamete_group_id or 0
int	getGenoidFromLine(String line_name) Return genoid
Map<Integer,net.maizegenetics.util.Tuple<String,byte[]>>	getHapCountsIDAndDataForVersionMethod(String method) This method pulls the haplotype_counts_id with corresponding genotypes line name and data for all DB entries based on the supplied method
Map<Integer,byte[]>	getHapCountsIDAndPathsForMethod(String method) THis method pulls the haplotype_counts_id and corresponding path for all entries in the paths table with the specified method.
int	getHapidForGenoidHapNumber(int genoid, int hap_number) Returns hapid for given line name and hap_number
Map<Integer,String>	getHapidHapNumberLineNamesForLines(List<String> lineNames) Retrieves line name and hapnumber, and returns them with the hapid.
Map<String,Integer>	getHapidMapFromLinenameHapNumber() Returns a map of created from the genotypes and haplotypes table.
List<Integer>	getHapidsForGenoid(int genoid) Returns list of hapids for a given line name
int	getHaplotypeIDFromFastaIDLine(String idLine, String methodName) Returns the haplotype_id from the haplotypes table based on the gamete_grp_id (calculated from the taxa list), the ref_range_id (calculated from the ref coordinates part of the idline) and the method.
com.google.common.collect.RangeMap<net.maizegenetics.dna.map.Position,Integer>	getIntervalRangesWithIDForChrom(String chrom) Returns sorted treeRangeMap of Positions for specified chromosome
net.maizegenetics.util.Tuple<String,Integer>	getLineNameHapNumberFromHapid(int hapid) Method to retrieve both a line name and the hap number given a hapid.
int	getMethodIdFromName(String method_name) Returns method_id given a method name.
int	getRefRangeIDFromString(String refData) Returns reference range id

Method Detail

getGenoidFromLine

int getGenoidFromLine(String line_name)

Return genoid

Parameters:

line_name -

Returns:

getHapidForGenoidHapNumber

int getHapidForGenoidHapNumber(int genoid,
                               int hap_number)

Returns hapid for given line name and hap_number

Parameters:

line_name -

Returns:

getHapidsForGenoid

List<Integer> getHapidsForGenoid(int genoid)

Returns list of hapids for a given line name

Parameters:

genoid -

Returns:

getLineNameHapNumberFromHapid

net.maizegenetics.util.Tuple<String,Integer> getLineNameHapNumberFromHapid(int hapid)

Method to retrieve both a line name and the hap number given a hapid.

Parameters:

hapid -

Returns:

Tuple consisting of Tuple

getHapidHapNumberLineNamesForLines

Map<Integer,String> getHapidHapNumberLineNamesForLines(List<String> lineNames)

Retrieves line name and hapnumber, and returns them with the hapid. hapid is the key in the map. THe line name and hap number are concatenated with an underscore and returned as the string value for each hapid.

Parameters:

lineNames -

Returns:

getChromNamesForHaplotype

List<String> getChromNamesForHaplotype(String line_name,
                                       int hap_number,
                                       String version)

Method grabs a list of distinct chromosome names for a genome_interval version

Parameters:

line_name -

hap_number -

version - Version name for anchors

Returns:

getMethodIdFromName

int getMethodIdFromName(String method_name)

Returns method_id given a method name. or 0 if no id found for the given name

Parameters:

method_name -

Returns:

getHapidMapFromLinenameHapNumber

Map<String,Integer> getHapidMapFromLinenameHapNumber()

Returns a map of created from the genotypes and haplotypes table.

Returns:

getGameteGroupIDFromTaxaList

int getGameteGroupIDFromTaxaList(List<String> gametes)

Takes a list of taxa and returns the corresponding gamete_group_id or 0

Parameters:

gametes - Items on the list must be of the form taxon_hapNumber

Returns:

getRefRangeIDFromString

int getRefRangeIDFromString(String refData)

Returns reference range id

Parameters:

refData - needs to be of form chr1:startpos:endPos

Returns:

getHaplotypeIDFromFastaIDLine

int getHaplotypeIDFromFastaIDLine(String idLine,
                                  String methodName)

Returns the haplotype_id from the haplotypes table based on the gamete_grp_id (calculated from the taxa list), the ref_range_id (calculated from the ref coordinates part of the idline) and the method.

Parameters:

idLine - expected form: refchr:refStartPos:refEndPos;taxa_hapnumber:taxa_hapnumber:etc

methodName - This is the method used for creating the haplotypes

Returns:

getIntervalRangesWithIDForChrom

com.google.common.collect.RangeMap<net.maizegenetics.dna.map.Position,Integer> getIntervalRangesWithIDForChrom(String chrom)

Returns sorted treeRangeMap of Positions for specified chromosome

Parameters:

chrom -

Returns:

getHapCountsIDAndPathsForMethod

Map<Integer,byte[]> getHapCountsIDAndPathsForMethod(String method)

THis method pulls the haplotype_counts_id and corresponding path for all entries in the paths table with the specified method.

Parameters:

method -

Returns:

Map of Haplotype_counts_id/paths

getHapCountsIDAndDataForVersionMethod

Map<Integer,net.maizegenetics.util.Tuple<String,byte[]>> getHapCountsIDAndDataForVersionMethod(String method)

This method pulls the haplotype_counts_id with corresponding genotypes line name and data for all DB entries based on the supplied method

Parameters:

method -

Returns:

Map of from haplotype_counts table