net.maizegenetics.pangenome.db_loading

Class PHGdbAccess

java.lang.Object

net.maizegenetics.pangenome.db_loading.PHGdbAccess

All Implemented Interfaces:

AutoCloseable, PHGData, PHGDataWriter

public class PHGdbAccess
extends Object
implements PHGDataWriter, AutoCloseable

Access methods for postgres or SQL PHG dbs. WHen making changes, or adding new methods, test the SQL statements in both PostgreSQL and SQL to ensure compatibility.

Author:

lcj34

Constructor Summary

Constructors

Constructor and Description
PHGdbAccess(Connection dbConnection)

Method Summary

Modifier and Type	Method and Description
void	close()
int	createRefRangeGroup(String method) Creates an entry in the ref_range_groups table using method_id associated with the name indicated via the method parameter.
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 gameteid) 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
boolean	putAllAnchors(List<AnchorDataPHG> adata, String refGroupMethod) Stores chrom, start pos, end pos to referenece_ranges table isFocus identifies focus intervals from the user's bed file
boolean	putAssemblyInterAnchorSequences(String line_name, int hapNumber, String method, com.google.common.collect.Multimap<Integer,AnchorDataPHG> anchorSequences) Adds inter-anchor sequences for the specified assembly to the anchor_sequences and anchor_haplotypes table.
void	putConsensusSequences(com.google.common.collect.Multimap<net.maizegenetics.dna.map.Position,net.maizegenetics.util.Tuple<AnchorDataPHG,List<String>>> consensusMap, int method_id) This method takes a map of consensus data, finds the anchorIds based on Position, finds the hapids of the taxa whose sequences at the specified anchorID map to the consensus.
boolean	putGameteGroupAndHaplotypes(List<String> gametes) Takes a list of gametes and stores to the gamete_groups and gamete_haplotypes table Skips if this grouping already exists
boolean	putGenoAndHaploTypeData(GenoHaploData ghData) Stores required data to the genotypes and haplotypes tables for each entry on the list.
void	putHaplotypeCountsData(String method, String methodDetails, String taxonName, String fastqFile, byte[] counts) This method adds data to the haplotype_counts table.
void	putHaplotypesForGamete(int gamete_grp_id, String method, Map<Integer,AnchorDataPHG> anchorSequences) Stores gamete sequence data to the haplotypes table This method associates all entries with the single gamete_grp_id which is passed.
void	putHaplotypesForMultipleGroups(com.google.common.collect.Multimap<net.maizegenetics.dna.map.Position,net.maizegenetics.util.Tuple<AnchorDataPHG,String>> mapWithGroupHash, int method_id) Add data to the haplotypes table.
int	putMethod(String name, DBLoadingUtils.MethodType type, String description) Adds a method, its type and its description to the anchor_methods table These are used to identify how sequences were created,how the were combined into consensus sequences, how haplotype counts were scores, how paths through the graph were create or how an edge was created.
void	putPathsData(String method, String methodDetails, com.google.common.collect.Multimap<Integer,HaplotypeNode> paths) This method stores paths data to the paths table.
boolean	putRefAnchorData(String line_name, int hapnumber, List<AnchorDataPHG> anchorData, String hapMethod, String refGrpMethod, String gvcf, String variant_list) Fills in the haplotypes table for the reference ranges.
void	putRefRangeRefRangeGroups(int group_method_id, List<Integer> refRangeIDList) Takes a method id and a list of reference ranges.

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

PHGdbAccess

public PHGdbAccess(Connection dbConnection)

Method Detail

getRefRangeIDFromString

public int getRefRangeIDFromString(String refData)

Description copied from interface: PHGData

Returns reference range id

Specified by:

getRefRangeIDFromString in interface PHGData

Parameters:

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

Returns:

getHaplotypeIDFromFastaIDLine

public int getHaplotypeIDFromFastaIDLine(String idLine,
                                         String methodName)

Description copied from interface: PHGData

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.

Specified by:

getHaplotypeIDFromFastaIDLine in interface PHGData

Parameters:

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

methodName - This is the method used for creating the haplotypes

Returns:

getMethodIdFromName

public int getMethodIdFromName(String method_name)

Description copied from interface: PHGData

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

Specified by:

getMethodIdFromName in interface PHGData

Returns:

getGameteGroupIDFromTaxaList

public int getGameteGroupIDFromTaxaList(List<String> gametes)

Description copied from interface: PHGData

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

Specified by:

getGameteGroupIDFromTaxaList in interface PHGData

Parameters:

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

Returns:

getGenoidFromLine

public int getGenoidFromLine(String line_name)

Description copied from interface: PHGData

Return genoid

Specified by:

getGenoidFromLine in interface PHGData

Returns:

getHapidForGenoidHapNumber

public int getHapidForGenoidHapNumber(int genoid,
                                      int hap_number)

Description copied from interface: PHGData

Returns hapid for given line name and hap_number

Specified by:

getHapidForGenoidHapNumber in interface PHGData

Returns:

getHapidsForGenoid

public List<Integer> getHapidsForGenoid(int genoid)

Description copied from interface: PHGData

Returns list of hapids for a given line name

Specified by:

getHapidsForGenoid in interface PHGData

Returns:

getLineNameHapNumberFromHapid

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

Description copied from interface: PHGData

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

Specified by:

getLineNameHapNumberFromHapid in interface PHGData

Returns:

Tuple consisting of Tuple

getHapidHapNumberLineNamesForLines

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

Description copied from interface: PHGData

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.

Specified by:

getHapidHapNumberLineNamesForLines in interface PHGData

Returns:

getIntervalRangesWithIDForChrom

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

Description copied from interface: PHGData

Returns sorted treeRangeMap of Positions for specified chromosome

Specified by:

getIntervalRangesWithIDForChrom in interface PHGData

Returns:

getChromNamesForHaplotype

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

Description copied from interface: PHGData

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

Specified by:

getChromNamesForHaplotype in interface PHGData

version - Version name for anchors

Returns:

getHapidMapFromLinenameHapNumber

public Map<String,Integer> getHapidMapFromLinenameHapNumber()

Description copied from interface: PHGData

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

Specified by:

getHapidMapFromLinenameHapNumber in interface PHGData

Returns:

getHapCountsIDAndPathsForMethod

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

Description copied from interface: PHGData

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

Specified by:

getHapCountsIDAndPathsForMethod in interface PHGData

Returns:

Map of Haplotype_counts_id/paths

getHapCountsIDAndDataForVersionMethod

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

Description copied from interface: PHGData

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

Specified by:

getHapCountsIDAndDataForVersionMethod in interface PHGData

Returns:

Map of from haplotype_counts table

putMethod

public int putMethod(String name,
                     DBLoadingUtils.MethodType type,
                     String description)

Description copied from interface: PHGDataWriter

Adds a method, its type and its description to the anchor_methods table These are used to identify how sequences were created,how the were combined into consensus sequences, how haplotype counts were scores, how paths through the graph were create or how an edge was created. The "type" field identifies the table to which the method belongs.

Specified by:

putMethod in interface PHGDataWriter

Returns:

the methodId from the methods table

putGameteGroupAndHaplotypes

public boolean putGameteGroupAndHaplotypes(List<String> gametes)

Description copied from interface: PHGDataWriter

Takes a list of gametes and stores to the gamete_groups and gamete_haplotypes table Skips if this grouping already exists

Specified by:

putGameteGroupAndHaplotypes in interface PHGDataWriter

Parameters:

gametes - list consisting of taxa/gamete number in the form taxaName_gameteNumber

Returns:

true if successful

putAllAnchors

public boolean putAllAnchors(List<AnchorDataPHG> adata,
                             String refGroupMethod)

Description copied from interface: PHGDataWriter

Stores chrom, start pos, end pos to referenece_ranges table isFocus identifies focus intervals from the user's bed file

Specified by:

putAllAnchors in interface PHGDataWriter

refGroupMethod - name of method used for creating this ref_range_group

Returns:

createRefRangeGroup

public int createRefRangeGroup(String method)

Description copied from interface: PHGDataWriter

Creates an entry in the ref_range_groups table using method_id associated with the name indicated via the method parameter.

Specified by:

createRefRangeGroup in interface PHGDataWriter

Returns:

putRefRangeRefRangeGroups

public void putRefRangeRefRangeGroups(int group_method_id,
                                      List<Integer> refRangeIDList)

Description copied from interface: PHGDataWriter

Takes a method id and a list of reference ranges. Populates the ref_range_ref_range_group table.

Specified by:

putRefRangeRefRangeGroups in interface PHGDataWriter

putGenoAndHaploTypeData

public boolean putGenoAndHaploTypeData(GenoHaploData ghData)

Description copied from interface: PHGDataWriter

Stores required data to the genotypes and haplotypes tables for each entry on the list.

Specified by:

putGenoAndHaploTypeData in interface PHGDataWriter

Returns:

putRefAnchorData

public boolean putRefAnchorData(String line_name,
                                int hapnumber,
                                List<AnchorDataPHG> anchorData,
                                String hapMethod,
                                String refGrpMethod,
                                String gvcf,
                                String variant_list)

Description copied from interface: PHGDataWriter

Fills in the haplotypes table for the reference ranges.

Specified by:

putRefAnchorData in interface PHGDataWriter

anchorData - Anchor data, including chrom, start/end positions

hapMethod - Name of method used to create anchors. Maps to method table for id.

refGrpMethod - Name of method used to create the ref_range_group

gvcf - String - name of gvcf file

variant_list - String - name of file containing list of variants

Returns:

putHaplotypesForMultipleGroups

public void putHaplotypesForMultipleGroups(com.google.common.collect.Multimap<net.maizegenetics.dna.map.Position,net.maizegenetics.util.Tuple<AnchorDataPHG,String>> mapWithGroupHash,
                                           int method_id)

Description copied from interface: PHGDataWriter

Add data to the haplotypes table. Entries on the map are for different gamete groups. The key is a Position item identifying the genome_interval id The value is a Tuple consisting of (x) AnchorDataPHG object with sequence, gvcf, etc; and (y) a List of taxa represented by the ANchorDataPHG sequence

Specified by:

putHaplotypesForMultipleGroups in interface PHGDataWriter

method_id - Id in the methods table for this group of sequences

putHaplotypesForGamete

public void putHaplotypesForGamete(int gamete_grp_id,
                                   String method,
                                   Map<Integer,AnchorDataPHG> anchorSequences)

Description copied from interface: PHGDataWriter

Stores gamete sequence data to the haplotypes table This method associates all entries with the single gamete_grp_id which is passed. It is used when loading genome_interval sequences or haplotype sequences for a single line.

Specified by:

putHaplotypesForGamete in interface PHGDataWriter

putConsensusSequences

public void putConsensusSequences(com.google.common.collect.Multimap<net.maizegenetics.dna.map.Position,net.maizegenetics.util.Tuple<AnchorDataPHG,List<String>>> consensusMap,
                                  int method_id)

Description copied from interface: PHGDataWriter

This method takes a map of consensus data, finds the anchorIds based on Position, finds the hapids of the taxa whose sequences at the specified anchorID map to the consensus. Adds the gamete_group and sequence data to the haplotpes table ; adds entries to gamete_groups and gamete_hapltoypes. *

Specified by:

putConsensusSequences in interface PHGDataWriter

Parameters:

consensusMap - Multimap>

method_id - method used for collapsing anchors

putHaplotypeCountsData

public void putHaplotypeCountsData(String method,
                                   String methodDetails,
                                   String taxonName,
                                   String fastqFile,
                                   byte[] counts)

Description copied from interface: PHGDataWriter

This method adds data to the haplotype_counts table. The "data" is a Snappy compressed byte buffer of a 3xn array, found in parameter "counts" To see how this data is stored, examine DBLoadingUtils.encodeHapCountsArrayFromFile(), DBLoadingUtils.encodeHapCountsArrayFromMultiset() and DBLoadingUtils.decodeHapCountsArray()

Specified by:

putHaplotypeCountsData in interface PHGDataWriter

putPathsData

public void putPathsData(String method,
                         String methodDetails,
                         com.google.common.collect.Multimap<Integer,HaplotypeNode> paths)

Description copied from interface: PHGDataWriter

This method stores paths data to the paths table.

Specified by:

putPathsData in interface PHGDataWriter

Parameters:

method - - Method Name for Path detemination process

methodDetails - Details of how these paths were created

paths - Compressed byte array of HaplotypeNode ids

putAssemblyInterAnchorSequences

public boolean putAssemblyInterAnchorSequences(String line_name,
                                               int hapNumber,
                                               String method,
                                               com.google.common.collect.Multimap<Integer,AnchorDataPHG> anchorSequences)

Description copied from interface: PHGDataWriter

Adds inter-anchor sequences for the specified assembly to the anchor_sequences and anchor_haplotypes table. This method takes a multi-map as assembly. Inter-anchors that do not map to a reference inter-anchor are all given the anchorid 0.

Specified by:

putAssemblyInterAnchorSequences in interface PHGDataWriter

Returns:

close

public void close()
           throws Exception

Specified by:

close in interface AutoCloseable

Throws:

Exception