All Implemented Interfaces:

java.lang.AutoCloseable , net.maizegenetics.pangenome.db_loading.PHGData , net.maizegenetics.pangenome.db_loading.PHGDataWriter
```
public class PHGdbAccess
 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.

Nested Class Summary

Nested Classes
Modifier and Type	Class	Description

Field Summary

Fields
Modifier and Type	Field	Description

Constructor Summary

Constructors
Constructor	Description
`PHGdbAccess(Connection dbConnection)`

Enum Constant Summary

Enum Constants
Enum Constant	Description

Method Summary

Modifier and Type	Method	Description
`void`	`updateReadMappingHash()`	This prompts a call to private method loadReadMappingHash() to update this hash table
`int`	`getRefRangeIDFromString(String refData)`	Returns reference range id
`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.
`int`	`getMethodIdFromName(String method_name)`	Returns method_id given a method name.
`Map<String, String>`	`getMethodDescriptionFromName(String method_name)`	Method queries the db methods table for the description field given a methods name
`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
`List<Integer>`	`getGenoidsForTaxa(List<String> taxa)`
`int`	`getGenomeFileIdFromGenoid(int genoid)`	Gets the id from the genome_file_data table based on the genoid .
`int`	`getGenomeFileIdFromGenoidAndFile(int genoid, String file)`	Gets the id from the genome_file_data table based on the genoid and a filename
`Pair<Integer, String>`	`getGenomeFileHashFromGenoidandFile(int genoid, String file)`	Given a genoid and a file name, return the hash value and id for that entry in the genome_file_data table.
`int`	`getHapidForGenoidHapNumber(int genoid, int hap_number)`	Returns hapid for given line name and hap_number
`List<Integer>`	`getHapidsForGenoid(int genoid)`	Returns list of hapids for a given line name
`Tuple<String, Integer>`	`getLineNameHapNumberFromHapid(int gameteid)`	Method to retrieve both a line name and the hap number given a hapid.
`Map<Integer, String>`	`getHapidHapNumberLineNamesForLines(List<String> lineNames)`	Retrieves line name and hapnumber, and returns them with the hapid.
`RangeMap<Position, Integer>`	`getIntervalRangesWithIDForChrom(String chrom)`	Returns sorted treeRangeMap of Positions for specified chromosome
`List<String>`	`getChromNamesForHaplotype(String line_name, int hap_number, String version)`	Method grabs a list of distinct chromosome names for a genome_interval version
`Map<String, Integer>`	`getHapidMapFromLinenameHapNumber()`	Returns a map of created from the genotypes and haplotypes table.
`Map<Integer, Array<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.
`Map<Integer, Tuple<String, Array<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
`HashSet<String>`	`getTaxaForPathMethod(String method_name)`	Method to get a list of all genoid line_names that have paths for method = method_name.
`Map<String, Array<byte>>`	`getTaxonPathsForMethod(String method_name)`	Returns a map of taxon to paths for that taxon from the paths table for a specified method name.
`int`	`getReadMappingId(String line_name, String method_name, String file_group_name)`	Method uses line_name, method_name and file_Group_name to fetch a read_mapping_id.
`List<Integer>`	`getHaplotypeList(int haplist_id)`	Given a haplotype_list_id, query the haplotype_list table and return a list of haplotypes stored for that ID, or an empty list if there were none.
`Pair<Array<byte>, Integer>`	`getReadMappingsForId(int readMappingId)`	Method to get the Read Mapping data from the DB using the read_mapping_id.
`List<Integer>`	`getReadMappingIdsForTaxaMethod(List<String> taxaList, String method)`	This method takes a list of taxa and a method name.
`List<Integer>`	`getPathIdsForReadMappingIds(List<Integer> readMappingIds)`	Returns path_ids from the read_mapping_paths table associated with the list of read_mapping_ids provided.
`List<ReadMappingDBRecord>`	`getReadMappingsForMethod(String methodName)`	Method to get the mapping ids and mapping data by method
`List<ReadMappingIdDBRecord>`	`getReadMappingIdsForReadMethod(String methodName)`	Method to get the mapping ids, taxa, and file group by method
`boolean`	`isFileGroupNew(String taxon, String fileGroupName, String methodName)`	Method to check to see if a given taxon and fileGroup are already in the readMapping table of the DB.
`List<Integer>`	`getRefRangesForMethod(String methodName)`	Method to return all reference ranges associated with a specified method name
`Map<String, List<List<Integer>>>`	`getPathsForTaxonMethod(List<String> taxon, String method_name)`	Method takes a list of taxa and a method name and returns the paths (if populated in the paths table) stored for each taxon/method pair.
`List<String>`	`getDbTaxaNames()`	Gets a list of the taxa currently in the database.
`int`	`getTaxaGroupIDFromName(String group_name)`	Returns taxa_grp_id given a taxa group name.
`List<String>`	`getTaxaForTaxaGroup(String group_name)`	Get the taxa that make up the specified taxa group
`List<String>`	`getAllTaxaGroupNames()`	Returns a list of all taxa group names from the taxa_groups table
`int`	`putMethod(String name, DBLoadingUtils.MethodType type, Map<String, String> descriptionMap)`	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.
`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`	`putAllAnchors(List<AnchorDataPHG> adata, int refGroupMethodID)`	Stores chrom, start pos, end pos to referenece_ranges table isFocus identifies focus intervals from the user's bed file
`void`	`putRefRangeRefRangeMethod(int method_id, List<Integer> refRangeIDList)`	Takes a method id and a list of reference ranges.
`boolean`	`putGenoAndHaploTypeData(GenoHaploData ghData)`	Stores required data to the genotypes and haplotypes tables for each entry on the list.
`boolean`	`putRefAnchorData(String line_name, int hapnumber, List<AnchorDataPHG> anchorData, int hapMethod, Set<String> refGrpMethods, String gvcf, String variant_list, int genomeFileId, int gvcfFileId)`	Fills in the haplotypes table for the reference ranges.
`void`	`putHaplotypesForMultipleGroups(Multimap<Position, Tuple<AnchorDataPHG, String>> mapWithGroupHash, int method_id)`	Add data to the haplotypes table.
`void`	`putHaplotypesForGamete(int gamete_grp_id, int method_id, Map<Integer, AnchorDataPHG> anchorSequences, int genomeFileId, int gvcfFileId)`	Stores gamete sequence data to the haplotypes table This method associates all entries with the single gamete_grp_id which is passed in.
`void`	`putHaplotypesData(int gamete_grp_id, int method, Map<Integer, AnchorDataPHG> anchorSequences, String chromosome, int genomeFileId, int gvcfFileId)`	Takes a gamete_grp_id, method_id, list of haplotype sequences, a chromosome and a genomeFileId.
`void`	`putHaplotypesData(int gamete_grp_id, int method, Map<Integer, AnchorDataPHG> anchorSequences, String chromosome, int genomeFileId, int gvcfFileId, int maxEntries)`	Takes a gamete_grp_id, method_id, list of haplotype sequences, a chromosome, genomeFileId, and a number of MaxEntries.
`void`	`processHaplotypesData(int gamete_grp_id, int method, Map<Integer, AnchorDataPHG> anchorSequences, String chromosome, int genomeFileId, int gvcfFileId)`
`void`	`putConsensusSequences(Multimap<Position, 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.
`void`	`putHaplotypeCountsData(String method, Map<String, String> methodDetails, String taxonName, String fastqFile, Array<byte> counts)`	This method adds data to the haplotype_counts table.
`int`	`putPathsData(String method, Map<String, String> methodDetails, String taxon, List<Integer> readMappingIds, Array<byte> pathBytes, boolean isTestMethod)`	This method stores paths data to the paths table.
`int`	`putReadMappingData(String method, Map<String, String> methodDetails, String taxon, String file_group_name, Array<byte> mapping_data, boolean isTestMethod, int haplotypeListId)`	Takes a method name, method details string, taxon name (should exist in the genotypes table), file_group_name, and a byte array of read mapping data.
`int`	`putHalotypeListData(List<Integer> hapids)`	put data to the haplotype Lists table.
`int`	`putGenomeFileData(String genome_server_path, String genome_file, int genoid, int type)`	Method takes information on a genome fasta file, stores to the PHG db, returns the genome_file_data entry id created for the table entry.
`int`	`putTaxaGroupName(String group_name)`	Creates an entry in the taxa_groups table.
`void`	`putTaxaTaxaGroups(String group_name, List<String> taxaList)`	Takes a taxa group name and a list of taxa.
`boolean`	`putAssemblyInterAnchorSequences(String line_name, int hapNumber, String method, Multimap<Integer, AnchorDataPHG> anchorSequences)`	Adds inter-anchor sequences for the specified assembly to the anchor_sequences and anchor_haplotypes table.
`void`	`deletePaths(String method, List<String> taxa)`	Deletes paths based on a method name and taxa.
`boolean`	`deleteReadMappingsCascade(List<Integer> readMappingIds)`	Delete read_mappings from the read_mapping table based on provided ids.
`void`	`deleteReadMappingPathsById(List<Integer> readMappingIds)`	Deletes from the read_mapping_paths table the ids in the ReadMappingIds List
`void`	`deleteReadMappingsById(List<Integer> readMappingIds)`	Deletes from the read_mapping table based on the ids in the input List
`void`	`deletePathsById(List<Integer> pathsIds)`
`int`	`deleteMethodByName(String method)`	Takes a method name and deletes the entry for it from the methods table.
`int`	`getHaplotypeListIDfromHash(String hash)`	Given an MD5 hash value, returns the db id for that entry, or 0 if none exist
`List<Array<int>>`	`getReferenceRangeHapidPairs(int haplotypeListId)`
`void`	`close()`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - PHGdbAccess
```
PHGdbAccess(Connection dbConnection)
```
- Method Detail
  - updateReadMappingHash
```
 void updateReadMappingHash()
```
    This prompts a call to private method loadReadMappingHash() to update this hash table
  - getRefRangeIDFromString
```
 int getRefRangeIDFromString(String refData)
```
    Returns reference range id
    
    Parameters:
    
    refData - needs to be of form chr1:startpos:endPos
  - 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
  - getMethodIdFromName
```
 int getMethodIdFromName(String method_name)
```
    Returns method_id given a method name. or 0 if no id found for the given name
  - getMethodDescriptionFromName
```
 Map<String, String> getMethodDescriptionFromName(String method_name)
```
    Method queries the db methods table for the description field given a methods name
    
    Parameters:
    
    method_name - : name of method
  - 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
  - getGenoidFromLine
```
 int getGenoidFromLine(String line_name)
```
    Return genoid
  - getGenoidsForTaxa
```
 List<Integer> getGenoidsForTaxa(List<String> taxa)
```
  - getGenomeFileIdFromGenoid
```
 int getGenomeFileIdFromGenoid(int genoid)
```
    Gets the id from the genome_file_data table based on the genoid .
  - getGenomeFileIdFromGenoidAndFile
```
 int getGenomeFileIdFromGenoidAndFile(int genoid, String file)
```
    Gets the id from the genome_file_data table based on the genoid and a filename
  - getGenomeFileHashFromGenoidandFile
```
 Pair<Integer, String> getGenomeFileHashFromGenoidandFile(int genoid, String file)
```
    Given a genoid and a file name, return the hash value and id for that entry in the genome_file_data table. If there is no entry, return null
  - getHapidForGenoidHapNumber
```
 int getHapidForGenoidHapNumber(int genoid, int hap_number)
```
    Returns hapid for given line name and hap_number
  - getHapidsForGenoid
```
 List<Integer> getHapidsForGenoid(int genoid)
```
    Returns list of hapids for a given line name
  - getLineNameHapNumberFromHapid
```
 Tuple<String, Integer> getLineNameHapNumberFromHapid(int gameteid)
```
    Method to retrieve both a line name and the hap number given a hapid.
  - 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.
  - getIntervalRangesWithIDForChrom
```
 RangeMap<Position, Integer> getIntervalRangesWithIDForChrom(String chrom)
```
    Returns sorted treeRangeMap of Positions for specified chromosome
  - 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:
    
    version - Version name for anchors
  - getHapidMapFromLinenameHapNumber
```
 Map<String, Integer> getHapidMapFromLinenameHapNumber()
```
    Returns a map of created from the genotypes and haplotypes table.
  - getHapCountsIDAndPathsForMethod
```
 Map<Integer, Array<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.
  - getHapCountsIDAndDataForVersionMethod
```
 Map<Integer, Tuple<String, Array<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
  - getTaxaForPathMethod
```
 HashSet<String> getTaxaForPathMethod(String method_name)
```
    Method to get a list of all genoid line_names that have paths for method = method_name.
  - getTaxonPathsForMethod
```
 Map<String, Array<byte>> getTaxonPathsForMethod(String method_name)
```
    Returns a map of taxon to paths for that taxon from the paths table for a specified method name.
  - getReadMappingId
```
 int getReadMappingId(String line_name, String method_name, String file_group_name)
```
    Method uses line_name, method_name and file_Group_name to fetch a read_mapping_id. -1 returned if the this combination is not present in the db.
  - getHaplotypeList
```
 List<Integer> getHaplotypeList(int haplist_id)
```
    Given a haplotype_list_id, query the haplotype_list table and return a list of haplotypes stored for that ID, or an empty list if there were none.
  - getReadMappingsForId
```
 Pair<Array<byte>, Integer> getReadMappingsForId(int readMappingId)
```
    Method to get the Read Mapping data from the DB using the read_mapping_id. Generally this is returned from PHGData.getReadMappingId(String line_name, String method_name, String file_group_name)
  - getReadMappingIdsForTaxaMethod
```
 List<Integer> getReadMappingIdsForTaxaMethod(List<String> taxaList, String method)
```
    This method takes a list of taxa and a method name. It returns a list of read_mapping Ids based on these 2 parameters
  - getPathIdsForReadMappingIds
```
 List<Integer> getPathIdsForReadMappingIds(List<Integer> readMappingIds)
```
    Returns path_ids from the read_mapping_paths table associated with the list of read_mapping_ids provided.
  - getReadMappingsForMethod
```
 List<ReadMappingDBRecord> getReadMappingsForMethod(String methodName)
```
    Method to get the mapping ids and mapping data by method
  - getReadMappingIdsForReadMethod
```
 List<ReadMappingIdDBRecord> getReadMappingIdsForReadMethod(String methodName)
```
    Method to get the mapping ids, taxa, and file group by method
  - isFileGroupNew
```
 boolean isFileGroupNew(String taxon, String fileGroupName, String methodName)
```
    Method to check to see if a given taxon and fileGroup are already in the readMapping table of the DB.
  - getRefRangesForMethod
```
 List<Integer> getRefRangesForMethod(String methodName)
```
    Method to return all reference ranges associated with a specified method name
    
    Parameters:
    
    methodName - name of method group for which the user wants reference range ids
  - getPathsForTaxonMethod
```
 Map<String, List<List<Integer>>> getPathsForTaxonMethod(List<String> taxon, String method_name)
```
    Method takes a list of taxa and a method name and returns the paths (if populated in the paths table) stored for each taxon/method pair. For each taxon, a List
  - getDbTaxaNames
```
 List<String> getDbTaxaNames()
```
    Gets a list of the taxa currently in the database. Taxa are identified by the line_name field of the genotypes table
  - getTaxaGroupIDFromName
```
 int getTaxaGroupIDFromName(String group_name)
```
    Returns taxa_grp_id given a taxa group name. or 0 if no id found for the given name
  - getTaxaForTaxaGroup
```
 List<String> getTaxaForTaxaGroup(String group_name)
```
    Get the taxa that make up the specified taxa group
  - getAllTaxaGroupNames
```
 List<String> getAllTaxaGroupNames()
```
    Returns a list of all taxa group names from the taxa_groups table
  - putMethod
```
 int putMethod(String name, DBLoadingUtils.MethodType type, Map<String, String> descriptionMap)
```
    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.
  - putGameteGroupAndHaplotypes
```
 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
    
    Parameters:
    
    gametes - list consisting of taxa/gamete number in the form taxaName_gameteNumber
  - putAllAnchors
```
 boolean putAllAnchors(List<AnchorDataPHG> adata, int refGroupMethodID)
```
    Stores chrom, start pos, end pos to referenece_ranges table isFocus identifies focus intervals from the user's bed file
    
    Parameters:
    
    refGroupMethodID - method_id used for creating this ref_range_group
  - putRefRangeRefRangeMethod
```
 void putRefRangeRefRangeMethod(int method_id, List<Integer> refRangeIDList)
```
    Takes a method id and a list of reference ranges. Populates the ref_range_ref_range_method table.
  - putGenoAndHaploTypeData
```
 boolean putGenoAndHaploTypeData(GenoHaploData ghData)
```
    Stores required data to the genotypes and haplotypes tables for each entry on the list.
  - putRefAnchorData
```
 boolean putRefAnchorData(String line_name, int hapnumber, List<AnchorDataPHG> anchorData, int hapMethod, Set<String> refGrpMethods, String gvcf, String variant_list, int genomeFileId, int gvcfFileId)
```
    Fills in the haplotypes table for the reference ranges.
    
    Parameters:
    
    hapMethod - Name of method used to create anchors.
    
    gvcf - String - name of gvcf file
    
    variant_list - String - name of file containing list of variants
    
    genomeFileId - int - id for ref fasta entry in the genome_file_data table
    
    gvcfFileId - int - id for ref gvcf file enty in the genome_file_data table
  - putHaplotypesForMultipleGroups
```
 void putHaplotypesForMultipleGroups(Multimap<Position, Tuple<AnchorDataPHG, String>> mapWithGroupHash, int method_id)
```
    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
    
    Parameters:
    
    method_id - Id in the methods table for this group of sequences
  - putHaplotypesForGamete
```
 void putHaplotypesForGamete(int gamete_grp_id, int method_id, Map<Integer, AnchorDataPHG> anchorSequences, int genomeFileId, int gvcfFileId)
```
    Stores gamete sequence data to the haplotypes table This method associates all entries with the single gamete_grp_id which is passed in. It is used when loading reference_ranges sequences or haplotype sequences for a single line. THe gidToVariantDataMap map is used to create the variant list blob for the db
    
    Parameters:
    
    genomeFileId - - genome_file_data table id for the fasta file this haplotype, -1 means none.
    
    gvcfFileId - - genome_file_data table id for the gvcf file for this haplotype, -1 mean none
  - putHaplotypesData
```
 void putHaplotypesData(int gamete_grp_id, int method, Map<Integer, AnchorDataPHG> anchorSequences, String chromosome, int genomeFileId, int gvcfFileId)
```
    Takes a gamete_grp_id, method_id, list of haplotype sequences, a chromosome and a genomeFileId. Starts the process of storing table data for the haplotypes to the db. This will set maxEntries to 10000 and will call the putHaplotypesData version below putHaplotypesData(int gamete_grp_id, int method, MapanchorSequences, String chromosome, int genomeFileId, gvcfFIleId)
  - putHaplotypesData
```
 void putHaplotypesData(int gamete_grp_id, int method, Map<Integer, AnchorDataPHG> anchorSequences, String chromosome, int genomeFileId, int gvcfFileId, int maxEntries)
```
    Takes a gamete_grp_id, method_id, list of haplotype sequences, a chromosome, genomeFileId, and a number of MaxEntries. Starts the process of storing table data for the haplotypes to the db
  - processHaplotypesData
```
 void processHaplotypesData(int gamete_grp_id, int method, Map<Integer, AnchorDataPHG> anchorSequences, String chromosome, int genomeFileId, int gvcfFileId)
```
  - putConsensusSequences
```
 void putConsensusSequences(Multimap<Position, 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. Adds the gamete_group and sequence data to the haplotpes table ; adds entries to gamete_groups and gamete_hapltoypes. *
    
    Parameters:
    
    consensusMap - Multimap
  - putHaplotypeCountsData
```
 void putHaplotypeCountsData(String method, Map<String, String> methodDetails, String taxonName, String fastqFile, Array<byte> counts)
```
    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()
  - putPathsData
```
 int putPathsData(String method, Map<String, String> methodDetails, String taxon, List<Integer> readMappingIds, Array<byte> pathBytes, boolean isTestMethod)
```
    This method stores paths data to the paths table.
    
    Parameters:
    
    method - - Method Name for Path detemination process
    
    methodDetails - Details of how these paths were created
    
    taxon - Name of line for which data is being added
    
    readMappingIds - List of read_mapping_ids
    
    pathBytes - Compressed byte array of paths data
    
    isTestMethod - Indicates if the method type should be PATHS ot TEST_PATHS
  - putReadMappingData
```
 int putReadMappingData(String method, Map<String, String> methodDetails, String taxon, String file_group_name, Array<byte> mapping_data, boolean isTestMethod, int haplotypeListId)
```
    Takes a method name, method details string, taxon name (should exist in the genotypes table), file_group_name, and a byte array of read mapping data. This is stored to the PHG read_mapping table
    
    Parameters:
    
    isTestMethod - : indicates if method type should be set to a TEST method
    
    haplotypeListId - : id from the haplotype_list table
  - putHalotypeListData
```
 int putHalotypeListData(List<Integer> hapids)
```
    put data to the haplotype Lists table.
    
    Parameters:
    
    hapids - - list of integers representing haplotype ids
  - putGenomeFileData
```
 int putGenomeFileData(String genome_server_path, String genome_file, int genoid, int type)
```
    Method takes information on a genome fasta file, stores to the PHG db, returns the genome_file_data entry id created for the table entry.
    
    Parameters:
    
    genome_file - local path to file name used for MD5 calculation
    
    genoid - genoid associated with this genome data
    
    type - the type of file, ie FASTA or GVCF from DBLoadingUtils.
  - putTaxaGroupName
```
 int putTaxaGroupName(String group_name)
```
    Creates an entry in the taxa_groups table. If one already exists with the specified name, the id for it is returned.
  - putTaxaTaxaGroups
```
 void putTaxaTaxaGroups(String group_name, List<String> taxaList)
```
    Takes a taxa group name and a list of taxa. Populates the taxa_groups and taxa_groups_genoid tables.
  - putAssemblyInterAnchorSequences
```
 boolean putAssemblyInterAnchorSequences(String line_name, int hapNumber, String method, Multimap<Integer, AnchorDataPHG> anchorSequences)
```
    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.
  - deletePaths
```
 void deletePaths(String method, List<String> taxa)
```
    Deletes paths based on a method name and taxa. It allows for either method or taxa to be null, but not both. Entries are deleted from both the read_mapping_paths and the paths
    
    Parameters:
    
    method - delete paths which have this method
    
    taxa - list of taxa for which the paths should be deleted
  - deleteReadMappingsCascade
```
 boolean deleteReadMappingsCascade(List<Integer> readMappingIds)
```
    Delete read_mappings from the read_mapping table based on provided ids. This will also delete entries from the read_mapping_paths and paths table that are associated with these read_mappings
  - deleteReadMappingPathsById
```
 void deleteReadMappingPathsById(List<Integer> readMappingIds)
```
    Deletes from the read_mapping_paths table the ids in the ReadMappingIds List
  - deleteReadMappingsById
```
 void deleteReadMappingsById(List<Integer> readMappingIds)
```
    Deletes from the read_mapping table based on the ids in the input List
  - deletePathsById
```
 void deletePathsById(List<Integer> pathsIds)
```
  - deleteMethodByName
```
 int deleteMethodByName(String method)
```
    Takes a method name and deletes the entry for it from the methods table.
  - getHaplotypeListIDfromHash
```
 int getHaplotypeListIDfromHash(String hash)
```
    Given an MD5 hash value, returns the db id for that entry, or 0 if none exist
  - getReferenceRangeHapidPairs
```
 List<Array<int>> getReferenceRangeHapidPairs(int haplotypeListId)
```
    Parameters:
    
    haplotypeListId - an id to a list of haplotype_ids in the database
  - close
```
 void close()
```

Class PHGdbAccess

Nested Class Summary

Field Summary

Constructor Summary

Enum Constant Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

PHGdbAccess

Method Detail

updateReadMappingHash

getRefRangeIDFromString

getHaplotypeIDFromFastaIDLine

getMethodIdFromName

getMethodDescriptionFromName

getGameteGroupIDFromTaxaList

getGenoidFromLine

getGenoidsForTaxa

getGenomeFileIdFromGenoid

getGenomeFileIdFromGenoidAndFile

getGenomeFileHashFromGenoidandFile

getHapidForGenoidHapNumber

getHapidsForGenoid

getLineNameHapNumberFromHapid

getHapidHapNumberLineNamesForLines

getIntervalRangesWithIDForChrom

getChromNamesForHaplotype

getHapidMapFromLinenameHapNumber

getHapCountsIDAndPathsForMethod

getHapCountsIDAndDataForVersionMethod

getTaxaForPathMethod

getTaxonPathsForMethod

getReadMappingId

getHaplotypeList

getReadMappingsForId

getReadMappingIdsForTaxaMethod

getPathIdsForReadMappingIds

getReadMappingsForMethod

getReadMappingIdsForReadMethod

isFileGroupNew

getRefRangesForMethod

getPathsForTaxonMethod

getDbTaxaNames

getTaxaGroupIDFromName

getTaxaForTaxaGroup

getAllTaxaGroupNames

putMethod

putGameteGroupAndHaplotypes

putAllAnchors

putRefRangeRefRangeMethod

putGenoAndHaploTypeData

putRefAnchorData

putHaplotypesForMultipleGroups

putHaplotypesForGamete

putHaplotypesData

putHaplotypesData

processHaplotypesData

putConsensusSequences

putHaplotypeCountsData

putPathsData

putReadMappingData

putHalotypeListData

putGenomeFileData

putTaxaGroupName

putTaxaTaxaGroups

putAssemblyInterAnchorSequences

deletePaths

deleteReadMappingsCascade

deleteReadMappingPathsById

deleteReadMappingsById

deletePathsById

deleteMethodByName

getHaplotypeListIDfromHash

getReferenceRangeHapidPairs

close