net.maizegenetics.pangenome.api

Class CreateGraphUtils

java.lang.Object

net.maizegenetics.pangenome.api.CreateGraphUtils

public class CreateGraphUtils
extends Object

Author:

Terry Casstevens Created August 21, 2017

Field Summary

Fields

Modifier and Type	Field and Description
static String	INNER_ANCHOR_METHOD
static String	NO_CONSENSUS_METHOD

Method Summary

Modifier and Type	Method and Description
static int	addInnerAnchorNodes(TreeMap<ReferenceRange,List<HaplotypeNode>> result, Connection database, Map<Integer,ReferenceRange> referenceRangeMap, Map<Integer,net.maizegenetics.taxa.TaxaList> taxaListMap, boolean includeVariantContext, int hapMethodId)
static HaplotypeGraph	addMissingSequenceNodes(HaplotypeGraph graph)
static int	addMissingSequenceNodes(TreeMap<ReferenceRange,List<HaplotypeNode>> result)
static void	addUnconsolidatedNodes(Connection database, Map<ReferenceRange,List<HaplotypeNode>> consensusNodes, Map<Integer,ReferenceRange> referenceRangeMap, Map<Integer,net.maizegenetics.taxa.TaxaList> taxaListMap, boolean onlyAnchors) Adds HaplotypeNodes to the given map for sequences that wasn't consolidated into a consensus sequence.
static Connection	connection(String propertiesFile) Creates a database connection given a properties file
static Connection	connection(String host, String user, String password, String dbName) Creates a Postgres database connection.
static List<HaplotypeEdge>	createEdges(Collection<HaplotypeNode> haplotypeNodes) Generates Edges based on HaplotypeNodes.
static List<HaplotypeEdge>	createEdges(TreeMap<ReferenceRange,List<HaplotypeNode>> rangeToNode) Generates Edges based on HaplotypeNodes.
static TreeMap<ReferenceRange,List<HaplotypeNode>>	createHaplotypeNodes(Connection database, Map<Integer,ReferenceRange> referenceRangeMap, Map<Integer,net.maizegenetics.taxa.TaxaList> taxaListMap, String method, boolean onlyAnchors, boolean includeVariantContext, SortedSet<Integer> includeHapids) Creates lists of HaplotypeNodes organized by reference Range based on the given method.
static TreeMap<ReferenceRange,List<HaplotypeNode>>	createHaplotypeNodes(Connection database, String method, boolean onlyAnchors, boolean includeVariantContext, SortedSet<Integer> includeHapids) Creates HaplotypeNode Lists with keys as ReferenceRanges.
static HaplotypeGraph	createHaplotypeNodesWithVariants(Connection database, HaplotypeGraph graph) Creates HaplotypeGraph with variant contexts corresponding to the given HaplotypeGraph.
static TreeMap<ReferenceRange,List<HaplotypeNode>>	createHaplotypeNodesWithVariants(Connection database, Set<HaplotypeNode> includeHapNodes) Creates lists of HaplotypeNodes with variant contexts corresponding to the specified nodes organized by reference Range.
static String	getRefLineName(Connection database) Returns the line name of the reference genotype
static HaplotypeGraph	keepRefRanges(HaplotypeGraph graph, List<ReferenceRange> ranges) Creates graph that includes specified reference ranges.
static int	methodId(Connection database, String method_name) Returns method id (methods.method_id) for given method name.
static HaplotypeGraph	nodesSplitByIndividualTaxa(HaplotypeGraph graph, double sameTaxonPercent)
static Map<Integer,ReferenceRange>	referenceRangeMap(Connection database) Retrieves all ReferenceRange instances
static SortedSet<ReferenceRange>	referenceRanges(Connection database) Retrieves all ReferenceRange instances with specified genome interval version name.
static HaplotypeGraph	removeRefRanges(HaplotypeGraph graph, double minPercentTaxa) Removes reference ranges from given graph that represent less than given minimum percent of total taxa.
static HaplotypeGraph	removeRefRanges(HaplotypeGraph graph, int minCountTaxa) Removes reference ranges from given graph that represent less than given minimum number of taxa.
static HaplotypeGraph	removeRefRanges(HaplotypeGraph graph, List<ReferenceRange> ranges) Removes specified reference ranges from graph.
static HaplotypeGraph	subsetGraph(HaplotypeGraph graph, net.maizegenetics.taxa.TaxaList taxa) Create graph that's a subset of the given graph which contains only nodes from the taxa list.
static net.maizegenetics.taxa.TaxaList	taxaInNodes(TreeMap<ReferenceRange,List<HaplotypeNode>> nodes)
static Map<Integer,net.maizegenetics.taxa.TaxaList>	taxaListMap(Connection database) Retrieves all groups of taxa.
static TreeMap<ReferenceRange,List<HaplotypeNode>>	tree(HaplotypeGraph graph)

Methods inherited from class java.lang.Object

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

Field Detail

NO_CONSENSUS_METHOD

public static final String NO_CONSENSUS_METHOD

See Also:

Constant Field Values

INNER_ANCHOR_METHOD

public static final String INNER_ANCHOR_METHOD

See Also:

Constant Field Values

Method Detail

connection

public static Connection connection(String propertiesFile)

Creates a database connection given a properties file

Parameters:

propertiesFile - properties file

Returns:

database connection

connection

public static Connection connection(String host,
                                    String user,
                                    String password,
                                    String dbName)

Creates a Postgres database connection.

Parameters:

host - hostname

user - user id

password - password

dbName - database name

Returns:

SQLite database connection

referenceRangeMap

public static Map<Integer,ReferenceRange> referenceRangeMap(Connection database)

Retrieves all ReferenceRange instances

Parameters:

database - database connection

Returns:

map of ReferenceRanges, key is references_ranges.ref_range_id

referenceRanges

public static SortedSet<ReferenceRange> referenceRanges(Connection database)

Retrieves all ReferenceRange instances with specified genome interval version name.

Parameters:

database - database connection

Returns:

ReferenceRanges

taxaListMap

public static Map<Integer,net.maizegenetics.taxa.TaxaList> taxaListMap(Connection database)

Retrieves all groups of taxa.

Parameters:

database - database connection

Returns:

map of TaxaList, key is gamete_groups.gamete_grp_id

createHaplotypeNodes

public static TreeMap<ReferenceRange,List<HaplotypeNode>> createHaplotypeNodes(Connection database,
                                                                               Map<Integer,ReferenceRange> referenceRangeMap,
                                                                               Map<Integer,net.maizegenetics.taxa.TaxaList> taxaListMap,
                                                                               String method,
                                                                               boolean onlyAnchors,
                                                                               boolean includeVariantContext,
                                                                               SortedSet<Integer> includeHapids)

Creates lists of HaplotypeNodes organized by reference Range based on the given method. In most cases use #createHaplotypeNodes(Connection, String, boolean, boolean, SortedSet).

Parameters:

database - database connection

referenceRangeMap - ReferenceRange map (referenceRangeMap(Connection)

taxaListMap - TaxaList map taxaListMap(Connection)

method - method name

onlyAnchors - whether to include only anchors (i.e. no regions between anchors)

includeVariantContext - whether to include variant contexts in haplotype nodes

includeHapids - includes specified hapids. include everything if null

Returns:

Map of HaplotypeNode Lists (keys are ReferenceRange)

createHaplotypeNodesWithVariants

public static TreeMap<ReferenceRange,List<HaplotypeNode>> createHaplotypeNodesWithVariants(Connection database,
                                                                                           Set<HaplotypeNode> includeHapNodes)

Creates lists of HaplotypeNodes with variant contexts corresponding to the specified nodes organized by reference Range.

Parameters:

database - database connection

includeHapNodes - includes specified hapids

Returns:

Map of HaplotypeNode Lists (keys are ReferenceRange)

createHaplotypeNodesWithVariants

public static HaplotypeGraph createHaplotypeNodesWithVariants(Connection database,
                                                              HaplotypeGraph graph)

Creates HaplotypeGraph with variant contexts corresponding to the given HaplotypeGraph.

Parameters:

database - database connection

graph - graph without variant contexts

Returns:

graph with variant contexts

addInnerAnchorNodes

public static int addInnerAnchorNodes(TreeMap<ReferenceRange,List<HaplotypeNode>> result,
                                      Connection database,
                                      Map<Integer,ReferenceRange> referenceRangeMap,
                                      Map<Integer,net.maizegenetics.taxa.TaxaList> taxaListMap,
                                      boolean includeVariantContext,
                                      int hapMethodId)

addUnconsolidatedNodes

public static void addUnconsolidatedNodes(Connection database,
                                          Map<ReferenceRange,List<HaplotypeNode>> consensusNodes,
                                          Map<Integer,ReferenceRange> referenceRangeMap,
                                          Map<Integer,net.maizegenetics.taxa.TaxaList> taxaListMap,
                                          boolean onlyAnchors)

Adds HaplotypeNodes to the given map for sequences that wasn't consolidated into a consensus sequence.

Parameters:

database - database connection

consensusNodes - nodes created from consensus sequences #createHaplotypeNodes(Connection, Map, Map, String, boolean, boolean, SortedSet)

referenceRangeMap - ReferenceRange map (referenceRangeMap(Connection)

taxaListMap - TaxaList map taxaListMap(Connection)

onlyAnchors - whether to include only anchors (i.e. no regions between anchors)

addMissingSequenceNodes

public static HaplotypeGraph addMissingSequenceNodes(HaplotypeGraph graph)

addMissingSequenceNodes

public static int addMissingSequenceNodes(TreeMap<ReferenceRange,List<HaplotypeNode>> result)

taxaInNodes

public static net.maizegenetics.taxa.TaxaList taxaInNodes(TreeMap<ReferenceRange,List<HaplotypeNode>> nodes)

tree

public static TreeMap<ReferenceRange,List<HaplotypeNode>> tree(HaplotypeGraph graph)

nodesSplitByIndividualTaxa

public static HaplotypeGraph nodesSplitByIndividualTaxa(HaplotypeGraph graph,
                                                        double sameTaxonPercent)

createHaplotypeNodes

public static TreeMap<ReferenceRange,List<HaplotypeNode>> createHaplotypeNodes(Connection database,
                                                                               String method,
                                                                               boolean onlyAnchors,
                                                                               boolean includeVariantContext,
                                                                               SortedSet<Integer> includeHapids)

Creates HaplotypeNode Lists with keys as ReferenceRanges.

Parameters:

database - database connection

method - method name

onlyAnchors - whether to include only anchors (i.e. no regions between anchors)

includeVariantContext - whether to include variant contexts in haplotype nodes

includeHapids - includes specified hapids. include everything if null

Returns:

HaplotypeNode List map with keys as ReferenceRanges.

createEdges

public static List<HaplotypeEdge> createEdges(Collection<HaplotypeNode> haplotypeNodes)

Generates Edges based on HaplotypeNodes. Database information not used.

Parameters:

haplotypeNodes - HaplotypeNodes

Returns:

Generated HaplotypeEdges

createEdges

public static List<HaplotypeEdge> createEdges(TreeMap<ReferenceRange,List<HaplotypeNode>> rangeToNode)

Generates Edges based on HaplotypeNodes. Database information not used.

Parameters:

rangeToNode - map of RefereneceRanges to List of HaplotypeNodes

Returns:

Generated HaplotypeEdges

getRefLineName

public static String getRefLineName(Connection database)

Returns the line name of the reference genotype

Parameters:

database -

Returns:

reference line name

methodId

public static int methodId(Connection database,
                           String method_name)

Returns method id (methods.method_id) for given method name.

Parameters:

database - database connection

method_name - method name

Returns:

method id

subsetGraph

public static HaplotypeGraph subsetGraph(HaplotypeGraph graph,
                                         net.maizegenetics.taxa.TaxaList taxa)

Create graph that's a subset of the given graph which contains only nodes from the taxa list.

Parameters:

taxa - taxa list

graph - original graph

Returns:

subset graph

removeRefRanges

public static HaplotypeGraph removeRefRanges(HaplotypeGraph graph,
                                             double minPercentTaxa)

Removes reference ranges from given graph that represent less than given minimum percent of total taxa.

Parameters:

graph - graph

minPercentTaxa - minimum percent taxa

Returns:

new graph

removeRefRanges

public static HaplotypeGraph removeRefRanges(HaplotypeGraph graph,
                                             int minCountTaxa)

Removes reference ranges from given graph that represent less than given minimum number of taxa.

Parameters:

graph - graph

minCountTaxa - minimum number of taxa

Returns:

new graph

removeRefRanges

public static HaplotypeGraph removeRefRanges(HaplotypeGraph graph,
                                             List<ReferenceRange> ranges)

Removes specified reference ranges from graph.

Parameters:

graph - graph

ranges - reference ranges to remove

Returns:

new graph

keepRefRanges

public static HaplotypeGraph keepRefRanges(HaplotypeGraph graph,
                                           List<ReferenceRange> ranges)

Creates graph that includes specified reference ranges.

Parameters:

graph - graph

ranges - ranges to keep

Returns:

new graph