org.forester.phylogeny

Class PhylogenyMethods

java.lang.Object

org.forester.phylogeny.PhylogenyMethods

public class PhylogenyMethods
extends Object

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	PhylogenyMethods.DESCENDANT_SORT_PRIORITY
static class	PhylogenyMethods.PhylogenyNodeField

Method Summary

Modifier and Type	Method and Description
static void	addMolecularSeqsToTree(Phylogeny phy, Msa msa)
static DescriptiveStatistics	calculateBranchLengthStatistics(Phylogeny phy)
static List<DescriptiveStatistics>	calculateConfidenceStatistics(Phylogeny phy)
static double	calculateDistance(PhylogenyNode node1, PhylogenyNode node2) Calculates the distance between PhylogenyNodes node1 and node2.
static PhylogenyNode	calculateLCA(PhylogenyNode node1, PhylogenyNode node2) Returns the LCA of PhylogenyNodes node1 and node2.
static PhylogenyNode	calculateLCAonTreeWithIdsInPreOrder(PhylogenyNode node1, PhylogenyNode node2) Returns the LCA of PhylogenyNodes node1 and node2.
static short	calculateMaxBranchesToLeaf(PhylogenyNode node)
static int	calculateMaxDepth(Phylogeny phy)
static double	calculateMaxDistanceToRoot(Phylogeny phy)
static PhylogenyNode	calculateNodeWithMaxDistanceToRoot(Phylogeny phy)
static DescriptiveStatistics	calculateNumberOfDescendantsPerNodeStatistics(Phylogeny phy)
static int	calculateNumberOfExternalNodesWithoutTaxonomy(PhylogenyNode node)
Object	clone()
static void	collapseSubtreeStructure(PhylogenyNode n)
static int	countNumberOfOneDescendantNodes(Phylogeny phy)
static int	countNumberOfPolytomies(Phylogeny phy)
static HashMap<String,PhylogenyNode>	createNameToExtNodeMap(Phylogeny phy)
static void	deleteExternalNodesNegativeSelection(Set<Long> to_delete, Phylogeny phy)
static void	deleteExternalNodesNegativeSelection(String[] node_names_to_delete, Phylogeny p)
static List<String>	deleteExternalNodesPositiveSelection(String[] node_names_to_keep, Phylogeny p)
static void	deleteExternalNodesPositiveSelectionT(List<Taxonomy> species_to_keep, Phylogeny phy)
static void	deleteInternalNodesWithOnlyOneDescendent(Phylogeny phy)
static void	deleteNonOrthologousExternalNodes(Phylogeny phy, PhylogenyNode n)
static List<List<PhylogenyNode>>	divideIntoSubTrees(Phylogeny phy, double min_distance_to_root)
static boolean	extractFastaInformation(Phylogeny phy)
static List<PhylogenyNode>	getAllDescendants(PhylogenyNode node)
static Color	getBranchColorValue(PhylogenyNode node) Convenience method
static double	getBranchWidthValue(PhylogenyNode node) Convenience method
static double	getConfidenceValue(PhylogenyNode node) Convenience method
static double[]	getConfidenceValuesAsArray(PhylogenyNode node) Convenience method
static Event	getEventAtLCA(PhylogenyNode n1, PhylogenyNode n2)
static Taxonomy	getExternalDescendantsTaxonomy(PhylogenyNode node) Returns taxonomy t if all external descendants have the same taxonomy t, null otherwise.
static PhylogenyNode	getFurthestDescendant(PhylogenyNode node)
static double	getMaximumConfidenceValue(Phylogeny phy) Returns the largest confidence value found on phy.
static int	getMinimumDescendentsPerInternalNodes(Phylogeny phy)
static String	getSpecies(PhylogenyNode node) Convenience method for display purposes.
static String	getTaxonomyIdentifier(PhylogenyNode node) Convenience method for display purposes.
static boolean	isAllDecendentsAreDuplications(PhylogenyNode n)
static boolean	isHasExternalDescendant(PhylogenyNode node)
static boolean	isInternalNamesLookLikeConfidences(Phylogeny phy)
static boolean	isTaxonomyHasIdentifierOfGivenProvider(Taxonomy tax, String[] providers)
static void	midpointRoot(Phylogeny phylogeny)
static void	normalizeBootstrapValues(Phylogeny phylogeny, double max_bootstrap_value, double max_normalized_value)
static List<PhylogenyNode>	obtainAllNodesAsList(Phylogeny phy)
static Map<Taxonomy,Integer>	obtainDistinctTaxonomyCounts(PhylogenyNode node) Returns a map of distinct taxonomies of all external nodes of node.
static void	orderAppearance(PhylogenyNode n, boolean order, boolean order_ext_alphabetically, PhylogenyMethods.DESCENDANT_SORT_PRIORITY pri) Arranges the order of childern for each node of this Phylogeny in such a way that either the branch with more children is on top (right) or on bottom (left), dependent on the value of boolean order.
static void	postorderBranchColorAveragingExternalNodeBased(Phylogeny p)
static void	preOrderReId(Phylogeny phy)
static Phylogeny[]	readPhylogenies(PhylogenyParser parser, File file)
static Phylogeny[]	readPhylogenies(PhylogenyParser parser, List<File> files)
static void	removeNode(PhylogenyNode remove_me, Phylogeny phylogeny)
static List<PhylogenyNode>	searchData(String query, Phylogeny phy, boolean case_sensitive, boolean partial, boolean regex, boolean search_domains, double domains_confidence_threshold)
static List<PhylogenyNode>	searchDataLogicalAnd(String[] queries, Phylogeny phy, boolean case_sensitive, boolean partial, boolean search_domains, double domains_confidence_threshold)
static void	setAllIndicatorsToZero(Phylogeny phy)
static void	setBootstrapConfidence(PhylogenyNode node, double bootstrap_confidence_value) Convenience method.
static void	setBranchColorValue(PhylogenyNode node, Color color)
static void	setBranchWidthValue(PhylogenyNode node, double branch_width_value) Convenience method
static void	setConfidence(PhylogenyNode node, double confidence_value) Convenience method.
static void	setConfidence(PhylogenyNode node, double confidence_value, String type) Convenience method.
static void	setScientificName(PhylogenyNode node, String scientific_name)
static void	setTaxonomyCode(PhylogenyNode node, String taxonomy_code) Convenience method to set the taxonomy code of a phylogeny node.
static void	sortNodeDescendents(PhylogenyNode node, PhylogenyMethods.DESCENDANT_SORT_PRIORITY pri)
static List<PhylogenyNode>	taxonomyBasedDeletionOfExternalNodes(Phylogeny reference, Phylogeny to_be_stripped) Removes from Phylogeny to_be_stripped all external Nodes which are associated with a species NOT found in Phylogeny reference.
static void	transferInternalNamesToBootstrapSupport(Phylogeny phy)
static void	transferInternalNodeNamesToConfidence(Phylogeny phy, String confidence_type)
static void	transferNodeNameToField(Phylogeny phy, PhylogenyMethods.PhylogenyNodeField field, boolean external_only)

Methods inherited from class java.lang.Object

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

Method Detail

clone

public Object clone()
             throws CloneNotSupportedException

Overrides:

clone in class Object

Throws:

CloneNotSupportedException

extractFastaInformation

public static boolean extractFastaInformation(Phylogeny phy)

calculateBranchLengthStatistics

public static DescriptiveStatistics calculateBranchLengthStatistics(Phylogeny phy)

calculateConfidenceStatistics

public static List<DescriptiveStatistics> calculateConfidenceStatistics(Phylogeny phy)

calculateDistance

public static double calculateDistance(PhylogenyNode node1,
                                       PhylogenyNode node2)

Calculates the distance between PhylogenyNodes node1 and node2.

Parameters:

node1 -

node2 -

Returns:

distance between node1 and node2

calculateLCA

public static final PhylogenyNode calculateLCA(PhylogenyNode node1,
                                               PhylogenyNode node2)

Returns the LCA of PhylogenyNodes node1 and node2.

Parameters:

node1 -

node2 -

Returns:

LCA of node1 and node2

calculateLCAonTreeWithIdsInPreOrder

public static final PhylogenyNode calculateLCAonTreeWithIdsInPreOrder(PhylogenyNode node1,
                                                                      PhylogenyNode node2)

Returns the LCA of PhylogenyNodes node1 and node2. Precondition: ids are in pre-order (or level-order).

Parameters:

node1 -

node2 -

Returns:

LCA of node1 and node2

calculateMaxBranchesToLeaf

public static short calculateMaxBranchesToLeaf(PhylogenyNode node)

calculateMaxDepth

public static int calculateMaxDepth(Phylogeny phy)

calculateMaxDistanceToRoot

public static double calculateMaxDistanceToRoot(Phylogeny phy)

calculateNodeWithMaxDistanceToRoot

public static PhylogenyNode calculateNodeWithMaxDistanceToRoot(Phylogeny phy)

calculateNumberOfExternalNodesWithoutTaxonomy

public static int calculateNumberOfExternalNodesWithoutTaxonomy(PhylogenyNode node)

calculateNumberOfDescendantsPerNodeStatistics

public static DescriptiveStatistics calculateNumberOfDescendantsPerNodeStatistics(Phylogeny phy)

collapseSubtreeStructure

public static final void collapseSubtreeStructure(PhylogenyNode n)

countNumberOfOneDescendantNodes

public static int countNumberOfOneDescendantNodes(Phylogeny phy)

countNumberOfPolytomies

public static int countNumberOfPolytomies(Phylogeny phy)

createNameToExtNodeMap

public static final HashMap<String,PhylogenyNode> createNameToExtNodeMap(Phylogeny phy)

deleteExternalNodesNegativeSelection

public static void deleteExternalNodesNegativeSelection(Set<Long> to_delete,
                                                        Phylogeny phy)

deleteExternalNodesNegativeSelection

public static void deleteExternalNodesNegativeSelection(String[] node_names_to_delete,
                                                        Phylogeny p)
                                                 throws IllegalArgumentException

Throws:

IllegalArgumentException

deleteExternalNodesPositiveSelection

public static List<String> deleteExternalNodesPositiveSelection(String[] node_names_to_keep,
                                                                Phylogeny p)

deleteExternalNodesPositiveSelectionT

public static void deleteExternalNodesPositiveSelectionT(List<Taxonomy> species_to_keep,
                                                         Phylogeny phy)

deleteInternalNodesWithOnlyOneDescendent

public static final void deleteInternalNodesWithOnlyOneDescendent(Phylogeny phy)

deleteNonOrthologousExternalNodes

public static final void deleteNonOrthologousExternalNodes(Phylogeny phy,
                                                           PhylogenyNode n)

divideIntoSubTrees

public static final List<List<PhylogenyNode>> divideIntoSubTrees(Phylogeny phy,
                                                                 double min_distance_to_root)

getAllDescendants

public static List<PhylogenyNode> getAllDescendants(PhylogenyNode node)

getBranchColorValue

public static Color getBranchColorValue(PhylogenyNode node)

Convenience method

Parameters:

node -

Returns:

getBranchWidthValue

public static double getBranchWidthValue(PhylogenyNode node)

Convenience method

getConfidenceValue

public static double getConfidenceValue(PhylogenyNode node)

Convenience method

getConfidenceValuesAsArray

public static double[] getConfidenceValuesAsArray(PhylogenyNode node)

Convenience method

getEventAtLCA

public static final Event getEventAtLCA(PhylogenyNode n1,
                                        PhylogenyNode n2)

getExternalDescendantsTaxonomy

public static Taxonomy getExternalDescendantsTaxonomy(PhylogenyNode node)

Returns taxonomy t if all external descendants have the same taxonomy t, null otherwise.

getFurthestDescendant

public static PhylogenyNode getFurthestDescendant(PhylogenyNode node)

getMaximumConfidenceValue

public static double getMaximumConfidenceValue(Phylogeny phy)

Returns the largest confidence value found on phy.

getMinimumDescendentsPerInternalNodes

public static int getMinimumDescendentsPerInternalNodes(Phylogeny phy)

getSpecies

public static String getSpecies(PhylogenyNode node)

Convenience method for display purposes. Not intended for algorithms.

getTaxonomyIdentifier

public static String getTaxonomyIdentifier(PhylogenyNode node)

Convenience method for display purposes. Not intended for algorithms.

isAllDecendentsAreDuplications

public static final boolean isAllDecendentsAreDuplications(PhylogenyNode n)

isHasExternalDescendant

public static boolean isHasExternalDescendant(PhylogenyNode node)

isTaxonomyHasIdentifierOfGivenProvider

public static boolean isTaxonomyHasIdentifierOfGivenProvider(Taxonomy tax,
                                                             String[] providers)

midpointRoot

public static void midpointRoot(Phylogeny phylogeny)

normalizeBootstrapValues

public static void normalizeBootstrapValues(Phylogeny phylogeny,
                                            double max_bootstrap_value,
                                            double max_normalized_value)

obtainAllNodesAsList

public static List<PhylogenyNode> obtainAllNodesAsList(Phylogeny phy)

obtainDistinctTaxonomyCounts

public static Map<Taxonomy,Integer> obtainDistinctTaxonomyCounts(PhylogenyNode node)

Returns a map of distinct taxonomies of all external nodes of node. If at least one of the external nodes has no taxonomy, null is returned.

orderAppearance

public static void orderAppearance(PhylogenyNode n,
                                   boolean order,
                                   boolean order_ext_alphabetically,
                                   PhylogenyMethods.DESCENDANT_SORT_PRIORITY pri)

Arranges the order of childern for each node of this Phylogeny in such a way that either the branch with more children is on top (right) or on bottom (left), dependent on the value of boolean order.

Parameters:

order - decides in which direction to order

pri -

postorderBranchColorAveragingExternalNodeBased

public static void postorderBranchColorAveragingExternalNodeBased(Phylogeny p)

preOrderReId

public static final void preOrderReId(Phylogeny phy)

readPhylogenies

public static final Phylogeny[] readPhylogenies(PhylogenyParser parser,
                                                File file)
                                         throws IOException

Throws:

IOException

readPhylogenies

public static final Phylogeny[] readPhylogenies(PhylogenyParser parser,
                                                List<File> files)
                                         throws IOException

Throws:

IOException

removeNode

public static void removeNode(PhylogenyNode remove_me,
                              Phylogeny phylogeny)

searchData

public static List<PhylogenyNode> searchData(String query,
                                             Phylogeny phy,
                                             boolean case_sensitive,
                                             boolean partial,
                                             boolean regex,
                                             boolean search_domains,
                                             double domains_confidence_threshold)

searchDataLogicalAnd

public static List<PhylogenyNode> searchDataLogicalAnd(String[] queries,
                                                       Phylogeny phy,
                                                       boolean case_sensitive,
                                                       boolean partial,
                                                       boolean search_domains,
                                                       double domains_confidence_threshold)

setAllIndicatorsToZero

public static void setAllIndicatorsToZero(Phylogeny phy)

setBootstrapConfidence

public static void setBootstrapConfidence(PhylogenyNode node,
                                          double bootstrap_confidence_value)

Convenience method. Sets value for the first confidence value (created if not present, values overwritten otherwise).

setBranchColorValue

public static void setBranchColorValue(PhylogenyNode node,
                                       Color color)

setBranchWidthValue

public static void setBranchWidthValue(PhylogenyNode node,
                                       double branch_width_value)

Convenience method

setConfidence

public static void setConfidence(PhylogenyNode node,
                                 double confidence_value)

Convenience method. Sets value for the first confidence value (created if not present, values overwritten otherwise).

setConfidence

public static void setConfidence(PhylogenyNode node,
                                 double confidence_value,
                                 String type)

Convenience method. Sets value for the first confidence value (created if not present, values overwritten otherwise).

setScientificName

public static void setScientificName(PhylogenyNode node,
                                     String scientific_name)

setTaxonomyCode

public static void setTaxonomyCode(PhylogenyNode node,
                                   String taxonomy_code)
                            throws PhyloXmlDataFormatException

Convenience method to set the taxonomy code of a phylogeny node.

Parameters:

node -

taxonomy_code -

Throws:

PhyloXmlDataFormatException

sortNodeDescendents

public static final void sortNodeDescendents(PhylogenyNode node,
                                             PhylogenyMethods.DESCENDANT_SORT_PRIORITY pri)

taxonomyBasedDeletionOfExternalNodes

public static List<PhylogenyNode> taxonomyBasedDeletionOfExternalNodes(Phylogeny reference,
                                                                       Phylogeny to_be_stripped)

Removes from Phylogeny to_be_stripped all external Nodes which are associated with a species NOT found in Phylogeny reference.

Parameters:

reference - a reference Phylogeny

to_be_stripped - Phylogeny to be stripped

Returns:

nodes removed from to_be_stripped

transferInternalNamesToBootstrapSupport

public static final void transferInternalNamesToBootstrapSupport(Phylogeny phy)

isInternalNamesLookLikeConfidences

public static final boolean isInternalNamesLookLikeConfidences(Phylogeny phy)

transferInternalNodeNamesToConfidence

public static final void transferInternalNodeNamesToConfidence(Phylogeny phy,
                                                               String confidence_type)

transferNodeNameToField

public static final void transferNodeNameToField(Phylogeny phy,
                                                 PhylogenyMethods.PhylogenyNodeField field,
                                                 boolean external_only)
                                          throws PhyloXmlDataFormatException

Throws:

PhyloXmlDataFormatException

addMolecularSeqsToTree

public static void addMolecularSeqsToTree(Phylogeny phy,
                                          Msa msa)