Class PhylogenyMethods

Method Details

• 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)