Method Detail

• clone

  public java.lang.Object clone()
                         throws java.lang.CloneNotSupportedException

  Overrides:

  clone in class java.lang.Object

  Throws:

  java.lang.CloneNotSupportedException

• extractFastaInformation

  public static boolean extractFastaInformation​(Phylogeny phy)

• calculateBranchLengthStatistics

  public static DescriptiveStatistics calculateBranchLengthStatistics​(Phylogeny phy)

• calculateConfidenceStatistics

  public static java.util.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 java.util.HashMap<java.lang.String,​PhylogenyNode> createNameToExtNodeMap​(Phylogeny phy)

• deleteExternalNodesNegativeSelection

  public static void deleteExternalNodesNegativeSelection​(java.util.Set<java.lang.Long> to_delete,
                                                          Phylogeny phy)

• deleteExternalNodesNegativeSelection

  public static void deleteExternalNodesNegativeSelection​(java.lang.String[] node_names_to_delete,
                                                          Phylogeny p)
                                                   throws java.lang.IllegalArgumentException

  Throws:

  java.lang.IllegalArgumentException

• deleteExternalNodesPositiveSelection

  public static java.util.List<java.lang.String> deleteExternalNodesPositiveSelection​(java.lang.String[] node_names_to_keep,
                                                                                      Phylogeny p)

• deleteExternalNodesPositiveSelectionT

  public static void deleteExternalNodesPositiveSelectionT​(java.util.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 java.util.List<java.util.List<PhylogenyNode>> divideIntoSubTrees​(Phylogeny phy,
                                                                                       double min_distance_to_root)

• getAllDescendants

  public static java.util.List<PhylogenyNode> getAllDescendants​(PhylogenyNode node)

• getBranchColorValue

  public static java.awt.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 java.lang.String getSpecies​(PhylogenyNode node)

  Convenience method for display purposes. Not intended for algorithms.

• getTaxonomyIdentifier

  public static java.lang.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,
                                                               java.lang.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 java.util.List<PhylogenyNode> obtainAllNodesAsList​(Phylogeny phy)

• obtainDistinctTaxonomyCounts

  public static java.util.Map<Taxonomy,​java.lang.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,
                                                  java.io.File file)
                                           throws java.io.IOException

  Throws:

  java.io.IOException

• readPhylogenies

  public static final Phylogeny[] readPhylogenies​(PhylogenyParser parser,
                                                  java.util.List<java.io.File> files)
                                           throws java.io.IOException

  Throws:

  java.io.IOException

• removeNode

  public static void removeNode​(PhylogenyNode remove_me,
                                Phylogeny phylogeny)

• searchData

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

• searchDataLogicalAnd

  public static java.util.List<PhylogenyNode> searchDataLogicalAnd​(java.lang.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,
                                         java.awt.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,
                                   java.lang.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,
                                       java.lang.String scientific_name)

• setTaxonomyCode

  public static void setTaxonomyCode​(PhylogenyNode node,
                                     java.lang.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 java.util.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,
                                                                 java.lang.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)