Uses of Class
edu.upenn.crimson.Species

Packages that use Species

edu.upenn.crimson

Uses of Species in edu.upenn.crimson

Fields in edu.upenn.crimson declared as Species

private Species[]	Species.children This contains the set of children.
private Species	Species.parent The parent will be null if this Species is the root.
private Species	Tree.root The root Species of the tree.

Methods in edu.upenn.crimson that return Species

Species	Species.copy(Tree tree) This will return a copy of the current species WITHOUT the parent, children, or level.
Species[]	Species.getChildren()
static Species	Tree.getLCA(Species s1, Species s2) Returns the LCA for the tree, assuming this species is the root of the tree.
Species	Species.getParent()
Species	Tree.getRoot()
Species	Tree.getRootLCA(int num) This will return the LCA for a random sampling of leaves from the tree.
Species	Tree.getSpeciesByID(java.lang.String id) This steps through every species in the tree and compares the species IDs until it finds the species requested.
Species	Species.nextChild() This will return the next child keeping track of the children returned.

Methods in edu.upenn.crimson with parameters of type Species

void	Species.addChild(Species child) This will add the child to the set of children and then set the parent of the child to be this Species object.
private java.util.Queue	Tree.addChildrenToQueue(java.util.Queue queue, Species[] children) This will add the children to the queue.
void	Tree.addSpecies(Species species)
static Species	Tree.getLCA(Species s1, Species s2) Returns the LCA for the tree, assuming this species is the root of the tree.
Tree	Tree.getSubtree(Species subroot) Returns the subtree given the specified root.
void	Species.removeChild(Species child) This will remove the child from the set of children.
void	Tree.removeSpecies(Species species)
void	Species.setParent(Species parent)
void	Tree.setRoot(Species root) The root's label will be set to "_Root" if there is currently no label.

Constructors in edu.upenn.crimson with parameters of type Species

Tree(java.lang.String id, Species root, Model model, java.lang.String notes, int numSpecies, int numLeaves, boolean binary, boolean ultrametric, int minLevel, int maxLevel, double minTempDepth, double maxTempDepth, double minStemLength, double maxStemLength)
Trees should not be instantiated by the user, using this routine.