Class GuideTree.Node

Method Details

• getChild1

  public GuideTreeNode<S,C> getChild1()

  Description copied from interface: GuideTreeNode

  Returns the first child node of this node. For leaf nodes (sequences), this will be null.

  Specified by:

  getChild1 in interface GuideTreeNode<S extends Sequence<C>,C extends Compound>

  Returns:

  the first child node of this node

• getChild2

  public GuideTreeNode<S,C> getChild2()

  Description copied from interface: GuideTreeNode

  Returns the second child node of this node. For leaf nodes (sequences), this will be null.

  Specified by:

  getChild2 in interface GuideTreeNode<S extends Sequence<C>,C extends Compound>

  Returns:

  the second child node of this node

• getDistanceToParent

  public double getDistanceToParent()

  Description copied from interface: GuideTreeNode

  Returns the difference in height of this node and it's parent node. A likely meaning of this distance is half the percent difference between this node and it's sibling node.

  Specified by:

  getDistanceToParent in interface GuideTreeNode<S extends Sequence<C>,C extends Compound>

  Returns:

  the difference in height of this node to it's parent node

• getName

  public String getName()

  Description copied from interface: GuideTreeNode

  Returns the name of this node. For leaf nodes (sequences), this will likely be the accession ID.

  Specified by:

  getName in interface GuideTreeNode<S extends Sequence<C>,C extends Compound>

  Returns:

  the name of this node

• getProfile

  public Profile<S,C> getProfile()

  Description copied from interface: GuideTreeNode

  Returns the profile stored at this node. If the node is a leaf, the profile is that of a single sequence. If not, this returns null until GuideTreeNode.setProfile(Profile) has been called.

  Specified by:

  getProfile in interface GuideTreeNode<S extends Sequence<C>,C extends Compound>

  Returns:

  the profile stored at this node

• getProfileFuture

  public Future<ProfilePair<S,C>> getProfileFuture()

  Description copied from interface: GuideTreeNode

  Returns the profile future stored at this node, but does not force the calculation, yet. This allows alignment tasks for the entire tree to be queued in a post-order traversal before concurrent execution.

  Specified by:

  getProfileFuture in interface GuideTreeNode<S extends Sequence<C>,C extends Compound>

  Returns:

  the profile future stored at this node

• setProfile

  public void setProfile(Profile<S,C> profile)

  Description copied from interface: GuideTreeNode

  Stores the given profile.

  Specified by:

  setProfile in interface GuideTreeNode<S extends Sequence<C>,C extends Compound>

  Parameters:

  profile - new profile stored at this node

• setProfileFuture

  public void setProfileFuture(Future<ProfilePair<S,C>> profileFuture)

  Description copied from interface: GuideTreeNode

  Stores the given profile future. This allows concurrent execution of alignment tasks.

  Specified by:

  setProfileFuture in interface GuideTreeNode<S extends Sequence<C>,C extends Compound>

  Parameters:

  profileFuture - new profile to be calculated and then stored at this node

• children

  public Enumeration<GuideTreeNode<S,C>> children()

  Specified by:

  children in interface TreeNode

• getAllowsChildren

  public boolean getAllowsChildren()

  Specified by:

  getAllowsChildren in interface TreeNode

• getChildAt

  public GuideTreeNode<S,C> getChildAt(int childIndex)

  Specified by:

  getChildAt in interface TreeNode

• getChildCount

  public int getChildCount()

  Specified by:

  getChildCount in interface TreeNode

• getIndex

  public int getIndex(TreeNode child)

  Specified by:

  getIndex in interface TreeNode

• getParent

  public GuideTreeNode<S,C> getParent()

  Specified by:

  getParent in interface TreeNode

• isLeaf

  public boolean isLeaf()

  Specified by:

  isLeaf in interface TreeNode