org::gel::mauve::tree::IntervalSequenceTree Class Reference

Collaboration diagram for org::gel::mauve::tree::IntervalSequenceTree:

Collaboration graph
[legend]
List of all members.

Public Member Functions

long erase (long point, long length)
Iterator insert (Key val, long point)

Protected Member Functions

IstNode recursiveFind (long[] point, IstNode node)

Package Functions

IstNode decrement (IstNode x)
IstNode increment (IstNode x)
long nodeCount ()
 Returns the total length of intervals contained in this interval sequence.

void propogateChanges (IstNode cur_node, long length_diff, long subtree_diff)
 propogates changes to node values up a tree


Package Attributes

IstNode leftmost
 < Root of the tree

IstNode rightmost
 < Left most tree node, for begin() method

IstNode root

Member Function Documentation

IstNode org::gel::mauve::tree::IntervalSequenceTree::decrement IstNode  x  )  [inline, package]
 

Definition at line 291 of file IntervalSequenceTree.java.

References org::gel::mauve::tree::IstNode::getKey(), org::gel::mauve::tree::IstNode::getLeft(), org::gel::mauve::tree::IstNode::getParent(), and org::gel::mauve::tree::IstNode::getRight().

Referenced by insert().

long org::gel::mauve::tree::IntervalSequenceTree::erase long  point,
long  length
[inline]
 

Definition at line 122 of file IntervalSequenceTree.java.

References org::gel::mauve::tree::Key::copy(), org::gel::mauve::tree::Key::cropEnd(), org::gel::mauve::tree::Key::cropStart(), org::gel::mauve::tree::IstNode::getKey(), org::gel::mauve::tree::IstNode::getLeft(), org::gel::mauve::tree::IstNode::getLength(), org::gel::mauve::tree::IstNode::getParent(), org::gel::mauve::tree::IstNode::getRight(), org::gel::mauve::tree::IstNode::getSubtreeSize(), increment(), leftmost, propogateChanges(), recursiveFind(), rightmost, org::gel::mauve::tree::IstNode::setKey(), org::gel::mauve::tree::IstNode::setLeft(), org::gel::mauve::tree::IstNode::setLength(), org::gel::mauve::tree::IstNode::setParent(), org::gel::mauve::tree::IstNode::setRight(), and org::gel::mauve::tree::IstNode::setSubtreeSize().

IstNode org::gel::mauve::tree::IntervalSequenceTree::increment IstNode  x  )  [inline, package]
 

Definition at line 264 of file IntervalSequenceTree.java.

References org::gel::mauve::tree::IstNode::getKey(), org::gel::mauve::tree::IstNode::getLeft(), org::gel::mauve::tree::IstNode::getParent(), and org::gel::mauve::tree::IstNode::getRight().

Referenced by erase(), org::gel::mauve::tree::IstIterator::hasNext(), and org::gel::mauve::tree::IstIterator::next().

Iterator org::gel::mauve::tree::IntervalSequenceTree::insert Key  val,
long  point
[inline]
 

Definition at line 23 of file IntervalSequenceTree.java.

References org::gel::mauve::tree::Key::copy(), org::gel::mauve::tree::Key::cropEnd(), org::gel::mauve::tree::Key::cropStart(), decrement(), org::gel::mauve::tree::IstNode::getKey(), org::gel::mauve::tree::IstNode::getLeft(), org::gel::mauve::tree::IstNode::getLength(), org::gel::mauve::tree::Key::getLength(), org::gel::mauve::tree::IstNode::getParent(), org::gel::mauve::tree::IstNode::getRight(), leftmost, propogateChanges(), recursiveFind(), rightmost, org::gel::mauve::tree::IstNode::setKey(), org::gel::mauve::tree::IstNode::setLeft(), org::gel::mauve::tree::IstNode::setLength(), org::gel::mauve::tree::IstNode::setParent(), org::gel::mauve::tree::IstNode::setRight(), and org::gel::mauve::tree::IstNode::setSubtreeSize().

long org::gel::mauve::tree::IntervalSequenceTree::nodeCount  )  [inline, package]
 

Returns the total length of intervals contained in this interval sequence.

Definition at line 19 of file IntervalSequenceTree.java.

References org::gel::mauve::tree::IstNode::getSubtreeSize().

void org::gel::mauve::tree::IntervalSequenceTree::propogateChanges IstNode  cur_node,
long  length_diff,
long  subtree_diff
[inline, package]
 

propogates changes to node values up a tree

Definition at line 235 of file IntervalSequenceTree.java.

References org::gel::mauve::tree::IstNode::getLength(), org::gel::mauve::tree::IstNode::getParent(), org::gel::mauve::tree::IstNode::getSubtreeSize(), org::gel::mauve::tree::IstNode::setLength(), and org::gel::mauve::tree::IstNode::setSubtreeSize().

Referenced by erase(), and insert().

IstNode org::gel::mauve::tree::IntervalSequenceTree::recursiveFind long[]  point,
IstNode  node
[inline, protected]
 

Definition at line 243 of file IntervalSequenceTree.java.

References org::gel::mauve::tree::IstNode::getKey(), org::gel::mauve::tree::IstNode::getLeft(), org::gel::mauve::tree::IstNode::getLength(), and org::gel::mauve::tree::IstNode::getRight().

Referenced by erase(), and insert().


Member Data Documentation

IstNode org::gel::mauve::tree::IntervalSequenceTree::leftmost [package]
 

< Root of the tree

Definition at line 9 of file IntervalSequenceTree.java.

Referenced by erase(), and insert().

IstNode org::gel::mauve::tree::IntervalSequenceTree::rightmost [package]
 

< Left most tree node, for begin() method

Definition at line 12 of file IntervalSequenceTree.java.

Referenced by erase(), and insert().

IstNode org::gel::mauve::tree::IntervalSequenceTree::root [package]
 

Definition at line 6 of file IntervalSequenceTree.java.


The documentation for this class was generated from the following file:
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