Class LightPairDPCursor

java.lang.Object
org.biojava.bio.dp.twohead.LightPairDPCursor
All Implemented Interfaces:
PairDPCursor

public class LightPairDPCursor extends Object implements PairDPCursor
A LIGHT implementation of PairDPCursor.

This object manages memory that is linear on the length of the shortest sequence. It does not maintain any data beyond that necessary for the next round of calcCell invocations.

Author:
Matthew Pocock, David Huen (fixes for magical state)
  • Field Details

  • Constructor Details

    • LightPairDPCursor

      public LightPairDPCursor(SymbolList seq1, SymbolList seq2, int depth1, int depth2, int numStates, EmissionCache eCache) throws IllegalSymbolException
      Constructor for the LightPairDPCursor object
      Parameters:
      seq1 - First sequence in this twohead DP.
      seq2 - Second sequence in this twohead DP.
      depth1 - The number of bases of context required in first sequence to compute DP matrix at a point (= max advance in first sequence + 1).
      depth2 - The number of bases of context required in second sequence to compute DP matrix at a point (= max advance in second sequence + 1).
      numStates - Total number of states in model.
      eCache - Emission cache to be used with this run.
      Throws:
      IllegalSymbolException - Description of Exception
  • Method Details

    • getDepth

      public int[] getDepth()
      Gets the Depth attribute of the LightPairDPCursor object
      Specified by:
      getDepth in interface PairDPCursor
      Returns:
      The Depth value
    • hasNext

      public boolean hasNext()
      Are there further Cells to be computed?
      Specified by:
      hasNext in interface PairDPCursor
      Returns:
      Description of the Returned Value
    • press

      public Cell[][] press()
      Returns the minimal context of the DP matrix necessary to compute the value of a single point in that matrix.

      The Cell [][] array has the origin as the current point to be evaluated and successive rows/columns represent rows/columns backwards within the DP matrix.

      Specified by:
      press in interface PairDPCursor
      Returns:
      An array representing the immediate context around the element to be computed.
    • next

      public void next(Cell[][] cells) throws IllegalSymbolException
      Description of the Method
      Specified by:
      next in interface PairDPCursor
      Parameters:
      cells - Description of Parameter
      Throws:
      IllegalSymbolException - Description of Exception