Package org.biojava.bio.dp.onehead

Interface DPCursor

All Known Implementing Classes:
SmallCursor
public interface DPCursor
Encapsulates the dynamic programmming matrix, and the context within algorithms work. The cursor should put DP.MAGICAL_SYMBOL symbols at either end of the sequence.
Author:
Matthew Pocock

  • Method Details

    • symList

      SymbolList symList()
      The symbol list being looped over.

    • length

      int length()

      The length of the sequence.

      The matrix may allocate length+1 columns.

    • currentCol

      double[] currentCol()
      The current column of the matrix.

    • lastCol

      double[] lastCol()
      The previous column.

    • currentRes

      Symbol currentRes()
      The current symbol.

    • lastRes

      Symbol lastRes()
      The previous symbol.

    • canAdvance

      boolean canAdvance()
      Can we advance?

    • advance

      void advance()
      Advance.