contextFold.rnaFolding
Class Traceback

java.lang.Object
  extended by contextFold.rnaFolding.Traceback

public class Traceback
extends java.lang.Object

Contains methods for tracing-back score tables, in order to produce optimal foldings.


Field Summary
static int BEST
           
static int JUST_ONE_BRANCH
           
static int MORE_THAN_ONE_BRANCH
           
static int PAIRED
           
static int UNPAIRED
           
 
Constructor Summary
Traceback()
           
 
Method Summary
protected  int[] traceback(int[][] _scores_3, int[] _cot, int[] _il, int[] _ml1, int[] _ml2, int[][] _rowOctIxs, StructreElementsScorer _es, int _n, int[] _hpBaseAccumScores, int[] _hpLengthScores, int[] _ilBaseScores, int[] _mlBaseScores, int[][] _ilLengthScores, int[] _ilAccumBases, StructureRecognizerImpl _csr)
           
 void traceback3(int leftXIBaseType, int leftXILengthType, int i)
          Resolving the next external branch, from left (5') to right (3').
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

JUST_ONE_BRANCH

public static final int JUST_ONE_BRANCH
See Also:
Constant Field Values

MORE_THAN_ONE_BRANCH

public static final int MORE_THAN_ONE_BRANCH
See Also:
Constant Field Values

PAIRED

public static final int PAIRED
See Also:
Constant Field Values

UNPAIRED

public static final int UNPAIRED
See Also:
Constant Field Values

BEST

public static final int BEST
See Also:
Constant Field Values
Constructor Detail

Traceback

public Traceback()
Method Detail

traceback

protected int[] traceback(int[][] _scores_3,
                          int[] _cot,
                          int[] _il,
                          int[] _ml1,
                          int[] _ml2,
                          int[][] _rowOctIxs,
                          StructreElementsScorer _es,
                          int _n,
                          int[] _hpBaseAccumScores,
                          int[] _hpLengthScores,
                          int[] _ilBaseScores,
                          int[] _mlBaseScores,
                          int[][] _ilLengthScores,
                          int[] _ilAccumBases,
                          StructureRecognizerImpl _csr)

traceback3

public void traceback3(int leftXIBaseType,
                       int leftXILengthType,
                       int i)
Resolving the next external branch, from left (5') to right (3').

Parameters:
leftXIBaseType -
leftXILengthType -
i - the starting index of the string's 3' suffix.