org.simtk.toon.secstruct
Class SecondaryStructureDiagramClass

java.lang.Object
  extended by org.simtk.toon.secstruct.SecondaryStructureDiagramClass
All Implemented Interfaces:
SecondaryStructureDiagram
Direct Known Subclasses:
NussinovDiagram

public class SecondaryStructureDiagramClass
extends java.lang.Object
implements SecondaryStructureDiagram


Constructor Summary
SecondaryStructureDiagramClass()
           
 
Method Summary
 java.util.List<BasePairPosition> basePairPositions()
           
 java.util.List<BasePosition> basePositions()
           
static java.util.Set<BasePair> findWorstPseudoknotBasePairs(java.util.Set<BasePair> basePairs)
          Identify a set of base pairs, which, if removed, leaves a set that has no pseudoknots and no bases with multiple base pairs.
 BoundingBox getBoundingBox()
           
 double getConsecutiveBaseDistance()
           
 java.util.List<NumberTick> majorTicks()
           
 java.util.List<NumberTick> minorTicks()
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

SecondaryStructureDiagramClass

public SecondaryStructureDiagramClass()
Method Detail

getConsecutiveBaseDistance

public double getConsecutiveBaseDistance()
Specified by:
getConsecutiveBaseDistance in interface SecondaryStructureDiagram

basePositions

public java.util.List<BasePosition> basePositions()
Specified by:
basePositions in interface SecondaryStructureDiagram

basePairPositions

public java.util.List<BasePairPosition> basePairPositions()
Specified by:
basePairPositions in interface SecondaryStructureDiagram

majorTicks

public java.util.List<NumberTick> majorTicks()
Specified by:
majorTicks in interface SecondaryStructureDiagram

minorTicks

public java.util.List<NumberTick> minorTicks()
Specified by:
minorTicks in interface SecondaryStructureDiagram

getBoundingBox

public BoundingBox getBoundingBox()
Specified by:
getBoundingBox in interface SecondaryStructureDiagram

findWorstPseudoknotBasePairs

public static java.util.Set<BasePair> findWorstPseudoknotBasePairs(java.util.Set<BasePair> basePairs)
Identify a set of base pairs, which, if removed, leaves a set that has no pseudoknots and no bases with multiple base pairs.

Parameters:
basePairs -
Returns:
a set of base pairs "most" responsible for pseudoknot conflicts