org.simtk.toon.secstruct
Class SecondaryStructureDiagramClass
java.lang.Object
org.simtk.toon.secstruct.SecondaryStructureDiagramClass
- All Implemented Interfaces:
- SecondaryStructureDiagram
- Direct Known Subclasses:
- NussinovDiagram
public class SecondaryStructureDiagramClass
- extends java.lang.Object
- implements SecondaryStructureDiagram
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
SecondaryStructureDiagramClass
public SecondaryStructureDiagramClass()
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