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getBottom()
- Method in enum
BasePair
Returns the nucleotide at the bottom of the base pair.
getBottom()
- Method in class
Tree
Returns the bottom RNA sequence.
getEnergy()
- Method in enum
Loop
Returns the free energy of the loop.
getEnergyProfile()
- Method in class
Tree
Returns the energy profile.
getLeft()
- Method in enum
Loop
Returns the left base pair.
getLoops(String, int, int)
- Static method in enum
Loop
This method returns all the Loops that 'fit' the given template and have an energy value in between the given upper and lower bound.
getMaxDist()
- Method in class
Tree
Returns the maximal distance to the energy profile.
getResults(ArrayList<String>, String)
- Method in class
Node
This method returns the sequences of the hairpins that are the result after building this tree.
getResults(String)
- Method in class
Tree
Returns the resulting RNA hairpins that fit the template and have a stability profile that fits the given energy profile.
getRight()
- Method in enum
Loop
Returns the right base pair.
getSize()
- Method in enum
Loop
Returns the size of the loop.
getTop()
- Method in enum
BasePair
Returns the nucleotide at the top of the base pair.
getTop()
- Method in class
Tree
Returns the top RNA sequence.
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