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java.lang.ObjectTree
public class Tree
This class represents a tree which is used as a data structure that stores multiple RNA hairpins. A branch within the tree represents a hairpin structure that is build up by a number of loops, which are the nodes. Each hairpin within the tree must have a stability profile that stays within the boundaries of the energyProfile and have a sequence that matches the given template sequence.
See also http://2008.igem.org/Team:TUDelft/Temperature_software
Node
Constructor Summary | |
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Tree(java.lang.String top,
java.lang.String bottom,
int[] energyProfile,
int maxDist)
Creates a new tree. |
Method Summary | |
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void |
buildTree()
Recursively builds up the tree. |
java.lang.String |
getBottom()
Returns the bottom RNA sequence. |
int[] |
getEnergyProfile()
Returns the energy profile. |
int |
getMaxDist()
Returns the maximal distance to the energy profile. |
java.util.ArrayList<java.lang.String> |
getResults(java.lang.String loop)
Returns the resulting RNA hairpins that fit the template and have a stability profile that fits the given energy profile. |
java.lang.String |
getTop()
Returns the top RNA sequence. |
Methods inherited from class java.lang.Object |
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equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public Tree(java.lang.String top, java.lang.String bottom, int[] energyProfile, int maxDist)
top
- A template for the top sequence of the hairpin.bottom
- A template for the bottom sequence of the hairpin.energyProfile
- The energy profile.maxDist
- The maximal allowed distance to the energy profile.Method Detail |
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public void buildTree()
Node.addChilds()
public java.util.ArrayList<java.lang.String> getResults(java.lang.String loop)
loop
- The sequense of the hairpin loop that connects the top and
bottom sequences.
public java.lang.String getTop()
public java.lang.String getBottom()
public int[] getEnergyProfile()
public int getMaxDist()
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