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java.lang.ObjectcontextFold.rnaFolding.Folder
public final class Folder
An object that implements the (dynamic programming Zuker-like) RNA folding prediction algorithm. The implementation utilizes sparsification techniques, which were presented in: Rolf Backofen, Dekel Tsur, Shay Zakov, and Michal Ziv-Ukelson. Sparse RNA Folding: Time and Space Efficient Algorithms. Journal of Discrete Algorithms, Volume 9, Issue 1, March 2011, Pages 12-31, 20th Anniversary Edition of the Annual Symposium on Combinatorial Pattern Matching (CPM 2009).
Field Summary | |
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long |
concatanations
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FeatureManager |
fm
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long |
naivSplits
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long[] |
octPerLength
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long[] |
seqPerLength
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boolean |
sparseByOcts
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boolean |
sparseBySteps
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long[] |
splitsPerLength
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Constructor Summary | |
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Folder()
Constructs a Folder object. |
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Folder(FeatureManager featureManager)
Construct a folder which uses the scoring model of the given feature manager. |
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Folder(java.lang.String modelPath)
Construct a folder which uses the scoring model of the given feature manager. |
Method Summary | |
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float |
computeDPTables(StructreElementsScorer es,
java.util.List<int[]> optFoldings,
int numOfOutputFoldings)
Fills the dynamic programming scoring tables. |
void |
initializeTables(int n)
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static void |
main(java.lang.String[] args)
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long |
naivSplits(long n)
Computes the number of split-points needed to be examined in order to find optimal branching structure, in which both subsequence endpoints i and j are paired (not to each other). |
java.lang.String |
predictFolding(java.lang.String sequence)
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static void |
printStructure(int[] S,
int[] matchIxs)
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void |
resetCounts()
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void |
setFeatureManager(FeatureManager featureManager)
A setter to the feature manager of the folder (the scoring model). |
void |
setFeatureManager(java.lang.String modelPath)
A setter to the feature manager of the folder (the scoring model). |
java.util.List<RNA> |
tagMany(java.lang.String listInput)
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RNA |
tagOne(java.lang.String sequence)
Deprecated. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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public FeatureManager fm
public long[] octPerLength
public long[] splitsPerLength
public long[] seqPerLength
public long concatanations
public long naivSplits
public boolean sparseByOcts
public boolean sparseBySteps
Constructor Detail |
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public Folder()
public Folder(FeatureManager featureManager)
featureManager
- a FeatureManager object that defines a
scoring model.public Folder(java.lang.String modelPath) throws java.io.IOException, java.lang.ClassNotFoundException
modelPath
- a path to a serialized (trained) FeatureManager object.
java.io.IOException
- - an I/O error has occurred.
java.lang.ClassNotFoundException
- - Class of a serialized object cannot be found.Method Detail |
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public void setFeatureManager(FeatureManager featureManager)
featureManager
- a FeatureManager object.public void setFeatureManager(java.lang.String modelPath) throws java.io.IOException, java.lang.ClassNotFoundException
modelPath
- a path to a serialized (trained) FeatureManager object.
java.io.IOException
- - an I/O error has occurred.
java.lang.ClassNotFoundException
- - Class of a serialized object cannot be found.public float computeDPTables(StructreElementsScorer es, java.util.List<int[]> optFoldings, int numOfOutputFoldings)
es
- a StructreElementsScorer
object that defines
structural element scores (this object wraps the input RNA string).optFoldings
- a handle in which computed optimal solutions are
returned. Currently only one optimal solution is computed (might change
in the future).numOfOutputFoldings
- CURRENTLY NOT WORKING. In the future: allows
to specify the number of returned (sub) optimal foldings.
public void initializeTables(int n)
public static void printStructure(int[] S, int[] matchIxs)
public long naivSplits(long n)
The minimum split-point index is i+MIN_HAIRPIN_LENGTH+2, and the maximum index is j-MIN_HAIRPIN_LENGTH-1, and thus there are j-i-2*MIN_HAIRPIN_LENGTH-2 split-points to examine (or 0, if j-i < 2*MIN_HAIRPIN_LENGTH+2). The return value of this function is the result of summing the above term for all pairs of indices i,j in the sequence.
n
- sequence length.
public java.util.List<RNA> tagMany(java.lang.String listInput)
tagMany
in interface Fold
@Deprecated public RNA tagOne(java.lang.String sequence)
tagOne
in interface Fold
public java.lang.String predictFolding(java.lang.String sequence) throws java.io.IOException, java.lang.ClassNotFoundException
java.io.IOException
java.lang.ClassNotFoundException
public void resetCounts()
public static void main(java.lang.String[] args) throws java.io.IOException, java.lang.ClassNotFoundException
java.io.IOException
java.lang.ClassNotFoundException
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