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java.lang.Objectutil.secondaryStructure.SecondaryStructureExtraction
public class SecondaryStructureExtraction
This method is primarily used for buiding the secondary structure of non-training files (although it can also be used for this purpose, there are better ways of doing this). This class allows a link the the native RNAfold method (which is assumed to be installed locally).
Constructor Summary | |
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SecondaryStructureExtraction(org.apache.log4j.Logger logger)
Constructor of the secondary structure builder class |
Method Summary | |
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java.lang.String |
extractSequenceString(java.lang.String sequence,
int location,
int maxUp,
int maxDown)
This method extracts a string of the same length for all possible maximum upstream and downstream lengths, relative to the splicesite location. |
SecondaryStructureData |
extractStructures(java.lang.String sequence,
java.util.List<java.lang.Integer> locations,
java.lang.String outputDirectory,
int maxUp,
int maxDown)
This method extracts the actual secondary structures from the sequence, given by the list of possible splicesites. |
static void |
main(java.lang.String[] args)
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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 SecondaryStructureExtraction(org.apache.log4j.Logger logger)
logger
- The logging facility for the projectMethod Detail |
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public SecondaryStructureData extractStructures(java.lang.String sequence, java.util.List<java.lang.Integer> locations, java.lang.String outputDirectory, int maxUp, int maxDown)
sequence
- The sequence that contains the splicesites and from which the sec structs will be extractedlocations
- The different (pseudo-) splice sites within the sequenceoutputDirectory
- The outputdirectory for temporary filesmaxUp
- maximum upstream range from the splicesitesmaxDown
- maximum downstream range from the splicesite
public java.lang.String extractSequenceString(java.lang.String sequence, int location, int maxUp, int maxDown)
sequence
- The sequencelocation
- The location of the splicesitemaxUp
- The maximum upstream locationmaxDown
- The maximum downstream location
public static void main(java.lang.String[] args)
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