util.parsers.fasta
Class ExtractTrainingData

java.lang.Object
  extended by util.parsers.fasta.ExtractTrainingData

public class ExtractTrainingData
extends java.lang.Object


Field Summary
static java.lang.String DATADIRECTORY
           
static int MAX_EXTRACT
           
static boolean PURE_DNA
           
 
Constructor Summary
ExtractTrainingData(java.lang.String dir)
           
ExtractTrainingData(java.lang.String[] args)
           
 
Method Summary
 java.lang.String extractFromSequence(int i, java.lang.String seq)
           
static void main(java.lang.String[] args)
           
 void parseFirstLine(util.parsers.fasta.ExtractTrainingData.AnnotationData data, java.lang.String s)
           
 util.parsers.fasta.ExtractTrainingData.AnnotationData readData(java.lang.String fileName)
           
 void reverse(util.parsers.fasta.ExtractTrainingData.AnnotationData data)
           
 void writeAcceptors(java.io.BufferedWriter posData, java.io.BufferedWriter negData, util.parsers.fasta.ExtractTrainingData.AnnotationData data)
           
 void writeDonors(java.io.BufferedWriter posData, java.io.BufferedWriter negData, util.parsers.fasta.ExtractTrainingData.AnnotationData data)
           
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

DATADIRECTORY

public static final java.lang.String DATADIRECTORY
See Also:
Constant Field Values

MAX_EXTRACT

public static final int MAX_EXTRACT
See Also:
Constant Field Values

PURE_DNA

public static boolean PURE_DNA
Constructor Detail

ExtractTrainingData

public ExtractTrainingData(java.lang.String dir)

ExtractTrainingData

public ExtractTrainingData(java.lang.String[] args)
Method Detail

main

public static void main(java.lang.String[] args)

reverse

public void reverse(util.parsers.fasta.ExtractTrainingData.AnnotationData data)

writeAcceptors

public void writeAcceptors(java.io.BufferedWriter posData,
                           java.io.BufferedWriter negData,
                           util.parsers.fasta.ExtractTrainingData.AnnotationData data)
                    throws java.io.IOException
Throws:
java.io.IOException

writeDonors

public void writeDonors(java.io.BufferedWriter posData,
                        java.io.BufferedWriter negData,
                        util.parsers.fasta.ExtractTrainingData.AnnotationData data)
                 throws java.io.IOException
Throws:
java.io.IOException

extractFromSequence

public java.lang.String extractFromSequence(int i,
                                            java.lang.String seq)

readData

public util.parsers.fasta.ExtractTrainingData.AnnotationData readData(java.lang.String fileName)

parseFirstLine

public void parseFirstLine(util.parsers.fasta.ExtractTrainingData.AnnotationData data,
                           java.lang.String s)