util.parsers
Class ExtractTrainingData

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

public class ExtractTrainingData
extends java.lang.Object


Nested Class Summary
static class ExtractTrainingData.DATATYPES
           
 
Field Summary
static java.lang.String DIRECTORY
           
static int SPLICESITE
           
 
Constructor Summary
ExtractTrainingData()
           
ExtractTrainingData(boolean temp)
           
ExtractTrainingData(java.lang.String[] args)
           
 
Method Summary
 void extractFromData(GeneTrainingData data, java.io.BufferedWriter posDon, java.io.BufferedWriter negDon, java.io.BufferedWriter posAcc, java.io.BufferedWriter negAcc)
           
 GeneTrainingData extractFromFile(java.io.File f, ExtractTrainingData.DATATYPES type)
           
 GeneTrainingData extractFromFileEctocarpus(java.io.File f)
           
 GeneTrainingData extractFromFileMicromonas(java.io.File f)
           
 GeneTrainingData extractFromFileOstreococcus(java.io.File f)
           
 void extractNegativeAcceptors(java.util.List<java.lang.Integer> acceptors, java.lang.String sequence, java.io.BufferedWriter negAcc)
           
 void extractNegativeDonors(java.util.List<java.lang.Integer> donors, java.lang.String sequence, java.io.BufferedWriter negDon)
           
 void extractPositiveAcceptors(java.util.List<java.lang.Integer> acceptors, java.lang.String sequence, java.io.BufferedWriter posAcc, boolean forward)
           
 void extractPositiveDonors(java.util.List<java.lang.Integer> donors, java.lang.String sequence, java.io.BufferedWriter posDon, boolean forward)
           
 java.lang.String extractUpDown(int place, java.lang.String sequence, boolean forward)
           
 java.lang.String filterEMBLSeq(java.lang.String s)
           
static void main(java.lang.String[] args)
           
 util.parsers.ExtractTrainingData.HeaderClass parseHeader1(java.lang.String s)
           
 util.parsers.ExtractTrainingData.HeaderClass parseHeader2(java.lang.String s)
           
 util.parsers.ExtractTrainingData.HeaderClass parseHeader3(java.util.List<java.lang.String> list)
           
 int parseSQ(java.lang.String s)
           
 ExtractTrainingData.DATATYPES parseType(java.lang.String s)
           
 GeneTestResult testData(GeneTrainingData data)
           
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

DIRECTORY

public static java.lang.String DIRECTORY

SPLICESITE

public static final int SPLICESITE
See Also:
Constant Field Values
Constructor Detail

ExtractTrainingData

public ExtractTrainingData(boolean temp)

ExtractTrainingData

public ExtractTrainingData()

ExtractTrainingData

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

main

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

parseType

public ExtractTrainingData.DATATYPES parseType(java.lang.String s)

extractFromData

public void extractFromData(GeneTrainingData data,
                            java.io.BufferedWriter posDon,
                            java.io.BufferedWriter negDon,
                            java.io.BufferedWriter posAcc,
                            java.io.BufferedWriter negAcc)
                     throws java.io.IOException
Throws:
java.io.IOException

extractNegativeDonors

public void extractNegativeDonors(java.util.List<java.lang.Integer> donors,
                                  java.lang.String sequence,
                                  java.io.BufferedWriter negDon)
                           throws java.io.IOException
Throws:
java.io.IOException

extractNegativeAcceptors

public void extractNegativeAcceptors(java.util.List<java.lang.Integer> acceptors,
                                     java.lang.String sequence,
                                     java.io.BufferedWriter negAcc)
                              throws java.io.IOException
Throws:
java.io.IOException

extractPositiveDonors

public void extractPositiveDonors(java.util.List<java.lang.Integer> donors,
                                  java.lang.String sequence,
                                  java.io.BufferedWriter posDon,
                                  boolean forward)
                           throws java.io.IOException
Throws:
java.io.IOException

extractPositiveAcceptors

public void extractPositiveAcceptors(java.util.List<java.lang.Integer> acceptors,
                                     java.lang.String sequence,
                                     java.io.BufferedWriter posAcc,
                                     boolean forward)
                              throws java.io.IOException
Throws:
java.io.IOException

extractUpDown

public java.lang.String extractUpDown(int place,
                                      java.lang.String sequence,
                                      boolean forward)

testData

public GeneTestResult testData(GeneTrainingData data)

extractFromFile

public GeneTrainingData extractFromFile(java.io.File f,
                                        ExtractTrainingData.DATATYPES type)

extractFromFileMicromonas

public GeneTrainingData extractFromFileMicromonas(java.io.File f)

extractFromFileOstreococcus

public GeneTrainingData extractFromFileOstreococcus(java.io.File f)

extractFromFileEctocarpus

public GeneTrainingData extractFromFileEctocarpus(java.io.File f)

parseSQ

public int parseSQ(java.lang.String s)

filterEMBLSeq

public java.lang.String filterEMBLSeq(java.lang.String s)

parseHeader2

public util.parsers.ExtractTrainingData.HeaderClass parseHeader2(java.lang.String s)

parseHeader3

public util.parsers.ExtractTrainingData.HeaderClass parseHeader3(java.util.List<java.lang.String> list)

parseHeader1

public util.parsers.ExtractTrainingData.HeaderClass parseHeader1(java.lang.String s)