util.parsers
Class ExtractTrainingData
java.lang.Object
util.parsers.ExtractTrainingData
public class ExtractTrainingData
- extends java.lang.Object
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 |
DIRECTORY
public static java.lang.String DIRECTORY
SPLICESITE
public static final int SPLICESITE
- See Also:
- Constant Field Values
ExtractTrainingData
public ExtractTrainingData(boolean temp)
ExtractTrainingData
public ExtractTrainingData()
ExtractTrainingData
public ExtractTrainingData(java.lang.String[] args)
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)