gov.nih.nci.caarray.services.fileparse2.parsers
Class BaseMicroarrayFileParser

java.lang.Object
  extended by gov.nih.nci.caarray.services.fileparse2.parsers.BaseMicroarrayFileParser
Direct Known Subclasses:
AffyCelFileParser, AffyChpFileParser, MicroarrayDelimitedFileParser

public abstract class BaseMicroarrayFileParser
extends java.lang.Object

Author:
TranP

Field Summary
protected  DataSet dataSet_
           
protected  DataSetMapper dataSetMapper_
           
protected  BaseMicroarrayFileHeaderParser headerParser_
           
protected  org.apache.log4j.Logger logger_
          Logger used by this class.
protected  boolean parsed_
           
 
Constructor Summary
BaseMicroarrayFileParser(DataSetMapper dataSetMapper)
           
 
Method Summary
protected  org.apache.commons.beanutils.BasicDynaClass createDataTableRowBeanClass()
           
 DataSet getDataSet()
           
 DataSetMapper getDataSetMapper()
           
abstract  void parse(SequenceInputFile inputFile)
           
protected static java.io.File readFile(java.lang.String fileName)
           
 LocalDynaBean[] readRows()
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

logger_

protected org.apache.log4j.Logger logger_
Logger used by this class.


dataSetMapper_

protected DataSetMapper dataSetMapper_

dataSet_

protected DataSet dataSet_

parsed_

protected boolean parsed_

headerParser_

protected BaseMicroarrayFileHeaderParser headerParser_
Constructor Detail

BaseMicroarrayFileParser

public BaseMicroarrayFileParser(DataSetMapper dataSetMapper)
Method Detail

parse

public abstract void parse(SequenceInputFile inputFile)
                    throws java.io.IOException
Throws:
java.io.IOException

readRows

public LocalDynaBean[] readRows()

getDataSet

public DataSet getDataSet()
Returns:
Returns the dataSet.

getDataSetMapper

public DataSetMapper getDataSetMapper()

createDataTableRowBeanClass

protected org.apache.commons.beanutils.BasicDynaClass createDataTableRowBeanClass()

readFile

protected static final java.io.File readFile(java.lang.String fileName)
                                      throws java.io.FileNotFoundException
Throws:
java.io.FileNotFoundException