gov.nih.nci.caarray.services.fileparse2.parsers
Class BaseMicroarrayFileHeaderParser
java.lang.Object
gov.nih.nci.caarray.services.fileparse2.parsers.BaseMicroarrayFileHeaderParser
- Direct Known Subclasses:
- ArrayDesignFileHeaderParser, MicroarrayTextFileHeaderParser
public abstract class BaseMicroarrayFileHeaderParser
- extends java.lang.Object
- Author:
- tranp
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
logger_
protected org.apache.log4j.Logger logger_
- Logger used by this class.
header_
protected org.apache.commons.beanutils.BasicDynaBean header_
dataSetMapper_
protected DataSetMapper dataSetMapper_
BaseMicroarrayFileHeaderParser
public BaseMicroarrayFileHeaderParser(DataSetMapper dataHeaderMap)
parse
public abstract void parse(SequenceInputFile inputFile)
throws java.io.IOException
- Throws:
java.io.IOException
validate
public abstract boolean validate(SequenceInputFile inputFile,
boolean resetPointerAfterDone)
throws java.io.IOException
- Validates the file if it's the right one before proceeding further. The
typical implementation for this is to look at some parameters in the
file's header and match certain string. However, anything could be
performed to prevent the file from further processing. When this method
returns, the file pointer could be repositioned to where it was before
the method is invoked so the data can be re-read by passing
true
for the argument resetPointerAfterDone
.
- Parameters:
inputFile
-
- Returns:
-
- Throws:
java.io.IOException
getHeader
public org.apache.commons.beanutils.BasicDynaBean getHeader()
getDataSetMapper
protected DataSetMapper getDataSetMapper()