Package ubic.gemma.core.analysis.preprocess.batcheffects

Class AgilentScanDateExtractor

java.lang.Object

ubic.gemma.core.analysis.preprocess.batcheffects.BaseScanDateExtractor

ubic.gemma.core.analysis.preprocess.batcheffects.AgilentScanDateExtractor

All Implemented Interfaces:

ScanDateExtractor

public class AgilentScanDateExtractor
extends BaseScanDateExtractor

Because agilent makes slides that work with any scanner, the formats are not that predictable. I've seen these so far:

• GPR format format.
• Agilent scanner files. These start with "TYPE" Example: GSE14466. The second line is "FEPARAMS", the fourth column is "Scan_date". The data are in the third line.

Author:

paul

Field Summary

Fields

Modifier and Type	Field	Description
static DateFormat	AGILENT_DATE_FORMAT

Fields inherited from class ubic.gemma.core.analysis.preprocess.batcheffects.BaseScanDateExtractor

GENEPIX_DATETIME_HEADER_REGEXP

Constructor Summary

Constructors

Constructor	Description
AgilentScanDateExtractor()

Method Summary

Modifier and Type	Method	Description
Date	extract(InputStream is)

Methods inherited from class ubic.gemma.core.analysis.preprocess.batcheffects.BaseScanDateExtractor

extractGenePix, parseGenePixDateTime, parseISO8601, parseLongFormat, parseStandardFormat

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details

AGILENT_DATE_FORMAT

public static DateFormat AGILENT_DATE_FORMAT

Constructor Details

AgilentScanDateExtractor

public AgilentScanDateExtractor()

Method Details

extract

public Date extract(InputStream is)
             throws IOException,
ParseException

Throws:

IOException

ParseException