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

Class BaseScanDateExtractor

java.lang.Object

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

All Implemented Interfaces:

ScanDateExtractor

Direct Known Subclasses:

AffyScanDateExtractor, AgilentScanDateExtractor, GenericScanFileDateExtractor

public abstract class BaseScanDateExtractor
extends Object
implements ScanDateExtractor

Author:

paul

Field Summary

Fields

Modifier and Type	Field	Description
protected static String	GENEPIX_DATETIME_HEADER_REGEXP

Constructor Summary

Constructors

Constructor	Description
BaseScanDateExtractor()

Method Summary

Modifier and Type	Method	Description
protected Date	extractGenePix(BufferedReader reader)	This method should be generic for GenePix/GPR/ATR file formats.
protected Date	parseGenePixDateTime(String line)
protected Date	parseISO8601(String string)
protected Date	parseLongFormat(String string)
protected Date	parseStandardFormat(String string)

Methods inherited from class java.lang.Object

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

Methods inherited from interface ubic.gemma.core.analysis.preprocess.batcheffects.ScanDateExtractor

extract

Field Detail

GENEPIX_DATETIME_HEADER_REGEXP

protected static final String GENEPIX_DATETIME_HEADER_REGEXP

See Also:

Constant Field Values

Constructor Detail

BaseScanDateExtractor

public BaseScanDateExtractor()

Method Detail

extractGenePix

protected Date extractGenePix(BufferedReader reader)
                       throws IOException

This method should be generic for GenePix/GPR/ATR file formats. Has DateType at the top formatted with quotes: "DateTime=2005/11/09 11:36:27". Example GSE15739 For more information see here.

Parameters:

reader - the reader

Returns:

date

Throws:

IOException - when there was a read error

parseGenePixDateTime

protected Date parseGenePixDateTime(String line)

Parameters:

line - like "DateTime=2005/11/09 11:36:27" (with the quotes) possibly with trailing whitespace.

Returns:

date

parseISO8601

protected Date parseISO8601(String string)

Parameters:

string - ISO 8601 date time in WSTRING format based on Universal Time Clock UTC (UTC is also known as GMT, or Greenwich Mean Time) E.g. "2005-11-23T13:45:53Z"

Returns:

date

parseLongFormat

protected Date parseLongFormat(String string)

Parameters:

string - E.g. "Mon Jun 17 21:26:34 CST 2002", but line has to have Date at start (possibly white-space padded) Shows up in Imagene files.

Returns:

date

parseStandardFormat

protected Date parseStandardFormat(String string)

Parameters:

string - Parse a common format, "MM[/-]dd[/-]yy hh:mm:ss", found for example in the "DatHeader" line from a CEL file and extract the date found there.

Returns:

date