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 Details

  • Constructor Details

    • BaseScanDateExtractor

      public BaseScanDateExtractor()

  • Method Details

    • 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