net.sf.basedb.util.importer.spotdata
Class SecondPassSectionSpotsParser
java.lang.Object
net.sf.basedb.util.importer.spotdata.SecondPassSectionSpotsParser
- All Implemented Interfaces:
- BaseFileSectionParser
public class SecondPassSectionSpotsParser
- extends Object
- implements BaseFileSectionParser
The second pass of the 'spots' section extracts spot and extra value
data.
- Version:
- 2.14
- Author:
- Nicklas
- Last modified
- $Date: 2010-09-10 13:09:05 +0200 (Fri, 10 Sep 2010) $
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
dc
private final DbControl dc
info
private final BaseFileInfo info
child
private final BioAssaySet child
linesToParse
private final int linesToParse
progressReportInterval
private final int progressReportInterval
nextProgressReport
private int nextProgressReport
channels
private final int channels
sectionCount
private int sectionCount
SecondPassSectionSpotsParser
public SecondPassSectionSpotsParser(DbControl dc,
BaseFileInfo info,
BioAssaySet child,
int linesToParse)
- Creates a new 'section spot' parser for the first pass. This
parser will only extract header and reporter/position mapping
information.
- Parameters:
dc
- A DbControl to use for database accessinfo
- Information about the file we are parsingchild
- The new child bioassay set that we are importing data to
parseSection
public void parseSection(BaseFileParser parser,
FlatFileParser ffp)
throws IOException
- Description copied from interface:
BaseFileSectionParser
- Parse the current section. The current parse position is right
after the section marker. If the section contains headers the
FlatFileParser.parseHeaders()
must be called. Use
FlatFileParser.nextData()
to parse data lines.
- Specified by:
parseSection
in interface BaseFileSectionParser
- Parameters:
parser
- The master BASEfile parser (can be used for
reporting progress, checking for interrupts, etc.)ffp
- The actual file parser, use this to get the data
- Throws:
IOException
- If there is a problem reading the data