public class SecondPassSectionSpotsParser extends Object implements BaseFileSectionParser
Modifier and Type | Field and Description |
---|---|
private int |
channels |
private BioAssaySet |
child |
private DbControl |
dc |
private BaseFileInfo |
info |
private int |
linesToParse |
private int |
nextProgressReport |
private int |
progressReportInterval |
private int |
sectionCount |
Constructor and Description |
---|
SecondPassSectionSpotsParser(DbControl dc,
BaseFileInfo info,
BioAssaySet child,
int linesToParse)
Creates a new 'section spot' parser for the first pass.
|
Modifier and Type | Method and Description |
---|---|
void |
parseSection(BaseFileParser parser,
FlatFileParser ffp)
Parse the current section.
|
private final DbControl dc
private final BaseFileInfo info
private final BioAssaySet child
private final int linesToParse
private final int progressReportInterval
private int nextProgressReport
private final int channels
private int sectionCount
public SecondPassSectionSpotsParser(DbControl dc, BaseFileInfo info, BioAssaySet child, int linesToParse)
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 topublic void parseSection(BaseFileParser parser, FlatFileParser ffp) throws IOException
BaseFileSectionParser
FlatFileParser.parseHeaders()
must be called. Use
FlatFileParser.nextData()
to parse data lines.parseSection
in interface BaseFileSectionParser
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 dataIOException
- If there is a problem reading the data