2.17.2: 2011-06-17

net.sf.basedb.util.importer.spotdata
Class SecondPassSectionSpotsParser

java.lang.Object
  extended by 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) $

Field Summary
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 Summary
SecondPassSectionSpotsParser(DbControl dc, BaseFileInfo info, BioAssaySet child, int linesToParse)
          Creates a new 'section spot' parser for the first pass.
 
Method Summary
 void parseSection(BaseFileParser parser, FlatFileParser ffp)
          Parse the current section.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

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
Constructor Detail

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 access
info - Information about the file we are parsing
child - The new child bioassay set that we are importing data to
Method Detail

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

2.17.2: 2011-06-17