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

java.lang.Object
  net.sf.basedb.util.importer.spotdata.SectionAssaysParser

All Implemented Interfaces:

BaseFileSectionParser

public class SectionAssaysParser
extends Object
implements BaseFileSectionParser

Parses the 'assays' section of a BASEfile with bioassay set spot data. This section is optional, but if it exists, it must define 'id' and 'name' columns of child bioassays. The 'id' must be the same as the id of a parent bioassay unless a 'parents' column is present. One or more parents can be given for each child. Separate the values with a /.

NOTE! The column names can be redefined by calling BaseFileParser.setRedefinedColumnName(String, String, String)

section assays
columns id\tname\tparents
count   2
%
100     The first child 1/2/3
101     The second child        4/5/6

Version:

2.14

Author:

Nicklas

Last modified

$Date: 2009-09-14 08:29:17 +0200 (Mon, 14 Sep 2009) $

Field Summary

private DbControl	dc
private BaseFileInfo	info

Constructor Summary

SectionAssaysParser(DbControl dc, BaseFileInfo info)
Creates a new 'section assays' parser.

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

Constructor Detail

SectionAssaysParser

public SectionAssaysParser(DbControl dc,
                           BaseFileInfo info)

Creates a new 'section assays' parser.

Parameters:

dc - The DbControl to use for database access

info - Information collector for the file we are parsing

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