2.17.2: 2011-06-17

Class SectionAssaysParser

  extended by net.sf.basedb.util.importer.spotdata.SectionAssaysParser
All Implemented Interfaces:

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

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


private final DbControl dc


private final BaseFileInfo info
Constructor Detail


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

dc - The DbControl to use for database access
info - Information collector for the file we are parsing
Method Detail


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
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
IOException - If there is a problem reading the data

2.17.2: 2011-06-17