Class SectionAssaysParser
- java.lang.Object
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- net.sf.basedb.util.importer.spotdata.SectionAssaysParser
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- 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: 2019-03-20 14:31:03 +0100 (ons, 20 mars 2019) $
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Field Summary
Fields Modifier and Type Field Description private DbControl
dc
private BaseFileInfo
info
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Constructor Summary
Constructors Constructor Description SectionAssaysParser(DbControl dc, BaseFileInfo info)
Creates a new 'section assays' parser.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
parseSection(BaseFileParser parser, FlatFileParser ffp)
Parse the current section.
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Field Detail
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dc
private final DbControl dc
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info
private final BaseFileInfo info
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Constructor Detail
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SectionAssaysParser
public SectionAssaysParser(DbControl dc, BaseFileInfo info)
Creates a new 'section assays' parser.- Parameters:
dc
- The DbControl to use for database accessinfo
- Information collector for the file we are parsing
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Method Detail
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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 theFlatFileParser.parseHeaders()
must be called. UseFlatFileParser.nextData()
to parse data lines.- Specified by:
parseSection
in interfaceBaseFileSectionParser
- 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
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