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: 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. -
Method Summary
Modifier and Type Method Description void
parseSection(BaseFileParser parser, FlatFileParser ffp)
Parse the current section.
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Field Details
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dc
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info
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Constructor Details
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SectionAssaysParser
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 Details
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parseSection
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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