Class TaxonParser
- java.lang.Object
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- ubic.gemma.core.loader.util.parser.BasicLineMapParser<Integer,Taxon>
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- ubic.gemma.core.loader.genome.taxon.TaxonParser
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- All Implemented Interfaces:
LineParser<Taxon>
,Parser<Taxon>
public class TaxonParser extends BasicLineMapParser<Integer,Taxon>
Parse the "names.dmp" file from NCBI, ftp://ftp.ncbi.nih.gov/pub/taxonomy/.- Author:
- pavlidis
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Field Summary
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Fields inherited from class ubic.gemma.core.loader.util.parser.BasicLineMapParser
COMMENT_MARK, log
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Fields inherited from interface ubic.gemma.core.loader.util.parser.LineParser
MIN_PARSED_LINES_FOR_UPDATE, PARSE_ALERT_TIME_FREQUENCY_MS
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Fields inherited from interface ubic.gemma.core.loader.util.parser.Parser
PARSE_ALERT_FREQUENCY
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Constructor Summary
Constructors Constructor Description TaxonParser()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description boolean
containsKey(Integer key)
Taxon
get(Integer key)
protected Integer
getKey(Taxon newItem)
Collection<Integer>
getKeySet()
Collection<Taxon>
getResults()
Taxon
parseOneLine(String line)
Handle the parsing of a single line from the input.protected void
put(Integer key, Taxon value)
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Methods inherited from class ubic.gemma.core.loader.util.parser.BasicLineMapParser
parse, parse, parse
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Method Detail
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containsKey
public boolean containsKey(Integer key)
- Specified by:
containsKey
in classBasicLineMapParser<Integer,Taxon>
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getKeySet
public Collection<Integer> getKeySet()
- Specified by:
getKeySet
in classBasicLineMapParser<Integer,Taxon>
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getResults
public Collection<Taxon> getResults()
- Specified by:
getResults
in interfaceParser<Taxon>
- Specified by:
getResults
in classBasicLineMapParser<Integer,Taxon>
- Returns:
- the results of the parse.
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parseOneLine
public Taxon parseOneLine(String line)
Description copied from interface:LineParser
Handle the parsing of a single line from the input.- Specified by:
parseOneLine
in interfaceLineParser<Taxon>
- Specified by:
parseOneLine
in classBasicLineMapParser<Integer,Taxon>
- Parameters:
line
- line to parse- Returns:
- parsed object
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getKey
protected Integer getKey(Taxon newItem)
- Specified by:
getKey
in classBasicLineMapParser<Integer,Taxon>
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