CompositeSequenceParser (Gemma 1.31.4 API)

java.lang.Object
- ubic.gemma.core.loader.util.parser.BasicLineParser<CompositeSequence>
- - ubic.gemma.core.loader.expression.arrayDesign.CompositeSequenceParser

All Implemented Interfaces:

LineParser<CompositeSequence>, Parser<CompositeSequence>
```
public class CompositeSequenceParser
extends BasicLineParser<CompositeSequence>
```
Parse the "old" array description format. This has three columns, with probe id, a genbank id, and a description. Note that this does not set the ArrayDesign for the CompositeSequences, this must be set by the caller.

Author:

pavlidis

Field Summary
- Fields inherited from class ubic.gemma.core.loader.util.parser.BasicLineParser
  log
- Fields inherited from interface ubic.gemma.core.loader.util.parser.LineParser
  MIN_PARSED_LINES_FOR_UPDATE, PARSE_ALERT_TIME_FREQUENCY_MS
- Fields inherited from interface ubic.gemma.core.loader.util.parser.Parser
  PARSE_ALERT_FREQUENCY

Constructor Summary

Constructors
Constructor Description

CompositeSequenceParser()

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`protected void`	`addResult(CompositeSequence obj)`
`Collection<CompositeSequence>`	`getResults()`
`CompositeSequence`	`parseOneLine(String line)`	Handle the parsing of a single line from the input.

Methods inherited from class ubic.gemma.core.loader.util.parser.BasicLineParser
parse, parse, parse

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - CompositeSequenceParser
```
public CompositeSequenceParser()
```
- Method Detail
  - getResults
```
public Collection<CompositeSequence> getResults()
```
    Specified by:
    
    getResults in interface Parser<CompositeSequence>
    
    Specified by:
    
    getResults in class BasicLineParser<CompositeSequence>
    
    Returns:
    
    the results of the parse.
  - addResult
```
protected void addResult(CompositeSequence obj)
```
    Specified by:
    
    addResult in class BasicLineParser<CompositeSequence>
  - parseOneLine
```
public CompositeSequence parseOneLine(String line)
```
    Description copied from interface: LineParser
    
    Handle the parsing of a single line from the input.
    
    Parameters:
    
    line - line to parse
    
    Returns:
    
    parsed object