ParseMiseqFile (SeqWare 1.1.2 API)

java.lang.Object
- net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.BatchMetadataParser
- - net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.ParseMiseqFile

public class ParseMiseqFile
extends BatchMetadataParser

Author:: mtaschuk

Nested Class Summary
- Nested classes/interfaces inherited from class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.BatchMetadataParser
  BatchMetadataParser.Field

Field Summary
- Fields inherited from class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.BatchMetadataParser
  defaults, fields, interactive

Constructor Summary

Constructors
Constructor and Description

ParseMiseqFile(Metadata metadata, Map<String,String> fields, boolean interactive)

Constructors
Constructor and Description
`ParseMiseqFile(Metadata metadata, Map<String,String> fields, boolean interactive)`

Method Summary

Methods
Modifier and Type	Method and Description
`Set<LaneInfo>`	`parseMiseqData(BufferedReader freader)`
`RunInfo`	`parseMiseqFile(String filepath)`
`RunInfo`	`parseMiseqHeader(BufferedReader freader, File file)`

Methods inherited from class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.BatchMetadataParser
choiceOf, findOrganismId, generateLaneInfo, generateRunInfo, generateSampleInfo, printLaneInfo, printRunInfo, printSampleInfo, promptAccession, promptInteger, promptPositiveInteger, promptString, promptString

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

Constructor Detail

ParseMiseqFile

public ParseMiseqFile(Metadata metadata,
              Map<String,String> fields,
              boolean interactive)

Method Detail

parseMiseqFile

public RunInfo parseMiseqFile(String filepath)
                       throws Exception

Throws:: Exception

parseMiseqData

public Set<LaneInfo> parseMiseqData(BufferedReader freader)
                             throws IOException,
                                    Exception

Throws:: IOException; Exception

parseMiseqHeader

public RunInfo parseMiseqHeader(BufferedReader freader,
                       File file)
                         throws IOException

Throws:: IOException

Class ParseMiseqFile

Nested Class Summary

Nested classes/interfaces inherited from class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.BatchMetadataParser

Field Summary

Fields inherited from class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.BatchMetadataParser

Constructor Summary

Method Summary

Methods inherited from class net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection.BatchMetadataParser

Methods inherited from class java.lang.Object

Constructor Detail

ParseMiseqFile

Method Detail

parseMiseqFile

parseMiseqData

parseMiseqHeader