Package net.sf.basedb.plugins.gtf
Class GtfReporterImporter
- java.lang.Object
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- net.sf.basedb.core.plugin.AbstractPlugin
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- net.sf.basedb.plugins.AbstractFlatFileImporter
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- net.sf.basedb.plugins.ReporterFlatFileImporter
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- net.sf.basedb.plugins.gtf.GtfReporterImporter
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- All Implemented Interfaces:
AutoDetectingImporter
,InteractivePlugin
,Plugin
,SignalTarget
,ConfigureByExample
,WrappedConfigureByExample
public class GtfReporterImporter extends ReporterFlatFileImporter implements WrappedConfigureByExample
Reporter importer implementation that create reporters from information in GTF files. The implementation builds on the regularReporterFlatFileImporter
but uses aGtfInputStream
as a wrapper to generate a pure column-based output which can be used by the regular tools for file parsing. The importer will also skip lines with a non-unique transcript_id+seqname.The default configuration is to use the transcript_id+seqname as the reporter id and name. gene_id is stored as "gene symbol" and seqname as "chromosome". The default configuration can be changed by user configurations depending on what additional attributes that are present in the GTF file.
- Since:
- 3.0
- Author:
- Nicklas
- Last modified
- $Date: 2011-09-29 13:27:33 +0200 (to, 29 sep 2011) $
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Nested Class Summary
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Nested classes/interfaces inherited from interface net.sf.basedb.core.plugin.Plugin
Plugin.MainType
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Field Summary
Fields Modifier and Type Field Description private InputStreamTracker
tracker
Needed for progress reporting since reading from the source will produce less bytes when wrapped.-
Fields inherited from class net.sf.basedb.plugins.ReporterFlatFileImporter
reporterIsUsedErrorParameter
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Fields inherited from class net.sf.basedb.plugins.AbstractFlatFileImporter
complexMappings, dataFooterRegexpParameter, dataHeaderRegexpParameter, dataSplitterRegexpParameter, defaultErrorParameter, errorSection, excelSheetParameter, fileParameter, fileType, headerRegexpParameter, ignoreRegexpParameter, invalidUseOfNullErrorParameter, mappingSection, maxDataColumnsParameter, minDataColumnsParameter, numberFormatErrorParameter, numberOutOfRangeErrorParameter, numDataColumnsType, optionalRegexpType, parserSection, requiredRegexpType, sectionRegexpParameter, stringTooLongErrorParameter, trimQuotesParameter
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Fields inherited from class net.sf.basedb.core.plugin.AbstractPlugin
annotationSection, configuration, COPY_ANNOTATIONS, job, OVERWRITE_ANNOTATIONS, sc
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Constructor Summary
Constructors Constructor Description GtfReporterImporter()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected long
getNumBytes(FlatFileParser ffp)
Get the number of bytes read from the original file.void
init(SessionControl sc, ParameterValues configuration, ParameterValues job)
Store copies of the session control, plugin and job configuration.InputStream
wrapInputStream(InputStream in)
Wrap the input stream with aGtfInputStream
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Methods inherited from class net.sf.basedb.plugins.ReporterFlatFileImporter
begin, beginData, configure, end, getGuiContexts, getPermissions, getRequestInformation, getSuccessMessage, handleData, isInContext, requiresConfiguration, supportsConfigurations
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Methods inherited from class net.sf.basedb.plugins.AbstractFlatFileImporter
addErrorHandler, checkColumnMapping, checkColumnMapping, continueWithNextFileAfterError, doImport, finish, getCharset, getCharset, getDateFormatter, getDecimalSeparator, getErrorHandler, getErrorOption, getFileIterator, getInitializedFlatFileParser, getMainType, getMapper, getMapper, getNumberFormat, getPattern, getProgress, getSignalHandler, getTimestampFormatter, getTotalFileSize, handleHeader, handleSection, isImportable, isImportable, log, log, log, log, run, setUpErrorHandling, start
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Methods inherited from class net.sf.basedb.core.plugin.AbstractPlugin
cloneParameterWithDefaultValue, closeLogFile, createLogFile, done, getCopyAnnotationsParmeter, getCurrentConfiguration, getCurrentJob, getJobOrConfigurationValue, getOverwriteAnnotationsParameters, log, log, storeValue, storeValue, storeValues, validateRequestParameters
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Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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Methods inherited from interface net.sf.basedb.core.plugin.Plugin
done, getMainType, getPermissions, requiresConfiguration, run, supportsConfigurations
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Field Detail
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tracker
private InputStreamTracker tracker
Needed for progress reporting since reading from the source will produce less bytes when wrapped.
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Method Detail
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init
public void init(SessionControl sc, ParameterValues configuration, ParameterValues job) throws BaseException
Description copied from class:AbstractPlugin
Store copies of the session control, plugin and job configuration. These are available to subclasses in theAbstractPlugin.sc
,AbstractPlugin.configuration
andAbstractPlugin.job
variables. If a subclass overrides this method it is recommended that it also callssuper.init(sc, configuration, job)
.- Specified by:
init
in interfacePlugin
- Overrides:
init
in classAbstractPlugin
- Parameters:
sc
- ASessionControl
object that the plugin can use to communicate with the core.configuration
- The configuration parameters for the pluginjob
- The job parameters for the plugin- Throws:
BaseException
- if there is an error.
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wrapInputStream
public InputStream wrapInputStream(InputStream in) throws IOException
Wrap the input stream with aGtfInputStream
.- Specified by:
wrapInputStream
in interfaceWrappedConfigureByExample
- Overrides:
wrapInputStream
in classAbstractFlatFileImporter
- Parameters:
in
- The input stream to wrap- Returns:
- The same or a different input stream
- Throws:
IOException
- If there is an error- See Also:
AbstractFlatFileImporter.getNumBytes(FlatFileParser)
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getNumBytes
protected long getNumBytes(FlatFileParser ffp)
Get the number of bytes read from the original file.- Overrides:
getNumBytes
in classAbstractFlatFileImporter
- Parameters:
ffp
- The file parser that is used to parsed the file- Returns:
- The number of bytes read from the original file
- See Also:
AbstractFlatFileImporter.wrapInputStream(InputStream)
,AbstractFlatFileImporter.getProgress(FlatFileParser)
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