Package net.sf.basedb.plugins.gtf

Class GtfReporterImporter

java.lang.Object

net.sf.basedb.core.plugin.AbstractPlugin

net.sf.basedb.plugins.AbstractFlatFileImporter

net.sf.basedb.plugins.ReporterFlatFileImporter

net.sf.basedb.plugins.gtf.GtfReporterImporter

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 regular ReporterFlatFileImporter but uses a GtfInputStream 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) $

Nested Class Summary

Nested classes/interfaces inherited from interface net.sf.basedb.core.plugin.Plugin

Plugin.MainType

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

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

Fields inherited from class net.sf.basedb.core.plugin.AbstractPlugin

annotationSection, configuration, COPY_ANNOTATIONS, job, OVERWRITE_ANNOTATIONS, sc

Constructor Summary

Constructors

Constructor	Description
GtfReporterImporter()

Method Summary

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 a GtfInputStream.

Methods inherited from class net.sf.basedb.plugins.ReporterFlatFileImporter

begin, beginData, configure, end, getGuiContexts, getPermissions, getRequestInformation, getSuccessMessage, handleData, isInContext, requiresConfiguration, supportsConfigurations

Methods inherited from class net.sf.basedb.plugins.AbstractFlatFileImporter

addErrorHandler, checkColumnMapping, checkColumnMapping, continueWithNextFileAfterError, doImport, finish, getCharset, getCharset, getDateFormatter, getDecimalSeparator, getErrorHandler, getErrorOption, getFileIterator, getInitializedFlatFileParser, getInitializedFlatFileParser, getMainType, getMapper, getMapper, getNumberFormat, getPattern, getPattern, getProgress, getSignalHandler, getTimestampFormatter, getTotalFileSize, handleHeader, handleSection, isImportable, isImportable, log, log, log, log, run, setUpErrorHandling, start

Methods inherited from class net.sf.basedb.core.plugin.AbstractPlugin

cloneParameterWithDefaultValue, closeLogFile, createLogFile, done, getCopyAnnotationsParmeter, getCurrentConfiguration, getCurrentJob, getJobOrConfigurationValue, getOverwriteAnnotationsParameters, isLogging, log, log, storeValue, storeValue, storeValues, validateRequestParameters

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface net.sf.basedb.core.plugin.Plugin

done, getMainType, getPermissions, requiresConfiguration, run, supportsConfigurations

Field Details

tracker

private InputStreamTracker tracker

Needed for progress reporting since reading from the source will produce less bytes when wrapped.

Constructor Details

GtfReporterImporter

public GtfReporterImporter()

Method Details

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 the AbstractPlugin.sc, AbstractPlugin.configuration and AbstractPlugin.job variables. If a subclass overrides this method it is recommended that it also calls super.init(sc, configuration, job).

Specified by:

init in interface Plugin

Overrides:

init in class AbstractPlugin

Parameters:

sc - A SessionControl object that the plugin can use to communicate with the core.

configuration - The configuration parameters for the plugin

job - The job parameters for the plugin

Throws:

BaseException - if there is an error.

wrapInputStream

public InputStream wrapInputStream(InputStream in)
                            throws IOException

Wrap the input stream with a GtfInputStream.

Specified by:

wrapInputStream in interface WrappedConfigureByExample

Overrides:

wrapInputStream in class AbstractFlatFileImporter

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)

getNumBytes

protected long getNumBytes(FlatFileParser ffp)

Get the number of bytes read from the original file.

Overrides:

getNumBytes in class AbstractFlatFileImporter

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)