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 (Thu, 29 Sep 2011) $
Field Summary |
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.AbstractFlatFileImporter |
complexMappings, dataFooterRegexpParameter, dataHeaderRegexpParameter, dataSplitterRegexpParameter, defaultErrorParameter, errorSection, fileParameter, fileType, headerRegexpParameter, ignoreRegexpParameter, invalidUseOfNullErrorParameter, mappingSection, maxDataColumnsParameter, minDataColumnsParameter, numberFormatErrorParameter, numberOutOfRangeErrorParameter, numDataColumnsType, optionalRegexpType, parserSection, requiredRegexpType, sectionRegexpParameter, stringTooLongErrorParameter, trimQuotesParameter |
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, getDecimalSeparator, getErrorHandler, getErrorOption, getFileIterator, getInitializedFlatFileParser, getMainType, getMapper, getMapper, getNumberFormat, getProgress, getSignalHandler, 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, log, log, storeValue, storeValue, storeValues, validateRequestParameters |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
tracker
private InputStreamTracker tracker
- Needed for progress reporting since reading from the source
will produce less bytes when wrapped.
GtfReporterImporter
public GtfReporterImporter()
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 pluginjob
- 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)