Package net.sf.basedb.plugins.gtf
Class GtfReporterMapImporter
java.lang.Object
net.sf.basedb.core.plugin.AbstractPlugin
net.sf.basedb.plugins.AbstractFlatFileImporter
net.sf.basedb.plugins.ReporterMapFlatFileImporter
net.sf.basedb.plugins.gtf.GtfReporterMapImporter
- All Implemented Interfaces:
AutoDetectingImporter
,InteractivePlugin
,Plugin
,SignalTarget
,ConfigureByExample
,WrappedConfigureByExample
public class GtfReporterMapImporter
extends ReporterMapFlatFileImporter
implements InteractivePlugin, WrappedConfigureByExample
Import features to an array design from a GTF file. The default
settings use transcript_id+seqname as the feature id and reporter id. This
can be changed by user configuration, but it is recommended that
transcript_id+seqname is used as feature id since other combinations of
values may not be unique in raw data files.
- Since:
- 3.0
- Author:
- Nicklas
- Last modified
- $Date: 2011-09-29 13:48:47 +0200 (to, 29 sep 2011) $
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Nested Class Summary
Nested classes/interfaces inherited from interface net.sf.basedb.core.plugin.Plugin
Plugin.MainType
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Field Summary
Modifier and TypeFieldDescriptionprivate List<PluginParameter<String>>
private RequestInformation
private RequestInformation
protected static final PluginParameter<String>
private InputStreamTracker
Needed for progress reporting since reading from the source will produce less bytes when wrapped.Fields inherited from class net.sf.basedb.plugins.ReporterMapFlatFileImporter
blockColumnMapping, columnColumnMapping, duplicateFeatureErrorParameter, featureIdColumnMapping, featureIdentificationParameter, metaGridXColumnMapping, metaGridYColumnMapping, missingReporterErrorParameter, positionColumnMapping, reporterIdColumnMapping, rowColumnMapping
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
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Constructor Summary
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Method Summary
Modifier and TypeMethodDescriptionvoid
configure
(GuiContext context, Request request, Response response) Store configuration settings forRequest.COMMAND_CONFIGURE_PLUGIN
andRequest.COMMAND_CONFIGURE_JOB
.private List<PluginParameter<String>>
private RequestInformation
getConfigurePluginParameters
(GuiContext context) protected long
Get the number of bytes read from the original file.getRequestInformation
(GuiContext context, String command) TheRequest.COMMAND_CONFIGURE_PLUGIN
command will ask for parser regular expressions and column mappings.void
init
(SessionControl sc, ParameterValues configuration, ParameterValues job) Store copies of the session control, plugin and job configuration.isInContext
(GuiContext context, Object item) Returns null if the item is aArrayDesign
that doesn't already have any features and is using a supported platform/variant.Wrap the input stream with aGtfInputStream
.Methods inherited from class net.sf.basedb.plugins.ReporterMapFlatFileImporter
begin, beginData, end, getGuiContexts, getPermissions, getSuccessMessage, handleData, 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.InteractivePlugin
getGuiContexts
Methods inherited from interface net.sf.basedb.core.plugin.Plugin
done, getMainType, getPermissions, requiresConfiguration, run, supportsConfigurations
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Field Details
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tracker
Needed for progress reporting since reading from the source will produce less bytes when wrapped. -
configurePlugin
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configureJob
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allColumnMappings
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requiredFeatureIdColumnMapping
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Constructor Details
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GtfReporterMapImporter
public GtfReporterMapImporter()
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Method Details
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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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isInContext
Description copied from class:ReporterMapFlatFileImporter
Returns null if the item is aArrayDesign
that doesn't already have any features and is using a supported platform/variant.- Specified by:
isInContext
in interfaceInteractivePlugin
- Overrides:
isInContext
in classReporterMapFlatFileImporter
- Parameters:
context
- The current context of the client application, it is one of the values found in set returned byInteractivePlugin.getGuiContexts()
item
- The currently active item, it's type should match theGuiContext.getItem()
type, or null if the context is a list context- Returns:
Null
if the plugin can use that item, or a warning-level message explaining why the plugin can't be used
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getRequestInformation
public RequestInformation getRequestInformation(GuiContext context, String command) throws BaseException Description copied from class:ReporterMapFlatFileImporter
TheRequest.COMMAND_CONFIGURE_PLUGIN
command will ask for parser regular expressions and column mappings. TheRequest.COMMAND_CONFIGURE_JOB
command will ask for a file and the array design that features should be added to.- Specified by:
getRequestInformation
in interfaceInteractivePlugin
- Overrides:
getRequestInformation
in classReporterMapFlatFileImporter
- Parameters:
context
- The current context of the client application, it is one of the values found in set returned byInteractivePlugin.getGuiContexts()
command
- The command- Returns:
- The
RequestInformation
for the command - Throws:
BaseException
- if there is an error
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configure
Description copied from class:ReporterMapFlatFileImporter
Store configuration settings forRequest.COMMAND_CONFIGURE_PLUGIN
andRequest.COMMAND_CONFIGURE_JOB
.- Specified by:
configure
in interfaceInteractivePlugin
- Overrides:
configure
in classReporterMapFlatFileImporter
- Parameters:
context
- The current context of the client application, it is one of the values found in set returned byInteractivePlugin.getGuiContexts()
request
- Request object with the command and parametersresponse
- Response object in for the plugin to response through
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wrapInputStream
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:
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getNumBytes
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:
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getAllColumnMappings
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getConfigurePluginParameters
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