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 (Thu, 29 Sep 2011) $

Nested Class Summary

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

Plugin.MainType

Field Summary

private List<PluginParameter<String>>	allColumnMappings
private RequestInformation	configureJob
private RequestInformation	configurePlugin
protected static PluginParameter<String>	requiredFeatureIdColumnMapping
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.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, 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

GtfReporterMapImporter()

Method Summary

void	configure(GuiContext context, Request request, Response response) Store configuration settings for Request.COMMAND_CONFIGURE_PLUGIN and Request.COMMAND_CONFIGURE_JOB.
private List<PluginParameter<String>>	getAllColumnMappings()
private RequestInformation	getConfigurePluginParameters(GuiContext context)
protected long	getNumBytes(FlatFileParser ffp) Get the number of bytes read from the original file.
RequestInformation	getRequestInformation(GuiContext context, String command) The Request.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.
String	isInContext(GuiContext context, Object item) Returns null if the item is a ArrayDesign that doesn't already have any features and is using a supported platform/variant.
InputStream	wrapInputStream(InputStream in) Wrap the input stream with a GtfInputStream.

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, 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

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

Field Detail

tracker

private InputStreamTracker tracker

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

configurePlugin

private RequestInformation configurePlugin

configureJob

private RequestInformation configureJob

allColumnMappings

private List<PluginParameter<String>> allColumnMappings

requiredFeatureIdColumnMapping

protected static final PluginParameter<String> requiredFeatureIdColumnMapping

Constructor Detail

GtfReporterMapImporter

public GtfReporterMapImporter()

Method Detail

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.

isInContext

public String isInContext(GuiContext context,
                          Object item)

Description copied from class: ReporterMapFlatFileImporter

Returns null if the item is a ArrayDesign that doesn't already have any features and is using a supported platform/variant.

Specified by:

isInContext in interface InteractivePlugin

Overrides:

isInContext in class ReporterMapFlatFileImporter

Parameters:

context - The current context of the client application, it is one of the values found in set returned by InteractivePlugin.getGuiContexts()

item - The currently active item, it's type should match the GuiContext.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

getRequestInformation

public RequestInformation getRequestInformation(GuiContext context,
                                                String command)
                                         throws BaseException

Description copied from class: ReporterMapFlatFileImporter

The Request.COMMAND_CONFIGURE_PLUGIN command will ask for parser regular expressions and column mappings. The Request.COMMAND_CONFIGURE_JOB command will ask for a file and the array design that features should be added to.

Specified by:

getRequestInformation in interface InteractivePlugin

Overrides:

getRequestInformation in class ReporterMapFlatFileImporter

Parameters:

context - The current context of the client application, it is one of the values found in set returned by InteractivePlugin.getGuiContexts()

command - The command

Returns:

The RequestInformation for the command

Throws:

BaseException - if there is an error

configure

public void configure(GuiContext context,
                      Request request,
                      Response response)

Description copied from class: ReporterMapFlatFileImporter

Store configuration settings for Request.COMMAND_CONFIGURE_PLUGIN and Request.COMMAND_CONFIGURE_JOB.

Specified by:

configure in interface InteractivePlugin

Overrides:

configure in class ReporterMapFlatFileImporter

Parameters:

context - The current context of the client application, it is one of the values found in set returned by InteractivePlugin.getGuiContexts()

request - Request object with the command and parameters

response - Response object in for the plugin to response through

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)

getAllColumnMappings

private List<PluginParameter<String>> getAllColumnMappings()

getConfigurePluginParameters

private RequestInformation getConfigurePluginParameters(GuiContext context)