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) $
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 |
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.
configurePlugin
private RequestInformation configurePlugin
configureJob
private RequestInformation configureJob
allColumnMappings
private List<PluginParameter<String>> allColumnMappings
requiredFeatureIdColumnMapping
protected static final PluginParameter<String> requiredFeatureIdColumnMapping
GtfReporterMapImporter
public GtfReporterMapImporter()
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.
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 parametersresponse
- 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)