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java.lang.Object net.sf.basedb.core.plugin.AbstractPlugin net.sf.basedb.plugins.CdfFileReporterImporter
public class CdfFileReporterImporter
This plug-in can import probesets from Affymetrix CDF files as reporters.
The plug-in uses the Affymetrix
class for the actual work.
AutoDetectingImporter
interface
we needed to duplicate the file format checks from the Fusion SDK
in this class. See isImportable(InputStream)
.Nested Class Summary |
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Nested classes/interfaces inherited from interface net.sf.basedb.core.plugin.Plugin |
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Plugin.MainType |
Field Summary | |
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private static About |
about
Plugin description |
private RequestInformation |
configureJob
|
private static Set<GuiContext> |
guiContexts
|
private static Set<Permissions> |
permissions
|
private ThreadSignalHandler |
signalHandler
|
Fields inherited from class net.sf.basedb.core.plugin.AbstractPlugin |
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annotationSection, configuration, COPY_ANNOTATIONS, job, OVERWRITE_ANNOTATIONS, sc |
Constructor Summary | |
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CdfFileReporterImporter()
Constructor should be empty. |
Method Summary | |
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void |
configure(GuiContext context,
Request request,
Response response)
Configure the plugin. |
void |
doImport(InputStream in,
ProgressReporter progress)
Import the data from the given InputStream . |
About |
getAbout()
Get information about the plugin, such as name, version, authors, etc. |
private RequestInformation |
getConfigureJobParameters(GuiContext context)
|
Set<GuiContext> |
getGuiContexts()
Get a set containing all items that the plugin handles. |
Plugin.MainType |
getMainType()
Get the type of the plugin. |
Collection<Permissions> |
getPermissions()
Request create and write access to Reporter:s and read access to File:s ArrayDesign:s, ReporterType:s, Platform:s and DataFileType:s |
RequestInformation |
getRequestInformation(GuiContext context,
String command)
This method will return the RequestInformation for a given command, i.e. |
SignalHandler |
getSignalHandler()
Get the signal handler that is handling signals on behalf of this object. |
private int |
importFromCdf(DbControl dc,
affymetrix.fusion.cdf.FusionCDFData cdf,
ProgressReporter progress)
|
boolean |
isImportable(InputStream in)
Check if the given InputStream can be imported by this
plugin. |
String |
isInContext(GuiContext context,
Object item)
If used from an array design context, verify that the array design is an affymetrix chip. |
boolean |
requiresConfiguration()
Returns FALSE, since that is how the plugins used to work before this method was introduced. |
void |
run(Request request,
Response response,
ProgressReporter progress)
Run the plugin. |
boolean |
supportsConfigurations()
Returns TRUE, since that is how the plugins used to work before this method was introduced. |
Methods inherited from class net.sf.basedb.core.plugin.AbstractPlugin |
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checkInterrupted, cloneParameterWithDefaultValue, closeLogFile, createLogFile, done, getCopyAnnotationsParmeter, getCurrentConfiguration, getCurrentJob, getJobOrConfigurationValue, getOverwriteAnnotationsParameters, init, log, log, storeValue, storeValue, storeValues, validateRequestParameters |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Methods inherited from interface net.sf.basedb.core.plugin.Plugin |
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done, init |
Field Detail |
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private static final About about
private static final Set<GuiContext> guiContexts
private static final Set<Permissions> permissions
private RequestInformation configureJob
private ThreadSignalHandler signalHandler
Constructor Detail |
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public CdfFileReporterImporter()
Method Detail |
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public About getAbout()
Plugin
getAbout
in interface Plugin
About
objectpublic boolean supportsConfigurations()
AbstractPlugin
supportsConfigurations
in interface Plugin
supportsConfigurations
in class AbstractPlugin
public boolean requiresConfiguration()
AbstractPlugin
requiresConfiguration
in interface Plugin
requiresConfiguration
in class AbstractPlugin
public Plugin.MainType getMainType()
Plugin
getMainType
in interface Plugin
public Collection<Permissions> getPermissions()
getPermissions
in interface Plugin
getPermissions
in class AbstractPlugin
public void run(Request request, Response response, ProgressReporter progress)
Plugin
run
in interface Plugin
request
- Request object with the command and parametersresponse
- Response object in for the plugin to response
throughprogress
- A ProgressReporter
where the plugin can report
its progess, can be nullpublic Set<GuiContext> getGuiContexts()
InteractivePlugin
Item.REPORTER
.
This information is used by client applications to put the plugin
in the proper place in the user interface.
getGuiContexts
in interface InteractivePlugin
Set
containing Item
:s, or null
if the plugin is not concerned about itemspublic String isInContext(GuiContext context, Object item)
isInContext
in interface InteractivePlugin
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
Null
if the plugin can use that item, or
a warning-level message explaining why the plugin can't be usedpublic RequestInformation getRequestInformation(GuiContext context, String command) throws BaseException
InteractivePlugin
RequestInformation
for a given command, i.e.
the list of parameters and some nice help text.
getRequestInformation
in interface InteractivePlugin
context
- The current context of the client application,
it is one of the values found in set returned by InteractivePlugin.getGuiContexts()
command
- The command
RequestInformation
for the command
BaseException
- if there is an errorpublic void configure(GuiContext context, Request request, Response response)
InteractivePlugin
InteractivePlugin.getRequestInformation(GuiContext, String)
.
configure
in interface InteractivePlugin
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
throughpublic final boolean isImportable(InputStream in) throws BaseException
AutoDetectingImporter
InputStream
can be imported by this
plugin.
isImportable
in interface AutoDetectingImporter
in
- The input stream to check
BaseException
- If something goes wrongpublic void doImport(InputStream in, ProgressReporter progress) throws BaseException
AutoDetectingImporter
InputStream
.
doImport
in interface AutoDetectingImporter
in
- The input stream to read fromprogress
- Progress reporter used by the caller to keep track of the progress.
Null is allowed
BaseException
- If something goes wrongpublic SignalHandler getSignalHandler()
SignalTarget
getSignalHandler
in interface SignalTarget
private RequestInformation getConfigureJobParameters(GuiContext context)
private int importFromCdf(DbControl dc, affymetrix.fusion.cdf.FusionCDFData cdf, ProgressReporter progress)
|
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