info.bioinfweb.jphyloio.formatinfo

Interface JPhyloIOFormatInfo

All Superinterfaces:

JPhyloIOFormatSpecificObject

All Known Implementing Classes:

DefaultFormatInfo

public interface JPhyloIOFormatInfo
extends JPhyloIOFormatSpecificObject

Classes implementing this interface provide information about a phylogenetic file format that is supported by JPhyloIO. and allow to create according file filters and provide information on the content and parameter set of associated implementations of JPhyloIOEventReader and JPhyloIOEventWriter.

Since:

0.0.0

Author:

Ben Stöver, Sarah Wiechers

Method Summary

Modifier and Type	Method and Description
JPhyloIOContentExtensionFileFilter	createFileFilter(ContentExtensionFileFilter.TestStrategy testStrategy) Creates a new file filter instance that is associated with the modeled format.
java.lang.String	getFormatName() Returns the human readable name of the modeled format.
MetadataModeling	getMetadataModeling(EventContentType parentContentType, boolean forReading) Determines which kind of metadata the represented format allows to model nested under the specified data element Readers will not produce metaevents under an unsupported type, while writers will accept but ignore metaevents under this type.
java.util.Set<java.lang.String>	getSupportedParameters(boolean forReading) Returns a set of the parameters supported by the associated reader or writer.
boolean	isElementModeled(EventContentType contentType, boolean forReading) Determines whether the represented format allows to model the specified data element (content type).

Methods inherited from interface info.bioinfweb.jphyloio.JPhyloIOFormatSpecificObject

getFormatID

Method Detail

getFormatName

java.lang.String getFormatName()

Returns the human readable name of the modeled format.

Returns:

the name of the format

createFileFilter

JPhyloIOContentExtensionFileFilter createFileFilter(ContentExtensionFileFilter.TestStrategy testStrategy)

Creates a new file filter instance that is associated with the modeled format. It will check valid file extensions and possibly the contents of the file, if the extension is not unique.

Parameters:

testStrategy - the strategy to be used to accept a file or not

Returns:

a new file filter instance

isElementModeled

boolean isElementModeled(EventContentType contentType,
                         boolean forReading)

Determines whether the represented format allows to model the specified data element (content type). Readers will not produce events of an unsupported type, while writers will accept but ignore events of this type.

Note that the values returned here indicate the capabilities of the provided readers and writers and not the capabilities of the respective format. It may happen that elements of a format are not supported by its reader and writer. In such cases false would be returned here for the according content type.

Note that this method will return true for content types that may occur at multiple positions in the event stream (e.g. EventContentType.LITERAL_META or EventContentType.SET_ELEMENT), if they are supported at least at one position. Use #isMetadataModeled(EventContentType) to check at which position metadata elements are supported.

Parameters:

contentType - the content type to be tested

forReading - Specify true here, if support for contentType in reading this format or false for writing it should be returned.

Returns:

true if the specified content type is supported, false otherwise

Since:

0.1.0

See Also:

#isMetadataModeled(EventContentType)

getMetadataModeling

MetadataModeling getMetadataModeling(EventContentType parentContentType,
                                     boolean forReading)

Determines which kind of metadata the represented format allows to model nested under the specified data element Readers will not produce metaevents under an unsupported type, while writers will accept but ignore metaevents under this type.

Note that the values returned here indicate the capabilities of the provided readers and writers and not the capabilities of the respective format.

Parameters:

contentType - the content type of the parent element of possibly supported metadata

forReading - Specify true here, if support for metadata nested under contentType in reading this format or false for writing it should be returned.

Returns:

an object describing which metadata is supported, never null

Since:

0.1.0

See Also:

#isElementModeled(EventContentType)

getSupportedParameters

java.util.Set<java.lang.String> getSupportedParameters(boolean forReading)

Returns a set of the parameters supported by the associated reader or writer. Parameter names used by readers and writers included in JPhyloIO are defined as string constants in ReadWriteParameterNames. Readers and writers from third party developers may introduce additional parameter names defined elsewhere.

Parameters:

forReading - Specify true here, if support for parameterName in reading this format or false for writing it should be returned.

Returns:

an unmodifiable set of supported parameters

Since:

0.1.0