Class FASTAWriter

java.lang.Object

org.episteme.core.io.AbstractResourceWriter<List<FASTAReader.Sequence>>

org.episteme.natural.biology.loaders.FASTAWriter

All Implemented Interfaces:

ResourceIO<List<FASTAReader.Sequence>>, ResourceWriter<List<FASTAReader.Sequence>>

public class FASTAWriter
extends AbstractResourceWriter<List<FASTAReader.Sequence>>

Writer for FASTA files.

Since:

1.0

Author:

Silvere Martin-Michiellot, Gemini AI (Google DeepMind)

Constructor Summary

Constructors

Constructor	Description
FASTAWriter()

Method Summary

Modifier and Type	Method	Description
String	getCategory()	Returns the category for grouping.
String	getDescription()	Returns a short description of this resource handler.
String	getLongDescription()	Returns a long description of this resource handler.
String	getName()	Returns the display name of this resource handler.
String	getResourcePath()	Returns the base path where this resource is located.
Class<List<FASTAReader.Sequence>>	getResourceType()	Returns the type of resource.
String[]	getSupportedVersions()	Returns the supported versions of the format this reader/writer handles.
void	save(List<FASTAReader.Sequence> sequences, String destination)	Saves the resource to a destination.

Methods inherited from class AbstractResourceWriter

createBufferedStream

Methods inherited from class Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface ResourceIO

getExpectedResourceFiles, getSupportedExtensions, isFileBased, isInput

Methods inherited from interface ResourceWriter

isOutput

Constructor Details

FASTAWriter

public FASTAWriter()

Method Details

getSupportedVersions

public String[] getSupportedVersions()

Description copied from interface: ResourceIO

Returns the supported versions of the format this reader/writer handles.

Each implementation MUST override this method to declare which versions of the underlying format are supported. The returned array should contain version strings in the format's standard notation (e.g., "3.0", "2.1", "Level 3 Version 2").

Examples:

• MathML: {"3.0", "2.0"}
• SBML: {"Level 3 Version 2", "Level 3 Version 1", "Level 2 Version 5"}
• PhyloXML: {"1.10", "1.00"}

Returns:

array of supported version strings, never null (empty array if version-agnostic)

getResourcePath

public String getResourcePath()

Description copied from interface: ResourceIO

Returns the base path where this resource is located.

getResourceType

public Class<List<FASTAReader.Sequence>> getResourceType()

Description copied from interface: ResourceIO

Returns the type of resource.

save

public void save(List<FASTAReader.Sequence> sequences,
 String destination)
          throws Exception

Description copied from interface: ResourceWriter

Saves the resource to a destination.

Throws:

Exception

getCategory

public String getCategory()

Description copied from interface: ResourceIO

Returns the category for grouping. MUST be implemented with I18N support.

Specified by:

getCategory in interface ResourceIO<List<FASTAReader.Sequence>>

Overrides:

getCategory in class AbstractResourceWriter<List<FASTAReader.Sequence>>

Returns:

the category name

getName

public String getName()

Description copied from interface: ResourceIO

Returns the display name of this resource handler. MUST be implemented with I18N support.

Specified by:

getName in interface ResourceIO<List<FASTAReader.Sequence>>

Overrides:

getName in class AbstractResourceWriter<List<FASTAReader.Sequence>>

Returns:

the display name

getDescription

public String getDescription()

Description copied from interface: ResourceIO

Returns a short description of this resource handler. MUST be implemented with I18N support.

Specified by:

getDescription in interface ResourceIO<List<FASTAReader.Sequence>>

Overrides:

getDescription in class AbstractResourceWriter<List<FASTAReader.Sequence>>

Returns:

the description

getLongDescription

public String getLongDescription()

Description copied from interface: ResourceIO

Returns a long description of this resource handler. MUST be implemented with I18N support.

Specified by:

getLongDescription in interface ResourceIO<List<FASTAReader.Sequence>>

Overrides:

getLongDescription in class AbstractResourceWriter<List<FASTAReader.Sequence>>

Returns:

the long description