Package de.uni_mannheim.informatik.dws.melt.yet_another_alignment_api

Class SSSOMSerializer

java.lang.Object

de.uni_mannheim.informatik.dws.melt.yet_another_alignment_api.SSSOMSerializer

public class SSSOMSerializer
extends Object

The SSSOMSerializer can serialize to SSSOM files following the convention described in the SSSOM github and userguide.

Author:

Sven Hertling

Field Summary

Fields

Modifier and Type	Field	Description
private static final Charset	ENCODING	Constant for UTF-8 encoding.
private static final org.slf4j.Logger	LOGGER
private static final String	NEWLINE
private static final Map<String,List<String>>	SSSOM_ALTERNATIVES

Constructor Summary

Constructors

Constructor	Description
SSSOMSerializer()

Method Summary

Modifier and Type	Method	Description
private static Map<String,List<String>>	initAlternatives()
static String	serialize(Alignment alignment)	Serializes an alignment as String.
static String	serialize(Alignment alignment, boolean includeNonSSSOMAttributes)	Serializes an alignment as String.
static void	serialize(Alignment alignment, File file)	Method to write the specified alignment to the specified file in the SSSOM format.
static void	serialize(Alignment alignment, OutputStream stream)	Method to write the specified alignment to the specified file in the SSSOM format.
static void	serialize(Alignment alignment, OutputStream stream, boolean includeNonSSSOMAttributes)	Method to write the specified alignment to the specified file in the SSSOM format.
private static void	writeMetadata(SSSOMPrefixMap prefixMap, Alignment a, OutputStreamWriter writer, boolean includeNonSSSOMAttributes)

Methods inherited from class java.lang.Object

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

Field Details

LOGGER

private static final org.slf4j.Logger LOGGER

ENCODING

private static final Charset ENCODING

Constant for UTF-8 encoding.

SSSOM_ALTERNATIVES

private static final Map<String,List<String>> SSSOM_ALTERNATIVES

NEWLINE

private static final String NEWLINE

Constructor Details

SSSOMSerializer

public SSSOMSerializer()

Method Details

serialize

public static void serialize(Alignment alignment,
 File file)
                      throws IOException

Method to write the specified alignment to the specified file in the SSSOM format.

Parameters:

alignment - The alignment that shall be written.

file - The file to which the alignment shall be written.

Throws:

IOException - Exception that occurred while serializing the alignment.

serialize

public static String serialize(Alignment alignment)
                        throws IOException

Serializes an alignment as String.

Parameters:

alignment - The alignment to be serialized.

Returns:

Alignment as String.

Throws:

IOException - in case of an io error

serialize

public static String serialize(Alignment alignment,
 boolean includeNonSSSOMAttributes)
                        throws IOException

Serializes an alignment as String.

Parameters:

alignment - The alignment to be serialized.

includeNonSSSOMAttributes - if true include also non SSSOM attributes in the output.

Returns:

Alignment as String.

Throws:

IOException - in case of an io error

initAlternatives

private static Map<String,List<String>> initAlternatives()

serialize

public static void serialize(Alignment alignment,
 OutputStream stream)
                      throws IOException

Method to write the specified alignment to the specified file in the SSSOM format. The provided OutputStream is not closed.

Parameters:

alignment - The alignment that shall be written.

stream - the stream where the serialized alignment should be written to (the stream is not closed)

Throws:

IOException - Exception that occurred while serializing the alignment.

serialize

public static void serialize(Alignment alignment,
 OutputStream stream,
 boolean includeNonSSSOMAttributes)
                      throws IOException

Method to write the specified alignment to the specified file in the SSSOM format. The provided OutputStream is not closed.

Parameters:

alignment - The alignment that shall be written.

stream - the stream where the serialized alignment should be written to (the stream is not closed)

includeNonSSSOMAttributes - if true include also non SSSOM attributes in the output.

Throws:

IOException - Exception that occurred while serializing the alignment.

writeMetadata

private static void writeMetadata(SSSOMPrefixMap prefixMap,
 Alignment a,
 OutputStreamWriter writer,
 boolean includeNonSSSOMAttributes)
                           throws IOException

Throws:

IOException