org.sbolstandard.core2

Class SBOLWriter

java.lang.Object

org.sbolstandard.core2.SBOLWriter

public class SBOLWriter
extends Object

Provides methods to output SBOL files in XML/RDF format.

Version:

2.1

Author:

Tramy Nguyen, Chris Myers, Matthew Pocock, Goksel Misirli

Field Summary

Fields

Modifier and Type	Field and Description
static boolean	keepGoing A true value of the keepGoing flag tells the SBOL writer to continue writing an output file, after it encounters an SBOL conversion exception; a false value forces the writer to stop writing after it encounters an SBOL conversion exception.

Constructor Summary

Constructors

Constructor and Description
SBOLWriter()

Method Summary

Modifier and Type	Method and Description
static void	clearErrors() Sets the error list that is used to store SBOL conversion exceptions during reading to empty.
static List<String>	getErrors() Returns the error list that is used to store SBOL conversion exceptions.
static int	getNumErrors() Returns the number of errors in the error list.
static boolean	isKeepGoing() Returns the value of the keepGoing flag.
static void	setKeepGoing(boolean keepGoing) Sets the value for the keepGoing flag to the given boolean value.
static void	write(SBOLDocument doc, File file) Outputs the given SBOL document's data from the RDF/XML serialization to the given file.
static void	write(SBOLDocument doc, File file, String fileType) Outputs this SBOL document's data from the serialization in the given serialization format to the given file.
static void	write(SBOLDocument doc, OutputStream out) Outputs this SBOL document's data from the RDF/XML serialization to the given output stream.
static void	write(SBOLDocument doc, OutputStream out, String fileType) Serializes a given SBOLDocument and outputs the data from the serialization to the given output stream in the specified fileType format.
static void	write(SBOLDocument doc, String filename) Outputs this SBOL document's data from the RDF/XML serialization to a new file with the given file name.
static void	write(SBOLDocument doc, String filename, String fileType) Outputs this SBOL document's data from serialization in the given serialization format to a new file with the given file name.

Methods inherited from class java.lang.Object

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

Field Detail

keepGoing

public static boolean keepGoing

A true value of the keepGoing flag tells the SBOL writer to continue writing an output file, after it encounters an SBOL conversion exception; a false value forces the writer to stop writing after it encounters an SBOL conversion exception.

Constructor Detail

SBOLWriter

public SBOLWriter()

Method Detail

isKeepGoing

public static boolean isKeepGoing()

Returns the value of the keepGoing flag.

Returns:

the value of the keepGoing flag

setKeepGoing

public static void setKeepGoing(boolean keepGoing)

Sets the value for the keepGoing flag to the given boolean value.

A true value means that reading will keep going after encountering an SBOL validation exception, and a false value means otherwise.

Parameters:

keepGoing - the boolean value for the keepGoing flag

clearErrors

public static void clearErrors()

Sets the error list that is used to store SBOL conversion exceptions during reading to empty.

getErrors

public static List<String> getErrors()

Returns the error list that is used to store SBOL conversion exceptions.

Returns:

the error list that is used to store SBOL conversion exceptions

getNumErrors

public static int getNumErrors()

Returns the number of errors in the error list.

Returns:

the number of errors in the error list

write

public static void write(SBOLDocument doc,
                         File file)
                  throws IOException,
                         SBOLConversionException

Outputs the given SBOL document's data from the RDF/XML serialization to the given file.

This method first creates a BufferedOutputStream from the given file, and then calls write(SBOLDocument, OutputStream).

Parameters:

doc - the given SBOL document

file - the given output file

Throws:

IOException - see IOException

SBOLConversionException - - problem found during serialization

write

public static void write(SBOLDocument doc,
                         File file,
                         String fileType)
                  throws IOException,
                         SBOLConversionException

Outputs this SBOL document's data from the serialization in the given serialization format to the given file.

This method first creates a BufferedOutputStream from the given file, and then calls write(SBOLDocument, OutputStream, String).

Parameters:

doc - the given SBOL document

file - the given output file

fileType - the given serialization format

Throws:

IOException - see IOException

SBOLConversionException - - problem found during serialization

write

public static void write(SBOLDocument doc,
                         OutputStream out)
                  throws SBOLConversionException

Outputs this SBOL document's data from the RDF/XML serialization to the given output stream.

Parameters:

doc - the given SBOL document

out - the given output stream

Throws:

SBOLConversionException - - problem found during serialization

write

public static void write(SBOLDocument doc,
                         String filename)
                  throws IOException,
                         SBOLConversionException

Outputs this SBOL document's data from the RDF/XML serialization to a new file with the given file name.

This method calls write(SBOLDocument, File) by passing this SBOL document, and a new file with the given file name.

Parameters:

doc - the given SBOL document

filename - the given output file name

Throws:

IOException - see IOException

SBOLConversionException - - problem found during serialization

write

public static void write(SBOLDocument doc,
                         String filename,
                         String fileType)
                  throws IOException,
                         SBOLConversionException

Outputs this SBOL document's data from serialization in the given serialization format to a new file with the given file name.

This method calls write(SBOLDocument, File, String) by passing this SBOL document, and a new file with the given file name and type.

Parameters:

doc - the given SBOLDocument object

filename - the name of the serialized output file

fileType - the given file format, such as RDF/XML, JSON, or Turtle.

Throws:

IOException - see IOException

SBOLConversionException - - problem found during serialization

write

public static void write(SBOLDocument doc,
                         OutputStream out,
                         String fileType)
                  throws SBOLConversionException,
                         IOException

Serializes a given SBOLDocument and outputs the data from the serialization to the given output stream in the specified fileType format.

Parameters:

doc - the given SBOLDocument object

out - the serialized output stream

fileType - the given file format, such as RDF/XML, JSON, or Turtle.

Throws:

SBOLConversionException - - problem found during serialization

IOException - see IOException