SBOLReader

java.lang.Object
- org.sbolstandard.core2.SBOLReader

```
public class SBOLReader
extends Object
```
Provides methods to read input SBOL files.

Version:

2.1

Author:

Tramy Nguyen, Chris Myers, Zhen Zhang, 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 reader to continue reading an SBOL input file, after it encounters an SBOL validation exception; a `false` value forces the reader to stop reading after it encounters an SBOL validation exception.
`static String`	`SBOLVERSION1` Constant representing SBOL version 1.1
`static String`	`SBOLVERSION2` Constant representing SBOL version 2.0

Constructor Summary

Constructors
Constructor and Description

SBOLReader()

Constructors
Constructor and Description
`SBOLReader()`

Method Summary

All Methods Static Methods Concrete Methods
Modifier and Type	Method and Description
`static void`	`clearErrors()` Sets the error list that is used to store SBOL validation exceptions during reading to empty.
`static URI`	`getDefaultSequenceEncoding()` Sets the default sequence encoding for FASTA conversion.
`static String`	`getDisplayId()` Get the SBOL default displayId for this reader.
`static List<String>`	`getErrors()` Returns the error list that is used to store SBOL validation exceptions.
`static int`	`getNumErrors()` Returns the number of errors in the error list.
`static String`	`getSBOLVersion(File file)` Takes in a given RDF file and returns its SBOL version.
`static String`	`getSBOLVersion(InputStream in)` Takes in a given RDF input stream and returns the SBOL version of the file.
`static String`	`getSBOLVersion(String fileName)` Takes in a given RDF file name and returns the SBOL version of the file.
`static String`	`getURIPrefix()` Returns the specified authority prefix.
`static String`	`getVersion()` Get the SBOL default version for this reader.
`static boolean`	`isCompliant()` Check if document is to be read as being compliant.
`static boolean`	`isDropObjectsWithDuplicateURIs()` Check if objects with duplicate URIs should be dropped.
`static boolean`	`isFastaFile(String fileName)` Check if a file begins with ">" or ";" indicating that it is Fasta file
`static boolean`	`isFastaString(String inputString)` Check if a string begins with ">" or ";" indicating that it is Fasta file string
`static boolean`	`isGenBankFile(String fileName)` Check if a file begins with LOCUS indicating that it is GenBank file
`static boolean`	`isGenBankString(String inputString)` Check if a string begins with LOCUS indicating that it is GenBank file string
`static boolean`	`isKeepGoing()` Checks if reading should continue after encountering an SBOL validation exception.
`static boolean`	`isSnapGeneFile(String fileName)` Check if a file begins with the byte sequence indicating it is a SnapGene file
`static SBOLDocument`	`read(File file)` Parses the given RDF file and stores its contents in an SBOLDocument object.
`static SBOLDocument`	`read(InputStream in)` Takes in a given RDF InputStream and converts the file to an SBOLDocument.
`static SBOLDocument`	`read(String fileName)` Takes in the given RDF filename and converts the file to an SBOLDocument.
`static void`	`setCompliant(boolean compliant)` Sets the compliant flag to the given value.
`static void`	`setDefaultSequenceEncoding(URI defaultSequenceEncoding)` Sets the defaultsequenceEndocding flag to the given value.
`static void`	`setDisplayId(String displayId)` Sets the SBOL default displayId for this reader.
`static void`	`setDropObjectsWithDuplicateURIs(boolean dropObjectsWithDuplicateURIs)` Sets the value of the dropObjectsWithDuplicateURIs flag.
`static void`	`setKeepGoing(boolean keepGoing)` Sets the value for the keepGoing flag to the given boolean value.
`static void`	`setTypesInURI(boolean typesInURI)` Sets the value for the typesInURI flag.
`static void`	`setURIPrefix(String URIprefix)` Sets the specified authority as the prefix.
`static void`	`setVersion(String version)` Sets the SBOL default version for this reader.
`static void`	`unsetURIPrefix()` Sets the URI prefix for this reader to `null`.

Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - SBOLVERSION1
```
public static final String SBOLVERSION1
```
    Constant representing SBOL version 1.1
    
    See Also:
    
    Constant Field Values
  - SBOLVERSION2
```
public static final String SBOLVERSION2
```
    Constant representing SBOL version 2.0
    
    See Also:
    
    Constant Field Values
  - keepGoing
```
public static boolean keepGoing
```
    A true value of the keepGoing flag tells the SBOL reader to continue reading an SBOL input file, after it encounters an SBOL validation exception; a false value forces the reader to stop reading after it encounters an SBOL validation exception.
- Constructor Detail
  - SBOLReader
```
public SBOLReader()
```
- Method Detail
  - isKeepGoing
```
public static boolean isKeepGoing()
```
    Checks if reading should continue after encountering an SBOL validation exception.
    
    Returns:
    
    true if it should continue, false otherwise
  - 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 validation exceptions during reading to empty.
  - getErrors
```
public static List<String> getErrors()
```
    Returns the error list that is used to store SBOL validation exceptions.
    
    Returns:
    
    the error list that is used to store SBOL validation exceptions
  - getNumErrors
```
public static int getNumErrors()
```
    Returns the number of errors in the error list.
    
    Returns:
    
    the number of errors in the error list
  - isCompliant
```
public static boolean isCompliant()
```
    Check if document is to be read as being compliant.
    
    Returns:
    
    true if document is to be read as being compliant, false otherwise
  - setCompliant
```
public static void setCompliant(boolean compliant)
```
    Sets the compliant flag to the given value.
    A true value means that the SBOL document is to be read as compliant, and a false value means otherwise.
    
    Parameters:
    
    compliant - the boolean value for the compliant flag
  - getURIPrefix
```
public static String getURIPrefix()
```
    Returns the specified authority prefix.
    
    Returns:
    
    the specified authority prefix.
  - setURIPrefix
```
public static void setURIPrefix(String URIprefix)
```
    Sets the specified authority as the prefix.
    
    Parameters:
    
    URIprefix - the given URI prefix
  - unsetURIPrefix
```
public static void unsetURIPrefix()
```
    Sets the URI prefix for this reader to null.
  - getDisplayId
```
public static String getDisplayId()
```
    Get the SBOL default displayId for this reader.
    
    Returns:
    
    the SBOL default displayId for this reader.
  - setDisplayId
```
public static void setDisplayId(String displayId)
```
    Sets the SBOL default displayId for this reader.
    
    Parameters:
    
    displayId - the given displayId
  - getVersion
```
public static String getVersion()
```
    Get the SBOL default version for this reader.
    
    Returns:
    
    the SBOL default version for this reader.
  - setVersion
```
public static void setVersion(String version)
```
    Sets the SBOL default version for this reader.
    
    Parameters:
    
    version - the given version
  - setTypesInURI
```
public static void setTypesInURI(boolean typesInURI)
```
    Sets the value for the typesInURI flag.
    A true value means that types are to be inserted into each top-level URI when it is created, and a false value means otherwise.
    
    Parameters:
    
    typesInURI - the boolean value for the typesInURI flag
  - isDropObjectsWithDuplicateURIs
```
public static boolean isDropObjectsWithDuplicateURIs()
```
    Check if objects with duplicate URIs should be dropped.
    
    Returns:
    
    true if objects with duplicate URIs should be dropped, false otherwise
  - setDropObjectsWithDuplicateURIs
```
public static void setDropObjectsWithDuplicateURIs(boolean dropObjectsWithDuplicateURIs)
```
    Sets the value of the dropObjectsWithDuplicateURIs flag.
    A true value means that instances with duplicate URIs should be dropped, and a false value means otherwise.
    
    Parameters:
    
    dropObjectsWithDuplicateURIs - the boolean value for the dropObjectsWithDuplicateURIs flag
  - getDefaultSequenceEncoding
```
public static URI getDefaultSequenceEncoding()
```
    Sets the default sequence encoding for FASTA conversion.
    
    Returns:
    
    the defaultSequenceEncoding
  - setDefaultSequenceEncoding
```
public static void setDefaultSequenceEncoding(URI defaultSequenceEncoding)
```
    Sets the defaultsequenceEndocding flag to the given value.
    
    Parameters:
    
    defaultSequenceEncoding - the given defaultSequenceEncoding URI
  - getSBOLVersion
```
public static String getSBOLVersion(String fileName)
                             throws FileNotFoundException,
                                    SBOLValidationException,
                                    SBOLConversionException
```
    Takes in a given RDF file name and returns the SBOL version of the file.
    
    Parameters:
    
    fileName - a given RDF file name
    
    Returns:
    
    the SBOL version of the file
    
    Throws:
    
    FileNotFoundException - if file was not found.
    
    SBOLValidationException - if any of the following SBOL validation rules was violated: 10101, 10102, 10105, 10201.
    
    SBOLConversionException - if file is empty
  - read
```
public static SBOLDocument read(String fileName)
                         throws SBOLValidationException,
                                IOException,
                                SBOLConversionException
```
    Takes in the given RDF filename and converts the file to an SBOLDocument.
    
    Parameters:
    
    fileName - the name of the given RDF file
    
    Returns:
    
    the converted SBOLDocument
    
    Throws:
    
    SBOLValidationException - if any of the following SBOL validation rules was violated: 10101, 10102, 10105, 10201, 10202, 10203, 10204, 10206, 10208, 10212, 10213, 10220, 10303, 10304, 10305, 10401, 10402, 10403, 10405, 10501, 10502, 10503, 10504, 10507, 10508, 10512, 10513, 10519, 10522, 10526, 10602, 10603, 10604, 10605, 10606, 10607, 10701, 10801, 10802, 10803, 10804, 10805, 10806, 10807, 10808, 10809, 10810, 10811, 10901, 10902, 10904, 10905, 11002, 11101, 11102, 11103, 11104, 11201, 11202, 11301, 11401, 11402, 11403, 11404, 11405, 11406, 11407, 11412, 11501, 11502, 11504, 11508, 11601, 11602, 11604, 11605, 11606, 11607, 11608, 11609, 11701, 11702, 11703, 11704, 11705, 11706, 11801, 11802, 11901, 11902, 11906, 12001, 12002, 12003, 12004, 12101, 12102, 12103, 12301, 12302.
    
    SBOLConversionException - see SBOLConversionException.SBOLConversionException(java.lang.Throwable)
    
    IOException - see IOException
  - getSBOLVersion
```
public static String getSBOLVersion(File file)
                             throws FileNotFoundException,
                                    SBOLValidationException,
                                    SBOLConversionException
```
    Takes in a given RDF file and returns its SBOL version.
    
    Parameters:
    
    file - the given RDF file
    
    Returns:
    
    the SBOL version of the file
    
    Throws:
    
    FileNotFoundException - if file was not found.
    
    SBOLValidationException - if any of the following SBOL validation rules was violated: 10101, 10102, 10105, 10201.
    
    SBOLConversionException - if file is empty
  - read
```
public static SBOLDocument read(File file)
                         throws SBOLValidationException,
                                IOException,
                                SBOLConversionException
```
    Parses the given RDF file and stores its contents in an SBOLDocument object.
    
    Parameters:
    
    file - the given RDF file
    
    Returns:
    
    an SBOLDocument object that stores the RDF file information
    
    Throws:
    
    SBOLValidationException - if any of the following SBOL validation rules was violated: 10101, 10102, 10105, 10201, 10202, 10203, 10204, 10206, 10208, 10212, 10213, 10220, 10221, 10222 10303, 10304, 10305, 10401, 10402, 10403, 10405, 10501, 10502, 10503, 10504, 10507, 10508, 10512, 10513, 10519, 10522, 10526, 10602, 10603, 10604, 10605, 10606, 10607, 10701, 10801, 10802, 10803, 10804, 10805, 10806, 10807, 10808, 10809, 10810, 10811, 10901, 10902, 10904, 10905, 11002, 11101, 11102, 11103, 11104, 11201, 11202, 11301, 11401, 11402, 11403, 11404, 11405, 11406, 11407, 11412, 11501, 11502, 11504, 11508, 11601, 11602, 11604, 11605, 11606, 11607, 11608, 11609, 11701, 11702, 11703, 11704, 11705, 11706, 11801, 11802, 11901, 11902, 11906, 12001, 12002, 12003, 12004, 12101, 12102, 12103, 12301, 12302, 12401, 12402, 12403, 12404, 12405, 12406, 12407 12501, 12502, 12503, 12601, 12602, 12603, 12604, 12605, 12606, 12701, 12801.
    
    SBOLConversionException - see SBOLConversionException
    
    IOException - see IOException
  - read
```
public static SBOLDocument read(InputStream in)
                         throws SBOLValidationException,
                                IOException,
                                SBOLConversionException
```
    Takes in a given RDF InputStream and converts the file to an SBOLDocument.
    
    Parameters:
    
    in - a given RDF InputStream
    
    Returns:
    
    the converted SBOLDocument instance
    
    Throws:
    
    SBOLConversionException - see SBOLConversionException
    
    IOException - see IOException
    
    SBOLValidationException - if any of the following SBOL validation rules was violated: 10101, 10102, 10105, 10201, 10202, 10203, 10204, 10206, 10208, 10212, 10213, 10220, 10303, 10304, 10305, 10401, 10402, 10403, 10405, 10501, 10502, 10503, 10504, 10507, 10508, 10512, 10513, 10519, 10522, 10526, 10602, 10603, 10604, 10605, 10606, 10607, 10701, 10801, 10802, 10803, 10804, 10805, 10806, 10807, 10808, 10809, 10810, 10811, 10901, 10902, 10904, 10905, 11002, 11101, 11102, 11103, 11104, 11201, 11202, 11301, 11401, 11402, 11403, 11404, 11405, 11406, 11407, 11412, 11501, 11502, 11504, 11508, 11601, 11602, 11604, 11605, 11606, 11607, 11608, 11609, 11701, 11702, 11703, 11704, 11705, 11706, 11801, 11802, 11901, 11902, 11906, 12001, 12002, 12003, 12004, 12101, 12102, 12103, 12301, 12302.
  - getSBOLVersion
```
public static String getSBOLVersion(InputStream in)
                             throws SBOLValidationException,
                                    SBOLConversionException
```
    Takes in a given RDF input stream and returns the SBOL version of the file.
    
    Parameters:
    
    in - a given RDF input stream
    
    Returns:
    
    the SBOL version of the file.
    
    Throws:
    
    SBOLValidationException - if any of the following SBOL validation rules was violated: 10101, 10102, 10105, 10201.
    
    SBOLConversionException - if file is empty
  - isGenBankString
```
public static boolean isGenBankString(String inputString)
```
    Check if a string begins with LOCUS indicating that it is GenBank file string
    
    Parameters:
    
    inputString - input string to check if it is a GenBank file string
    
    Returns:
    
    true if the string begins with LOCUS indicating that it is a GenBank file string
  - isGenBankFile
```
public static boolean isGenBankFile(String fileName)
                             throws IOException
```
    Check if a file begins with LOCUS indicating that it is GenBank file
    
    Parameters:
    
    fileName - file name of file to check if it is a GenBank file
    
    Returns:
    
    true if the string begins with LOCUS indicating that it is a GenBank file
    
    Throws:
    
    IOException - if there is an I/O exception reading the file
  - isFastaString
```
public static boolean isFastaString(String inputString)
```
    Check if a string begins with ">" or ";" indicating that it is Fasta file string
    
    Parameters:
    
    inputString - input string to check if it is a Fasta file string
    
    Returns:
    
    true if the string begins with ">" or ";" indicating that it is a Fasta file string
  - isFastaFile
```
public static boolean isFastaFile(String fileName)
                           throws IOException
```
    Check if a file begins with ">" or ";" indicating that it is Fasta file
    
    Parameters:
    
    fileName - file name of file to check if it is a Fasta file
    
    Returns:
    
    true if the string begins with ">" or ";" indicating that it is a Fasta file
    
    Throws:
    
    IOException - if there is an I/O exception reading the file
  - isSnapGeneFile
```
public static boolean isSnapGeneFile(String fileName)
                              throws IOException
```
    Check if a file begins with the byte sequence indicating it is a SnapGene file
    
    Parameters:
    
    fileName - file name of file to check if it is a Fasta file
    
    Returns:
    
    true if the string begins with ">" or ";" indicating that it is a Fasta file
    
    Throws:
    
    IOException - if there is an I/O exception reading the file

Class SBOLReader

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

SBOLVERSION1

SBOLVERSION2

keepGoing

Constructor Detail

SBOLReader

Method Detail

isKeepGoing

setKeepGoing

clearErrors

getErrors

getNumErrors

isCompliant

setCompliant

getURIPrefix

setURIPrefix

unsetURIPrefix

getDisplayId

setDisplayId

getVersion

setVersion

setTypesInURI

isDropObjectsWithDuplicateURIs

setDropObjectsWithDuplicateURIs

getDefaultSequenceEncoding

setDefaultSequenceEncoding

getSBOLVersion

read

getSBOLVersion

read

read

getSBOLVersion

isGenBankString

isGenBankFile

isFastaString

isFastaFile

isSnapGeneFile