org.jbei.ice.lib.parsers.sbol

Class SBOLParser

java.lang.Object

org.jbei.ice.lib.entry.HasEntry

org.jbei.ice.lib.parsers.AbstractParser

org.jbei.ice.lib.parsers.sbol.SBOLParser

public class SBOLParser
extends AbstractParser

Parse SBOL files that are imported by the user. As an initial support for version 2, it converts the file to genBank and then the ICE genBank parser is used to convert to the data model

Author:

Hector Plahar

Field Summary

Fields inherited from class org.jbei.ice.lib.parsers.AbstractParser

entry, fileName, partData, userId

Fields inherited from class org.jbei.ice.lib.entry.HasEntry

accountDAO, entryDAO

Constructor Summary

Constructors

Constructor and Description
SBOLParser(String userId, String entryId, boolean extractHierarchy)

Method Summary

Modifier and Type	Method and Description
protected void	createICEComponentDefinitionRecord(org.sbolstandard.core2.SBOLDocument document, org.sbolstandard.core2.ComponentDefinition componentDefinition)
protected void	createICEModuleDefinitionRecord(org.sbolstandard.core2.SBOLDocument document, org.sbolstandard.core2.ModuleDefinition moduleDefinition)
protected long	createNewEntry(org.sbolstandard.core2.TopLevel moduleDefinition, org.sbolstandard.core2.SBOLDocument document)
SequenceInfo	parseToEntry(String textSequence, String fileName)
protected SequenceInfo	parseToGenBank(org.sbolstandard.core2.SBOLDocument sbolDocument, String fileName, Entry entry, String uri) Parse the SBOL document to genbank format, save and associate with entry

Methods inherited from class org.jbei.ice.lib.parsers.AbstractParser

cleanSequence, parse, save

Methods inherited from class org.jbei.ice.lib.entry.HasEntry

getEntry

Methods inherited from class java.lang.Object

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

Constructor Detail

SBOLParser

public SBOLParser(String userId,
                  String entryId,
                  boolean extractHierarchy)

Method Detail

parseToEntry

public SequenceInfo parseToEntry(String textSequence,
                                 String fileName)
                          throws InvalidFormatParserException

Throws:

InvalidFormatParserException

parseToGenBank

protected SequenceInfo parseToGenBank(org.sbolstandard.core2.SBOLDocument sbolDocument,
                                      String fileName,
                                      Entry entry,
                                      String uri)

Parse the SBOL document to genbank format, save and associate with entry

Parameters:

sbolDocument - SBOL document to parse

fileName - name of file that was parsed to extract the SBOL information

entry - ICE entry to associate sequence document with

uri - optional uri to associate with sequence

Returns:

Sequence info data transfer object for saved sequence

createNewEntry

protected long createNewEntry(org.sbolstandard.core2.TopLevel moduleDefinition,
                              org.sbolstandard.core2.SBOLDocument document)

createICEModuleDefinitionRecord

protected void createICEModuleDefinitionRecord(org.sbolstandard.core2.SBOLDocument document,
                                               org.sbolstandard.core2.ModuleDefinition moduleDefinition)
                                        throws org.sbolstandard.core2.SBOLValidationException

Throws:

org.sbolstandard.core2.SBOLValidationException

createICEComponentDefinitionRecord

protected void createICEComponentDefinitionRecord(org.sbolstandard.core2.SBOLDocument document,
                                                  org.sbolstandard.core2.ComponentDefinition componentDefinition)
                                           throws org.sbolstandard.core2.SBOLValidationException

Throws:

org.sbolstandard.core2.SBOLValidationException