Package org.helm.notation2
Class NucleotideFactory
java.lang.Object
org.helm.notation2.NucleotideFactory
public class NucleotideFactory extends Object
This is a factory class to build nucleotide templates
- Author:
- zhangtianhong
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Field Summary
Fields Modifier and Type Field Description static StringDEFAULT_NAME_SPACEstatic StringEXTERNAL_SCHEMA_LOCATION_KEYstatic StringLOCAL_NUCLEOTIDE_TEMPLATE_FILE_NAMEstatic StringLOCAL_NUCLEOTIDE_TEMPLATE_FILE_PATHstatic StringNOTATION_DIRECTORYstatic StringNUCLEOTIDE_TEMPLATE_SCHEMA_RESOURCEstatic StringNUCLEOTIDE_TEMPLATE_XML_RESOURCEstatic StringXML_SCHEMA_VALIDATION_FEATURE -
Method Summary
Modifier and Type Method Description Map<String,Map<String,String>>buildNucleotideTemplatesFromXML(String nucleotideTemplatesXML)static NucleotideFactorygetInstance()Map<String,Map<String,String>>getNucleotideTemplates()Map<String,String>getReverseNucleotideTemplateMap()static voidinitializeNucleotideTemplatesFromWebService()voidsaveNucleotideTemplates()save Nucleotide Templates to disk filevoidsetNucleotideTemplates(Map<String,Map<String,String>> newNucleotideTemplates)
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Field Details
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NOTATION_DIRECTORY
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LOCAL_NUCLEOTIDE_TEMPLATE_FILE_NAME
- See Also:
- Constant Field Values
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LOCAL_NUCLEOTIDE_TEMPLATE_FILE_PATH
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NUCLEOTIDE_TEMPLATE_XML_RESOURCE
- See Also:
- Constant Field Values
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NUCLEOTIDE_TEMPLATE_SCHEMA_RESOURCE
- See Also:
- Constant Field Values
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XML_SCHEMA_VALIDATION_FEATURE
- See Also:
- Constant Field Values
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EXTERNAL_SCHEMA_LOCATION_KEY
- See Also:
- Constant Field Values
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DEFAULT_NAME_SPACE
- See Also:
- Constant Field Values
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Method Details
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getNucleotideTemplates
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setNucleotideTemplates
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getInstance
- Throws:
NucleotideLoadingException
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buildNucleotideTemplatesFromXML
public Map<String,Map<String,String>> buildNucleotideTemplatesFromXML(String nucleotideTemplatesXML) throws IOException, org.jdom2.JDOMException- Throws:
IOExceptionorg.jdom2.JDOMException
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initializeNucleotideTemplatesFromWebService
- Throws:
NucleotideLoadingException
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saveNucleotideTemplates
save Nucleotide Templates to disk file- Throws:
IOException- if it can't be saved
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getReverseNucleotideTemplateMap
- Returns:
- reverse nucleotide template map for 'HELM Notation'
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