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

Field Summary

Fields

Modifier and Type	Field	Description
static String	DEFAULT_NAME_SPACE
static String	EXTERNAL_SCHEMA_LOCATION_KEY
static String	LOCAL_NUCLEOTIDE_TEMPLATE_FILE_NAME
static String	LOCAL_NUCLEOTIDE_TEMPLATE_FILE_PATH
static String	NOTATION_DIRECTORY
static String	NUCLEOTIDE_TEMPLATE_SCHEMA_RESOURCE
static String	NUCLEOTIDE_TEMPLATE_XML_RESOURCE
static String	XML_SCHEMA_VALIDATION_FEATURE

Method Summary

Modifier and Type	Method	Description
Map<String,Map<String,String>>	buildNucleotideTemplatesFromXML(String nucleotideTemplatesXML)
static NucleotideFactory	getInstance()
Map<String,Map<String,String>>	getNucleotideTemplates()
Map<String,String>	getReverseNucleotideTemplateMap()
static void	initializeNucleotideTemplatesFromWebService()
void	saveNucleotideTemplates()	save Nucleotide Templates to disk file
void	setNucleotideTemplates(Map<String,Map<String,String>> newNucleotideTemplates)

Methods inherited from class java.lang.Object

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

Field Details

NOTATION_DIRECTORY

public static final String NOTATION_DIRECTORY

LOCAL_NUCLEOTIDE_TEMPLATE_FILE_NAME

public static final String LOCAL_NUCLEOTIDE_TEMPLATE_FILE_NAME

See Also:

Constant Field Values

LOCAL_NUCLEOTIDE_TEMPLATE_FILE_PATH

public static final String LOCAL_NUCLEOTIDE_TEMPLATE_FILE_PATH

NUCLEOTIDE_TEMPLATE_XML_RESOURCE

public static final String NUCLEOTIDE_TEMPLATE_XML_RESOURCE

See Also:

Constant Field Values

NUCLEOTIDE_TEMPLATE_SCHEMA_RESOURCE

public static final String NUCLEOTIDE_TEMPLATE_SCHEMA_RESOURCE

See Also:

Constant Field Values

XML_SCHEMA_VALIDATION_FEATURE

public static final String XML_SCHEMA_VALIDATION_FEATURE

See Also:

Constant Field Values

EXTERNAL_SCHEMA_LOCATION_KEY

public static final String EXTERNAL_SCHEMA_LOCATION_KEY

See Also:

Constant Field Values

DEFAULT_NAME_SPACE

public static final String DEFAULT_NAME_SPACE

See Also:

Constant Field Values

Method Details

getNucleotideTemplates

public Map<String,Map<String,String>> getNucleotideTemplates()

setNucleotideTemplates

public void setNucleotideTemplates(Map<String,Map<String,String>> newNucleotideTemplates)

getInstance

public static NucleotideFactory getInstance() throws NucleotideLoadingException

Throws:

NucleotideLoadingException

buildNucleotideTemplatesFromXML

public Map<String,Map<String,String>> buildNucleotideTemplatesFromXML(String nucleotideTemplatesXML) throws IOException, org.jdom2.JDOMException

Throws:

IOException

org.jdom2.JDOMException

initializeNucleotideTemplatesFromWebService

public static void initializeNucleotideTemplatesFromWebService() throws NucleotideLoadingException

Throws:

NucleotideLoadingException

saveNucleotideTemplates

public void saveNucleotideTemplates() throws IOException

save Nucleotide Templates to disk file

Throws:

IOException - if it can't be saved

getReverseNucleotideTemplateMap

public Map<String,String> getReverseNucleotideTemplateMap()

Returns:

reverse nucleotide template map for 'HELM Notation'