Package biotransformer.biosystems
Class BioSystem
- java.lang.Object
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- biotransformer.biosystems.BioSystem
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
BioSystem.BioSystemName
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Field Summary
Fields Modifier and Type Field Description MReactionsFilter
mrFilter
BioSystem.BioSystemName
name
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Constructor Summary
Constructors Constructor Description BioSystem(BioSystem.BioSystemName bsName, java.util.ArrayList<Enzyme> enzymes)
BioSystem(BioSystem.BioSystemName bsName, org.codehaus.jackson.map.ObjectMapper mapper)
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description java.util.LinkedHashMap<Enzyme.EnzymeName,Enzyme>
getEnzymeHash()
java.util.ArrayList<Enzyme>
getEnzymesList()
java.util.LinkedHashMap<MetabolicPathway.MPathwayName,java.util.ArrayList<Enzyme>>
getMetPathwaysHash()
java.util.LinkedHashMap<java.lang.String,MetabolicReaction>
getReactionsHash()
java.util.LinkedHashMap<java.lang.String,java.lang.Double>
getReactionsORatios()
ambit2.smarts.SMIRKSManager
getSmirksManager()
static void
main(java.lang.String[] args)
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Field Detail
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mrFilter
public MReactionsFilter mrFilter
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name
public BioSystem.BioSystemName name
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Constructor Detail
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BioSystem
public BioSystem(BioSystem.BioSystemName bsName, org.codehaus.jackson.map.ObjectMapper mapper) throws org.codehaus.jackson.JsonParseException, org.codehaus.jackson.map.JsonMappingException, java.io.IOException
- Throws:
org.codehaus.jackson.JsonParseException
org.codehaus.jackson.map.JsonMappingException
java.io.IOException
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BioSystem
public BioSystem(BioSystem.BioSystemName bsName, java.util.ArrayList<Enzyme> enzymes)
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Method Detail
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main
public static void main(java.lang.String[] args) throws org.codehaus.jackson.JsonParseException, org.codehaus.jackson.map.JsonMappingException, java.io.IOException
- Throws:
org.codehaus.jackson.JsonParseException
org.codehaus.jackson.map.JsonMappingException
java.io.IOException
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getEnzymesList
public java.util.ArrayList<Enzyme> getEnzymesList()
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getSmirksManager
public ambit2.smarts.SMIRKSManager getSmirksManager()
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getReactionsHash
public java.util.LinkedHashMap<java.lang.String,MetabolicReaction> getReactionsHash()
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getReactionsORatios
public java.util.LinkedHashMap<java.lang.String,java.lang.Double> getReactionsORatios()
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getEnzymeHash
public java.util.LinkedHashMap<Enzyme.EnzymeName,Enzyme> getEnzymeHash()
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getMetPathwaysHash
public java.util.LinkedHashMap<MetabolicPathway.MPathwayName,java.util.ArrayList<Enzyme>> getMetPathwaysHash()
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