public class PsiToBiopax3Converter extends Object
Constructor and Description |
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PsiToBiopax3Converter()
Constructor.
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PsiToBiopax3Converter(String xmlBase)
Constructor.
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Modifier and Type | Method and Description |
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void |
convert(psidev.psi.mi.xml.model.EntrySet entrySet,
OutputStream outputStream,
boolean forceInteractionToComplex)
Converts the PSI interactions from the EntrySet and places into BioPAX output stream.
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void |
convert(InputStream inputStream,
OutputStream outputStream,
boolean forceInteractionToComplex)
Converts the PSI-MI inputStream into BioPAX outputStream.
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void |
convertTab(InputStream inputStream,
OutputStream outputStream,
boolean forceInteractionToComplex)
Converts the PSI-MITAB inputStream into BioPAX outputStream.
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String |
getXmlBase() |
public PsiToBiopax3Converter()
public PsiToBiopax3Converter(String xmlBase)
xmlBase
- xml:base to be used when generating non-canonical BioPAX objects' URIspublic void convert(InputStream inputStream, OutputStream outputStream, boolean forceInteractionToComplex) throws IOException, psidev.psi.mi.xml.PsimiXmlReaderException
inputStream
- PSI-MIoutputStream
- BioPAXforceInteractionToComplex
- - always generate Complex instead of MolecularInteractionIOException
- when an I/O error occurpsidev.psi.mi.xml.PsimiXmlReaderException
- when an error in the PSI-MI parser happenspublic void convertTab(InputStream inputStream, OutputStream outputStream, boolean forceInteractionToComplex) throws IOException, psidev.psi.mi.tab.PsimiTabException
inputStream
- psi-mitaboutputStream
- biopaxforceInteractionToComplex
- - always generate Complex instead of MolecularInteractionIOException
- when an I/O error occurpsidev.psi.mi.tab.PsimiTabException
- when there's a problem within the PSI-MITAB parserpublic void convert(psidev.psi.mi.xml.model.EntrySet entrySet, OutputStream outputStream, boolean forceInteractionToComplex)
entrySet
- PSI-MI entry setoutputStream
- output stream for writing the BioPAX RDF/XML resultforceInteractionToComplex
- true/false - whether to always generate Complex instead of MolecularInteractionpublic String getXmlBase()
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