public class GOFactory extends Object
Modifier and Type | Field and Description |
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static String |
separator
The separator used to separate line contents.
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Modifier and Type | Method and Description |
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void |
clearFactory()
Clears the mappings.
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void |
close()
Closes connections.
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ArrayList<String> |
getAccessions(String goTerm)
Returns the protein accessions linked to a GO term.
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ArrayList<String> |
getGoTerms(String accession)
Returns the go terms linked to a given accession.
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static GOFactory |
getInstance()
Static method returning the instance of the factory.
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int |
getNProteinsForTerm(String goTerm)
Returns the total number of accessions mapping to a given GO term.
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int |
getNTermsForProtein(String accession)
Returns the total number of GO terms mapping to a given protein.
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int |
getNumberOfProteins()
Returns the total number of proteins in this mapping.
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int |
getNumberOfTerms()
Returns the total number of GO terms in this mapping.
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ArrayList<String> |
getProteinMapped()
Returns a non redundant list of all the proteins mapped.
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ArrayList<String> |
getProteinMatchTerms(String matchKey)
Returns a list of non redundant go terms corresponding to a protein
match.
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String |
getTermDescription(String goTerm)
Returns the description of a GO term.
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ArrayList<String> |
getTermsMapped()
Returns a non redundant list of all the GO terms mapped.
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void |
initialize(File file,
WaitingHandler waitingHandler)
Initializes the factory on the given file
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public static final String separator
public static GOFactory getInstance()
public void initialize(File file, WaitingHandler waitingHandler) throws IOException
file
- the file containing the GO mappingwaitingHandler
- a waiting handler allowing display of the progress
and canceling of the process.IOException
public ArrayList<String> getGoTerms(String accession) throws IOException
accession
- the accession of the protein of interestIOException
public ArrayList<String> getProteinMatchTerms(String matchKey) throws IOException
matchKey
- the key of the protein matchIOException
public ArrayList<String> getAccessions(String goTerm) throws IOException
goTerm
- the go termIOException
public String getTermDescription(String goTerm) throws IOException
goTerm
- the go term of interestIOException
public int getNumberOfProteins()
public int getNumberOfTerms()
public int getNProteinsForTerm(String goTerm)
goTerm
- the GO term of interestpublic int getNTermsForProtein(String accession)
accession
- the accession of the proteinpublic ArrayList<String> getProteinMapped()
public ArrayList<String> getTermsMapped()
public void close() throws IOException
IOException
public void clearFactory()
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