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 |
closeFiles()
Closes connections.
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ArrayList<String> |
getAccessions(String goAccession)
Returns the protein accessions linked to a GO accession number.
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ArrayList<String> |
getGoAccessions(String proteinAccession)
Returns the GO accession numbers linked to a given protein accession
number.
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static GOFactory |
getInstance()
Static method returning the instance of the factory.
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int |
getNProteinsForTerm(String goAccession)
Returns the total number of protein 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> |
getProteinGoAccessions(String matchKey)
Returns a list of non redundant GO accession numbers corresponding to a
protein match.
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ArrayList<String> |
getProteinGoDescriptions(String matchKey)
Returns a list of non redundant GO term descriptions corresponding to a
protein match.
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ArrayList<String> |
getProteinMapped()
Returns a non redundant list of all the proteins mapped.
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String |
getTermAccession(String goTerm)
Returns the accession number of a GO term.
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String |
getTermDescription(String goAccession)
Returns the description of a GO term.
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ArrayList<String> |
getTermNamesMapped()
Returns a non redundant list of all the GO term descriptions mapped.
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ArrayList<String> |
getTermsMapped()
Returns a non redundant list of all the GO accession numbers mapped.
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void |
initialize(File file,
WaitingHandler waitingHandler)
Initializes the factory on the given file.
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boolean |
isMappingFileOpen()
Returns true of the mapping file is currently open.
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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> getGoAccessions(String proteinAccession) throws IOException
proteinAccession
- the accession number of the protein of interestIOException
public ArrayList<String> getProteinGoAccessions(String matchKey) throws IOException
matchKey
- the key of the protein matchIOException
public ArrayList<String> getProteinGoDescriptions(String matchKey) throws IOException
matchKey
- the key of the protein matchIOException
public ArrayList<String> getAccessions(String goAccession) throws IOException
goAccession
- the GO accession numberIOException
public String getTermDescription(String goAccession) throws IOException
goAccession
- the accession number of the GO term of interestIOException
public String getTermAccession(String goTerm) throws IOException
goTerm
- the description of the GO term of interestIOException
public int getNumberOfProteins()
public int getNumberOfTerms()
public int getNProteinsForTerm(String goAccession)
goAccession
- the GO accession number of interestpublic int getNTermsForProtein(String accession)
accession
- the accession of the proteinpublic ArrayList<String> getProteinMapped()
public ArrayList<String> getTermsMapped()
public ArrayList<String> getTermNamesMapped()
public void closeFiles() throws IOException
IOException
public void clearFactory()
public boolean isMappingFileOpen()
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