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java.lang.Objectcom.compomics.util.experiment.annotation.go.GOFactory
public class GOFactory
The GOFactory annotates identification results based on Ensembl Gene Ontology terms.
Field Summary | |
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static String |
separator
The separator used to separate line contents. |
Method Summary | |
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void |
clearFactory()
Clears the mappings. |
void |
closeFiles()
Closes connections. |
ArrayList<String> |
getAccessions(String goAccession)
Returns the protein accessions linked to a GO accession number. |
ArrayList<String> |
getGoAccessions(String proteinAccession)
Returns the GO accession numbers linked to a given protein accession number. |
static GOFactory |
getInstance()
Static method returning the instance of the factory. |
int |
getNProteinsForTerm(String goAccession)
Returns the total number of protein accessions mapping to a given GO term. |
int |
getNTermsForProtein(String accession)
Returns the total number of GO terms mapping to a given protein. |
int |
getNumberOfProteins()
Returns the total number of proteins in this mapping. |
int |
getNumberOfTerms()
Returns the total number of GO terms in this mapping. |
ArrayList<String> |
getProteinGoAccessions(String matchKey)
Returns a list of non redundant GO accession numbers corresponding to a protein match. |
ArrayList<String> |
getProteinGoDescriptions(String matchKey)
Returns a list of non redundant GO term descriptions corresponding to a protein match. |
ArrayList<String> |
getProteinMapped()
Returns a non redundant list of all the proteins mapped. |
String |
getTermAccession(String goTerm)
Returns the accession number of a GO term. |
String |
getTermDescription(String goAccession)
Returns the description of a GO term. |
ArrayList<String> |
getTermNamesMapped()
Returns a non redundant list of all the GO term descriptions mapped. |
ArrayList<String> |
getTermsMapped()
Returns a non redundant list of all the GO accession numbers mapped. |
void |
initialize(File file,
WaitingHandler waitingHandler)
Initializes the factory on the given file |
boolean |
isMappingFileOpen()
Returns true of the mapping file is currently open. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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public static final String separator
Method Detail |
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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 interest
IOException
public ArrayList<String> getProteinGoAccessions(String matchKey) throws IOException
matchKey
- the key of the protein match
IOException
public ArrayList<String> getProteinGoDescriptions(String matchKey) throws IOException
matchKey
- the key of the protein match
IOException
public ArrayList<String> getAccessions(String goAccession) throws IOException
goAccession
- the GO accession number
IOException
public String getTermDescription(String goAccession) throws IOException
goAccession
- the accession number of the GO term of interest
IOException
public String getTermAccession(String goTerm) throws IOException
goTerm
- the description of the GO term of interest
IOException
public int getNumberOfProteins()
public int getNumberOfTerms()
public int getNProteinsForTerm(String goAccession)
goAccession
- the GO accession number of interest
public int getNTermsForProtein(String accession)
accession
- the accession of the protein
public 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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