public class GOFactory
extends java.lang.Object
Modifier and Type | Field and Description |
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static java.lang.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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java.util.ArrayList<java.lang.String> |
getAccessions(java.lang.String goAccession)
Returns the protein accessions linked to a GO accession number.
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java.util.ArrayList<java.lang.String> |
getGoAccessions(java.lang.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(java.lang.String goAccession)
Returns the total number of protein accessions mapping to a given GO
term.
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int |
getNTermsForProtein(java.lang.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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java.util.ArrayList<java.lang.String> |
getProteinGoAccessions(java.lang.String matchKey)
Returns a list of non redundant GO accession numbers corresponding to a
protein match.
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java.util.ArrayList<java.lang.String> |
getProteinGoDescriptions(java.lang.String matchKey)
Returns a list of non redundant GO term descriptions corresponding to a
protein match.
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java.util.ArrayList<java.lang.String> |
getProteinMapped()
Returns a non redundant list of all the proteins mapped.
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java.lang.String |
getTermAccession(java.lang.String goTerm)
Returns the accession number of a GO term.
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java.lang.String |
getTermDescription(java.lang.String goAccession)
Returns the description of a GO term.
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java.util.ArrayList<java.lang.String> |
getTermNamesMapped()
Returns a non redundant list of all the GO term descriptions mapped.
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java.util.ArrayList<java.lang.String> |
getTermsMapped()
Returns a non redundant list of all the GO accession numbers mapped.
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void |
initialize(java.io.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 java.lang.String separator
public static GOFactory getInstance()
public void initialize(java.io.File file, WaitingHandler waitingHandler) throws java.io.IOException
file
- the file containing the GO mappingwaitingHandler
- a waiting handler allowing display of the progress
and canceling of the process.java.io.IOException
public java.util.ArrayList<java.lang.String> getGoAccessions(java.lang.String proteinAccession) throws java.io.IOException
proteinAccession
- the accession number of the protein of interestjava.io.IOException
public java.util.ArrayList<java.lang.String> getProteinGoAccessions(java.lang.String matchKey) throws java.io.IOException
matchKey
- the key of the protein matchjava.io.IOException
public java.util.ArrayList<java.lang.String> getProteinGoDescriptions(java.lang.String matchKey) throws java.io.IOException
matchKey
- the key of the protein matchjava.io.IOException
public java.util.ArrayList<java.lang.String> getAccessions(java.lang.String goAccession) throws java.io.IOException
goAccession
- the GO accession numberjava.io.IOException
public java.lang.String getTermDescription(java.lang.String goAccession) throws java.io.IOException
goAccession
- the accession number of the GO term of interestjava.io.IOException
public java.lang.String getTermAccession(java.lang.String goTerm) throws java.io.IOException
goTerm
- the description of the GO term of interestjava.io.IOException
public int getNumberOfProteins()
public int getNumberOfTerms()
public int getNProteinsForTerm(java.lang.String goAccession)
goAccession
- the GO accession number of interestpublic int getNTermsForProtein(java.lang.String accession)
accession
- the accession of the proteinpublic java.util.ArrayList<java.lang.String> getProteinMapped()
public java.util.ArrayList<java.lang.String> getTermsMapped()
public java.util.ArrayList<java.lang.String> getTermNamesMapped()
public void closeFiles() throws java.io.IOException
java.io.IOException
public void clearFactory()
public boolean isMappingFileOpen()
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