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java.lang.Objectcom.compomics.util.experiment.annotation.gene.GeneFactory
public class GeneFactory
The gene factory provides gene information for protein accessions.
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 files. |
String |
getChromosomeForGeneName(String geneName)
Returns the chromosome for a given gene. |
String |
getChromosomeFromGeneId(String geneID)
Returns the chromosome where a gene can be located, null if not found. |
String |
getChromosomeFromGeneName(String geneName)
Returns the chromosome where a gene can be located, null if not found. |
Integer |
getCurrentEnsemblVersion(String ensemblType)
Returns the current Ensembl version number. |
String |
getGeneEnsemblId(String geneName)
Returns the Ensembl ID of a gene, null if not found. |
String |
getGeneName(String geneID)
Returns the name of a gene, null if not found. |
String |
getGeneNameForUniProtProtein(String proteinAccession)
Returns the gene name attached to a protein. |
static GeneFactory |
getInstance()
Static method returning the instance of the factory. |
ArrayList<String> |
getMappedGeneNames()
Returns a list of the mapped genes indexed by their gene names. |
ArrayList<String> |
getMappedGenes()
Returns a list of the mapped genes indexed by their Ensembl Gene ID. |
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 GeneFactory getInstance()
public void initialize(File file, WaitingHandler waitingHandler) throws IOException
file
- the file containing the mappingwaitingHandler
- a waiting handler allowing display of the progress
and canceling of the process.
IOException
public String getChromosomeForGeneName(String geneName)
geneName
- the gene name
public ArrayList<String> getMappedGenes()
public ArrayList<String> getMappedGeneNames()
public String getGeneName(String geneID) throws IOException
geneID
- the Ensembl ID of the gene of interest
IOException
public String getGeneEnsemblId(String geneName) throws IOException
geneName
- the gene name of the gene of interest
IOException
public String getChromosomeFromGeneId(String geneID) throws IOException
geneID
- the Ensembl ID of the gene of interest
IOException
public String getChromosomeFromGeneName(String geneName) throws IOException
geneName
- the gene name of the gene of interest
IOException
public String getGeneNameForUniProtProtein(String proteinAccession) throws IOException, IllegalArgumentException, InterruptedException, FileNotFoundException, ClassNotFoundException
proteinAccession
- the accession of the protein of interest
IOException
IllegalArgumentException
InterruptedException
FileNotFoundException
ClassNotFoundException
- REpublic void closeFiles() throws IOException
IOException
public void clearFactory()
public boolean isMappingFileOpen()
public Integer getCurrentEnsemblVersion(String ensemblType)
ensemblType
- the Ensembl type, e.g., ensembl or plants
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