Package ubic.gemma.core.analysis.service

Class ArrayDesignAnnotationServiceImpl

java.lang.Object

ubic.gemma.core.analysis.service.ArrayDesignAnnotationServiceImpl

All Implemented Interfaces:

ArrayDesignAnnotationService

@Component
public class ArrayDesignAnnotationServiceImpl
extends Object
implements ArrayDesignAnnotationService

Author:

Paul

See Also:

ArrayDesignAnnotationService

Nested Class Summary

Nested classes/interfaces inherited from interface ubic.gemma.core.analysis.service.ArrayDesignAnnotationService

ArrayDesignAnnotationService.OutputType

Field Summary

Fields inherited from interface ubic.gemma.core.analysis.service.ArrayDesignAnnotationService

ANNOT_DATA_DIR, ANNOTATION_FILE_DIRECTORY_NAME, ANNOTATION_FILE_SUFFIX, BIO_PROCESS_FILE_SUFFIX, NO_PARENTS_FILE_SUFFIX, STANDARD_FILE_SUFFIX

Constructor Summary

Constructors

Constructor	Description
ArrayDesignAnnotationServiceImpl()

Method Summary

Modifier and Type	Method	Description
void	create(ArrayDesign inputAd, Boolean useGO, boolean deleteOtherFiles)	Create (or update) all the annotation files for the given platform.
void	deleteExistingFiles(ArrayDesign ad)
int	generateAnnotationFile(Writer writer, Collection<Gene> genes, Boolean useGO)	Generate an annotation for a list of genes, instead of probes.
static File	getFileName(String fileBaseName)
static String	mungeFileName(String fileBaseName)	Remove file separators (e.g., "/") from the file names.
static Map<Long,Collection<Gene>>	readAnnotationFile(ArrayDesign arrayDesign)
static Map<Long,String[]>	readAnnotationFileAsString(ArrayDesign arrayDesign)	This tries to read one of the annotation files (noparents, bioprocess or regular) to get the gene information - GO annotations are not part of the result.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

ArrayDesignAnnotationServiceImpl

public ArrayDesignAnnotationServiceImpl()

Method Detail

getFileName

public static File getFileName(String fileBaseName)

mungeFileName

public static String mungeFileName(String fileBaseName)

Remove file separators (e.g., "/") from the file names.

Parameters:

fileBaseName - file base name

Returns:

munged name

readAnnotationFile

public static Map<Long,Collection<Gene>> readAnnotationFile(ArrayDesign arrayDesign)

Parameters:

arrayDesign - array design

Returns:

Map of composite sequence ids and transient (incomplete) genes. The genes only have the symbol filled in.

readAnnotationFileAsString

public static Map<Long,String[]> readAnnotationFileAsString(ArrayDesign arrayDesign)

This tries to read one of the annotation files (noparents, bioprocess or regular) to get the gene information - GO annotations are not part of the result.

Parameters:

arrayDesign - array design

Returns:

Map of composite sequence ids to an array of delimited strings: [probe name,genes symbol, gene Name, gemma gene id, ncbi id] for a given probe id. format of string is geneSymbol then geneNames same as found in annotation file.

create

public void create(ArrayDesign inputAd,
                   Boolean useGO,
                   boolean deleteOtherFiles)
            throws IOException

Description copied from interface: ArrayDesignAnnotationService

Create (or update) all the annotation files for the given platform. Side effect: any expression experiment data files that use this platform will be deleted. Format details: There is a one-line header. The columns are:

1. Probe name
2. Gene symbol. Genes located at different genome locations are delimited by "|"; multiple genes at the same location are delimited by ",". Both can happen simultaneously.
3. Gene name, delimited as for the symbol except '$' is used instead of ','.
4. GO terms, delimited by '|'; multiple genes are not handled specially (for compatibility with ermineJ) -- unless useGO is false
5. Gemma's gene ids, delimited by '|'
6. NCBI gene ids, delimited by '|'
7. Ensembl gene ids, delimited by '|'

Specified by:

create in interface ArrayDesignAnnotationService

Parameters:

inputAd - platform to process

useGO - if true, GO terms will be included

deleteOtherFiles - if true, other files conaining the annotations for this platform will be deleted, such as DEA results and data flat files.

Throws:

IOException

deleteExistingFiles

public void deleteExistingFiles(ArrayDesign ad)

Specified by:

deleteExistingFiles in interface ArrayDesignAnnotationService

generateAnnotationFile

public int generateAnnotationFile(Writer writer,
                                  Collection<Gene> genes,
                                  Boolean useGO)

Description copied from interface: ArrayDesignAnnotationService

Generate an annotation for a list of genes, instead of probes. The second column will contain the NCBI id, if available. Will generate the 'short' version.

Specified by:

generateAnnotationFile in interface ArrayDesignAnnotationService

Parameters:

writer - the writer

genes - genes

useGO - if true, GO terms will be included

Returns:

code