All Known Implementing Classes:

ArrayDesignAnnotationServiceImpl
```
public interface ArrayDesignAnnotationService
```
Methods to generate annotations for array designs, based on information already in the database. This can be used to generate annotation files used for ermineJ, for example. The file format:
- The file is tab-delimited text. Comma-delimited files or Excel spreadsheets (for example) are not supported.
- There is a one-line header included in the file for readability.
- The first column contains the probe identifier
- The second column contains a gene symbol(s). Clusters are delimited by '|' and genes within clusters are delimited by ','
- The third column contains the gene names (or description). Clusters are delimited by '|' and names within clusters are delimited by '$'
- The fourth column contains a delimited list of GO identifiers. These include the "GO:" prefix. Thus they read "GO:00494494" and not "494494". Delimited by '|'.
Note that for backwards compatibility, GO terms are not segregated by gene cluster.
Author:

paul

Nested Class Summary

Nested Classes
Modifier and Type Interface Description

static class ArrayDesignAnnotationService.OutputType

Field Summary

Fields
Modifier and Type	Field	Description
`static String`	`ANNOT_DATA_DIR`
`static String`	`ANNOTATION_FILE_DIRECTORY_NAME`
`static String`	`ANNOTATION_FILE_SUFFIX`
`static String`	`BIO_PROCESS_FILE_SUFFIX`
`static String`	`NO_PARENTS_FILE_SUFFIX`
`static String`	`STANDARD_FILE_SUFFIX`	String included in file names for standard (default) annotation files.

Method Summary

All Methods Instance Methods Abstract Methods
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 arrayDesign)`
`int`	`generateAnnotationFile(Writer writer, Collection<Gene> genes, Boolean useGO)`	Generate an annotation for a list of genes, instead of probes.

- Field Detail
  - ANNOTATION_FILE_SUFFIX
```
static final String ANNOTATION_FILE_SUFFIX
```
    See Also:
    
    Constant Field Values
  - BIO_PROCESS_FILE_SUFFIX
```
static final String BIO_PROCESS_FILE_SUFFIX
```
    See Also:
    
    Constant Field Values
  - NO_PARENTS_FILE_SUFFIX
```
static final String NO_PARENTS_FILE_SUFFIX
```
    See Also:
    
    Constant Field Values
  - STANDARD_FILE_SUFFIX
```
static final String STANDARD_FILE_SUFFIX
```
    String included in file names for standard (default) annotation files. These include GO terms and all parents.
    
    See Also:
    
    Constant Field Values
  - ANNOTATION_FILE_DIRECTORY_NAME
```
static final String ANNOTATION_FILE_DIRECTORY_NAME
```
    See Also:
    
    Constant Field Values
  - ANNOT_DATA_DIR
```
static final String ANNOT_DATA_DIR
```
- Method Detail
  - deleteExistingFiles
```
void deleteExistingFiles(ArrayDesign arrayDesign)
```
  - create
```
void create(ArrayDesign inputAd,
            Boolean useGO,
            boolean deleteOtherFiles)
     throws IOException
```
    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:
    
    Probe name
    Gene symbol. Genes located at different genome locations are delimited by "|"; multiple genes at the same location are delimited by ",". Both can happen simultaneously.
    Gene name, delimited as for the symbol except '$' is used instead of ','.
    GO terms, delimited by '|'; multiple genes are not handled specially (for compatibility with ermineJ) -- unless useGO is false
    Gemma's gene ids, delimited by '|'
    NCBI gene ids, delimited by '|'
    Ensembl gene ids, delimited by '|'
    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
  - generateAnnotationFile
```
int generateAnnotationFile(Writer writer,
                           Collection<Gene> genes,
                           Boolean useGO)
```
    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.
    
    Parameters:
    
    writer - the writer
    
    genes - genes
    
    useGO - if true, GO terms will be included
    
    Returns:
    
    code

Interface ArrayDesignAnnotationService

Nested Class Summary

Field Summary

Method Summary

Field Detail

ANNOTATION_FILE_SUFFIX

BIO_PROCESS_FILE_SUFFIX

NO_PARENTS_FILE_SUFFIX

STANDARD_FILE_SUFFIX

ANNOTATION_FILE_DIRECTORY_NAME

ANNOT_DATA_DIR

Method Detail

deleteExistingFiles

create

generateAnnotationFile