# Jalview Rest(-like) API

## Launch Jalview with API active on specified port

`java -jar jalview_all.jar -nosplash -nowebservicediscovery -startapi -serverport 2021`
(-nosplash and -nowebservicediscovery just to save time/output)

## Open a MSA window with existing data

`*POST* http://localhost:2021/jalview/api/inputalignment`
with body of HTTP request being content of file (automatic parsing by Jalview)

`*GET* http://localhost:2021/jalview/api/inputalignment?data=<data>`
with <data> being content of file (limited size)

`*GET* http://localhost:2021/jalview/api/inputalignment?file=<fileURI>`
with <fileURI> being a file

`*GET* http://localhost:2021/jalview/api/inputalignment?url=<URL>`
with <URL> being a URL to a file

## Open a MSA window with online resource fetch

`http://localhost:2021/jalview/api/fetchsequences/<resource name>/<sequence ids>`
<resource name> is one of "ensemble", "pdb", "ensembl-tr", "ensembl-gn", ["uniprotkb/swiss-prot", "uniprotkb/trembl", ""uniprot/sptrembl", "uniprot/swissprot" not yet implemented]
<sequence ids> ids for fetch

### optional parameters
`id=<your specified id for this request>`

### Returns (as key=value pairs in the body of the response)
```
id=<the given id for this request>
status=<STARTED|IN_PROGRESS|FINISHED|ERROR|NOT_RUN>