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 being content of file (limited size)

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

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

Open a MSA window with online resource fetch

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