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The command line client comes as a part of client package which you are welcome to download. The command line client can be used to align sequences using any of JABAWS supported web services. The client is OS independent and supports most of the functions which can be accessed programmatically via JABAWS API. Using this client you could align sequences using presets or custom parameters, please see examples of this below. Here is the list of options supported by the command line client.
Usage: java -jar <path_to_jar_file> -h=host_and_context -s=serviceName ACTION [OPTIONS] -h=<host_and_context> - a full URL to the JABAWS web server including context path e.g. http://10.31.10.159:8080/ws -s=<ServiceName> - one of [MafftWS, MuscleWS, ClustalWS, ClustalOWS, TcoffeeWS, ProbconsWS, AAConWS, JronnWS, DisemblWS, GlobPlotWS, IUPredWS]
ACTIONS: -i=<inputFile> - full path to fasta formatted sequence file, from which to align sequences -parameters - lists parameters supported by web service -presets - lists presets supported by web service -limits - lists web services limits Please note that if input file is specified other actions are ignored
OPTIONS: (only for use with -i action): -r=<presetName> - name of the preset to use -o=<outputFile> - full path to the file where to write an alignment -f=<parameterInputFile> - the name of the file with the list of parameters to use.
Please note that -r and -f options cannot be used together. Alignment is done with either preset or aparameters from the file, but not both!
Align sequences from input.fasta file using Mafft web service with default settings, print alignment in Clustal format to console.
java -jar jabaws-min-client.jar -h=http://myhost.compbio.ac.uk:8080/jabaws -s=MafftWS -i=d:\input.fasta
Content of input.fasta file is show below (please note sequences has been trimmed for clarity)
>Foobar MTADGPRELLQLRAAVRHRPQDFVAWL >Bar MGDTTAGEMAVQRGLALHQ >Foofriend MTADGPRELLQLRAAV
Align as in above example, but write output alignment in a file out.clustal, using parameters defined in prm.in file
java -jar jabaws-min-client.jar -h=http://myhost.compbio.ac.uk:8080/jabaws -s=MafftWS -i=d:\input.fasta -o=d:\out.clustal -f=prm.in
The content of the prm.in file is shown below
--nofft
--noscore
--fastaparttree
--retree=10
--op=2.2
The format of the file is the same for all JABAWS web services.
Parameters are specified in exactly the same way as for native
executables - alignment programs like Mafft etc. So parameters
which you can use with command line version of an alignment program
can be used with JABAWS. Most of the settings controlling alignment
process are supported, but because any output has to be handled by
JABAWS, settings controlling output are not allowed to be changed.
For a list of parameters supported by a web service see the next example.
In
java -jar jabaws-min-client.jar -h=http://myhost.compbio.ac.uk:8080/jabaws -s=MafftWS -parameters
The same client can be used to access JABAWS on different hosts. Just point the client to the host you want to use by changing the value of -h key.
For example you used