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EBIEMBL-EBI Web Servicesservicesmsamview_soap
Table of Contents

MView (SOAP)

Description

MView 1) re-formats the results of a sequence database search (BLAST, FASTA, etc) or a multiple alignment (MSF, PIR, CLUSTAL, etc) adding optional HTML markup to control colouring and web page layout.

When generating a multiple sequence alignment from a sequence database search result MView uses only the sequence data which appears in the search result. As a consequence regions of the query sequence and/or the hits found which are not matched do not appear in the generated alignment, however the alignments found in the search are retained as part of the multiple alignment. This contrasts with the method used by DbClustal (DbClustal (REST) or DbClustal (SOAP)) which uses the full length sequences (query and hits) to generate the alignment.

For more information see:

Web service registry entries:

Important

We kindly ask all users of EMBL-EBI Web Services to submit tool jobs in batches of up to 25 at a time and to not submit more until the results and processing has completed for these. This enables users as well as the service maintainers to deal more easily with local and remote network outages as well as scheduled or unscheduled downtime.

Service provision happens on a fair-share basis. Overzealous usage of a particular resource will be dealt with in accordance to the EMBL-EBI's Terms of Use.

Clients

Sample clients are provided for a number of programming languages. For details of how to use these clients, download the client and run the program without any arguments.

Language Download Requirements
C# .NET Executable: MViewCliClient.exe; Source: AbstractWsClient.cs, MViewClient.cs, MViewCliClient.cs A .NET runtime environment. If building from source development tools are also required. See the .NET tutorial for details.
Java Executable jar: MView_Axis1.jar; Source: AbstractWsToolClient.java, MViewClient.java Axis 1.4; All dependencies, including Axis 1.4 and Commons-CLI, are available in lib-1.4.zip.
Perl mview_soaplite.pl SOAP::Lite

For further details of these tool-kits and workflow platforms see our Guide to Web Services.

WSDL

The WSDL for the MView SOAP service: http://www.ebi.ac.uk/Tools/services/soap/mview?wsdl

Operations

getParameters()

Get a list of the parameter names.

Arguments: none

Returns: a list of strings giving the names of the parameters.

getParameterDetails(parameterId)

Get details of a specific parameter.

Arguments:

  • parameterId: identifier/name of the parameter to fetch details of.

Returns: a wsParameterDetails describing the parameter and its values.

run(email, title, params)

Submit a job to the service.

Arguments:

Returns: a string containing the job identifier (jobId).

getStatus(jobId)

Get the status of a submitted job.

Arguments:

  • jobId: (required) job identifier.

Returns: a string containing the status.

The values for the status are:

  • RUNNING: the job is currently being processed.
  • FINISHED: job has finished, and the results can then be retrieved.
  • ERROR: an error occurred attempting to get the job status.
  • FAILURE: the job failed.
  • NOT_FOUND: the job cannot be found.

Further details can be found in Synchronous and Asynchronous Access: JDispatcher.

getResultTypes(jobId)

Get the available result types for a finished job.

Arguments:

  • jobId: (required) job identifier.

Returns: a list of wsResultType data structures describing the available result types.

getResult(jobId, type, parameters)

Get the result of a job of the specified type.

Arguments:

  • jobId: (required) job identifier.
  • type: (required) string specifying the result type to fetch. See getResultTypes(jobId) for details of the available types.
  • parameters: optional list of wsRawOutputParameter used to provide additional parameters for derived result types.

Returns: the result data for the specified type, base64 encoded. Depending on the SOAP library and programming language used the result may be returned in decoded form. For some result types (e.g. images) this will be binary data rather than a text string.

Data Types

InputParameters

The input parameters for the job:

Attribute Type Description
stype string Input sequence type.
informat string Input alignment or sequence similarity search result format.
outformat string Output alignment format.
htmlmarkup string Type of HTML mark-up used for output.
css boolean Enable/disable use of Cascading Style Sheets (CSS) in output HTML.
pcid string Basis for percent identity calculation.
alignment boolean Show/hide alignment in output.
ruler boolean Show/hide ruler in output.
width int Width for output alignment.
coloring string Basic style of colouring.
colormap string Colour map.
groupmap string Group map.
consensus boolean Show/hide consensus.
concoloring string Basic style of consensus colouring.
concolormap string Consensus colour map.
congroupmap string Consensus group map.
congaps boolean Enable/disable counting of gaps during consensus computations.
sequence string Input alignment or sequence similarity search result. For sequence similarity search jobs run on the EMBL-EBI services with supported output formats an EMBL-EBI job identifier can be used as input.

More detailed information about each parameter, including valid values can be obtained using the getParameterDetails(parameterId) operation.

wsParameterDetails

Descriptive information about a tool parameter. Returned by getParameterDetails(parameterId).

Attribute Type Description
name string Name of the parameter.
description string Description of the parameter, suitable for use in option help interfaces.
type string Data type of the parameter.
values list of wsParameterValue List of valid values for the option.

wsParameterValue

Description of a tool parameter value. Used in wsParameterDetails.

Attribute Type Description
label string Display name of the value, for use in interfaces.
value string String representation of the value to be passed to the tool parameter.
defaultValue boolean Flag indicating if this value is the default.
properties list of wsProperty List of key/value pairs providing further information.

wsProperty

Properties of a tool parameter value. Used in wsParameterValue.

Attribute Type Description
key string name of property
value string value for property

wsRawOutputParameter

Additional parameters passed when requesting a result. See getResult(jobId, type, parameters).

Attribute Type Description
name string name of parameter
value list of string values for parameter

wsResultType

Description of a result type. Returned by getResultTypes(jobId).

Attribute Type Description
identifier string Identifier for the result type. Passed as type to getResult(jobId, type, parameters).
label string Display name for use in user interfaces.
description string Description of the result type, for use in help interfaces.
mediaType string MIME type of the returned data.
fileSuffix string Suggested suffix for file name, if writing data to disk.
1) Brown N.P., Leroy C. and Sander C. (1998)
MView: a web-compatible database search or multiple alignment viewer.
Bioinformatics 14(4):380-1
PubMed: 9632837
DOI: 10.1093/bioinformatics/14.4.380
 
services/msa/mview_soap.txt · Last modified: 2013/04/30 10:24 by hpm
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