Method (extension point)

Identifier

ru.biosoft.analysis.method

Registry

ru.biosoft.analysis.AnalysisMethodRegistry

Description

This extension point allows you to define new analyses method. Analysis methods appear under analyses/Methods path in the repository.

Configuration Markup

<!ELEMENT analysisClass>
<!ATTLIST analysisClass
     class        CDATA #REQUIRED
     group        CDATA #REQUIRED
     name         CDATA #REQUIRED
     description  CDATA #REQUIRED
     js           CDATA #IMPLIED
>

class

fully-qualified name of method class. This class must implement ru.biosoft.analysis.AnalysisMethod interface.

exporter

the fully-qualified name of a class which implements ru.biosoft.access.DataElementExporter interface. In most of the cases it's easier to subclass AnalysisMethodSupport.

group

analysis group (subfolder under analyses/Methods) to place the analysis to.

name

analysis name

description

either textual description or path to method description HTML file.

js

name of autogenerated JavaScript function which represents this analysis in the hostObject.function format.

Examples

The following example defines "Track statistics" analysis method:

<extension id="Track statistics" point="ru.biosoft.analysis.method"> 
  <analysisClass
    class="ru.biosoft.bsa.analysis.stats.SequenceStatistics"
    group="BSA"
    name="Track statistics"
    description="Gather various statistics about track or FASTQ file"
    js="siteAnalysis.trackStats"/> 
</extension>

JavaScript implementation

JavaScript analysis implementation will be automatically generated if you perform the following steps:

• Create JavaScript host object class which extends ru.biosoft.analysis.javascript.JavaScriptAnalysisHost.
• Register it via hostObject extension point.
• Add "js" attribute with registered host object name and desired method name separated by point as "siteAnalysis.trackStats" in the example above.