org.expasy.mzjava.script

Interface ScriptConfiguredTool<C>

public interface ScriptConfiguredTool<C>

A tool interface that allows the tool to be configured using a scripting language such as javascript, groovy or python.

Here is how a typical Tool is implemented:

First an java interface for the configuration needs to be defined. Here the configuration needs to provide a tolerance and a peptide.

     public interface SearchConfiguration {

         Tolerance getTolerance();

         Peptide getPeptide();

     }
 

The application is implemented as follows

     public class MyApp extends ScriptConfiguredTool<SearchConfiguration> {

         @Override
         public Class<SearchConfiguration> getConfigurationClass() {

             return SearchConfiguration.class;
         }

         @Override
         public int run(SearchConfiguration configuration) {

             Tolerance tolerance = configuration.getTolerance();
             Peptide peptide = configuration.getPeptide();

             //Run the search using the tolerance and peptide
             return 0;
         }

         public static void main(String[] args) throws Exception {

             File file = new File("/path/to/Config.js");

             ScriptConfiguredToolRunner.run(file, new MyApp());
         }
     }
 

The javascript script that provides configured objects is:

 function getTolerance(){

     return new org.expasy.mzjava.core.ms.AbsoluteTolerance(0.2);
 }

 function getPeptide(){

     return org.expasy.mzjava.proteomics.mol.Peptide.parse('CERVILAS');
 }
 

and the same script in groovy:

 import org.expasy.mzjava.core.ms.AbsoluteTolerance
 import org.expasy.mzjava.proteomics.mol.Peptide

 def getTolerance(){

     new AbsoluteTolerance(0.2)
 }

 def getPeptide(){

     Peptide.parse("CERVILAS")
 }
 

Version:

sqrt -1

Author:

Oliver Horlacher

Method Summary

Methods

Modifier and Type	Method and Description
Class<C>	getConfigurationClass() Returns the interface that the configuration implements
int	run(C configuration) Execute the tool with the given configuration

Method Detail

run

int run(C configuration)
        throws Exception

Execute the tool with the given configuration

Parameters:

configuration - the configuration

Returns:

exit code.

Throws:

Exception

getConfigurationClass

Class<C> getConfigurationClass()

Returns the interface that the configuration implements

Returns:

the interface that the configuration implements