Analysis method development

BioUML analysis method is a function which takes some user-defined parameters, processes them somehow (probably using repository elements and databases) and produces some results, storing them in the repository. This page describes implementation details on how to create your own analysis method.

If you want to create your analysis method in new plugin, please read plugin development page first.

Classes

To create analysis method, you should create at least three classes:

1. Analysis class: class implementing AnalysisMethod interface. It's strongly recommended to extend AnalysisMethodSupport class parameterizing it via parameters class.
2. Parameters class: bean class for analysis parameters, which must implement AnalysisParameters interface. It's strongly recommended to extend AbstractAnalysisParameters class.
3. Bean info for parameters class: class implementing BeanInfo interface which describes parameters class. Must have the same name as parameters class with BeanInfo suffix. It's strongly recommended to extend BeanInfoEx2 class.

The following naming conventions are used. Consider, you want to create some analysis to "process data". Then analysis class should be named as ProcessData or ProcessDataAnalysis, parameters class should be named as ProcessDataParameters and bean info for parameters class should be named as ProcessDataParametersBeanInfo.

If your analysis has not very much code, you may consider putting parameters class and its bean info as nested static classes into analysis class in the following manner:

public class ProcessDataAnalysis extends AnalysisMethodSupport<ProcessDataAnalysis.ProcessDataParameters>
{
  ...
  public static class ProcessDataParameters extends AbstractAnalysisParameters
  {
    ...
  }

  public static class ProcessDataParametersBeanInfo extends BeanInfoEx2
  {
    ...
  }
}

Extension

To make your analysis available in the tree, you must register it as extension for ru.biosoft.analysis.method extension point. Consider also creating method description HTML file and JavaScript host object (or use existing one).

Implementing parameters

Parameters class must have default constructor and getter and setter methods for all parameters used in analysis method. Setters must call Option.firePropertyChange superclass method. Getters can be annotated using @PropertyName and @PropertyDescription annotations. Usual implementation look like this:

public class ProcessDataParameters extends AbstractAnalysisParameters
{
  private DataElementPath inputPath, outputPath;
  private String myStringParameter;
  private boolean myBooleanParameter;

  @PropertyName("Input table")
  @PropertyDescription("Table to process")
  public DataElementPath getInputPath()
  {
    return inputPath;
  }
    
  public void setInputPath(DataElementPath inputPath)
  {
    Object oldValue = this.inputPath;
    this.inputPath = inputPath;
    firePropertyChange("inputPath", oldValue, this.inputPath);
  }

  @PropertyName("String parameter")
  @PropertyDescription("String which will be used during processing")
  public String getMyStringParameter()
  {
    return myStringParameter;
  }

  public void setMyStringParameter(String myStringParameter)
  {
    Object oldValue = this.myStringParameter;
    this.myStringParameter = myStringParameter;
    firePropertyChange("myStringParameter", oldValue, myStringParameter);
  }

  @PropertyName("Verbose output")
  @PropertyDescription("Whether to print additional messages during processing")
  public boolean isMyBooleanParameter()
  {
    return myBooleanParameter;
  }

  public void setMyBooleanParameter(boolean myBooleanParameter)
  {
    Object oldValue = this.myBooleanParameter;
    this.myBooleanParameter = myBooleanParameter;
    firePropertyChange("myBooleanParameter", oldValue, myBooleanParameter);
  }
}

Parameter types

Many parameter types are supported, including (but not limited to) the following:

• Primitive types (boolean, short, int, long, float, double);
• String for textual parameters;
• DataElementPath for paths to the repository elements (both for inputs and outputs);
• DataElementPathSet for sets of input repository elements;
• Species for selection of species from preinstalled list;
• BasicGenomeSelector and GenomeSelector for convenient selection of the genome (either in preinstalled database or user-uploaded);
• Color for color selection;
• Java arrays of any supported types (array elements can be added or deleted by user).

You may use your own bean as complex parameter type, but the following requirements should be met:

• Your bean should extend Option class.
• Your bean should be serializable via TextUtil.fromString/TextUtil.toString methods. See text serialization for details.

Writing bean info class for parameters

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Advanced parameters features

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Implementing analysis

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Logging

To log messages during analysis execution, use AnalysisMethodSupport.log logger instance. This instance is connected with analysis or workflow log. In case of unrecoverable error, it's better to throw BioUML exception out of justAnalyzeAndPut method than to log it by yourself.