Proteome Informatics Group > Java Proteomic Library

Coding Conventions

About conventions in JPL

Fixme (nikitin)

Coding Style

Coding style, formatter and code templates.

Writing clean code helps other developers read, understand, and maintain the code you write. However, not everyone agrees on the definitions of pretty, nice, or clean. Different developers possess different styles and aesthetic sensibilities (reference).

Eclipse Style

  • A new 'JPLStyleProfile.xml' has been created and stored in JPLlib/lib that we will need to discuss format and at the end apply everywhere in the project
  • A new 'JPLCodeTemplates.xml'
  • A new 'JPLFormatterProfile.xml'
  • Share profiles for importation in JPLLib/profile project
  • DO NOT FORGET TO CONFIGURE ECLIPSE EDITOR (prop->Java Code ->Style->Clean up Code Template and Formatter) + prop->Java Editor ->Save Actions to define previously set prefs to couple with saving file

To apply an external profile from an XML file to your project, you must import it first. Click Import in the main cleanup preferences, select the file, and click OK.

Naming Conventions

We try in the jpl to call methods in a consistency way:

Creating instances:

  • with dedicated Builders when many optional parameters implement the build() method.
  • with Static Factory methods, when we want to control instanciation with getInstance() else newInstance()
  • with classic constructors (rarely)

In general, we try to follow the naming conventions given by java. The most proper way to do that is to implement interfaces proposed in the core java, propagating the contracts and propagating naming conventions.

If it is not possible we try to fit the naming convention of an approching concept.

For example, every interval met in jpl follows the same rules defined in core java. The start index is inclusive and the end index is exclusive ([begin, end[).

As another example, Sequence<T> is a generalisation of CharSequence and as such methods names are pretty close.

	public interface CharSequence {
	  char charAt(int index);
	  CharSequence subSequence(int start, int end);
	  int length();

	public interface Sequence<T> {
 	  T valueAt(int index);  
	  Sequence<T> subSequence(int start, int end);
	  int length();
Each time a concept is develop in a method via the naming mechanism, it has to be propagated everywhere the same concept appears.
	In older version of jpl, in peaklist object, we had a method named
	getPeakNumber(), and even getNumberOfPeak()
	else where in a closed object that returned the number of peaks in 
	the object. As peaklist are basically list of peaks it is more 
	consistent to name them size() (ref).