[Joelib-help] PMD 'coupling' code cleanup

[Joerg K. W. <we...@in...>]

Dear users,

default users of the main functionality should not be affected by these 
changes.
------------

Dear developers,
I've started with refactoring the sources following the PMD rules.

First, this is important to hide the internal JOELib development 
process, e.g. using a more efficient implementation.
Second, these changes are at the moment only available in the CVS and if 
you are a developer this may affect your implementation. So, the next 
JOELib release will switch back into beta-release mode with focus on a 
more stable release for the future.
Beta-release mode for the next release means that i've decided to change 
method calls and signatures if necessary. So developers ... be warned.

Example: Load descriptors of unkown size. Load them into a data 
structure, e.g. Vector, which causes a lot of memory swapping processes. 
So, a LinkedList would be more efficient here.
So, the PMD coupling rule recommend to use always a List interface for 
the user, so the user have not to know which implementation is used 
internally.
This was not the case, because i've often used a Vector in method headers.

Until now i've corrected the 'basic','coupling' and 'import' rules. Two 
of them causes no problems.
But the 'coupling' rule has forced me to change 'Vector-->List',
'HashMap-->Map'. So, this affects method calls and forces you to
change these things also, if you are using the JOELib library for
your own implementations.
This causes three main changes for you:
      0. joelibMethod(myVector);
         Nothing to do here, because List is an interface for the Vector
         class
      1. Vector myVector=joelibMethod();
         Must be changed to:
         List myList=joelibMethod();
         or you should use casting from Vector to List and vice versa.
         Depends on your implementation.
      2. Vector myVector=joelibMethod();
         Enumeration enum=myVector.enumeration();
         enum.hasNextElement();
         enum.nextElement();
         Must be changed to:
         Iteration iter=myVector.iterator();
	iter.hasNext();
         iter.next();
      3. All users which have used the 'addElement', 'getElementAt'
         should use the access method, which are recommended from the
         interface:
         'add' and 'get'
         And 'setElementAt(object, index)' should be replaced by
         'setElementAt(index, object)' interchanging the order of the
         arguments.

Kind regards, Joerg
-- 
Dipl. Chem. Joerg K. Wegner
Center of Bioinformatics Tuebingen (ZBIT)
Department of Computer Architecture
Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany
Phone: (+49/0) 7071 29 78970
Fax: (+49/0) 7071 29 5091
E-Mail: mailto:we...@in...
WWW:    http://www-ra.informatik.uni-tuebingen.de
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