[Bioperl-pipeline] <dev docs> innovated converter subsystem, integrating more closely to the biopipe core.

[Juguang Xiao]

Hi all,

As people wants to see 

1. the xml setup for ensembl converter has no duplicated information of database connection and analysis; and 
2. the ensembl converter is in charge to fill in the ensembl analysis table if the analysis is new.

I do the following changes to make them.

1. made the Converter.pm have get/setter biopipe analysis and iohandler; modified the constructor of it to accept these information.

2. AnalysisAdaptor and ConverterAdaptor is changed, since these are the only places to form a Converter object. AnalysisAdaptor provider the analysis and iohanlder objects.

3. BaseEnsEMBLConverter's constructor has the new task to 1) convert biopipe analysis to ensmebl analysis, 2) setup the ensembl dbadaptor fetching the db information from the iohandler, and 3) store the ensmebl analysis into db if it is new.

4. All subclasses of BaseEnsEMBLConverter are changed accordingly. (I will give you an overview on these 6 classes for EnsEMBL core tables, later)

The only difference of this effect for users presents on the converter part in xml file. 

Before:

   <converter id="1" module="FeaturePairToEnsEMBLConverter">
      <method name="new" rank="1">
         <argument tag = "-host" value = "mysql"/>
         <argument tag = "-driver" value = "mysql"/>
         <argument tag = "-dbname" value = "juguang_homo_core_9_30"/>
         <argument tag = "-user" value = "root"/>
         <argument id = "15" tag = "-passwd" value = ""/ >
         <argument tag="-analysis_logic_name" value="RepeatMask"/>
      </method >
      <method name="contig_name" rank="2">
         <argument value="INPUT" type="SCALAR" rank="1"/>
      </method>
      <method name="convert" rank="3"/>
  </converter>

After:

   <converter id="1" module="FeaturePairToEnsEMBLConverter">
      <method name="new" rank="1"/ >
      <method name="contig_name" rank="2">
         <argument value="INPUT" type="SCALAR" rank="1"/>
      </method>
      <method name="convert" rank="3"/>
  </converter>


Enjoy the neat xml :)

Juguang.