Revision history for Bio-DOOP-DOOP
0.27    2007/07/06
        The Mofext object and the Fuzznuc object now have same methods. Easy to use. Correct some
        documentation errors.
0.26    2007/06/24
        New methods in the Graphics::Feature (draw_fuzz_result), Util::Run::Fuzznuc (new_by_tmp).
        Change the Util::Run::Mofext. Now it is returns the subquery because it is needed by the
        alignemnt creating script.
0.25    2007/06/15
        The Mofext results now return the full hit sequence and the positions for the alignment
0.24    2007/06/11
        Modified the Sequence module to return -1 in the get_xref_value method.
        The Sort and Filt modules have finished
        Modified the help messages in the Cluster module
        Add new method to the Search module to return just ids, not objects. (This
        take lower load on our webserver.)
0.23    2007/05/29
        I have started to coding the Sort and Filt modules. The Mofext is
        write out the score and extended score.
0.22    2007/05/22
        New method in the Mofext.pm. Now you can use previously defined
        tmp file for the mofext search. Time save option.
0.21    2007/05/21
        Fix the Mofext.pm, now the installer won't give error messages
0.20    2007/05/14
        Fix a Makefile.pm error. Now no problem at the installation
0.19    2007/05/10
        Tha database have been changed, so the modules also changed. New
        methods not added, but some old stuff have been removed.
0.18    2007/05/09
        Modification in the Motif module. Correct the get_seqfeature_ids method
0.17    2007/04/24
        Changes in the Sequence objects
0.16    2007/04/12
        The Graphics::Feature module fixed, but Endre found some bug :-(
0.15    2007/04/12
        The ClusterSubset class can manage the chordata database
0.14    2007/04/01
        New module Util::Run::Fuzznuc.
	New modification in Graphics::Feature, because it is not correct.
0.13    2007/03/28
        The motifs in the Graphics::Feature module drawed incorrectly. Now fixed. Maybe
0.12    2007/03/19
        The motifs in the Graphics::Feature module drawed correctly
        The ClusterSubset module get_all_seqs method returns sorted sequences
0.11    2007/03/14
        The motifs is the Graphics::Feature module drawed reverse order. Fixed
        The first sequence in the graphics is a reference species
        The UTR doesn't hide the species name
        If no have motifs the Graphics::Feature module also create picture
0.10    2007/02/15
        Add new object (Util::Run::Admin) to handle the running processes
0.09    2007/02/10
        Add new methods to Cluster.pm (get_subset_by_type, get_availables_types)
        Add new methods to Util::Run::Mofext object (run_background, get_results_from_file)
        Now you can run mofext in the background.
0.08    2007/01/31
        Add new method for Sequence.pm (get_raw_seq)
        Fixed the motif drawing in Graphics::Feature module
        Fixed the get_fasta method (add a new line to the end :-))
        Add new method for SequenceFeature.pm (length)
        Add new object (Util::Run::Mofext)
        Fixed the get_subset_id methods in Bio::DOOP::Motif
        Add more warning messages to the Cluster and ClusterSubset objects
0.07    2007/01/12
        Add more comment for the documentation
        Remove hungarian comments
0.06    2007/01/05
        New method in Cluster class: get_ref_seq
        Carp uses for module warnings
        Some methods add warning messages if has an error in the MySQL database
0.05    2007/01/03
	Search module recoding. The get_cluster_by_* methods
	not give back redundant elements
0.04    2006/12/20
	Bug fixes. New method in Cluster class: get_orig_subset.
0.03    2006/12/13
        Advanced color handling in the Graphics::Feature module
        Full access to the TSS annotation
0.02    2006/12/06
        First version with correct CPAN install
0.01    2006/12/04
        First version, released on an unsuspecting world.