Revision history for Bio-DOOP-DOOP 1.04 2009/08/17 Purge Proc:Processtable from module & deps. Remove Bio::DOOP::Util::Run::Admin module. Other minor corrections. 1.03 2009/05/20 Moar documentation and some minor corrections. 1.02 2009/04/23 Fuzznuc and Mofext wrapper changed. Documentation extended with useful informations about connecting to our database. 1.01 2008/08/29 Help messages corrections. 1.00 2008/08/05 GeneMerge module added. Some minor changes to optimize the MySQL queries. 0.29 2008/06/22 Modifying the draw_fuzz_result. 0.28 2007/09/18 Grammatical corrections. Thanx for Endre. 0.27 2007/07/06 The Mofext object and the Fuzznuc object now have the same easy to use methods. Corrected some documentation errors. 0.26 2007/06/24 New methods in the Graphics::Feature (draw_fuzz_result), Util::Run::Fuzznuc (new_by_tmp). Changed Util::Run::Mofext. Now it returns the subquery because the alignment creating script needs it. 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 are finished. Modified the help messages in the Cluster module. Added new method to the Search module to return just ids, not objects. (This takes lower load on our webserver.) 0.23 2007/05/29 Started coding the Sort and Filt modules. The Mofext module writes out the score and extended score. 0.22 2007/05/22 New method in the Mofext.pm. Now you can use a previously defined tmp file for the mofext search. Time saving 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 has 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 new bugs. :-( 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 the png is not correct. 0.13 2007/03/28 The motifs in the Graphics::Feature module were drawn incorrectly. Now fixed. Maybe. 0.12 2007/03/19 The motifs in the Graphics::Feature module drawn correctly. The ClusterSubset module get_all_seqs method returns sorted sequences. 0.11 2007/03/14 The motifs is the Graphics::Feature module were drawn in reverse order. Fixed. The first sequence in the graphics is the reference species. The UTR doesn't hide the species name. If we don't have motifs, the Graphics::Feature module still creates the picture. 0.10 2007/02/15 Added new object (Util::Run::Admin) to handle the running processes. 0.09 2007/02/10 Added new methods to Cluster.pm (get_subset_by_type, get_availables_types). Added 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 Added 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 :-)). Added new method for SequenceFeature.pm (length). Added new object (Util::Run::Mofext). Fixed the get_subset_id methods in Bio::DOOP::Motif. Added more warning messages to the Cluster and ClusterSubset objects. 0.07 2007/01/12 Added more comments for the documentation. Removed hungarian comments. 0.06 2007/01/05 New method in Cluster class: get_ref_seq. Carp for module warnings. Some methods throw warning messages, if they have problems with the MySQL database. 0.05 2007/01/03 Search module recoding. The get_cluster_by_* methods do 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.