Revision history for g-language package

1.6.10   2007.06.10
	-bug fixes. 
	-packaging for MacOS X 10.4 (Intel)

1.6.9    2007.06.07
        -added G::Tools::Statistics
         exported methods are:
                 mean
                 sum
                 variance
                 standard_deviation
                 min
                 mindex
                 max
                 maxdex
                 median
                 least_squares_fit
                 cor
                 ttest
         where cor include options for Spearman's, Pearson's, and Kendall's methods,
         and ttest supports both independent and paired Student's t-test.

1.6.8    2007.06.06
	-clened up the codes of G-language Shell
	-logging features are moved to G::Shell::Log
	 logging now works quite nicely
	-modified the loading message
	- '-h' option shows help message for G command

	-removed "without annotation" option for new G()
	-removed "long sequence" option for new G()

	-fixed a bug in EMBL parser (multiple-locus, join)

1.6.7    2007.06.05
	-added $gb->rRNA(), $gb->tRNA(), $gb->gene()
		or  $gb->feature("rRNA"), $gb->feature("tRNA"), $gb->feature("gene")
		or $gb->feature("any feature type")
		which functions like $gb->cds()

	-added $gb->previous_feature(), $gb->next_feature()
        	$gb->previous_cds(), $gb->next_cds()
        	which returns the feature ID of the next or previous
        	features or CDS. See help for details.

	-added manual for 35 "prelude" methods
	-removed G::G.pm

1.6.6    2007.06.01
	- Added G::Shell::EUtils
	- This module provides
	  pubmed and entrez commands to search through
          NCBI Entrez from G-language Shell use the 
          help function of G-language Shell for details.

1.6.5    2007.05.31
	- Added help command to G-language Shell
        - Added G::Shell::Help to do the above purpose
	- help also searches for Bioperl functions :-)

1.6.4    2007.05.29
	- First package using Module::Install

1.6.3    2007.01.12
	- G::Seq::, G::SystemsBiology::, G::Tools:: classes now use
	  SelfLoader. This resulted in 20% speed-up.

1.6.2    2006.05.13
	- porting to MacOS X

1.6.1    2006.04.11
	- porting to KNOB (Knoppix for Bio)

1.4.9    2004.11.14
	- porting to Windows (final version for Windows)
	  We are no longer supporting Windows
	- Included G-language Shell (Interpreter)

1.1.0    2002.07.31
	1. micro module core
	   The former 'Prelude' core has been subdivided into micro module cores 
	   each responsible for specific functions. This enables more Object Oriented
	   style of architecture, and better flexibility in plugging. Another advantage
	   is to use Skyline core functions without doing 'use G;'. This can be alternatively
	   called internally as 'use G::Skyline'.
	
	   G::Skyline succeeds G::IO::GenBankO, which succeeds G::IO::GenBankI, which succeeds
	   G::Prelude.

	   The following is the explanation of [new|altered] modules:

	   G.pm              Succeeds G::Skyline. Now only responsible for 'new G()' options and output options
	   G::Prelude        Core of core. Base class with manipulation methods only.
	   G::IO::GenBankI   Succeeds G::Prelude. Embedded with GenBank parsers.
	   G::IO::GenBankO   Succeeds G::GenBankI. Responsible for GenBank flatfile output.	
	   G::IO::Bioperl    Responsible for the conversion of Bio::Seq::RichSeq to G::Skyline
	   G::IO::Annotation Embedded with annotation functions
	   G::Skyline        Dummy class that multiply inherit the above classes
	
	   complement() and translate() are moved to G::Seq::Primitive so that they can be 'use'-ed internally
	   from odyssey modules.

	   As stated above, with stronger object oriented form, it is easier to expand the functions without 
	   risking new bugs, and G::IO:: can be plugged with new parsers, such as that for FASTA, EMBL, and 
	   so on for more speed. 

	2. enhanced bioperl porting
	   Conversion of Bio::Seq::RichSeq object to G::Skyline object is further enhanced, now almost
	   perfectly mirroring including the header and the 'join' field.
	
	   G::IO::Bioperl::convert(struct Bio::Seq::RichSeq, struct G::Skyline); easily converts the 
	   bioperl object.
	
	   SubOpt protocol is also enhanced so that now it can take bioperl object as well as G object.
	   Therefore, all odyssey functions can be directly accessed from bioperl as follows:
	     $in = new Bio::SeqIO('-file'=>"hoge.embl");
	     $bioperl = $in->next_seq();
	     gcskew($bioperl, -window=>1000, -output=>"show");
	
	3. new interpreter for loading options
	   Multiple options can now be used. For example, 
	   $gb = new G("hoge.embl", "EMBL", "no msg", "without annotation", "longest ORF annotation", "multiple locus");
	   is now possible. Order can be random.

	   Database formats supported is also expanded, now supporting all of the following:
	   GenBank, Fasta, SCF, PIR, EMBL, raw, GCG, ace, BSML, swiss, phd, game, qual
	   Moreover, file format option is now case insensitive. 'GENBANK', 'GenBank', 'genbank' all point to the
	   same old GenBank. Furthermore, Skyline core can now automatically guess the format of the database 
	   even without the format options. Thus 'new G("hoge.gbk")' load genbank file, and 'new G("hoge.bsml")' 
	   automatically loads in BSML format. From now on, you probably do no have to care about the database
	   formats at the input to G-language GAE.

	   Network retrieval is also automatically interpreted, and enhanced. Accession numbers starting with NC_
	   is taken from RefSeq in NCBI, and other accession numbers are taken from ordinary GenBank ftps. Again,
	   here you do not have to enter 'net GenBank' option, although if you prefer that, you can.

	4. BSML and LabBook Genome XML Viewer (TM)
	   Because BSML output is enabled, annotated G object can directly be put into the LabBook Genome XML Viewer (TM)
	   which is a free genome viewer and editer of BSML files. This enables graphical genome view, circular plasmid
	   view, with zooming and refering functions. Also, it is worth noting that it is the first step of G-language GAE
	   to be able to input/output XML formats of databases. GAME XML format is also supported.

	5. Bug fix and addition of modules
	   Bug in Prelude ($gb->del_key(), parsing of FT w/o value, -w switch compliancy) is fixed, and several new
	   modules are incorporated into the Odyssey functions layer. The documentations for the new functions will be
	   available at our website by the official release of version 2.

1.0.0    2001.09.11
	- initial relase

