Version 2.4.1
	Fixed error reading multiple databases
	Fixed MacOSX reading of incomplete sequence files
	Fixed indexing of REFSEQ

Version 2.4.0
        New Jemboss authorising server code. This uses a new set-uid
	program (jembossctl) to perform tasks as the user.

	New alignment output format "match" for wordmatch, reports the
	length, sequence names, and range in each sequence.

	emboss.default.template has been changed to include the new SRSWWW
	access method and the fields definitions for the test databases.

	In dbiblast, renamed the -filename option -filenames to match the
	other dbi indexing programs, and because wildcard filenames are
	supported.
	
	Removed the -staden option for the dbi indexing programs. This had
	no efect (it was originally included to rename files as
	division.lookup for use by internal utilities at the Sanger
	Centre).
	
	In qatest.pl test script, added test for missing expected file.
	Only seen for obsolete secondary output files, no tests were passing
	that should have failed.

	Script (scripts/dbilist.pl) to report the contents of EMBLCD
	database indices created by dbiflat, dbigcg, dbifasta or dbiblast.

	Proxy HTTP access for remote servers. Define EMBOSS_PROXY as an
	environment variable, or in emboss.defaults. Can also be set for
	any database as proxy: "hostname:port" or overridden with
	proxy: ":" to use a local server for a database. This is used by
	both the URL and SRSWWW access methods.

	New ajListUnique function to remove duplicate nodes in a list.

	New embxyz.c / .h embXyzSeqsetNRRange functions added

	Report format "table" is the default for several applications. In
	this format, the sequence USA has been removed because it already
	appears in the sequenec header part of the report. A new format
	"-rformat nametable" will produce the previous report output for
	users who are relying on parsing it.

	Output files defined with the "nullok" attribute in ACD are not
	created unless requested. The file name and extension are ignored.
	It is possible to add a new associated qualifier to control this
	behaviour, but its use may be confusing with more than one output
	file.
	
	Precision attribute for report score (default is 3). Other
	floating point report values are written as strings by the
	original application so their precision is defined in the
	code. The score is a float, as part of the internal (GFF) feature
	structure.  A zero value produces an integer score (strictly, it
	uses %.0f as the format). Set precision for etandem, fuzznuc,
	fuzzpro, fuzztran, patmatdb, patmatmotifs (integer scores) and
	restrict (no score)
	
	Report output for equicktandem and etandem, with -origfile to
	write the original output format for sites (Sanger for example)
	who still require it. By default, the origfile output file is
	not created.

	Report output for patmatdb and patmatmotifs. For patmatmotifs the
	prosite documentation appears in the report footer, with the
	addition of the motif name and the number of matches in the
	sequence.

	Report headers and footers automatically trim last newline.
	
	Reports in -rformat SeqTable right-align numbers.

	Report output for marscan (-rformat GFF by default)

	Report output for fuzztran (-rformat table with the translation
	included as a report field). Using -rformat seqtable with fuzztran
	now also shows the original DNA sequence.
	
	Report output for fuzznuc and fuzzpro (-rformat SeqTable by default)

	New report qualifiers -raccshow to include accession in header
	and -rdesshow to include description in header
	
	Two access methods "file" and "offset" were defined as valid in
	database definitions, but are really reserved for simple file reading.
	They are removed from the database access methods list.

	Two access methods "cmd" and "nbrf" are obsolete (cmd was never
	implemented, nbrf is replaced by gcg which includes a query
	mechanism). Both are removed from the database access methods list,
	and the source code is commented out.
	
	SRS, SRSFASTA and SRSWWW database access can read all entries This
	is not recommended for SRSWWW access because it will read
	everything into memory - all of EMBL for example - then strip out
	HTML tags before reading. For SRS it is not recommended because
	"methodall: direct" is faster. For SRSFASTA it is necessary
	because using SRSFASTA implies EMBOSS does not read the original
	data format. However, not iomplementing an "all" search left a gap
	in the SRS access methods which would generate a bad SRS command
	line or URL.
	
	NBRF sequence reading trims last character only if it is '*'
	to catch cases where SRS reports the sequence as 'plain'

	GCG database text has the spaces in ". ." strings removed.

	Database entry text and sequence saved for binary formats (GCG, BLAST)
	for use by entret and other applications

	dbiblast indices with split databases (formatdb -v) fixed for reading
	all entries (was only reading the first file)

	dbiblast and dbigcg indices support exclude and file definitions
	to create database subsets

	Database include and file definitions can use the simple filename.
	In some cases the full path was used. Database files are checked
	both with and without the directory path for back-compatibility.

	srswww access method created to query a remote web server.
	Preferred to using URL access as SRS queries can be built

	Sequence objects include the SeqVersion, Keyword list and Taxonomy
	list.

	The GI number is read as an alternative SeqVersion where it is
	available (GenBank and some NCBI formats). The GI number is
	reported in GenBank format if available, but the GenBank VERSION
	line may have only the SeqVersion if, for example, the sequence
	was reead from an EMBL entry. "sv" queries check both the
	SeqVersion and GI number.

	Accession numbers have a strict definition, which covers the old
	and new EMBL/GenBank format, SwissProt, PIR, and REFSEQ
	(NM_nnnnnn). Earlier versions would accept any "accession number"
	in some sequence formats, especially NCBI format.

	SeqVersion (EMBL SV line, GenBank VERSION line) is used in preference
	to accession number where available. Can also be read in FASTA
	and NCBI formats. Where only the SeqVersion is available, the
	accession number is generated.
	
	USA queries implement searches by SV, DES, ORG and KEY. These work
	with SRS access methods (SRS, SRSFASTA, SRSWWW) by building SRS
	queries, and with direct access (simple file reading) by
	testing the sequence object.

	Key and Org queries are for full keywords (including spaces) and
	for each level of the taxonomy.

	Des queries, if the access method does not provide a mechanism,
	(if the access method does not have its own index) are applied to
	words within the description. Words start with a letter or number,
	and end with a letter or number. SRS typically does the same, but
	allows a single quote at the end. This catches words such as 3'
	and 5' but is a problem with some quoted text.

	Queries for ID ACC SV DES ORG and KEY are valid for all file
	access methods, including URL, external, cmd, app, file and by
	default any new method added. If the internal query data is not
	flagged by the access method (to show the database has been
	queried) the sequence object is automatically tested.

	Missing description, keyword, organism, or seqversion fields cause
	queries to fail if they are used on inappropriate data.

	dbiflat, dbigcg dbifasta and dbiblast can index the new
	fields. All fields are available in dbiflat and dbigcg. The sv and
	des fields are available in dbifasta and dbiblast. If any specific
	formats make it possible to parse the org (or key) field they can
	be added as new formats.

	The new EMBLCD index files are named as follows: des for the
	descriptions (no obvious standard name), seqvn for the seqversion
	(no obvious standard name), keyword for keywords (EMBLCD
	distribution name) and taxon to organism (EMBCD distribution
	name). The EMBLCD distribution also included a freetext index
	which is similar to the SRS alltext search so we did not use the
	name for the desctription index.

	We are working through the EMBLCD format documentation to make
	EMBOSS indices more compatible. For example, all tokens in the TRG
	index files should have trailing spaces. We use a NULL to mark the
	end of the string.

	EMBLCD index files now expand to fit the longest token, including
	the entryname index which was limited to 12 characters (only one
	site reported a problem with this in dbifasta with long ID names).

	A new qualifier -maxindex sets an upper limit (25 is recommended)
	to limit the size of all index files. Currently this applies to
	all indices. We can add separate maxima for each field if
	needed. We expect very few sites to use the extra index fields
	as SRS is a simpler alternative.
	
	New database definition token 'fields' with a list of indexed fields
	can be set to 'sv des org key' for SRS databases. 

	USAs check the query field against the database 'fields'
	definition. ID and ACC are always allowed. dbname:name still
	searches ID and ACC (no change from previous version)

	USAs with a filename can include the new query fields. The syntax is
	filename:field:query for example empro.dat:id:eclaci (the extended
	syntax is because empro.dat-id:eclaci looks like a filename ending
	in -id)

	Application 'tranalign' added. 
	This aligns nucleic coding regions based on a set of aligned proteins.

	
Version 2.3.1

	est2genome fixed for large alignments (over 40Mbase for
	est * genomic sequence length)
	sequence reading for ABI files fixed (and selex files tested)
	genbank feature input working
	pepinfo PNG output larger to make the text readable (only affects
	PNG output)
	empty sequence file input fails gracefully
	empty sequence input fails gracefully (and only needs one
	^D from stdin)
	
Version 2.3.0

	Seqretall, seqretallfeat and seqretset moved to 'make check'.
	Seqret has all the functionality of the above.
	Fix for NBRF accession number reading (ajseqread.c)
	Whichdb program added.
	Fix for dbifasta and wormpep
	Fix for problem reading plain format sequences by primer3.
	Primer3 renamed eprimer3 to avoid conflicts with the Whitehead's
	primer3 version 3.0.6.
	transeq's '-frame' can have a list of values, as: '-frame=1,2,3'
	Non-existent files in lists are again ignored
	Various wildcard database search fixes
	ESIM4 added as an embassy package
