* (version 1.28) * Boulder::Store fixes from Aaron Wangberg Mon Feb 4 17:52:03 EST 2002 * (Version 1.27) * Batch entrez queries work again using semi-published, semi-private interface The problem with the published interface is there's no way to pass a list of Genbank ACCESSION numbers, just GI numbers. So I have to use the XML demo. * Patches from Michael Peterson to fix BLAST parsing. Thu Jan 24 14:21:02 EST 2002 * (Version 1.26) * Partial fix for Entrez retrieval, but Entrez queries don't work :-( 2001-12-28 Lincoln Stein * (version 1.25) * fixed GB_Stone bugs that prevented parsing of some of the feature fields * fixed Boulder/Genbank bugs that prevented parsing of some newer genbank entries that use the ORIGIN field. * fixed problems parsing genomic entries that contain gaps. 2001-06-14 Lincoln Stein * (version 1.24) * Fixed bugs introduced into 1.23 version when parsing Boulder::Genbank records from Entrez 2001-06-13 Lincoln Stein * (version 1.23) * Boulder::Genbank now correctly handles sequences that use whitespace to represent gaps 2001-06-11 Lincoln Stein * (version 1.22) * now reports BatchEntry errors to standard error * patch from Will Fitzhugh to correct problems with Yank accessor 2001-03-09 Lincoln Stein * (version 1.21) * fixed loop termination problem in Boulder::Genbank 2000-07-13 Lincoln Stein * (version 1.20) * Fixes to Boulder::Genbank provided by Lester Hui. Now handles repeated multivalued features better. 2000-06-08 Lincoln Stein * Fixed Boulder::Blast::NCBI parsing error that caused it to miss some HSPs * Fixed Boulder::Blast::{NCBI,WU} treatment of % identity -- had been returning identity as a fraction of 1 rather than a percentage (as documented) 1999-12-02 Lincoln Stein * Fixed parameter bug in File accessor for Boulder::Genbank. * Documented problems with flock() across NFS filesystems. * Boulder::Genbank no longer "eats" the list of accession numbers passed to it.