Common-lisp.net GIT projects - projects/mirror/cl-bio.git/shortlog

common-lisp.net / projects/mirror/cl-bio.git / shortlog

2011-01-25	Cyrus Harmon	update to work with new smarkup master	commit \| commitdiff \| tree
2011-01-25	Cyrus Harmon	resurrect the ability to build the documentation	commit \| commitdiff \| tree
2011-01-24	Cyrus Harmon	alignment improvements -- special variables for gap...	commit \| commitdiff \| tree
2011-01-24	Cyrus Harmon	only loop (lenth residues) times when setf'ing residues...	commit \| commitdiff \| tree
2011-01-07	Cyrus Harmon	add alexandria dependency	commit \| commitdiff \| tree
2011-01-07	Cyrus Harmon	pessimize code, removing speed/safety/inline declarations	commit \| commitdiff \| tree
2010-10-09	Cyrus Harmon	fix typo and remove bio-io prefix	commit \| commitdiff \| tree
2010-10-09	Cyrus Harmon	remove the bio-io package. just put everything in bio...	commit \| commitdiff \| tree
2010-10-09	Cyrus Harmon	remove bogus file reference	commit \| commitdiff \| tree
2010-10-09	Cyrus Harmon	remove some debugging declamations	commit \| commitdiff \| tree
2010-10-09	Cyrus Harmon	fix ASDF dependencies	commit \| commitdiff \| tree
2010-10-09	Cyrus Harmon	removed unused res loop variable in (setf residues...	commit \| commitdiff \| tree
2010-06-25	Cyrus Harmon	udpate taxonomy download instructions and path.	commit \| commitdiff \| tree
2010-06-24	Cyrus Harmon	Added gene-summary and entrez-gene parsing of gene...	commit \| commitdiff \| tree
2010-05-23	Cyrus Harmon	bump version to 0.2.7. remove bogus asdf-related package.	commit \| commitdiff \| tree
2010-05-23	Cyrus Harmon	really add the NCBI_Variation DTD	commit \| commitdiff \| tree
2010-05-23	Cyrus Harmon	update scratch entrez examples	commit \| commitdiff \| tree
2010-05-23	Cyrus Harmon	added variation DTD	commit \| commitdiff \| tree
2010-05-23	Cyrus Harmon	udpate DTDs and fix DTD entity resolving for the case...	commit \| commitdiff \| tree
2010-05-23	Cyrus Harmon	use &rest and fix whitespace typo	commit \| commitdiff \| tree
2010-05-23	Cyrus Harmon	more version.lisp-expr removal	commit \| commitdiff \| tree
2010-05-23	Cyrus Harmon	various code cleanup items	commit \| commitdiff \| tree
2010-05-23	Cyrus Harmon	use &rest for bio:fetch (object entrez-dictionary)	commit \| commitdiff \| tree
2010-05-23	Cyrus Harmon	add copyright and add some date-parsing stuff	commit \| commitdiff \| tree
2010-05-23	Cyrus Harmon	check for empty node and empty node-set	commit \| commitdiff \| tree
2010-05-23	Cyrus Harmon	add comment about origin of the article and article...	commit \| commitdiff \| tree
2010-05-23	Cyrus Harmon	remove bogus dependencies (ch-asdf, alexandria).	commit \| commitdiff \| tree
2009-07-27	Cyrus Harmon	add string-if and number-value-if	commit \| commitdiff \| tree
2009-07-27	Cyrus Harmon	get-search-result-ids now takes :id-class arg	commit \| commitdiff \| tree
2009-07-27	Cyrus Harmon	add some pubmed examples	commit \| commitdiff \| tree
2009-07-27	Cyrus Harmon	fore-name -> forenames cleanup and deal with some nil...	commit \| commitdiff \| tree
2009-07-27	Cyrus Harmon	remove some debug declarations	commit \| commitdiff \| tree
2009-07-27	Cyrus Harmon	split :cache into :use-cache-for-lookup and :cache...	commit \| commitdiff \| tree
2009-07-27	Cyrus Harmon	add ncbi-pmid identifier	commit \| commitdiff \| tree
2009-07-27	Cyrus Harmon	export some new symbols	commit \| commitdiff \| tree
2009-07-27	Cyrus Harmon	fore-name -> forenames	commit \| commitdiff \| tree
2009-07-25	Cyrus Harmon	add pubmed and article lisp files	commit \| commitdiff \| tree
2009-07-25	Cyrus Harmon	add string-value-if	commit \| commitdiff \| tree
2009-07-25	Cyrus Harmon	entrez pubmed parsing improvements	commit \| commitdiff \| tree
2009-07-25	Cyrus Harmon	article improvements:	commit \| commitdiff \| tree
2009-07-25	Cyrus Harmon	use :supersede instead of :overwrite for existing files...	commit \| commitdiff \| tree
2009-07-25	Cyrus Harmon	fix NCBI DTD's that got hosed due to using :overwrite...	commit \| commitdiff \| tree
2009-07-25	Cyrus Harmon	forgot to add article.lisp to last commit	commit \| commitdiff \| tree
2009-07-25	Cyrus Harmon	first pass at Pubmed stuff	commit \| commitdiff \| tree
2009-07-25	Cyrus Harmon	add new NCBI DTDs	commit \| commitdiff \| tree
2009-07-25	Cyrus Harmon	add some new NCBI DTDs and support multiple public...	commit \| commitdiff \| tree
2009-06-13	Cyrus Harmon	update generated documentation	commit \| commitdiff \| tree
2009-06-13	Cyrus Harmon	Merge branch 'master' of git+ssh://cyrusharmon.org...	commit \| commitdiff \| tree
2008-10-02	Cyrus Harmon	formatting	commit \| commitdiff \| tree
2008-10-02	Cyrus Harmon	formatting	commit \| commitdiff \| tree
2008-10-02	Cyrus Harmon	print-alignment -> alignment-results	commit \| commitdiff \| tree
2008-10-02	Cyrus Harmon	added a find-matches example	commit \| commitdiff \| tree
2008-10-02	Cyrus Harmon	newline at end of file	commit \| commitdiff \| tree
2008-10-02	Cyrus Harmon	performance improvements and gf's	commit \| commitdiff \| tree
2008-10-02	Cyrus Harmon	various example cleanups	commit \| commitdiff \| tree
2008-10-02	Cyrus Harmon	added aa and rna alignment examples	commit \| commitdiff \| tree
2008-09-06	Cyrus Harmon	Merge branch 'master' of git+ssh://cyrusharmon.org...	commit \| commitdiff \| tree
2008-09-06	Cyrus Harmon	autogen'ed doc changes	commit \| commitdiff \| tree
2008-07-03	Cyrus Harmon	version 0.2.6	commit \| commitdiff \| tree
2008-07-03	Cyrus Harmon	* use bio: prefixes	commit \| commitdiff \| tree
2008-07-03	Cyrus Harmon	split-string-into-lines-string -> split-string-into...	commit \| commitdiff \| tree
2008-07-03	Cyrus Harmon	* read-fasta-file arg file -> filespec	commit \| commitdiff \| tree
2008-07-03	Cyrus Harmon	* use change-class for adjustable-seqeunces	commit \| commitdiff \| tree
2008-07-03	Cyrus Harmon	don't explicity check for mRNA type	commit \| commitdiff \| tree
2008-07-03	Cyrus Harmon	minor doc updates	commit \| commitdiff \| tree
2008-07-03	Cyrus Harmon	minor documentation updates	commit \| commitdiff \| tree
2008-07-03	Cyrus Harmon	* export write-fasta-file	commit \| commitdiff \| tree
2008-07-03	Cyrus Harmon	* annotated-sequence no longer explicitly declares...	commit \| commitdiff \| tree
2008-04-21	Cyrus Harmon	add stp-document->list and stp->node-list. use in scratch.	commit \| commitdiff \| tree
2008-04-21	Cyrus Harmon	robustify asdf-loading of cl-bio and cl-bio-rucksack...	commit \| commitdiff \| tree
2008-04-21	Cyrus Harmon	Revert "retrieve this for the moment, at least..."	commit \| commitdiff \| tree
2008-04-21	Cyrus Harmon	retrieve this for the moment, at least...	commit \| commitdiff \| tree
2008-04-21	Cyrus Harmon	princ-to-string the object name in entrez-dictionary...	commit \| commitdiff \| tree
2008-04-21	Cyrus Harmon	make tax-nodes-file and tax-names-file be symbol...	commit \| commitdiff \| tree
2008-04-21	Cyrus Harmon	add cl-bio-taxonomy and cl-bio-entrez to the :depends...	commit \| commitdiff \| tree
2008-04-21	Cyrus Harmon	make the ncbi-gi id be an integer if possible.	commit \| commitdiff \| tree
2008-04-21	Cyrus Harmon	export some taxonomy symbols and clean up the scratch...	commit \| commitdiff \| tree
2008-04-20	Cyrus Harmon	start adding dictionary documentation.	commit \| commitdiff \| tree
2008-04-20	Cyrus Harmon	export bio-rucksack::bio-rucksack and use bio-rucksac...	commit \| commitdiff \| tree
2008-04-20	Cyrus Harmon	dictionary gf docstrings	commit \| commitdiff \| tree
2008-04-20	Cyrus Harmon	adding .gitignore	commit \| commitdiff \| tree
2008-04-20	Cyrus Harmon	starting to add documentation about modules	commit \| commitdiff \| tree
2008-04-20	Cyrus Harmon	note that the cl-bio-entrez-doc has gone away, but...	commit \| commitdiff \| tree
2008-04-20	Cyrus Harmon	add entrez:: around some temporary entrez debugging...	commit \| commitdiff \| tree
2008-04-20	Cyrus Harmon	remove optimize debug 3	commit \| commitdiff \| tree
2008-04-20	Cyrus Harmon	remove xmls parsing stuff.	commit \| commitdiff \| tree
2008-04-20	Cyrus Harmon	remove xml.lisp symbols and add generif symbols.	commit \| commitdiff \| tree
2008-04-20	Cyrus Harmon	remove entrez/xml.lisp	commit \| commitdiff \| tree
2008-04-20	Cyrus Harmon	cleaning up taxonomy and rucksack moves.	commit \| commitdiff \| tree
2008-04-20	Cyrus Harmon	moving align into its own package and fix cl-bio.asd...	commit \| commitdiff \| tree
2008-04-20	Cyrus Harmon	moving rucksack and taxonomy stuff into their own modules.	commit \| commitdiff \| tree
2008-04-19	Cyrus Harmon	cl-bio 0.2.5	commit \| commitdiff \| tree
2008-04-19	Cyrus Harmon	use (dirname "$0") so that running make-dist.sh from...	commit \| commitdiff \| tree
2008-04-19	Cyrus Harmon	make write-pdb-header a function instead of a generic...	commit \| commitdiff \| tree
2008-04-19	Cyrus Harmon	Revert "Use bio: prefix in doc fasta examples"	commit \| commitdiff \| tree
2008-04-19	Cyrus Harmon	use bio: prefix in doc examples	commit \| commitdiff \| tree
2008-04-19	Cyrus Harmon	Use bio: prefix in doc fasta examples	commit \| commitdiff \| tree
2008-04-19	Cyrus Harmon	Adding cl-bio-entrez module	commit \| commitdiff \| tree
2008-03-30	Cyrus Harmon	* add asdf:load-op line at the top	commit \| commitdiff \| tree
2008-03-30	Cyrus Harmon	* export dna->rna, 3-letter-residues-string, 3-letter...	commit \| commitdiff \| tree
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