This is the cl-gene-searcher Reference Manual, version 0.1, generated automatically by Declt version 4.0 beta 2 "William Riker" on Tue Jul 15 03:53:17 2025 GMT+0.
The main system appears first, followed by any subsystem dependency.
Files are sorted by type and then listed depth-first from the systems components trees.
cl-gene-searcher/cl-gene-searcher.asdcl-gene-searcher/lib/cl-gene-searcher/package.lispcl-gene-searcher/lib/cl-gene-searcher/db-connections.lispcl-gene-searcher/lib/cl-gene-searcher/db-defs.lispcl-gene-searcher/lib/cl-gene-searcher/cl-gene-searcher.lispcl-gene-searcher/cl-gene-searcher.asdcl-gene-searcher (system).
cl-gene-searcher/lib/cl-gene-searcher/package.lispcl-gene-searcher (system).
cl-gene-searcher/lib/cl-gene-searcher/db-connections.lispcl-gene-searcher (system).
*global-db-connection-object* (special variable).
connect-db (generic function).
db-connection (class).
db-connection-sqlite (class).
db-type (reader method).
db-type (reader method).
(setf db-type) (writer method).
disconnect-db (function).
path (reader method).
(setf path) (writer method).
cl-gene-searcher/lib/cl-gene-searcher/db-defs.lispcl-gene-searcher (system).
chr (reader method).
chr (reader method).
(setf chr) (writer method).
(setf chr) (writer method).
id (reader method).
id (reader method).
name (reader method).
name (reader method).
(setf name) (writer method).
(setf name) (writer method).
platform (reader method).
(setf platform) (writer method).
powner (reader method).
(setf powner) (writer method).
start_region (reader method).
start_region (reader method).
(setf start_region) (writer method).
(setf start_region) (writer method).
stop_region (reader method).
stop_region (reader method).
(setf stop_region) (writer method).
(setf stop_region) (writer method).
strand (reader method).
strand (reader method).
(setf strand) (writer method).
(setf strand) (writer method).
dgv (class).
geneplatform (class).
genes (class).
cl-gene-searcher/lib/cl-gene-searcher/cl-gene-searcher.lispcl-gene-searcher (system).
getdatabasepath (function).
query-dgv-by-range (function).
query-gene-by-name (function).
query-gene-by-range (function).
query-refflat-gene-by-range (function).
query-ucsc-gene-by-range (function).
setdatabasepath (function).
*database-path* (special variable).
query-error (condition).
text (reader method).
with-generic-sqlite-db (macro).
Packages are listed by definition order.
cl-gene-searcherclsql-sqlite3.
common-lisp.
chr (generic reader).
(setf chr) (generic writer).
getdatabasepath (function).
id (generic reader).
name (generic reader).
(setf name) (generic writer).
platform (generic reader).
(setf platform) (generic writer).
powner (generic reader).
(setf powner) (generic writer).
query-dgv-by-range (function).
query-gene-by-name (function).
query-gene-by-range (function).
query-refflat-gene-by-range (function).
query-ucsc-gene-by-range (function).
setdatabasepath (function).
start_region (generic reader).
(setf start_region) (generic writer).
stop_region (generic reader).
(setf stop_region) (generic writer).
strand (generic reader).
(setf strand) (generic writer).
*database-path* (special variable).
*global-db-connection-object* (special variable).
connect-db (generic function).
db-connection (class).
db-connection-sqlite (class).
db-type (generic reader).
(setf db-type) (generic writer).
dgv (class).
disconnect-db (function).
geneplatform (class).
genes (class).
path (generic reader).
(setf path) (generic writer).
query-error (condition).
text (generic reader).
with-generic-sqlite-db (macro).
Definitions are sorted by export status, category, package, and then by lexicographic order.
Generic method for which the various database types will be supported
db-connection-sqlite)) ¶db-connection-sqlite)) ¶automatically generated reader method
type.
db-connection)) ¶automatically generated reader method
type.
db-connection)) ¶automatically generated writer method
type.
db-connection-sqlite)) ¶automatically generated reader method
path.
db-connection-sqlite)) ¶automatically generated writer method
path.
query-error)) ¶text.
error.
text.
The foundation datbase connection class, that the others will inherit
common-lisp.
:type
The specific connection object for SQLite
standard-db-object.
(or null integer)
:start_region
(or null integer)
:stop_region
(or null string)
:strand
standard-db-object.
id.
(setf name).
name.
standard-db-object.
(or null integer)
:start_region
(or null integer)
:stop_region
(or null string)
:strand
(or null integer)
:platform
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