The cl-gene-searcher Reference Manual
Table of Contents
The cl-gene-searcher Reference Manual
This is the cl-gene-searcher Reference Manual, version 0.1,
generated automatically by Declt version 2.4 "Will Decker"
on Wed Jun 20 11:06:49 2018 GMT+0.
1 Introduction
cl-gene-searcher is a very simple library to allow searching for information available through UCSC, in a local form. The current database utilized is sqlite, with eventual support for utilizing the API interface for UCSC.
Installation
1) git clone the repository
2) Symlink the asd file to your central asdf systems directory
3) Download hg18.sqlite (hg19 coming soon) - Location: (still working on this)
Sample Usage:
(require :cl-gene-searcher)
You can create your own package that uses cl-gene-searcher, or just (in-package :cl-gene-searcher)
You will need to point the library to your hg18 database:
(setDatabasePath "/Users/dthole/programming/cl-gene-searcher/data/hg18.sqlite")
To search by a gene name (or multiple gene names):
CL-GENE-SEARCHER> (loop for x in (query-gene-by-name "RPS6KA2" "FAM20C") do (format t "name: ~a~%" (name x)))
name: RPS6KA2
name: RPS6KA2
name: FAM20C
NIL
To look up genes based off some genomic location:
CL-GENE-SEARCHER> (query-gene-by-range :chr "chr1" :start 1 :stop 5000)
(# # #
# # #
# # #
# # #
# # #)
And to get their useful information:
CL-GENE-SEARCHER> (loop for x in (query-gene-by-range :chr "chr1" :start 1 :stop 5000) do (format t "chr: ~a | start: ~a | end: ~a | name: ~a~%" (chr x) (start_region x) (stop_region x) (name x)))
chr: chr1 | start: 1115 | end: 4121 | name: uc001aaa.2
chr: chr1 | start: 1115 | end: 4272 | name: uc009vip.1
chr: chr1 | start: 4268 | end: 6628 | name: uc009vis.1
chr: chr1 | start: 4268 | end: 9622 | name: uc009vit.1
chr: chr1 | start: 4268 | end: 9622 | name: uc009viu.1
chr: chr1 | start: 4268 | end: 9622 | name: uc001aae.2
chr: chr1 | start: 4268 | end: 14764 | name: uc001aab.2
chr: chr1 | start: 4268 | end: 19221 | name: uc009viq.1
chr: chr1 | start: 4268 | end: 19221 | name: uc009vir.1
chr: chr1 | start: 4268 | end: 19221 | name: uc001aac.2
chr: chr1 | start: 4269 | end: 19221 | name: uc009viv.1
chr: chr1 | start: 4269 | end: 19221 | name: uc009viw.1
chr: chr1 | start: 4832 | end: 19672 | name: uc001aaf.1
chr: chr1 | start: 4224 | end: 7502 | name: LOC100288778
chr: chr1 | start: 4224 | end: 19233 | name: WASH7P
NIL
If you wanted just the refFlat version of this information:
CL-GENE-SEARCHER> (loop for x in (query-refflat-gene-by-range :chr "chr1" :start 1 :stop 5000) do (format t "chr: ~a | start: ~a | end: ~a | name: ~a~%" (chr x) (start_region x) (stop_region x) (name x)))
chr: chr1 | start: 4224 | end: 7502 | name: LOC100288778
chr: chr1 | start: 4224 | end: 19233 | name: WASH7P
NIL
2 Systems
The main system appears first, followed by any subsystem dependency.
2.1 cl-gene-searcher
- Maintainer
David Thole
- Author
David Thole
- License
LGPL
- Description
A simple interface to a SQLite database for querying information for genes, and DGV Tracks.
- Version
0.1
- Dependency
clsql-sqlite3
- Source
cl-gene-searcher.asd (file)
- Components
-
3 Files
Files are sorted by type and then listed depth-first from the systems
components trees.
3.1 Lisp
3.1.1 cl-gene-searcher.asd
- Location
cl-gene-searcher.asd
- Systems
cl-gene-searcher (system)
- Packages
cl-gene-searcher-asd
3.1.2 cl-gene-searcher/lib/cl-gene-searcher/package.lisp
- Parent
cl-gene-searcher (system)
- Location
lib/cl-gene-searcher/package.lisp
- Packages
cl-gene-searcher
3.1.3 cl-gene-searcher/lib/cl-gene-searcher/db-connections.lisp
- Dependency
lib/cl-gene-searcher/package.lisp (file)
- Parent
cl-gene-searcher (system)
- Location
lib/cl-gene-searcher/db-connections.lisp
- Internal Definitions
-
3.1.4 cl-gene-searcher/lib/cl-gene-searcher/db-defs.lisp
- Dependency
lib/cl-gene-searcher/db-connections.lisp (file)
- Parent
cl-gene-searcher (system)
- Location
lib/cl-gene-searcher/db-defs.lisp
- Exported Definitions
-
- Internal Definitions
-
3.1.5 cl-gene-searcher/lib/cl-gene-searcher/cl-gene-searcher.lisp
- Dependency
lib/cl-gene-searcher/db-defs.lisp (file)
- Parent
cl-gene-searcher (system)
- Location
lib/cl-gene-searcher/cl-gene-searcher.lisp
- Exported Definitions
-
- Internal Definitions
-
4 Packages
Packages are listed by definition order.
4.1 cl-gene-searcher-asd
- Source
cl-gene-searcher.asd
- Use List
common-lisp
4.2 cl-gene-searcher
- Source
lib/cl-gene-searcher/package.lisp (file)
- Use List
- clsql-sqlite3
- common-lisp
- Exported Definitions
-
- Internal Definitions
-
5 Definitions
Definitions are sorted by export status, category, package, and then by
lexicographic order.
5.1 Exported definitions
5.1.1 Functions
- Function: getdatabasepath ()
-
- Package
cl-gene-searcher
- Source
lib/cl-gene-searcher/cl-gene-searcher.lisp (file)
- Function: query-dgv-by-range &key CHR START STOP
-
- Package
cl-gene-searcher
- Source
lib/cl-gene-searcher/cl-gene-searcher.lisp (file)
- Function: query-gene-by-name NAME &rest NAMES
-
- Package
cl-gene-searcher
- Source
lib/cl-gene-searcher/cl-gene-searcher.lisp (file)
- Function: query-gene-by-range &key CHR START STOP
-
- Package
cl-gene-searcher
- Source
lib/cl-gene-searcher/cl-gene-searcher.lisp (file)
- Function: query-refflat-gene-by-range &key CHR START STOP
-
- Package
cl-gene-searcher
- Source
lib/cl-gene-searcher/cl-gene-searcher.lisp (file)
- Function: query-ucsc-gene-by-range &key CHR START STOP
-
- Package
cl-gene-searcher
- Source
lib/cl-gene-searcher/cl-gene-searcher.lisp (file)
- Function: setdatabasepath PATH
-
- Package
cl-gene-searcher
- Source
lib/cl-gene-searcher/cl-gene-searcher.lisp (file)
5.1.2 Generic functions
- Generic Function: chr OBJECT
-
- Generic Function: (setf chr) NEW-VALUE OBJECT
-
- Package
cl-gene-searcher
- Methods
- Method: chr (DGV dgv)
-
automatically generated reader method
- Source
lib/cl-gene-searcher/db-defs.lisp (file)
- Method: (setf chr) NEW-VALUE (DGV dgv)
-
automatically generated writer method
- Source
lib/cl-gene-searcher/db-defs.lisp (file)
- Method: chr (GENES genes)
-
automatically generated reader method
- Source
lib/cl-gene-searcher/db-defs.lisp (file)
- Method: (setf chr) NEW-VALUE (GENES genes)
-
automatically generated writer method
- Source
lib/cl-gene-searcher/db-defs.lisp (file)
- Generic Function: id OBJECT
-
- Package
cl-gene-searcher
- Methods
- Method: id (DGV dgv)
-
automatically generated reader method
- Source
lib/cl-gene-searcher/db-defs.lisp (file)
- Method: id (GENEPLATFORM geneplatform)
-
automatically generated reader method
- Source
lib/cl-gene-searcher/db-defs.lisp (file)
- Generic Function: name OBJECT
-
- Generic Function: (setf name) NEW-VALUE OBJECT
-
- Package
cl-gene-searcher
- Methods
- Method: name (GENES genes)
-
automatically generated reader method
- Source
lib/cl-gene-searcher/db-defs.lisp (file)
- Method: (setf name) NEW-VALUE (GENES genes)
-
automatically generated writer method
- Source
lib/cl-gene-searcher/db-defs.lisp (file)
- Method: name (GENEPLATFORM geneplatform)
-
automatically generated reader method
- Source
lib/cl-gene-searcher/db-defs.lisp (file)
- Method: (setf name) NEW-VALUE (GENEPLATFORM geneplatform)
-
automatically generated writer method
- Source
lib/cl-gene-searcher/db-defs.lisp (file)
- Generic Function: platform OBJECT
-
- Generic Function: (setf platform) NEW-VALUE OBJECT
-
- Package
cl-gene-searcher
- Methods
- Method: platform (GENES genes)
-
automatically generated reader method
- Source
lib/cl-gene-searcher/db-defs.lisp (file)
- Method: (setf platform) NEW-VALUE (GENES genes)
-
automatically generated writer method
- Source
lib/cl-gene-searcher/db-defs.lisp (file)
- Generic Function: powner OBJECT
-
- Generic Function: (setf powner) NEW-VALUE OBJECT
-
- Package
cl-gene-searcher
- Methods
- Method: powner (GENES genes)
-
automatically generated reader method
- Source
lib/cl-gene-searcher/db-defs.lisp (file)
- Method: (setf powner) NEW-VALUE (GENES genes)
-
automatically generated writer method
- Source
lib/cl-gene-searcher/db-defs.lisp (file)
- Generic Function: start_region OBJECT
-
- Generic Function: (setf start_region) NEW-VALUE OBJECT
-
- Package
cl-gene-searcher
- Methods
- Method: start_region (DGV dgv)
-
automatically generated reader method
- Source
lib/cl-gene-searcher/db-defs.lisp (file)
- Method: (setf start_region) NEW-VALUE (DGV dgv)
-
automatically generated writer method
- Source
lib/cl-gene-searcher/db-defs.lisp (file)
- Method: start_region (GENES genes)
-
automatically generated reader method
- Source
lib/cl-gene-searcher/db-defs.lisp (file)
- Method: (setf start_region) NEW-VALUE (GENES genes)
-
automatically generated writer method
- Source
lib/cl-gene-searcher/db-defs.lisp (file)
- Generic Function: stop_region OBJECT
-
- Generic Function: (setf stop_region) NEW-VALUE OBJECT
-
- Package
cl-gene-searcher
- Methods
- Method: stop_region (DGV dgv)
-
automatically generated reader method
- Source
lib/cl-gene-searcher/db-defs.lisp (file)
- Method: (setf stop_region) NEW-VALUE (DGV dgv)
-
automatically generated writer method
- Source
lib/cl-gene-searcher/db-defs.lisp (file)
- Method: stop_region (GENES genes)
-
automatically generated reader method
- Source
lib/cl-gene-searcher/db-defs.lisp (file)
- Method: (setf stop_region) NEW-VALUE (GENES genes)
-
automatically generated writer method
- Source
lib/cl-gene-searcher/db-defs.lisp (file)
- Generic Function: strand OBJECT
-
- Generic Function: (setf strand) NEW-VALUE OBJECT
-
- Package
cl-gene-searcher
- Methods
- Method: strand (DGV dgv)
-
automatically generated reader method
- Source
lib/cl-gene-searcher/db-defs.lisp (file)
- Method: (setf strand) NEW-VALUE (DGV dgv)
-
automatically generated writer method
- Source
lib/cl-gene-searcher/db-defs.lisp (file)
- Method: strand (GENES genes)
-
automatically generated reader method
- Source
lib/cl-gene-searcher/db-defs.lisp (file)
- Method: (setf strand) NEW-VALUE (GENES genes)
-
automatically generated writer method
- Source
lib/cl-gene-searcher/db-defs.lisp (file)
5.2 Internal definitions
5.2.1 Special variables
- Special Variable: *database-path*
-
- Package
cl-gene-searcher
- Source
lib/cl-gene-searcher/cl-gene-searcher.lisp (file)
- Special Variable: *global-db-connection-object*
-
- Package
cl-gene-searcher
- Source
lib/cl-gene-searcher/db-connections.lisp (file)
5.2.2 Macros
- Macro: with-generic-sqlite-db (VAR) &body BODY
-
- Package
cl-gene-searcher
- Source
lib/cl-gene-searcher/cl-gene-searcher.lisp (file)
5.2.3 Functions
- Function: disconnect-db ()
-
- Package
cl-gene-searcher
- Source
lib/cl-gene-searcher/db-connections.lisp (file)
5.2.4 Generic functions
- Generic Function: connect-db DB-CONNECTION
-
Generic method for which the various database types will be supported
- Package
cl-gene-searcher
- Source
lib/cl-gene-searcher/db-connections.lisp (file)
- Methods
- Method: connect-db (DB db-connection-sqlite)
-
- Generic Function: db-type OBJECT
-
- Generic Function: (setf db-type) NEW-VALUE OBJECT
-
- Package
cl-gene-searcher
- Methods
- Method: db-type (DB-CONNECTION-SQLITE db-connection-sqlite)
-
automatically generated reader method
- Source
lib/cl-gene-searcher/db-connections.lisp (file)
- Method: db-type (DB-CONNECTION db-connection)
-
automatically generated reader method
- Source
lib/cl-gene-searcher/db-connections.lisp (file)
- Method: (setf db-type) NEW-VALUE (DB-CONNECTION db-connection)
-
automatically generated writer method
- Source
lib/cl-gene-searcher/db-connections.lisp (file)
- Generic Function: path OBJECT
-
- Generic Function: (setf path) NEW-VALUE OBJECT
-
- Package
cl-gene-searcher
- Methods
- Method: path (DB-CONNECTION-SQLITE db-connection-sqlite)
-
automatically generated reader method
- Source
lib/cl-gene-searcher/db-connections.lisp (file)
- Method: (setf path) NEW-VALUE (DB-CONNECTION-SQLITE db-connection-sqlite)
-
automatically generated writer method
- Source
lib/cl-gene-searcher/db-connections.lisp (file)
- Generic Function: text CONDITION
-
- Package
cl-gene-searcher
- Methods
- Method: text (CONDITION query-error)
-
- Source
lib/cl-gene-searcher/cl-gene-searcher.lisp (file)
5.2.5 Conditions
- Condition: query-error ()
-
- Package
cl-gene-searcher
- Source
lib/cl-gene-searcher/cl-gene-searcher.lisp (file)
- Direct superclasses
error (condition)
- Direct methods
text (method)
- Direct slots
- Slot: text
-
- Initargs
:text
- Readers
text (generic function)
5.2.6 Classes
- Class: db-connection ()
-
The foundation datbase connection class, that the others will inherit
- Package
cl-gene-searcher
- Source
lib/cl-gene-searcher/db-connections.lisp (file)
- Direct superclasses
standard-object (class)
- Direct subclasses
db-connection-sqlite (class)
- Direct methods
-
- Direct slots
- Slot: type
-
- Initargs
:type
- Readers
db-type (generic function)
- Writers
(setf db-type) (generic function)
- Class: db-connection-sqlite ()
-
The specific connection object for SQLite
- Package
cl-gene-searcher
- Source
lib/cl-gene-searcher/db-connections.lisp (file)
- Direct superclasses
db-connection (class)
- Direct methods
-
- Direct slots
- Slot: type
-
- Initform
"sqlite3"
- Readers
db-type (generic function)
- Slot: path
-
- Initargs
:path
- Readers
path (generic function)
- Writers
(setf path) (generic function)
- Class: dgv ()
-
- Package
cl-gene-searcher
- Source
lib/cl-gene-searcher/db-defs.lisp (file)
- Direct superclasses
standard-db-object (class)
- Direct methods
-
- Direct slots
- Slot: id
-
- Type
(or null integer)
- Readers
id (generic function)
- Slot: chr
-
- Type
(or null string)
- Initargs
:chr
- Readers
chr (generic function)
- Writers
(setf chr) (generic function)
- Slot: start_region
-
- Type
(or null integer)
- Initargs
:start_region
- Readers
start_region (generic function)
- Writers
(setf start_region) (generic function)
- Slot: stop_region
-
- Type
(or null integer)
- Initargs
:stop_region
- Readers
stop_region (generic function)
- Writers
(setf stop_region) (generic function)
- Slot: strand
-
- Type
(or null string)
- Initargs
:strand
- Readers
strand (generic function)
- Writers
(setf strand) (generic function)
- Class: geneplatform ()
-
- Package
cl-gene-searcher
- Source
lib/cl-gene-searcher/db-defs.lisp (file)
- Direct superclasses
standard-db-object (class)
- Direct methods
- name (method)
- name (method)
- id (method)
- Direct slots
- Slot: id
-
- Type
(or null integer)
- Readers
id (generic function)
- Slot: name
-
- Type
(or null string)
- Initargs
:name
- Readers
name (generic function)
- Writers
(setf name) (generic function)
- Class: genes ()
-
- Package
cl-gene-searcher
- Source
lib/cl-gene-searcher/db-defs.lisp (file)
- Direct superclasses
standard-db-object (class)
- Direct methods
-
- Direct slots
- Slot: name
-
- Type
(or null string)
- Initargs
:name
- Readers
name (generic function)
- Writers
(setf name) (generic function)
- Slot: chr
-
- Type
(or null string)
- Initargs
:chr
- Readers
chr (generic function)
- Writers
(setf chr) (generic function)
- Slot: start_region
-
- Type
(or null integer)
- Initargs
:start_region
- Readers
start_region (generic function)
- Writers
(setf start_region) (generic function)
- Slot: stop_region
-
- Type
(or null integer)
- Initargs
:stop_region
- Readers
stop_region (generic function)
- Writers
(setf stop_region) (generic function)
- Slot: strand
-
- Type
(or null string)
- Initargs
:strand
- Readers
strand (generic function)
- Writers
(setf strand) (generic function)
- Slot: platform
-
- Type
(or null integer)
- Initargs
:platform
- Readers
platform (generic function)
- Writers
(setf platform) (generic function)
- Slot: powner
-
- Readers
powner (generic function)
- Writers
(setf powner) (generic function)
Appendix A Indexes
A.1 Concepts
| Index Entry | | Section |
|
C | | |
| cl-gene-searcher.asd: | | The cl-gene-searcher<dot>asd file |
| cl-gene-searcher/lib/cl-gene-searcher/cl-gene-searcher.lisp: | | The cl-gene-searcher/lib/cl-gene-searcher/cl-gene-searcher<dot>lisp file |
| cl-gene-searcher/lib/cl-gene-searcher/db-connections.lisp: | | The cl-gene-searcher/lib/cl-gene-searcher/db-connections<dot>lisp file |
| cl-gene-searcher/lib/cl-gene-searcher/db-defs.lisp: | | The cl-gene-searcher/lib/cl-gene-searcher/db-defs<dot>lisp file |
| cl-gene-searcher/lib/cl-gene-searcher/package.lisp: | | The cl-gene-searcher/lib/cl-gene-searcher/package<dot>lisp file |
|
F | | |
| File, Lisp, cl-gene-searcher.asd: | | The cl-gene-searcher<dot>asd file |
| File, Lisp, cl-gene-searcher/lib/cl-gene-searcher/cl-gene-searcher.lisp: | | The cl-gene-searcher/lib/cl-gene-searcher/cl-gene-searcher<dot>lisp file |
| File, Lisp, cl-gene-searcher/lib/cl-gene-searcher/db-connections.lisp: | | The cl-gene-searcher/lib/cl-gene-searcher/db-connections<dot>lisp file |
| File, Lisp, cl-gene-searcher/lib/cl-gene-searcher/db-defs.lisp: | | The cl-gene-searcher/lib/cl-gene-searcher/db-defs<dot>lisp file |
| File, Lisp, cl-gene-searcher/lib/cl-gene-searcher/package.lisp: | | The cl-gene-searcher/lib/cl-gene-searcher/package<dot>lisp file |
|
L | | |
| Lisp File, cl-gene-searcher.asd: | | The cl-gene-searcher<dot>asd file |
| Lisp File, cl-gene-searcher/lib/cl-gene-searcher/cl-gene-searcher.lisp: | | The cl-gene-searcher/lib/cl-gene-searcher/cl-gene-searcher<dot>lisp file |
| Lisp File, cl-gene-searcher/lib/cl-gene-searcher/db-connections.lisp: | | The cl-gene-searcher/lib/cl-gene-searcher/db-connections<dot>lisp file |
| Lisp File, cl-gene-searcher/lib/cl-gene-searcher/db-defs.lisp: | | The cl-gene-searcher/lib/cl-gene-searcher/db-defs<dot>lisp file |
| Lisp File, cl-gene-searcher/lib/cl-gene-searcher/package.lisp: | | The cl-gene-searcher/lib/cl-gene-searcher/package<dot>lisp file |
|
A.2 Functions
| Index Entry | | Section |
|
( | | |
| (setf chr) : | | Exported generic functions |
| (setf chr) : | | Exported generic functions |
| (setf chr) : | | Exported generic functions |
| (setf db-type) : | | Internal generic functions |
| (setf db-type) : | | Internal generic functions |
| (setf name) : | | Exported generic functions |
| (setf name) : | | Exported generic functions |
| (setf name) : | | Exported generic functions |
| (setf path) : | | Internal generic functions |
| (setf path) : | | Internal generic functions |
| (setf platform) : | | Exported generic functions |
| (setf platform) : | | Exported generic functions |
| (setf powner) : | | Exported generic functions |
| (setf powner) : | | Exported generic functions |
| (setf start_region) : | | Exported generic functions |
| (setf start_region) : | | Exported generic functions |
| (setf start_region) : | | Exported generic functions |
| (setf stop_region) : | | Exported generic functions |
| (setf stop_region) : | | Exported generic functions |
| (setf stop_region) : | | Exported generic functions |
| (setf strand) : | | Exported generic functions |
| (setf strand) : | | Exported generic functions |
| (setf strand) : | | Exported generic functions |
|
C | | |
| chr : | | Exported generic functions |
| chr : | | Exported generic functions |
| chr : | | Exported generic functions |
| connect-db : | | Internal generic functions |
| connect-db : | | Internal generic functions |
|
D | | |
| db-type : | | Internal generic functions |
| db-type : | | Internal generic functions |
| db-type : | | Internal generic functions |
| disconnect-db : | | Internal functions |
|
F | | |
| Function, disconnect-db : | | Internal functions |
| Function, getdatabasepath : | | Exported functions |
| Function, query-dgv-by-range : | | Exported functions |
| Function, query-gene-by-name : | | Exported functions |
| Function, query-gene-by-range : | | Exported functions |
| Function, query-refflat-gene-by-range : | | Exported functions |
| Function, query-ucsc-gene-by-range : | | Exported functions |
| Function, setdatabasepath : | | Exported functions |
|
G | | |
| Generic Function, (setf chr) : | | Exported generic functions |
| Generic Function, (setf db-type) : | | Internal generic functions |
| Generic Function, (setf name) : | | Exported generic functions |
| Generic Function, (setf path) : | | Internal generic functions |
| Generic Function, (setf platform) : | | Exported generic functions |
| Generic Function, (setf powner) : | | Exported generic functions |
| Generic Function, (setf start_region) : | | Exported generic functions |
| Generic Function, (setf stop_region) : | | Exported generic functions |
| Generic Function, (setf strand) : | | Exported generic functions |
| Generic Function, chr : | | Exported generic functions |
| Generic Function, connect-db : | | Internal generic functions |
| Generic Function, db-type : | | Internal generic functions |
| Generic Function, id : | | Exported generic functions |
| Generic Function, name : | | Exported generic functions |
| Generic Function, path : | | Internal generic functions |
| Generic Function, platform : | | Exported generic functions |
| Generic Function, powner : | | Exported generic functions |
| Generic Function, start_region : | | Exported generic functions |
| Generic Function, stop_region : | | Exported generic functions |
| Generic Function, strand : | | Exported generic functions |
| Generic Function, text : | | Internal generic functions |
| getdatabasepath : | | Exported functions |
|
I | | |
| id : | | Exported generic functions |
| id : | | Exported generic functions |
| id : | | Exported generic functions |
|
M | | |
| Macro, with-generic-sqlite-db : | | Internal macros |
| Method, (setf chr) : | | Exported generic functions |
| Method, (setf chr) : | | Exported generic functions |
| Method, (setf db-type) : | | Internal generic functions |
| Method, (setf name) : | | Exported generic functions |
| Method, (setf name) : | | Exported generic functions |
| Method, (setf path) : | | Internal generic functions |
| Method, (setf platform) : | | Exported generic functions |
| Method, (setf powner) : | | Exported generic functions |
| Method, (setf start_region) : | | Exported generic functions |
| Method, (setf start_region) : | | Exported generic functions |
| Method, (setf stop_region) : | | Exported generic functions |
| Method, (setf stop_region) : | | Exported generic functions |
| Method, (setf strand) : | | Exported generic functions |
| Method, (setf strand) : | | Exported generic functions |
| Method, chr : | | Exported generic functions |
| Method, chr : | | Exported generic functions |
| Method, connect-db : | | Internal generic functions |
| Method, db-type : | | Internal generic functions |
| Method, db-type : | | Internal generic functions |
| Method, id : | | Exported generic functions |
| Method, id : | | Exported generic functions |
| Method, name : | | Exported generic functions |
| Method, name : | | Exported generic functions |
| Method, path : | | Internal generic functions |
| Method, platform : | | Exported generic functions |
| Method, powner : | | Exported generic functions |
| Method, start_region : | | Exported generic functions |
| Method, start_region : | | Exported generic functions |
| Method, stop_region : | | Exported generic functions |
| Method, stop_region : | | Exported generic functions |
| Method, strand : | | Exported generic functions |
| Method, strand : | | Exported generic functions |
| Method, text : | | Internal generic functions |
|
N | | |
| name : | | Exported generic functions |
| name : | | Exported generic functions |
| name : | | Exported generic functions |
|
P | | |
| path : | | Internal generic functions |
| path : | | Internal generic functions |
| platform : | | Exported generic functions |
| platform : | | Exported generic functions |
| powner : | | Exported generic functions |
| powner : | | Exported generic functions |
|
Q | | |
| query-dgv-by-range : | | Exported functions |
| query-gene-by-name : | | Exported functions |
| query-gene-by-range : | | Exported functions |
| query-refflat-gene-by-range : | | Exported functions |
| query-ucsc-gene-by-range : | | Exported functions |
|
S | | |
| setdatabasepath : | | Exported functions |
| start_region : | | Exported generic functions |
| start_region : | | Exported generic functions |
| start_region : | | Exported generic functions |
| stop_region : | | Exported generic functions |
| stop_region : | | Exported generic functions |
| stop_region : | | Exported generic functions |
| strand : | | Exported generic functions |
| strand : | | Exported generic functions |
| strand : | | Exported generic functions |
|
T | | |
| text : | | Internal generic functions |
| text : | | Internal generic functions |
|
W | | |
| with-generic-sqlite-db : | | Internal macros |
|
A.3 Variables
| Index Entry | | Section |
|
* | | |
| *database-path* : | | Internal special variables |
| *global-db-connection-object* : | | Internal special variables |
|
C | | |
| chr : | | Internal classes |
| chr : | | Internal classes |
|
I | | |
| id : | | Internal classes |
| id : | | Internal classes |
|
N | | |
| name : | | Internal classes |
| name : | | Internal classes |
|
P | | |
| path : | | Internal classes |
| platform : | | Internal classes |
| powner : | | Internal classes |
|
S | | |
| Slot, chr : | | Internal classes |
| Slot, chr : | | Internal classes |
| Slot, id : | | Internal classes |
| Slot, id : | | Internal classes |
| Slot, name : | | Internal classes |
| Slot, name : | | Internal classes |
| Slot, path : | | Internal classes |
| Slot, platform : | | Internal classes |
| Slot, powner : | | Internal classes |
| Slot, start_region : | | Internal classes |
| Slot, start_region : | | Internal classes |
| Slot, stop_region : | | Internal classes |
| Slot, stop_region : | | Internal classes |
| Slot, strand : | | Internal classes |
| Slot, strand : | | Internal classes |
| Slot, text : | | Internal conditions |
| Slot, type : | | Internal classes |
| Slot, type : | | Internal classes |
| Special Variable, *database-path* : | | Internal special variables |
| Special Variable, *global-db-connection-object* : | | Internal special variables |
| start_region : | | Internal classes |
| start_region : | | Internal classes |
| stop_region : | | Internal classes |
| stop_region : | | Internal classes |
| strand : | | Internal classes |
| strand : | | Internal classes |
|
T | | |
| text : | | Internal conditions |
| type : | | Internal classes |
| type : | | Internal classes |
|
A.4 Data types