The cl-gene-searcher Reference Manual

This is the cl-gene-searcher Reference Manual, version 0.1, generated automatically by Declt version 4.0 beta 2 "William Riker" on Wed May 15 03:59:49 2024 GMT+0.

Table of Contents


1 Introduction


2 Systems

The main system appears first, followed by any subsystem dependency.


2.1 cl-gene-searcher

A simple interface to a SQLite database for querying information for genes, and DGV Tracks.

Maintainer

David Thole

Author

David Thole

License

LGPL

Version

0.1

Dependency

clsql-sqlite3 (system).

Source

cl-gene-searcher.asd.

Child 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/cl-gene-searcher.asd

Source

cl-gene-searcher.asd.

Parent Component

cl-gene-searcher (system).

ASDF Systems

cl-gene-searcher.

Packages

cl-gene-searcher-asd.


3.1.2 cl-gene-searcher/lib/cl-gene-searcher/package.lisp

Source

cl-gene-searcher.asd.

Parent Component

cl-gene-searcher (system).

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).

Source

cl-gene-searcher.asd.

Parent Component

cl-gene-searcher (system).

Internals

3.1.4 cl-gene-searcher/lib/cl-gene-searcher/db-defs.lisp

Dependency

lib/cl-gene-searcher/db-connections.lisp (file).

Source

cl-gene-searcher.asd.

Parent Component

cl-gene-searcher (system).

Public Interface
Internals

3.1.5 cl-gene-searcher/lib/cl-gene-searcher/cl-gene-searcher.lisp

Dependency

lib/cl-gene-searcher/db-defs.lisp (file).

Source

cl-gene-searcher.asd.

Parent Component

cl-gene-searcher (system).

Public Interface
Internals

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.

Use List
  • clsql-sqlite3.
  • common-lisp.
Public Interface
Internals

5 Definitions

Definitions are sorted by export status, category, package, and then by lexicographic order.


5.1 Public Interface


5.1.1 Ordinary functions

Function: getdatabasepath ()
Package

cl-gene-searcher.

Source

lib/cl-gene-searcher/cl-gene-searcher.lisp.

Function: query-dgv-by-range (&key chr start stop)
Package

cl-gene-searcher.

Source

lib/cl-gene-searcher/cl-gene-searcher.lisp.

Function: query-gene-by-name (name &rest names)
Package

cl-gene-searcher.

Source

lib/cl-gene-searcher/cl-gene-searcher.lisp.

Function: query-gene-by-range (&key chr start stop)
Package

cl-gene-searcher.

Source

lib/cl-gene-searcher/cl-gene-searcher.lisp.

Function: query-refflat-gene-by-range (&key chr start stop)
Package

cl-gene-searcher.

Source

lib/cl-gene-searcher/cl-gene-searcher.lisp.

Function: query-ucsc-gene-by-range (&key chr start stop)
Package

cl-gene-searcher.

Source

lib/cl-gene-searcher/cl-gene-searcher.lisp.

Function: setdatabasepath (path)
Package

cl-gene-searcher.

Source

lib/cl-gene-searcher/cl-gene-searcher.lisp.


5.1.2 Generic functions

Generic Reader: chr (object)
Package

cl-gene-searcher.

Methods
Reader Method: chr ((dgv dgv))

automatically generated reader method

Source

lib/cl-gene-searcher/db-defs.lisp.

Target Slot

chr.

Reader Method: chr ((genes genes))

automatically generated reader method

Source

lib/cl-gene-searcher/db-defs.lisp.

Target Slot

chr.

Generic Writer: (setf chr) (object)
Package

cl-gene-searcher.

Methods
Writer Method: (setf chr) ((dgv dgv))

automatically generated writer method

Source

lib/cl-gene-searcher/db-defs.lisp.

Target Slot

chr.

Writer Method: (setf chr) ((genes genes))

automatically generated writer method

Source

lib/cl-gene-searcher/db-defs.lisp.

Target Slot

chr.

Generic Reader: id (object)
Package

cl-gene-searcher.

Methods
Reader Method: id ((dgv dgv))

automatically generated reader method

Source

lib/cl-gene-searcher/db-defs.lisp.

Target Slot

id.

Reader Method: id ((geneplatform geneplatform))

automatically generated reader method

Source

lib/cl-gene-searcher/db-defs.lisp.

Target Slot

id.

Generic Reader: name (object)
Package

cl-gene-searcher.

Methods
Reader Method: name ((genes genes))

automatically generated reader method

Source

lib/cl-gene-searcher/db-defs.lisp.

Target Slot

name.

Reader Method: name ((geneplatform geneplatform))

automatically generated reader method

Source

lib/cl-gene-searcher/db-defs.lisp.

Target Slot

name.

Generic Writer: (setf name) (object)
Package

cl-gene-searcher.

Methods
Writer Method: (setf name) ((genes genes))

automatically generated writer method

Source

lib/cl-gene-searcher/db-defs.lisp.

Target Slot

name.

Writer Method: (setf name) ((geneplatform geneplatform))

automatically generated writer method

Source

lib/cl-gene-searcher/db-defs.lisp.

Target Slot

name.

Generic Reader: platform (object)
Package

cl-gene-searcher.

Methods
Reader Method: platform ((genes genes))

automatically generated reader method

Source

lib/cl-gene-searcher/db-defs.lisp.

Target Slot

platform.

Generic Writer: (setf platform) (object)
Package

cl-gene-searcher.

Methods
Writer Method: (setf platform) ((genes genes))

automatically generated writer method

Source

lib/cl-gene-searcher/db-defs.lisp.

Target Slot

platform.

Generic Reader: powner (object)
Package

cl-gene-searcher.

Methods
Reader Method: powner ((genes genes))

automatically generated reader method

Source

lib/cl-gene-searcher/db-defs.lisp.

Target Slot

powner.

Generic Writer: (setf powner) (object)
Package

cl-gene-searcher.

Methods
Writer Method: (setf powner) ((genes genes))

automatically generated writer method

Source

lib/cl-gene-searcher/db-defs.lisp.

Target Slot

powner.

Generic Reader: start_region (object)
Package

cl-gene-searcher.

Methods
Reader Method: start_region ((dgv dgv))

automatically generated reader method

Source

lib/cl-gene-searcher/db-defs.lisp.

Target Slot

start_region.

Reader Method: start_region ((genes genes))

automatically generated reader method

Source

lib/cl-gene-searcher/db-defs.lisp.

Target Slot

start_region.

Generic Writer: (setf start_region) (object)
Package

cl-gene-searcher.

Methods
Writer Method: (setf start_region) ((dgv dgv))

automatically generated writer method

Source

lib/cl-gene-searcher/db-defs.lisp.

Target Slot

start_region.

Writer Method: (setf start_region) ((genes genes))

automatically generated writer method

Source

lib/cl-gene-searcher/db-defs.lisp.

Target Slot

start_region.

Generic Reader: stop_region (object)
Package

cl-gene-searcher.

Methods
Reader Method: stop_region ((dgv dgv))

automatically generated reader method

Source

lib/cl-gene-searcher/db-defs.lisp.

Target Slot

stop_region.

Reader Method: stop_region ((genes genes))

automatically generated reader method

Source

lib/cl-gene-searcher/db-defs.lisp.

Target Slot

stop_region.

Generic Writer: (setf stop_region) (object)
Package

cl-gene-searcher.

Methods
Writer Method: (setf stop_region) ((dgv dgv))

automatically generated writer method

Source

lib/cl-gene-searcher/db-defs.lisp.

Target Slot

stop_region.

Writer Method: (setf stop_region) ((genes genes))

automatically generated writer method

Source

lib/cl-gene-searcher/db-defs.lisp.

Target Slot

stop_region.

Generic Reader: strand (object)
Package

cl-gene-searcher.

Methods
Reader Method: strand ((dgv dgv))

automatically generated reader method

Source

lib/cl-gene-searcher/db-defs.lisp.

Target Slot

strand.

Reader Method: strand ((genes genes))

automatically generated reader method

Source

lib/cl-gene-searcher/db-defs.lisp.

Target Slot

strand.

Generic Writer: (setf strand) (object)
Package

cl-gene-searcher.

Methods
Writer Method: (setf strand) ((dgv dgv))

automatically generated writer method

Source

lib/cl-gene-searcher/db-defs.lisp.

Target Slot

strand.

Writer Method: (setf strand) ((genes genes))

automatically generated writer method

Source

lib/cl-gene-searcher/db-defs.lisp.

Target Slot

strand.


5.2 Internals


5.2.1 Special variables

Special Variable: *database-path*
Package

cl-gene-searcher.

Source

lib/cl-gene-searcher/cl-gene-searcher.lisp.

Special Variable: *global-db-connection-object*
Package

cl-gene-searcher.

Source

lib/cl-gene-searcher/db-connections.lisp.


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.


5.2.3 Ordinary functions

Function: disconnect-db ()
Package

cl-gene-searcher.

Source

lib/cl-gene-searcher/db-connections.lisp.


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.

Methods
Method: connect-db ((db db-connection-sqlite))
Generic Reader: db-type (object)
Package

cl-gene-searcher.

Methods
Reader Method: db-type ((db-connection-sqlite db-connection-sqlite))

automatically generated reader method

Source

lib/cl-gene-searcher/db-connections.lisp.

Target Slot

type.

Reader Method: db-type ((db-connection db-connection))

automatically generated reader method

Source

lib/cl-gene-searcher/db-connections.lisp.

Target Slot

type.

Generic Writer: (setf db-type) (object)
Package

cl-gene-searcher.

Methods
Writer Method: (setf db-type) ((db-connection db-connection))

automatically generated writer method

Source

lib/cl-gene-searcher/db-connections.lisp.

Target Slot

type.

Generic Reader: path (object)
Package

cl-gene-searcher.

Methods
Reader Method: path ((db-connection-sqlite db-connection-sqlite))

automatically generated reader method

Source

lib/cl-gene-searcher/db-connections.lisp.

Target Slot

path.

Generic Writer: (setf path) (object)
Package

cl-gene-searcher.

Methods
Writer Method: (setf path) ((db-connection-sqlite db-connection-sqlite))

automatically generated writer method

Source

lib/cl-gene-searcher/db-connections.lisp.

Target Slot

path.

Generic Reader: text (condition)
Package

cl-gene-searcher.

Methods
Reader Method: text ((condition query-error))
Source

lib/cl-gene-searcher/cl-gene-searcher.lisp.

Target Slot

text.


5.2.5 Conditions

Condition: query-error
Package

cl-gene-searcher.

Source

lib/cl-gene-searcher/cl-gene-searcher.lisp.

Direct superclasses

error.

Direct methods

text.

Direct slots
Slot: text
Initargs

:text

Readers

text.

Writers

This slot is read-only.


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.

Direct subclasses

db-connection-sqlite.

Direct methods
Direct slots
Slot: type
Package

common-lisp.

Initargs

:type

Readers

db-type.

Writers

(setf db-type).

Class: db-connection-sqlite

The specific connection object for SQLite

Package

cl-gene-searcher.

Source

lib/cl-gene-searcher/db-connections.lisp.

Direct superclasses

db-connection.

Direct methods
Direct slots
Slot: type
Package

common-lisp.

Initform

"sqlite3"

Readers

db-type.

Writers

This slot is read-only.

Slot: path
Initargs

:path

Readers

path.

Writers

(setf path).

Class: dgv
Package

cl-gene-searcher.

Source

lib/cl-gene-searcher/db-defs.lisp.

Direct superclasses

standard-db-object.

Direct methods
Direct slots
Slot: id
Type

(or null integer)

Readers

id.

Writers

This slot is read-only.

Slot: chr
Type

(or null string)

Initargs

:chr

Readers

chr.

Writers

(setf chr).

Slot: start_region
Type

(or null integer)

Initargs

:start_region

Readers

start_region.

Writers

(setf start_region).

Slot: stop_region
Type

(or null integer)

Initargs

:stop_region

Readers

stop_region.

Writers

(setf stop_region).

Slot: strand
Type

(or null string)

Initargs

:strand

Readers

strand.

Writers

(setf strand).

Class: geneplatform
Package

cl-gene-searcher.

Source

lib/cl-gene-searcher/db-defs.lisp.

Direct superclasses

standard-db-object.

Direct methods
Direct slots
Slot: id
Type

(or null integer)

Readers

id.

Writers

This slot is read-only.

Slot: name
Type

(or null string)

Initargs

:name

Readers

name.

Writers

(setf name).

Class: genes
Package

cl-gene-searcher.

Source

lib/cl-gene-searcher/db-defs.lisp.

Direct superclasses

standard-db-object.

Direct methods
Direct slots
Slot: name
Type

(or null string)

Initargs

:name

Readers

name.

Writers

(setf name).

Slot: chr
Type

(or null string)

Initargs

:chr

Readers

chr.

Writers

(setf chr).

Slot: start_region
Type

(or null integer)

Initargs

:start_region

Readers

start_region.

Writers

(setf start_region).

Slot: stop_region
Type

(or null integer)

Initargs

:stop_region

Readers

stop_region.

Writers

(setf stop_region).

Slot: strand
Type

(or null string)

Initargs

:strand

Readers

strand.

Writers

(setf strand).

Slot: platform
Type

(or null integer)

Initargs

:platform

Readers

platform.

Writers

(setf platform).

Slot: powner
Readers

powner.

Writers

(setf powner).


Appendix A Indexes


A.1 Concepts


A.2 Functions

Jump to:   (  
C   D   F   G   I   M   N   P   Q   S   T   W  
Index Entry  Section

(
(setf chr): Public generic functions
(setf chr): Public generic functions
(setf chr): Public generic functions
(setf db-type): Private generic functions
(setf db-type): Private generic functions
(setf name): Public generic functions
(setf name): Public generic functions
(setf name): Public generic functions
(setf path): Private generic functions
(setf path): Private generic functions
(setf platform): Public generic functions
(setf platform): Public generic functions
(setf powner): Public generic functions
(setf powner): Public generic functions
(setf start_region): Public generic functions
(setf start_region): Public generic functions
(setf start_region): Public generic functions
(setf stop_region): Public generic functions
(setf stop_region): Public generic functions
(setf stop_region): Public generic functions
(setf strand): Public generic functions
(setf strand): Public generic functions
(setf strand): Public generic functions

C
chr: Public generic functions
chr: Public generic functions
chr: Public generic functions
connect-db: Private generic functions
connect-db: Private generic functions

D
db-type: Private generic functions
db-type: Private generic functions
db-type: Private generic functions
disconnect-db: Private ordinary functions

F
Function, disconnect-db: Private ordinary functions
Function, getdatabasepath: Public ordinary functions
Function, query-dgv-by-range: Public ordinary functions
Function, query-gene-by-name: Public ordinary functions
Function, query-gene-by-range: Public ordinary functions
Function, query-refflat-gene-by-range: Public ordinary functions
Function, query-ucsc-gene-by-range: Public ordinary functions
Function, setdatabasepath: Public ordinary functions

G
Generic Function, (setf chr): Public generic functions
Generic Function, (setf db-type): Private generic functions
Generic Function, (setf name): Public generic functions
Generic Function, (setf path): Private generic functions
Generic Function, (setf platform): Public generic functions
Generic Function, (setf powner): Public generic functions
Generic Function, (setf start_region): Public generic functions
Generic Function, (setf stop_region): Public generic functions
Generic Function, (setf strand): Public generic functions
Generic Function, chr: Public generic functions
Generic Function, connect-db: Private generic functions
Generic Function, db-type: Private generic functions
Generic Function, id: Public generic functions
Generic Function, name: Public generic functions
Generic Function, path: Private generic functions
Generic Function, platform: Public generic functions
Generic Function, powner: Public generic functions
Generic Function, start_region: Public generic functions
Generic Function, stop_region: Public generic functions
Generic Function, strand: Public generic functions
Generic Function, text: Private generic functions
getdatabasepath: Public ordinary functions

I
id: Public generic functions
id: Public generic functions
id: Public generic functions

M
Macro, with-generic-sqlite-db: Private macros
Method, (setf chr): Public generic functions
Method, (setf chr): Public generic functions
Method, (setf db-type): Private generic functions
Method, (setf name): Public generic functions
Method, (setf name): Public generic functions
Method, (setf path): Private generic functions
Method, (setf platform): Public generic functions
Method, (setf powner): Public generic functions
Method, (setf start_region): Public generic functions
Method, (setf start_region): Public generic functions
Method, (setf stop_region): Public generic functions
Method, (setf stop_region): Public generic functions
Method, (setf strand): Public generic functions
Method, (setf strand): Public generic functions
Method, chr: Public generic functions
Method, chr: Public generic functions
Method, connect-db: Private generic functions
Method, db-type: Private generic functions
Method, db-type: Private generic functions
Method, id: Public generic functions
Method, id: Public generic functions
Method, name: Public generic functions
Method, name: Public generic functions
Method, path: Private generic functions
Method, platform: Public generic functions
Method, powner: Public generic functions
Method, start_region: Public generic functions
Method, start_region: Public generic functions
Method, stop_region: Public generic functions
Method, stop_region: Public generic functions
Method, strand: Public generic functions
Method, strand: Public generic functions
Method, text: Private generic functions

N
name: Public generic functions
name: Public generic functions
name: Public generic functions

P
path: Private generic functions
path: Private generic functions
platform: Public generic functions
platform: Public generic functions
powner: Public generic functions
powner: Public generic functions

Q
query-dgv-by-range: Public ordinary functions
query-gene-by-name: Public ordinary functions
query-gene-by-range: Public ordinary functions
query-refflat-gene-by-range: Public ordinary functions
query-ucsc-gene-by-range: Public ordinary functions

S
setdatabasepath: Public ordinary functions
start_region: Public generic functions
start_region: Public generic functions
start_region: Public generic functions
stop_region: Public generic functions
stop_region: Public generic functions
stop_region: Public generic functions
strand: Public generic functions
strand: Public generic functions
strand: Public generic functions

T
text: Private generic functions
text: Private generic functions

W
with-generic-sqlite-db: Private macros


A.4 Data types

Jump to:   C   D   F   G   L   P   Q   S  
Index Entry  Section

C
cl-gene-searcher: The cl-gene-searcher system
cl-gene-searcher: The cl-gene-searcher package
cl-gene-searcher-asd: The cl-gene-searcher-asd package
cl-gene-searcher.asd: The cl-gene-searcher/cl-gene-searcher․asd file
Class, db-connection: Private classes
Class, db-connection-sqlite: Private classes
Class, dgv: Private classes
Class, geneplatform: Private classes
Class, genes: Private classes
Condition, query-error: Private conditions

D
db-connection: Private classes
db-connection-sqlite: Private classes
dgv: Private classes

F
File, cl-gene-searcher.asd: The cl-gene-searcher/cl-gene-searcher․asd file
File, lib/cl-gene-searcher/cl-gene-searcher.lisp: The cl-gene-searcher/lib/cl-gene-searcher/cl-gene-searcher․lisp file
File, lib/cl-gene-searcher/db-connections.lisp: The cl-gene-searcher/lib/cl-gene-searcher/db-connections․lisp file
File, lib/cl-gene-searcher/db-defs.lisp: The cl-gene-searcher/lib/cl-gene-searcher/db-defs․lisp file
File, lib/cl-gene-searcher/package.lisp: The cl-gene-searcher/lib/cl-gene-searcher/package․lisp file

G
geneplatform: Private classes
genes: Private classes

L
lib/cl-gene-searcher/cl-gene-searcher.lisp: The cl-gene-searcher/lib/cl-gene-searcher/cl-gene-searcher․lisp file
lib/cl-gene-searcher/db-connections.lisp: The cl-gene-searcher/lib/cl-gene-searcher/db-connections․lisp file
lib/cl-gene-searcher/db-defs.lisp: The cl-gene-searcher/lib/cl-gene-searcher/db-defs․lisp file
lib/cl-gene-searcher/package.lisp: The cl-gene-searcher/lib/cl-gene-searcher/package․lisp file

P
Package, cl-gene-searcher: The cl-gene-searcher package
Package, cl-gene-searcher-asd: The cl-gene-searcher-asd package

Q
query-error: Private conditions

S
System, cl-gene-searcher: The cl-gene-searcher system