The cl-gene-searcher Reference Manual

Table of Contents

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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.

• Introduction:  What cl-gene-searcher is all about
• Systems:  The systems documentation
• Files:  The files documentation
• Packages:  The packages documentation
• Definitions:  The symbols documentation
• Indexes:  Concepts, functions, variables and data types

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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

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2 Systems

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

• The cl-gene-searcher system:  

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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

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3 Files

Files are sorted by type and then listed depth-first from the systems components trees.

• Lisp files:  

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3.1 Lisp

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

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3.1.1 cl-gene-searcher.asd

Location

cl-gene-searcher.asd

Systems

cl-gene-searcher (system)

Packages

cl-gene-searcher-asd

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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

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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

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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

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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

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4 Packages

Packages are listed by definition order.

• The cl-gene-searcher-asd package:  
• The cl-gene-searcher package:  

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4.1 cl-gene-searcher-asd

Source

cl-gene-searcher.asd

Use List

common-lisp

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4.2 cl-gene-searcher

Source

lib/cl-gene-searcher/package.lisp (file)

Use List
Exported Definitions
Internal Definitions

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5 Definitions

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

• Exported definitions:  
• Internal definitions:  

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5.1 Exported definitions

• Exported functions:  
• Exported generic functions:  

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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)

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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)

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5.2 Internal definitions

• Internal special variables:  
• Internal macros:  
• Internal functions:  
• Internal generic functions:  
• Internal conditions:  
• Internal classes:  

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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)

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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)

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5.2.3 Functions

Function: disconnect-db ()
Package

cl-gene-searcher

Source

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

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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)

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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)

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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
  • db-type (method)
  • db-type (method)
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)

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Appendix A Indexes

• Concept index:  
• Function index:  
• Variable index:  
• Data type index:  

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A.1 Concepts

Jump to:   C   F   L  
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
Jump to:   C   F   L  

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A.2 Functions

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

Next: , Previous: , Up: Indexes   [Contents][Index]

A.3 Variables

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C   I   N   P   S   T  
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
Jump to:   *  
C   I   N   P   S   T  

Previous: , Up: Indexes   [Contents][Index]

A.4 Data types

Jump to:   C   D   G   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
Class, db-connection: Internal classes
Class, db-connection-sqlite: Internal classes
Class, dgv: Internal classes
Class, geneplatform: Internal classes
Class, genes: Internal classes
Condition, query-error: Internal conditions
D
db-connection: Internal classes
db-connection-sqlite: Internal classes
dgv: Internal classes
G
geneplatform: Internal classes
genes: Internal classes
P
Package, cl-gene-searcher: The cl-gene-searcher package
Package, cl-gene-searcher-asd: The cl-gene-searcher-asd package
Q
query-error: Internal conditions
S
System, cl-gene-searcher: The cl-gene-searcher system
Jump to:   C   D   G   P   Q   S