Common Lisp Package: CL-GENE-SEARCHER

README:

FUNCTION

Public

Undocumented

GETDATABASEPATH

QUERY-DGV-BY-RANGE (&KEY CHR START STOP)

QUERY-GENE-BY-NAME (NAME &REST NAMES)

QUERY-GENE-BY-RANGE (&KEY CHR START STOP)

QUERY-REFFLAT-GENE-BY-RANGE (&KEY CHR START STOP)

QUERY-UCSC-GENE-BY-RANGE (&KEY CHR START STOP)

SETDATABASEPATH (PATH)

Private

CONNECT (CONNECTION-SPEC &KEY (IF-EXISTS *CONNECT-IF-EXISTS*) (MAKE-DEFAULT T) (POOL NIL) (DATABASE-TYPE *DEFAULT-DATABASE-TYPE*) (ENCODING NIL))

Connects to a database of the supplied DATABASE-TYPE which defaults to *DEFAULT-DATABASE-TYPE*, using the type-specific connection specification CONNECTION-SPEC. The value of IF-EXISTS, which defaults to *CONNECT-IF-EXISTS*, determines what happens if a connection to the database specified by CONNECTION-SPEC is already established. A value of :new means create a new connection. A value of :warn-new means warn the user and create a new connect. A value of :warn-old means warn the user and use the old connection. A value of :error means fail, notifying the user. A value of :old means return the old connection. MAKE-DEFAULT is t by default which means that *DEFAULT-DATABASE* is set to the new connection, otherwise *DEFAULT-DATABASE* is not changed. If POOL is t the connection will be taken from the general pool, if POOL is a CONN-POOL object the connection will be taken from this pool.

DISCONNECT (&KEY (DATABASE *DEFAULT-DATABASE*) (ERROR NIL))

Closes the connection to DATABASE and resets *DEFAULT-DATABASE* if that database was disconnected. If DATABASE is a database instance, this object is closed. If DATABASE is a string, then a connected database whose name matches DATABASE is sought in the list of connected databases. If no matching database is found and ERROR and DATABASE are both non-nil an error is signaled, otherwise nil is returned. If the database is from a pool it will be released to this pool.

Undocumented

DISCONNECT-DB

MACRO

Private

DEF-VIEW-CLASS (CLASS SUPERS SLOTS &REST CL-OPTIONS)

Creates a View Class called CLASS whose slots SLOTS can map onto the attributes of a table in a database. If SUPERS is nil then the superclass of CLASS will be STANDARD-DB-OBJECT, otherwise SUPERS is a list of superclasses for CLASS which must include STANDARD-DB-OBJECT or a descendent of this class. The syntax of DEFCLASS is extended through the addition of a class option :base-table which defines the database table onto which the View Class maps and which defaults to CLASS. The DEFCLASS syntax is also extended through additional slot options. The :db-kind slot option specifies the kind of DB mapping which is performed for this slot and defaults to :base which indicates that the slot maps to an ordinary column of the database table. A :db-kind value of :key indicates that this slot is a special kind of :base slot which maps onto a column which is one of the unique keys for the database table, the value :join indicates this slot represents a join onto another View Class which contains View Class objects, and the value :virtual indicates a standard CLOS slot which does not map onto columns of the database table. If a slot is specified with :db-kind :join, the slot option :db-info contains a list which specifies the nature of the join. For slots of :db-kind :base or :key, the :type slot option has a special interpretation such that Lisp types, such as string, integer and float are automatically converted into appropriate SQL types for the column onto which the slot maps. This behaviour may be over-ridden using the :db-type slot option which is a string specifying the vendor-specific database type for this slot's column definition in the database. The :column slot option specifies the name of the SQL column which the slot maps onto, if :db-kind is not :virtual, and defaults to the slot name. The :void-value slot option specifies the value to store if the SQL value is NULL and defaults to NIL. The :db-constraints slot option is a string representing an SQL table constraint expression or a list of such strings.

Undocumented

WITH-GENERIC-SQLITE-DB ((VAR) &BODY BODY)

GENERIC-FUNCTION

Private

CONNECT-DB (DB-CONNECTION)

Generic method for which the various database types will be supported

Undocumented

TEXT (CONDITION)

SLOT-ACCESSOR

Public

Undocumented

CHR (OBJECT)

SETFCHR (NEW-VALUE OBJECT)

ID (OBJECT)

NAME (OBJECT)

SETFNAME (NEW-VALUE OBJECT)

PLATFORM (OBJECT)

SETFPLATFORM (NEW-VALUE OBJECT)

POWNER (OBJECT)

SETFPOWNER (NEW-VALUE OBJECT)

START_REGION (OBJECT)

SETFSTART_REGION (NEW-VALUE OBJECT)

STOP_REGION (OBJECT)

SETFSTOP_REGION (NEW-VALUE OBJECT)

STRAND (OBJECT)

SETFSTRAND (NEW-VALUE OBJECT)

Private

Undocumented

DATABASE-STATE (OBJECT)

DB-TYPE (OBJECT)

SETFDB-TYPE (NEW-VALUE OBJECT)

PATH (OBJECT)

SETFPATH (NEW-VALUE OBJECT)

VARIABLE

Private

Undocumented

*DATABASE-PATH*

*GLOBAL-DB-CONNECTION-OBJECT*

CLASS

Private

DB-CONNECTION

The foundation datbase connection class, that the others will inherit

DB-CONNECTION-SQLITE

The specific connection object for SQLite

Undocumented

DGV

GENEPLATFORM

GENES

CONDITION

Private

Undocumented

QUERY-ERROR