;;; -*- Mode: Lisp -*-

#|CLARITY: Common Lisp Data Alignment Repository
Copyright (c) 2006 Samantha Kleinberg
All rights reserved.

This library is free software; you can redistribute it and/or modify it under the terms of the GNU
Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the 
License, or (at your option) any later version.

This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even 
the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser 
General Public License for more details.

You should have received a copy of the GNU Lesser General Public License along with this library; 
if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA

contact: Samantha AT Bioinformatics DOT nyu DOT edu
715 Broadway, 10th floor
New York, NY 10003|#

(defpackage "CLARITY" (:use "CL")
  (:export 
   "ALIGN-CHARTS"
   "SCORE"
   "SCORE-PAIR"
   "ALIGN-TO-CONSENSUS"
   "SCORE-PAIR-CONSENSUS"
   "STRING-ALIGNMENT"
   "GET-ROOT"

   "TREE-INSERT"
   "TREE-INSERT-RECURSIVE"
   "INSERT-NODE"
   "BUILD-CONSENSUS"
   "BUILD-INTERNAL-CONSENSUS"
   "STORE-CONSENSUS-SEQUENCE"
   "GET-CONSENSUS-TERMS"
   "GET-DATA-TERMS")
  (:export
   "CLARITY-HANDLE"
   "CLARITY-HANDLE-P"
   "*CURRENT-CLARITY-HANDLE*"
   "MAKE-CLARITY-HANDLE"
   "DISCONNECT-CLARITY-DBS"
   "CONNECT"
   "NUMBER-TO-STRING"
   "INSERT"
   "INSERT-WITH-PROBES"
   "GANTTIFY"
   "GANTTIFY-WITH-PROBES"
   "STORE-GANTT-CHARTS"
   "STORE-GANTT-CHART"
   "STORE-NUMERICAL-DATA"
   "STORE-NUMERICAL-AND-PROBE-DATA"
   "FLATTEN"
   "LASTID"
   "FILE-LINES"
   "GET-CHILDREN"
   "GET-NODE-TERMS"
   "GET-ALL-DATA")

  (:export
   "READ-STRING-WHILE"
   "DECIMAL-READER"
   "PARSE-DECIMAL"
   "USE-DECIMAL")

  (:export
   "INSERT-FILE-POPUP"
   "GET-FILENAME"
   "DATABASE-SWITCH-CALLBACK"
   "PRINT-PARTIAL-FILENAME"
   )
  (:export
   "START-CLARITY-GUI"
   "START-SETUP-INTERFACE"
   )
   
     (:export
   "*CLARITY-DB-NAME*"
   "*CLARITY-DB-USER*"
   "*CLARITY-DB-PASSWORD*"
   )

  (:export
   "INSERT-FILE-POPUP"
   "INSERT-DATA-INTERFACE"
   "GET-FILENAME"
   "GET-PHYLOGENY-ROOT"
   "GET-PHYLOGENY-CHILDREN"
   "DATABASE-SWITCH-CALLBACK"
   "PRINT-PARTIAL-FILENAME"
   )
  (:export
   "START-CLARITY-GUI"
   "START-CLARITY-INTERFACE"
   "START-SETUP-INTERFACE"
   "START-WINDOWS-DATA-SOURCE-SETUP"
   "START-MACOSX-DATA-SOURCE-SETUP"
   "CLARITY-DATABASE-SETUP-INTERFACE"
   )
  (:export
   "PHYLOGENY-ITEM"
   "PHYLOGENY-TERM"
   "PHYLOGENY-WINDOW"
   )
  )




;;; end of file -- clarity-package.lisp --