/* File: cdnainit.h * Author: mieg * Copyright (c) J Thierry-Mieg and R Durbin, 1999 * ------------------------------------------------------------------- * Acedb is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * This program 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 General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. * or see the on-line version at http://www.gnu.org/copyleft/gpl.txt * ------------------------------------------------------------------- * This file is part of the ACEDB genome database package, written by * Richard Durbin (Sanger Centre, UK) rd@sanger.ac.uk, and * Jean Thierry-Mieg (CRBM du CNRS, France) mieg@kaa.crbm.cnrs-mop.fr * * Description: * Exported functions: * HISTORY: * Last edited: Aug 26 17:56 1999 (fw) * Created: Thu Aug 26 17:55:41 1999 (fw) * CVS info: $Id: cdnainit.h,v 1.8 2000/04/14 21:46:38 mieg Exp $ *------------------------------------------------------------------- */ #ifndef ACEDB_CDNAINIT_H #define ACEDB_CDNAINIT_H char B2[255] ; KEY _VTranscribed_gene, _Transcribed_gene, _VTranscript, _Transcript, _VAnnotation, _VcDNA_clone, _VSage, _Sage, _VClone_Group , _Clone_Group, _From_gene, _cDNA_clone, _Hit = 0, _Forward, _Reverse, _Confirmed_intron = 0, _Confirmed_exon = 0, _First_exon = 0, _Last_exon = 0, _Splicing, _Read, _Nb_possible_exons, _Nb_alternative_exons, _Nb_confirmed_introns, _Nb_confirmed_alternative_introns, _Intron, _Exon, _Gap, _Alternative_exon, _Alternative_first_exon, _Alternative_intron, _Partial_exon, _Alternative_partial_exon, _3prime_UTR, _5prime_UTR, _Begin_not_found, /* _End_not_found, */ _Total_length, _Total_intron_length, _Total_gap_length, _Transpliced_to, _Transcribed_from, _Genomic_sequence, _PolyA_after_base, _Intron_boundaries, _Fake_internal_poly_A, _Vector_clipping, _Reversed_by, _Other, _Read_matchingLength_nerrors, _PCR_product_size, _Primed_on_polyA, _Assembled_from_cDNA_clone, _Genomic_sequence, _Spliced_sequence, _From_gene, _NewName, _3prime_UTR_length, _Longest_cDNA_clone, _Overlap_right, _Overlap_left, _Is_chain, _Is_gap, _Genomic, _IntMap, _Hits, _Problem, _Gene_wall, _Mosaic, _Relabelled, _Discarded_cDNA, _Discarded_from, _Derived_sequence, _CTF_File ; void cDNAAlignInit (void) { int i ; KEY key ; if (_Hit) return ; i = 256 ; while (i--) B2[i] = 0 ; B2[A_] = 0x0 ; B2[T_] = 0x3 ; B2[G_] = 0x1 ; B2[C_] = 0x2 ; lexaddkey ("Transcribed_gene", &key, _VMainClasses) ; _VTranscribed_gene = KEYKEY(key) ; lexaddkey ("Transcript", &key, _VMainClasses) ; _VTranscript = KEYKEY(key) ; lexaddkey ("cDNA_clone", &key, _VMainClasses) ; _VcDNA_clone = KEYKEY(key) ; lexaddkey ("Clone_Group", &key, _VMainClasses) ; _VClone_Group = KEYKEY(key) ; lexaddkey ("Annotation", &key, _VMainClasses) ; _VAnnotation = KEYKEY(key) ; lexaddkey ("Sage", &key, _VMainClasses) ; _VSage = KEYKEY(key) ; _Transcribed_gene = str2tag ("Transcribed_gene") ; _Transcript = str2tag ("Transcript") ; _From_gene = str2tag ("From_gene") ; _cDNA_clone = str2tag ("cDNA_clone") ; _Sage = str2tag ("Sage") ; _Hit = str2tag ("Hit") ; _Forward = str2tag ("Forward") ; _Reverse = str2tag ("Reverse") ; _Confirmed_intron = str2tag ("Confirmed_intron") ; _Confirmed_exon = str2tag ("Confirmed_exon") ; _First_exon = str2tag ("First_exon") ; _Last_exon = str2tag ("Last_exon") ; _Splicing = str2tag ("Splicing") ; _Read = str2tag ("Read") ; _Clone_Group = str2tag ("Clone_Group") ; _Nb_possible_exons = str2tag ("Nb_possible_exons") ; _Nb_alternative_exons = str2tag ("Nb_alternative_exons") ; _Nb_confirmed_introns = str2tag ("Nb_confirmed_introns") ; _Nb_confirmed_alternative_introns = str2tag ("Nb_confirmed_alternative_introns") ; _Intron = str2tag ("Intron") ; _Exon = str2tag ("Exon") ; _Gap = str2tag ("Gap") ; _Alternative_exon = str2tag ("Alternative_exon") ; _Alternative_first_exon = str2tag ("Alternative_first_exon") ; _Alternative_intron = str2tag ("Alternative_intron") ; _Partial_exon = str2tag ("Partial_exon") ; _Alternative_partial_exon = str2tag ("Alternative_partial_exon") ; _3prime_UTR = str2tag ("3prime_UTR") ; _5prime_UTR = str2tag ("5prime_UTR") ; _Begin_not_found = str2tag ("Begin_not_found") ; /* _End_not_found = str2tag ("End_not_found") ; in tags.h */ _Total_length = str2tag ("Total_length") ; _Total_intron_length = str2tag ("Total_intron_length") ; _Total_gap_length = str2tag ("Total_gap_length") ; _Transpliced_to = str2tag ("Transpliced_to") ; _Transcribed_from = str2tag ("Transcribed_from") ; _Genomic_sequence = str2tag ("Genomic_sequence") ; _PolyA_after_base = str2tag ("PolyA_after_base") ; _Intron_boundaries = str2tag ("Intron_boundaries") ; _Discarded_cDNA = str2tag ("Discarded_cDNA") ; _Discarded_from = str2tag ("Discarded_from") ; _Derived_sequence = str2tag ("Derived_sequence") ; _CTF_File = str2tag ("CTF_File") ; _Fake_internal_poly_A = str2tag ("Fake_internal_poly_A") ; _Vector_clipping = str2tag ("Vector_clipping") ; _Reversed_by = str2tag ("Reversed_by") ; _Other = str2tag ("Other") ; _Read_matchingLength_nerrors = str2tag ("Read_matchingLength_nerrors") ; _PCR_product_size = str2tag ("PCR_product_size") ; _Primed_on_polyA = str2tag ("Primed_on_polyA") ; _Assembled_from_cDNA_clone = str2tag ("Assembled_from_cDNA_clone") ; _Genomic_sequence = str2tag ("Genomic_sequence") ; _Spliced_sequence = str2tag ("Spliced_sequence") ; _From_gene = str2tag ("From_gene") ; _NewName = str2tag ("NewName") ; _3prime_UTR_length = str2tag ("3prime_UTR_length") ; _Longest_cDNA_clone = str2tag ("Longest_cDNA_clone") ; _Overlap_right = str2tag ("Overlap_right") ; _Overlap_left = str2tag ("Overlap_left") ; _Is_chain = str2tag ("Is_chain") ; _Is_gap = str2tag ("Is_gap") ; _Genomic = str2tag ("Genomic") ; _IntMap = str2tag ("IntMap") ; _Hits = str2tag ("Hits") ; _Mosaic = str2tag ("Mosaic") ; _Problem = str2tag ("Problem") ; _Gene_wall = str2tag ("Gene_wall") ; _Relabelled = str2tag ("Relabelled") ; /* _ = str2tag ("") ; */ } #endif /* !ACEDB_CDNAINIT_H */