NCBI C Toolkit Cross Reference

C/desktop/ingenext.h

  1 /* ingenext.h
  2 
  3 * ===========================================================================
  4 *
  5 *                            PUBLIC DOMAIN NOTICE
  6 *            National Center for Biotechnology Information (NCBI)
  7 *
  8 *  This software/database is a "United States Government Work" under the
  9 *  terms of the United States Copyright Act.  It was written as part of
 10 *  the author's official duties as a United States Government employee and
 11 *  thus cannot be copyrighted.  This software/database is freely available
 12 *  to the public for use. The National Library of Medicine and the U.S.
 13 *  Government do not place any restriction on its use or reproduction.
 14 *  We would, however, appreciate having the NCBI and the author cited in
 15 *  any work or product based on this material
 16 *
 17 *  Although all reasonable efforts have been taken to ensure the accuracy
 18 *  and reliability of the software and data, the NLM and the U.S.
 19 *  Government do not and cannot warrant the performance or results that
 20 *  may be obtained by using this software or data. The NLM and the U.S.
 21 *  Government disclaim all warranties, express or implied, including
 22 *  warranties of performance, merchantability or fitness for any particular
 23 *  purpose.
 24 *
 25 * ===========================================================================
 26 *
 27 * File Name:  ingenext.h
 28 *
 29 * Author:  Fasika Aklilu
 30 *
 31 * Version Creation Date:   8/9/01
 32 *
 33 * $Revision: 6.5 $
 34 *
 35 * File Description: 
 36 *
 37 * Modifications:  
 38 * --------------------------------------------------------------------------
 39 * Date     Name        Description of modification
 40 * -------  ----------  -----------------------------------------------------
 41 *
 42 *
 43 * ==========================================================================
 44 */
 45 
 46 #ifndef _INGENEXT_
 47 #define _INGENEXT_
 48 
 49 #ifdef __cplusplus
 50 extern "C" {
 51 #endif
 52 
 53 #include <ingenwin.h>
 54 #include <dotviewer.h>
 55 #include <spidey.h>
 56 #include <qblastapi.h>
 57 #include <alignmgr2.h>
 58 
 59 #define Ing_NUM_DBS 20
 60 #define MAX_BLASTN_LEN 8000
 61 #define MAX_BLASTP_LEN 4000
 62 #define MAX_BLASTX_LEN 3000
 63 #define MAX_TBLASTN_LEN 2000
 64 #define OVERLAP_SPACE 1000
 65 #define POST_PROCESS_BANDALGN  1
 66 #define POST_PROCESS_NONE      2
 67 
 68 
 69 
 70 /******************************************************
 71  *
 72  *  typedefs
 73  *
 74 ******************************************************/
 75 
 76 typedef struct dotinfo{
 77   SeqAlignPtr sap;
 78   SeqIdPtr    sip1;
 79   SeqIdPtr    sip2;
 80   TexT from1;
 81   TexT to1;
 82   TexT from2;
 83   TexT to2;
 84   TexT wordsize;
 85   TexT numhits;
 86   TexT strand;
 87 } DotInfo;
 88 
 89 typedef struct ig_blastdlgdata {
 90   ValNode *pvnSips;               /* list of sips in structure */
 91   LisT bsp_list;          /* listbox of bsps */
 92   PopuP db_list;          /* listbox of databases */
 93   ButtoN bGap;   /* should the alignment be gapped? */
 94   TexT tMax;
 95   TexT tExpect;
 96   TexT wordsize;
 97   ButtoN     maskrep;
 98   ButtoN     masksimple;
 99   ButtoN     megablast;
100   SeqAlign *salp;  /* resulting seqalign */
101 }Ing_BlastDlgData;
102 
103 
104 
105 typedef struct ig_blast2info
106 {
107   BioseqPtr  bsp1;
108   BioseqPtr  bsp2;
109   CharPtr    path;
110   CharPtr    GI_list;
111   GrouP      localorglobal;
112   GrouP      progname;
113   GrouP      gapped;
114   TexT       from;
115   TexT       to;
116   TexT       eval;
117   TexT       wordsize;
118   ButtoN     maskrep;
119   ButtoN     masksimple;
120   ButtoN     megablast;
121   IngGenomeViewerPtr igvp;
122 } IngBlast2Info, PNTR IngBlast2InfoPtr;
123 
124 
125 typedef struct ig_spideyform
126 {
127   BioseqPtr  bsp1;
128   BioseqPtr  bsp2;
129   CharPtr    path;
130   CharPtr    GI_list;
131   ButtoN     inters;
132   PopuP      org;
133   TexT       idcutoff;
134   TexT       lencutoff;
135   TexT       firstpasseval;
136   TexT       secondpasseval;
137   TexT       thirdpasseval;
138   TexT       numreturns;
139   TexT       from;
140   TexT       to;
141 } IngSpideyForm , PNTR IngSpideyFormPtr;
142 
143 
144 extern  Uint2 primID_cntr;
145 
146 static CharPtr ig_nucdbs [] = {
147   "nr", "est", "est_human", "est_mouse", "est_others", "gss","htgs", "pat", "yeast",  "mito", "vector", "ecoli", "pdb", "drosoph", "month", "sts", "kabat",
148   "epd",  "alu", NULL
149 };
150 
151 static CharPtr ig_nucdbsnames [] = {
152   "nr", "est", "est_human", "est_mouse", "est_others", "gss (single-pass genomic)", "htgs", "patent", "yeast", "mito", "vector", "ecoli", "pdb (3-D prot)", "Drosophila", "month", "sts",  "kabat (immunologic)", "epd (eukaryotic promoter)",   "Alu repeats", NULL
153 };
154 
155 
156 /******************************************************
157  *
158  *  Function Declarations
159  *
160 ******************************************************/
161 
162 
163 #ifdef __cplusplus
164 }
165 #endif
166 
167 #endif /* ndef _GENVIEW_ */
168 
169
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