1 /** @source taxgetup
2 **
3 ** Find taxons at higher ranks
4 **
5 ** @author Copyright (C) 2010 Jon Ison / EMBOSS
6 ** @version 1 First version</replaceable>
7 ** @modified July 2010 Jon Ison First version</replaceable>
8 ** @@
9 **
10 ** This program is free software; you can redistribute it and/or
11 ** modify it under the terms of the GNU General Public License
12 ** as published by the Free Software Foundation; either version 2
13 ** of the License, or (at your option) any later version.
14 **
15 ** This program is distributed in the hope that it will be useful,
16 ** but WITHOUT ANY WARRANTY; without even the implied warranty of
17 ** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
18 ** GNU General Public License for more details.
19 **
20 ** You should have received a copy of the GNU General Public License
21 ** along with this program; if not, write to the Free Software
22 ** Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
23 ********************************************************************/
24
25
26 /* ==================================================================== */
27 /* ========================== include files =========================== */
28 /* ==================================================================== */
29
30 #include "emboss.h"
31
32 /* Inclusion of system and local header files goes here */
33
34
35
36 /* ==================================================================== */
37 /* ============================ constants ============================= */
38 /* ==================================================================== */
39
40 /* #define and enum statements go here */
41
42
43
44 /* ==================================================================== */
45 /* ======================== global variables ========================== */
46 /* ==================================================================== */
47
48 /* Global variables definitions go here */
49
50
51
52 /* ==================================================================== */
53 /* ============================== data ================================ */
54 /* ==================================================================== */
55
56 /* Definition of datatypes go here */
57
58
59
60 /* ==================================================================== */
61 /* ==================== function prototypes =========================== */
62 /* ==================================================================== */
63
64 /* Function prototypes for public (external) functions go here */
65
66
67
68
69 /* @prog taxgetup ************************************************************
70 **
71 ** Find NCBI taxons above search term
72 **
73 ******************************************************************************/
74
main(int argc,char ** argv)75 int main(int argc, char **argv)
76 {
77 /* Variable declarations */
78 AjPOutfile outfile = NULL;
79 AjBool hidden = ajFalse;
80
81 AjPTax tax = NULL;
82 AjPTax taxparent = NULL;
83 AjPTaxall taxall = NULL;
84 AjPTaxin taxinparent = NULL;
85
86 AjPStr taxqryup = NULL;
87 AjPTable foundtable = NULL;
88
89 ajuint up;
90 AjPList uplist = NULL;
91
92 /* ACD processing */
93 embInit("taxgetup", argc, argv);
94
95 taxall = ajAcdGetTaxonall("taxons");
96 outfile = ajAcdGetOuttaxon("outfile");
97 hidden = ajAcdGetBoolean("hidden");
98
99 taxinparent = ajTaxinNew();
100 taxparent = ajTaxNew();
101 uplist = ajListNew();
102
103 foundtable = ajTablestrNew(600);
104
105 while(ajTaxallNext(taxall, &tax))
106 {
107 up = ajTaxGetParent(tax);
108 while (up > 1)
109 {
110 ajFmtPrintS(&taxqryup, "%S-id:%u", ajTaxGetDb(tax), up);
111 ajTaxinQryS(taxinparent, taxqryup);
112
113 if(!ajTaxinRead(taxinparent, taxparent))
114 break;
115
116 if(hidden || !ajTaxIsHidden(taxparent))
117 {
118 if(!ajTableMatchS(foundtable, taxparent->Id))
119 {
120 ajTaxoutWrite(outfile, taxparent);
121 ajTablePut(foundtable,
122 ajStrNewS(taxparent->Id),
123 (void *) 1);
124 }
125 }
126
127 up = ajTaxGetParent(taxparent);
128 }
129 }
130
131 /* Memory clean-up and exit */
132
133 ajTaxallDel(&taxall);
134 ajTaxinDel(&taxinparent);
135 ajTaxDel(&tax);
136 ajTaxDel(&taxparent);
137
138 ajListFree(&uplist);
139
140 ajTablestrFreeKey(&foundtable);
141
142 ajStrDel(&taxqryup);
143
144 ajOutfileClose(&outfile);
145
146 embExit();
147
148 return 0;
149 }
150
151
152 /* ==================================================================== */
153 /* ============================ functions ============================= */
154 /* ==================================================================== */
155
156