29 GBS_strcat(strstruct,
"xterm -sl 1000 -sb -e sh -c 'LD_LIBRARY_PATH=\"");
31 GBS_strcat(strstruct,
"\";export LD_LIBRARY_PATH;for i in ");
102 if (i<j) sprintf(var,
"naligner/%c%c",
"acgt-"[i],
"acgt-"[j]);
103 else sprintf(var,
"naligner/%c%c",
"acgt-"[j],
"acgt-"[i]);
109 GBS_strcat(strstruct,
" || echo \"Aligner failed\";done;");
112 GBS_strcat(strstruct,
"echo press \"(return)\" to close window;read a' &");
115 if (error)
fputs(error, stderr);
121 root->
awar_int(
"naligner/what", 0, db1);
123 root->
awar_int (
"naligner/against", 0, db1);
125 root->
awar_int (
"naligner/pt_server", -1, db1);
127 root->
awar_int(
"naligner/mark_profile", 1, db1);
128 root->
awar_int(
"naligner/unmark_sequence", 0, db1);
140 root->
awar_float(
"naligner/gap_panelty", 5.0, db1);
141 root->
awar_float(
"naligner/igap_panelty", 0.2, db1);
142 root->
awar_int (
"naligner/minf", 3, db1);
143 root->
awar_int (
"naligner/maxf", 30, db1);
148 root->
awar_float(
"naligner/det/cl", .25, db1);
151 root->
awar_int (
"naligner/det/ib", 5, db1);
152 root->
awar_int (
"naligner/det/ic", 5, db1);
156 const int mwidth = 5;
157 AW_window_simple *aws =
new AW_window_simple;
158 aws->init(root,
"ALIGNER_V2_EXPERT2",
"ALIGNER V2.0 EXPERT 2");
163 aws->create_button(
"CLOSE",
"CLOSE",
"C");
165 aws->at(
"minw"); aws->create_input_field(
"naligner/minw", mwidth);
166 aws->at(
"maxew"); aws->create_input_field(
"naligner/maxew", mwidth);
168 aws->at(
"ib"); aws->create_input_field(
"naligner/det/ib", mwidth);
169 aws->at(
"ic"); aws->create_input_field(
"naligner/det/ic", mwidth);
170 aws->at(
"cl"); aws->create_input_field(
"naligner/det/cl", mwidth);
171 aws->at(
"cm"); aws->create_input_field(
"naligner/det/cm", mwidth);
172 aws->at(
"ch"); aws->create_input_field(
"naligner/det/ch", mwidth);
178 AW_window_simple *aws =
new AW_window_simple;
179 const int mwidth = 3;
181 aws->init(root,
"ALIGNER_V2_EXPERT",
"ALIGNER V2.0 EXPERT");
184 aws->label_length(22);
188 aws->create_button(
"CLOSE",
"CLOSE",
"C");
190 aws->at(
"minr"); aws->create_input_field(
"naligner/minf", 6);
191 aws->at(
"maxr"); aws->create_input_field(
"naligner/maxf", 6);
193 aws->at(
"aa"); aws->create_input_field(
"naligner/aa", mwidth);
194 aws->at(
"ac"); aws->create_input_field(
"naligner/ac", mwidth);
195 aws->at(
"ag"); aws->create_input_field(
"naligner/ag", mwidth);
196 aws->at(
"at"); aws->create_input_field(
"naligner/at", mwidth);
198 aws->at(
"ca"); aws->create_input_field(
"naligner/ac", mwidth);
199 aws->at(
"cc"); aws->create_input_field(
"naligner/cc", mwidth);
200 aws->at(
"cg"); aws->create_input_field(
"naligner/cg", mwidth);
201 aws->at(
"ct"); aws->create_input_field(
"naligner/ct", mwidth);
203 aws->at(
"ga"); aws->create_input_field(
"naligner/ag", mwidth);
204 aws->at(
"gc"); aws->create_input_field(
"naligner/cg", mwidth);
205 aws->at(
"gg"); aws->create_input_field(
"naligner/gg", mwidth);
206 aws->at(
"gt"); aws->create_input_field(
"naligner/gt", mwidth);
208 aws->at(
"ta"); aws->create_input_field(
"naligner/at", mwidth);
209 aws->at(
"tc"); aws->create_input_field(
"naligner/ct", mwidth);
210 aws->at(
"tg"); aws->create_input_field(
"naligner/gt", mwidth);
211 aws->at(
"tt"); aws->create_input_field(
"naligner/tt", mwidth);
213 aws->at(
"gap"); aws->create_input_field(
"naligner/gap_panelty", 4);
214 aws->at(
"igap"); aws->create_input_field(
"naligner/igap_panelty", 4);
218 aws->create_button(
"EXPERT_OPTIONS",
"EXPERT2",
"E");
224 AW_window_simple *aws =
new AW_window_simple;
225 aws->init(root,
"ALIGNER_V2",
"ALIGNER V2.0");
228 aws->label_length(10);
229 aws->button_length(10);
233 aws->create_button(
"CLOSE",
"CLOSE",
"O");
237 aws->create_button(
"HELP",
"HELP");
242 aws->create_button(
"GO",
"GO",
"G");
246 aws->create_button(
"OPTIONS",
"PARAMETERS",
"E");
249 aws->create_toggle_field(
"naligner/what",
"Align");
250 aws->insert_toggle(
"Selected Species:",
"S", 0);
251 aws->insert_default_toggle(
"Marked Species",
"M", 1);
252 aws->update_toggle_field();
258 aws->create_toggle_field(
"naligner/against",
"Reference");
259 aws->insert_toggle(
"Species by name",
"S", 0);
260 aws->insert_default_toggle(
"Auto search by pt_server",
"S", 1);
261 aws->update_toggle_field();
264 aws->create_input_field(
"naligner/sagainst", 2);
266 aws->label_length(25);
268 aws->at(
"pt_server");
269 aws->label(
"PT_SERVER:");
273 aws->label_length(40);
274 aws->label(
"Mark sequences found by the pt_server");
275 aws->create_toggle(
"naligner/mark_profile");
GB_ERROR GBK_system(const char *system_command)
GBDATA * GBT_first_marked_species(GBDATA *gb_main)
void load_xfig(const char *file, bool resize=true)
void GBS_intcat(GBS_strstruct *strstr, long val)
void AW_POPDOWN(AW_window *window)
char buffer[MESSAGE_BUFFERSIZE]
GBS_strstruct * GBS_stropen(long init_size)
WindowCallback makeHelpCallback(const char *helpfile)
static AW_window * create_expert_naligner_window(AW_root *root)
AW_awar * awar_float(const char *var_name, float default_value=0.0, AW_default default_file=AW_ROOT_DEFAULT)
static AW_window * create_special_naligner_window(AW_root *root)
void GBS_strcat(GBS_strstruct *strstr, const char *ptr)
static void error(const char *msg)
void create_naligner_variables(AW_root *root, AW_default db1)
GBDATA * GBT_next_marked_species(GBDATA *gb_species)
static void aed_start_naligning(AW_window *aw, GBDATA *gb_main)
#define AWAR_SPECIES_NAME
char * read_string() const
AW_awar * awar(const char *awar)
void awt_create_PTSERVER_selection_button(AW_window *aws, const char *varname)
GB_CSTR GB_getenv(const char *env)
void GBS_chrcat(GBS_strstruct *strstr, char ch)
fputs(TRACE_PREFIX, stderr)
AW_awar * awar_int(const char *var_name, long default_value=0, AW_default default_file=AW_ROOT_DEFAULT)
AW_window * create_naligner_window(AW_root *root, GBDATA *gb_main)
char * GBS_strclose(GBS_strstruct *strstr)
void GBS_floatcat(GBS_strstruct *strstr, double val)
GB_transaction ta(gb_var)
AW_awar * awar_string(const char *var_name, const char *default_value="", AW_default default_file=AW_ROOT_DEFAULT)
GB_CSTR GBT_get_name_or_description(GBDATA *gb_item)