int iplink_ifla_xstats(int argc, char **argv)
{
struct link_util *lu = NULL;
__u32 filt_mask;
if (!argc) {
fprintf(stderr, "xstats: missing argument\n");
return -1;
}
if (matches(*argv, "type") == 0) {
NEXT_ARG();
lu = get_link_kind(*argv);
if (!lu)
invarg("invalid type", *argv);
} else if (matches(*argv, "help") == 0) {
print_explain(stdout);
return 0;
} else {
invarg("unknown argument", *argv);
}
if (!lu) {
print_explain(stderr);
return -1;
}
if (!lu->print_ifla_xstats) {
fprintf(stderr, "xstats: link type %s doesn't support xstats\n",
lu->id);
return -1;
}
if (lu->parse_ifla_xstats &&
lu->parse_ifla_xstats(lu, argc-1, argv+1))
return -1;
if (strstr(lu->id, "_slave"))
filt_mask = IFLA_STATS_FILTER_BIT(IFLA_STATS_LINK_XSTATS_SLAVE);
else
filt_mask = IFLA_STATS_FILTER_BIT(IFLA_STATS_LINK_XSTATS);
if (rtnl_wilddump_stats_req_filter(&rth, AF_UNSPEC,
RTM_GETSTATS,
filt_mask) < 0) {
perror("Cannont send dump request");
return -1;
}
if (rtnl_dump_filter(&rth, lu->print_ifla_xstats, stdout) < 0) {
fprintf(stderr, "Dump terminated\n");
return -1;
}
return 0;
}
/* Prints the helptext for options in a generated form */
static tvalue print_flags(option_clone *opts,
gen_cli_helpstr *opts_explain,
unsigned int arglen,unsigned int cols)
{
register unsigned int beta=0, gamma;
unsigned int optcount = 0, curlen;
unsigned int conslen = PRINTSPACELEN+2;
if(opts)
while(opts[optcount].longflag != NULL || opts[optcount].has_arg != 0
|| opts[optcount].shortflag != 0)
optcount++;
/* do the printing */
for(beta = 0; beta < optcount; beta++)
{
curlen = conslen;
print_out(PRINTSPACE);
if(opts[beta].shortflag != 0)
print_out("-%c", opts[beta].shortflag);
if(opts[beta].longflag != NULL)
{
curlen += 4 + strlen(opts[beta].longflag);
if(opts[beta].shortflag != 0)
iolet_out_char(IL_IOStd,',');
else
print_out(" ");
print_out(" --%s", opts[beta].longflag);
if(opts_explain[beta].arg != NULL)
{
curlen += 1 + strlen(opts_explain[beta].arg);
print_out(" %s", opts_explain[beta].arg);
}
}
for(gamma = curlen; gamma < arglen; gamma++)
iolet_out_char(IL_IOStd,' ');
print_explain(arglen, opts_explain[beta].desc,cols);
}
iolet_out_char(IL_IOStd,'\n');
return TRUE;
}
void get_explanation(pnode_t p)
{
char buffer[EXPLAIN_LEN];
FILE *fp;
if (( fp = fopen(DICT_FILENAME, "r+")) == NULL)
IERROR("Open '%s'failed!", DICT_FILENAME);
fseek(fp, p->pos, SEEK_SET);
fgets(buffer, WORD_LEN, fp);
fgets(buffer, EXPLAIN_LEN, fp);
print_explain(buffer);
fclose(fp);
}
static void explain(void)
{
print_explain(stderr);
}
static void bridge_print_help(struct link_util *lu, int argc, char **argv,
FILE *f)
{
print_explain(f);
}
static void
format_pairs(FILE *f,
const p3_global_settings *pa,
const seq_args *sa,
const p3retval *retval,
const pair_array_t *best_pairs,
const char *pr_release,
const pr_append_str *combined_retval_err,
int explain_flag)
{
char *warning;
int print_lib_sim = lib_sim_specified(pa);
primer_rec *h = NULL;
PR_ASSERT(NULL != f);
PR_ASSERT(NULL != pa);
PR_ASSERT(NULL != sa);
/* If there are errors, print them and return */
if (!pr_is_empty(combined_retval_err)) {
format_error(f, sa->sequence_name,
pr_append_str_chars(combined_retval_err));
return;
}
/* Print the sequence name if it is provided */
if (NULL != sa->sequence_name)
fprintf(f, "PRIMER PICKING RESULTS FOR %s\n\n", sa->sequence_name);
/* Print if a mispriming libraby was used and which one */
if (pa->p_args.repeat_lib != NULL)
fprintf(f, "Using mispriming library %s\n",
pa->p_args.repeat_lib->repeat_file);
else
fprintf(f, "No mispriming library specified\n");
/* Print if a mispriming libraby for the internal oligo
* was used and which one */
if ( pa->pick_internal_oligo == 1 ) {
if (pa->o_args.repeat_lib != NULL)
fprintf(f, "Using internal oligo mishyb library %s\n",
pa->o_args.repeat_lib->repeat_file);
else
fprintf(f, "No internal oligo mishyb library specified\n");
}
/* Does the sequence start at position 0 or 1 ? */
fprintf(f, "Using %d-based sequence positions\n",
pa->first_base_index);
/* Complain if no primers are in the array */
if (best_pairs->num_pairs == 0) fprintf(f, "NO PRIMERS FOUND\n\n");
/* Print out the warings */
if ((warning = p3_get_rv_and_gs_warnings(retval, pa)) != NULL) {
fprintf(f, "WARNING: %s\n\n", warning);
free(warning);
}
/* Print the results for the best pair */
print_summary(f, pa, sa, best_pairs, 0);
fprintf(f, "\n");
/* Print nicely out the sequence with the best pair */
if (print_seq(f, pa, sa, retval, h, best_pairs, 0)) exit(-2); /* ENOMEM */
/* Print out the alternative pairs */
if (best_pairs->num_pairs > 1 ) print_rest(f, pa, sa, best_pairs);
/* Print the primer picking statistics */
if (explain_flag)
print_explain(f, pa, sa, retval, print_lib_sim, pr_release);
/* Flush the buffers and return */
fprintf(f, "\n\n");
if (fflush(f) == EOF) {
perror("fflush(f) failed");
exit(-1);
}
}
static void
format_oligos(FILE *f,
const p3_global_settings *pa,
const seq_args *sa,
const p3retval *retval,
const char* pr_release,
const pr_append_str *combined_retval_err,
int explain_flag)
{
char *warning;
int print_lib_sim = lib_sim_specified(pa);
int i;
int print_primers = 0;
primer_rec *h = NULL;
pair_array_t *best_pairs;
primer_rec *p;
int rest_count = 0;
PR_ASSERT(NULL != f);
PR_ASSERT(NULL != pa);
PR_ASSERT(NULL != sa);
best_pairs = NULL;
if (!pr_is_empty(combined_retval_err)) {
format_error(f, sa->sequence_name, pr_append_str_chars(combined_retval_err));
return;
}
if (NULL != sa->sequence_name)
fprintf(f, "PRIMER PICKING RESULTS FOR %s\n\n", sa->sequence_name);
if (pa->pick_left_primer || pa->pick_right_primer) {
if (pa->p_args.repeat_lib != NULL)
fprintf(f, "Using mispriming library %s\n",
pa->p_args.repeat_lib->repeat_file);
else
fprintf(f, "No mispriming library specified\n");
}
if (pa->pick_internal_oligo) {
if (pa->o_args.repeat_lib != NULL)
fprintf(f, "Using internal probe mishyb library %s\n", pa->o_args.repeat_lib->repeat_file);
else
fprintf(f, "No internal probe mishyb library specified\n");
}
fprintf(f, "Using %d-based sequence positions\n", pa->first_base_index);
if (pa->pick_left_primer) {
if (retval->fwd.num_elem == 0) {
fprintf(f, "NO LEFT PRIMER FOUND\n\n");
} else {
print_primers = 1;
}
}
if (pa->pick_internal_oligo) {
if (retval->intl.num_elem == 0) {
fprintf(f, "NO INTERNAL PROBE FOUND\n\n");
} else {
print_primers = 1;
}
}
if (pa->pick_right_primer) {
if (retval->rev.num_elem == 0) {
fprintf(f, "NO RIGHT PRIMER FOUND\n\n");
} else {
print_primers = 1;
}
}
if ((warning = p3_get_rv_and_gs_warnings(retval, pa)) != NULL) {
fprintf(f, "\nWARNING: %s\n", warning);
free(warning);
}
if ((pa->primer_task != pick_primer_list ) && (pa->primer_task != pick_sequencing_primers)) {
if (print_primers == 1) {
print_oligo_header(f, "OLIGO", print_lib_sim, pa->thermodynamic_alignment, sa->tar2.genotyping);
}
/* Print out the first line with the best primers */
if ((pa->pick_left_primer) && (&retval->fwd != NULL ) && (retval->fwd.num_elem > 0)) {
if(pa->modify_left_primer==1) {
print_oligo_Z(f, TITLE_MOD_LEFT, sa, retval->fwd.oligo, OT_LEFT, pa, pa->p_args.repeat_lib, print_lib_sim);
} else {
print_oligo_Z(f, TITLE_LEFT, sa, retval->fwd.oligo, OT_LEFT, pa, pa->p_args.repeat_lib, print_lib_sim);
}
h = retval->fwd.oligo;
rest_count = 1;
}
if ((pa->pick_internal_oligo) && (&retval->intl != NULL ) && (retval->intl.num_elem > 0)) {
if(pa->modify_internal_oligo==1) {
if((retval->intl.oligo)->oligo_dir==0) {
print_oligo_Z(f, TITLE_MOD_INTL_FW, sa, retval->intl.oligo, OT_INTL, pa, pa->p_args.repeat_lib, print_lib_sim);
} else if((retval->intl.oligo)->oligo_dir==1) {
print_oligo_Z(f, TITLE_MOD_INTL_RV, sa, retval->intl.oligo, OT_INTL, pa, pa->p_args.repeat_lib, print_lib_sim);
}
} else {
if((retval->intl.oligo)->oligo_dir==0) {
print_oligo_Z(f, TITLE_INTL_FW, sa, retval->intl.oligo, OT_INTL, pa, pa->p_args.repeat_lib, print_lib_sim);
} else if((retval->intl.oligo)->oligo_dir==1) {
print_oligo_Z(f, TITLE_INTL_RV, sa, retval->intl.oligo, OT_INTL, pa, pa->p_args.repeat_lib, print_lib_sim);
}
}
h = retval->intl.oligo;
rest_count = 1;
}
if ((pa->pick_right_primer) && (&retval->rev != NULL ) && (retval->rev.num_elem > 0)) {
if(pa->modify_right_primer==1) {
print_oligo_Z(f, TITLE_MOD_RIGHT, sa, retval->rev.oligo, OT_RIGHT, pa, pa->p_args.repeat_lib, print_lib_sim);
} else {
print_oligo_Z(f, TITLE_RIGHT, sa, retval->rev.oligo, OT_RIGHT, pa, pa->p_args.repeat_lib, print_lib_sim);
}
h = retval->rev.oligo;
rest_count = 1;
}
}
if(print_primers == 1) {
fprintf(f, "SEQUENCE SIZE: %ld\n", (long int) strlen(sa->sequence));
fprintf(f, "INCLUDED REGION SIZE: %d\n\n", sa->incl_l);
if(sa->tar2.genotyping==0) {
print_pair_array(f, "TARGETS", sa->tar2.count, sa->tar2.pairs, pa, sa);
} else if(sa->tar2.genotyping==1) {
fprintf(f,"TARGET VARIANT * (position,size):");
if(sa->tar2.char_count==sa->tar2.VAR_sequence_number) {
fprintf(f," %d,%d",sa->tar2.VAR_start[0],sa->tar2.char_num[sa->tar2.VAR_sequence_number]-1);
} else {
fprintf(f," %d,%d",sa->tar2.VAR_start[0],sa->tar2.char_num[sa->tar2.VAR_sequence_number]);
}
fprintf(f,"\n\n");
}
print_pair_array(f, "EXCLUDED REGIONS", sa->excl2.count, sa->excl2.pairs, pa, sa);
print_pair_array(f, "INTERNAL PROBE EXCLUDED REGIONS", sa->excl_internal2.count, sa->excl_internal2.pairs, pa, sa);
print_2_pair_array(f, "PAIR_OK_REGIONS", sa->ok_regions.count, sa->ok_regions.left_pairs, sa->ok_regions.right_pairs, pa, sa);
}
if (pa->primer_task != pick_primer_list ) {
if(pa->pick_internal_oligo==1) {
if(print_seq(f,pa,sa,retval,retval->intl.oligo,best_pairs,0)) exit(-2);
}
else if(pa->pick_left_primer==1) {
if(print_seq(f,pa,sa,retval,retval->fwd.oligo,best_pairs,0)) exit(-2);
}
else if(pa->pick_right_primer==1) {
if(print_seq(f,pa,sa,retval,retval->rev.oligo,best_pairs,0)) exit(-2);
}
else if (print_seq(f, pa, sa, retval, h, best_pairs, 0)) exit(-2); /* ENOMEM */
}
fprintf(f, "\n");
/* Print out the other primers */
if ((pa->pick_left_primer) && (&retval->fwd != NULL ) && (retval->fwd.num_elem > rest_count)) {
int n = retval->fwd.num_elem;
h = retval->fwd.oligo;
if (rest_count == 1) {
fprintf(f, "ADDITIONAL OLIGOS\n");
}
fprintf(f, " ");
print_oligo_header(f, "", print_lib_sim, pa->thermodynamic_alignment, sa->tar2.genotyping);
for (i = rest_count; i < pa->num_return; i++) {
if(i > n-1) break;
p = h + i;
fprintf(f, "%2d ", i + 1 - rest_count);
if(pa->modify_left_primer==1) {
print_oligo_Z(f, TITLE_MOD_LEFT, sa, p, OT_LEFT, pa, pa->p_args.repeat_lib, print_lib_sim);
} else {
print_oligo_Z(f, TITLE_LEFT, sa, p, OT_LEFT, pa, pa->p_args.repeat_lib, print_lib_sim);
}
}
if (rest_count == 0) {
fprintf(f, "\n ");
}
}
if ((pa->pick_internal_oligo) && (&retval->intl != NULL ) && (retval->intl.num_elem > rest_count)) {
int n = retval->intl.num_elem;
h = retval->intl.oligo;
if (rest_count == 1) {
fprintf(f, "ADDITIONAL OLIGOS\n");
}
fprintf(f, " ");
print_oligo_header(f, "", print_lib_sim, pa->thermodynamic_alignment, sa->tar2.genotyping);
for (i = rest_count; i < pa->num_return; i++) {
if(i > n-1) break;
p = h + i;
fprintf(f, "%2d ", i + 1 - rest_count);
if(pa->modify_internal_oligo==1) {
if(p->oligo_dir==0) {
print_oligo_Z(f, TITLE_MOD_INTL_FW, sa, p, OT_INTL, pa, pa->p_args.repeat_lib, print_lib_sim);
} else if(p->oligo_dir==1) {
print_oligo_Z(f, TITLE_MOD_INTL_RV, sa, p, OT_INTL, pa, pa->p_args.repeat_lib, print_lib_sim);
}
} else {
if(p->oligo_dir==0) {
print_oligo_Z(f, TITLE_INTL_FW, sa, p, OT_INTL, pa, pa->p_args.repeat_lib, print_lib_sim);
} else if(p->oligo_dir==1) {
print_oligo_Z(f, TITLE_INTL_RV, sa, p, OT_INTL, pa, pa->p_args.repeat_lib, print_lib_sim);
}
}
}
if (rest_count == 0) {
fprintf(f, "\n ");
}
}
if ((pa->pick_right_primer) && (&retval->rev != NULL ) && (retval->rev.num_elem > rest_count)) {
int n = retval->rev.num_elem;
h = retval->rev.oligo;
if (rest_count == 1) {
fprintf(f, "ADDITIONAL OLIGOS\n");
}
fprintf(f, " ");
print_oligo_header(f, "", print_lib_sim, pa->thermodynamic_alignment, sa->tar2.genotyping);
for (i = rest_count; i < pa->num_return; i++) {
if(i > n-1) break;
p = h + i;
fprintf(f, "%2d ", i + 1 - rest_count);
if(pa->modify_right_primer==1) {
print_oligo_Z(f, TITLE_MOD_RIGHT, sa, p, OT_RIGHT, pa, pa->p_args.repeat_lib, print_lib_sim);
} else {
print_oligo_Z(f, TITLE_RIGHT, sa, p, OT_RIGHT, pa, pa->p_args.repeat_lib, print_lib_sim);
}
}
}
if (explain_flag)
print_explain(f, pa, sa, retval, print_lib_sim, pr_release);
fprintf(f, "\n\n");
if (fflush(f) == EOF) {
perror("fflush(f) failed");
exit(-1);
}
}
static void explain(struct link_util *lu)
{
print_explain(lu, stderr);
}
static void macvlan_print_help(struct link_util *lu, int argc, char **argv,
FILE *f)
{
print_explain(lu, f);
}
/* Recursive help */
tvalue gen_cli_print_help(char *prog_name,gen_cli_argument *arg)
{
unsigned int arglen;
unsigned int rows,cols;
char *format_mand=" <%s>",*format_opt=" [%s]";
char *cmd_fmt=format_mand,*flag_fmt=format_mand;
ARG_ASSERT(!prog_name || !arg,FALSE);
print_out("\nUsage: ");
if(arg->cmd != NULL)
print_command_path(prog_name,arg);
else
print_out("%s",prog_name);
if(arg->helpcmdparameter != NULL)
print_out(" %s",arg->helpcmdparameter);
/* check if commands or flags are optional */
if(arg->flags & GEN_CLI_CMDS_OPTIONAL)
cmd_fmt=format_opt;
if(arg->flags & GEN_CLI_FLAGS_OPTIONAL)
flag_fmt=format_opt;
if(arg->subcmds)
print_out(cmd_fmt,"command");
if(arg->opt.options != NULL)
print_out(flag_fmt,"options");
if(arg->helpcmdextra != NULL)
print_out(" %s",arg->helpcmdextra);
print_out("\n\n");
get_win_size(&rows,&cols);
print_explain(0,arg->cmdhelp,cols);
print_out("\n\n");
arglen = getprintpos(arg);
/* print short descriptions of the subcommands */
if(arg->subcmds)
{
register unsigned int beta,gamma;
unsigned int curlen=0;
/*
if(arg->cmd != NULL)
print_out("Subc");
else
print_out("C");
*/
print_out("%sommands:\n", (arg->cmd) ? "Subc" : "C");
for(beta=0;arg->subcmds[beta];beta++)
{
curlen=PRINTSPACELEN + strlen(arg->subcmds[beta]->cmd);
print_out(PRINTSPACE "%s",arg->subcmds[beta]->cmd);
if(arg->subcmds[beta]->shortcmd != 0)
print_out(" (%c)",arg->subcmds[beta]->shortcmd);
for(gamma = curlen; gamma < arglen; gamma++)
print_out(" ");
print_explain(arglen-1,arg->subcmds[beta]->cmdhelp,cols);
}
print_out("\n");
}
/* print out the flags */
if(arg->opt.options)
{
print_out("Options:\n");
print_flags(arg->opt.options,arg->opt.help_strs,arglen,cols);
}
return TRUE;
}
