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* Option '--ipknot' sets optimized parameters for IPknot decoding.
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satoken committed Sep 15, 2012
1 parent 524759b commit 193d0d4
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Showing 4 changed files with 118 additions and 76 deletions.
103 changes: 64 additions & 39 deletions src/cmdline.c
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
/*
File autogenerated by gengetopt version 2.22.5
generated with the following command:
gengetopt --unamed
gengetopt -u
The developers of gengetopt consider the fixed text that goes in all
gengetopt output files to be in the public domain:
Expand Down Expand Up @@ -32,32 +32,33 @@ const char *gengetopt_args_info_usage = "Usage: " CMDLINE_PARSER_PACKAGE " [OPTI
const char *gengetopt_args_info_description = "";

const char *gengetopt_args_info_full_help[] = {
" -h, --help Print help and exit",
" --full-help Print help, including hidden options, and exit",
" -V, --version Print version and exit",
" -r, --refinement=INT The number of iteration of the iterative refinment \n (default=`0')",
" -w, --weight=FLOAT Weight of the expected accuracy score for secondary \n structures (default=`4.0')",
" --eta=FLOAT Initial step width for the subgradient optimization \n (default=`0.5')",
" -m, --max-iter=INT The maximum number of iteration of the subgradient \n optimization (default=`600')",
" -f, --fourway-pct=FLOAT Weight of four-way PCT (default=`0.0')",
" -v, --verbose=INT The level of verbose outputs (default=`0')",
" -h, --help Print help and exit",
" --full-help Print help, including hidden options, and exit",
" -V, --version Print version and exit",
" -r, --refinement=INT The number of iteration of the iterative refinment \n (default=`0')",
" -w, --weight=FLOAT Weight of the expected accuracy score for \n secondary structures (default=`4.0')",
" --eta=FLOAT Initial step width for the subgradient \n optimization (default=`0.5')",
" -m, --max-iter=INT The maximum number of iteration of the subgradient \n optimization (default=`600')",
" -f, --fourway-pct=FLOAT Weight of four-way PCT (default=`0.0')",
" -v, --verbose=INT The level of verbose outputs (default=`0')",
"\nOptions for alignments:",
" -a, --align-model=STRING Alignment model for calcualating matching \n probablities (possible values=\"CONTRAlign\", \n \"ProbCons\" default=`ProbCons')",
" -p, --align-pct=FLOAT Weight of PCT for matching probabilities \n (default=`0.25')",
" -u, --align-th=FLOAT Threshold for matching probabilities \n (default=`0.01')",
" --align-aux=FILENAME Load matching probability matrices from FILENAME",
" -a, --align-model=STRING Alignment model for calcualating matching \n probablities (possible values=\"CONTRAlign\", \n \"ProbCons\" default=`ProbCons')",
" -p, --align-pct=FLOAT Weight of PCT for matching probabilities \n (default=`0.25')",
" -u, --align-th=FLOAT Threshold for matching probabilities \n (default=`0.01')",
" --align-aux=FILENAME Load matching probability matrices from FILENAME",
"\nOptions for folding:",
" -s, --fold-model=STRING Folding model for calculating base-pairing \n probablities (possible values=\"Boltzmann\", \n \"Vienna\", \"CONTRAfold\" default=`Boltzmann')",
" -q, --fold-pct=FLOAT Weight of PCT for base-pairing probabilities \n (default=`0.25')",
" -t, --fold-th=FLOAT Threshold for base-pairing probabilities \n (default=`0.2')",
" -g, --gamma=FLOAT Specify the threshold for base-pairing \n probabilities by 1/(gamma+1))",
" --no-alifold No use of RNAalifold for calculating base-pairing \n probabilities (default=off)",
" -T, --fold-th1=FLOAT Threshold for base-pairing probabilities of the \n conclusive common secondary structures",
" -G, --gamma1=FLOAT Specify the threshold for base-pairing \n probabilities of the conclusive common secondary \n structuresby 1/(gamma+1))",
" --ipknot Use IPknot decoding (default=off)",
" --bp-update Use the iterative update of BPs (default=off)",
" --bp-update1 Use the iterative update of BPs for the final \n prediction (default=off)",
" --fold-aux=FILENAME Load base-pairing probability matrices from \n FILENAME",
" -s, --fold-model=STRING Folding model for calculating base-pairing \n probablities (possible values=\"Boltzmann\", \n \"Vienna\", \"CONTRAfold\" default=`Boltzmann')",
" --fold-decoder=STRING Decoder for common secondary structure prediction \n (possible values=\"Nussinov\", \"IPknot\" \n default=`Nussinov')",
" -q, --fold-pct=FLOAT Weight of PCT for base-pairing probabilities \n (default=`0.25')",
" -t, --fold-th=FLOAT Threshold for base-pairing probabilities \n (default=`0.2')",
" -g, --gamma=FLOAT Specify the threshold for base-pairing \n probabilities by 1/(gamma+1))",
" --no-alifold No use of RNAalifold for calculating base-pairing \n probabilities (default=off)",
" -T, --fold-th1=FLOAT Threshold for base-pairing probabilities of the \n conclusive common secondary structures",
" -G, --gamma1=FLOAT Specify the threshold for base-pairing \n probabilities of the conclusive common secondary \n structuresby 1/(gamma+1))",
" --ipknot Set optimized parameters for IPknot decoding \n (--fold-decoder=IPknot -g4,8 -G2,4 --bp-update1) \n (default=off)",
" --bp-update Use the iterative update of BPs (default=off)",
" --bp-update1 Use the iterative update of BPs for the final \n prediction (default=off)",
" --fold-aux=FILENAME Load base-pairing probability matrices from \n FILENAME",
0
};

Expand All @@ -75,9 +76,9 @@ init_help_array(void)
gengetopt_args_info_help[8] = gengetopt_args_info_full_help[12];
gengetopt_args_info_help[9] = gengetopt_args_info_full_help[14];
gengetopt_args_info_help[10] = gengetopt_args_info_full_help[15];
gengetopt_args_info_help[11] = gengetopt_args_info_full_help[17];
gengetopt_args_info_help[12] = gengetopt_args_info_full_help[20];
gengetopt_args_info_help[13] = gengetopt_args_info_full_help[22];
gengetopt_args_info_help[11] = gengetopt_args_info_full_help[18];
gengetopt_args_info_help[12] = gengetopt_args_info_full_help[21];
gengetopt_args_info_help[13] = gengetopt_args_info_full_help[23];
gengetopt_args_info_help[14] = 0;

}
Expand Down Expand Up @@ -105,6 +106,7 @@ cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *pro

const char *cmdline_parser_align_model_values[] = {"CONTRAlign", "ProbCons", 0}; /*< Possible values for align-model. */
const char *cmdline_parser_fold_model_values[] = {"Boltzmann", "Vienna", "CONTRAfold", 0}; /*< Possible values for fold-model. */
const char *cmdline_parser_fold_decoder_values[] = {"Nussinov", "IPknot", 0}; /*< Possible values for fold-decoder. */

static char *
gengetopt_strdup (const char *s);
Expand All @@ -126,6 +128,7 @@ void clear_given (struct gengetopt_args_info *args_info)
args_info->align_th_given = 0 ;
args_info->align_aux_given = 0 ;
args_info->fold_model_given = 0 ;
args_info->fold_decoder_given = 0 ;
args_info->fold_pct_given = 0 ;
args_info->fold_th_given = 0 ;
args_info->gamma_given = 0 ;
Expand Down Expand Up @@ -164,6 +167,8 @@ void clear_args (struct gengetopt_args_info *args_info)
args_info->align_aux_orig = NULL;
args_info->fold_model_arg = gengetopt_strdup ("Boltzmann");
args_info->fold_model_orig = NULL;
args_info->fold_decoder_arg = gengetopt_strdup ("Nussinov");
args_info->fold_decoder_orig = NULL;
args_info->fold_pct_arg = 0.25;
args_info->fold_pct_orig = NULL;
args_info->fold_th_arg = NULL;
Expand Down Expand Up @@ -202,24 +207,25 @@ void init_args_info(struct gengetopt_args_info *args_info)
args_info->align_th_help = gengetopt_args_info_full_help[12] ;
args_info->align_aux_help = gengetopt_args_info_full_help[13] ;
args_info->fold_model_help = gengetopt_args_info_full_help[15] ;
args_info->fold_pct_help = gengetopt_args_info_full_help[16] ;
args_info->fold_th_help = gengetopt_args_info_full_help[17] ;
args_info->fold_decoder_help = gengetopt_args_info_full_help[16] ;
args_info->fold_pct_help = gengetopt_args_info_full_help[17] ;
args_info->fold_th_help = gengetopt_args_info_full_help[18] ;
args_info->fold_th_min = 0;
args_info->fold_th_max = 0;
args_info->gamma_help = gengetopt_args_info_full_help[18] ;
args_info->gamma_help = gengetopt_args_info_full_help[19] ;
args_info->gamma_min = 0;
args_info->gamma_max = 0;
args_info->no_alifold_help = gengetopt_args_info_full_help[19] ;
args_info->fold_th1_help = gengetopt_args_info_full_help[20] ;
args_info->no_alifold_help = gengetopt_args_info_full_help[20] ;
args_info->fold_th1_help = gengetopt_args_info_full_help[21] ;
args_info->fold_th1_min = 0;
args_info->fold_th1_max = 0;
args_info->gamma1_help = gengetopt_args_info_full_help[21] ;
args_info->gamma1_help = gengetopt_args_info_full_help[22] ;
args_info->gamma1_min = 0;
args_info->gamma1_max = 0;
args_info->ipknot_help = gengetopt_args_info_full_help[22] ;
args_info->bp_update_help = gengetopt_args_info_full_help[23] ;
args_info->bp_update1_help = gengetopt_args_info_full_help[24] ;
args_info->fold_aux_help = gengetopt_args_info_full_help[25] ;
args_info->ipknot_help = gengetopt_args_info_full_help[23] ;
args_info->bp_update_help = gengetopt_args_info_full_help[24] ;
args_info->bp_update1_help = gengetopt_args_info_full_help[25] ;
args_info->fold_aux_help = gengetopt_args_info_full_help[26] ;

}

Expand Down Expand Up @@ -372,6 +378,8 @@ cmdline_parser_release (struct gengetopt_args_info *args_info)
free_string_field (&(args_info->align_aux_orig));
free_string_field (&(args_info->fold_model_arg));
free_string_field (&(args_info->fold_model_orig));
free_string_field (&(args_info->fold_decoder_arg));
free_string_field (&(args_info->fold_decoder_orig));
free_string_field (&(args_info->fold_pct_orig));
free_multiple_field (args_info->fold_th_given, (void *)(args_info->fold_th_arg), &(args_info->fold_th_orig));
args_info->fold_th_arg = 0;
Expand Down Expand Up @@ -495,6 +503,8 @@ cmdline_parser_dump(FILE *outfile, struct gengetopt_args_info *args_info)
write_into_file(outfile, "align-aux", args_info->align_aux_orig, 0);
if (args_info->fold_model_given)
write_into_file(outfile, "fold-model", args_info->fold_model_orig, cmdline_parser_fold_model_values);
if (args_info->fold_decoder_given)
write_into_file(outfile, "fold-decoder", args_info->fold_decoder_orig, cmdline_parser_fold_decoder_values);
if (args_info->fold_pct_given)
write_into_file(outfile, "fold-pct", args_info->fold_pct_orig, 0);
write_multiple_into_file(outfile, args_info->fold_th_given, "fold-th", args_info->fold_th_orig, 0);
Expand Down Expand Up @@ -1109,6 +1119,7 @@ cmdline_parser_internal (
{ "align-th", 1, NULL, 'u' },
{ "align-aux", 1, NULL, 0 },
{ "fold-model", 1, NULL, 's' },
{ "fold-decoder", 1, NULL, 0 },
{ "fold-pct", 1, NULL, 'q' },
{ "fold-th", 1, NULL, 't' },
{ "gamma", 1, NULL, 'g' },
Expand Down Expand Up @@ -1329,6 +1340,20 @@ cmdline_parser_internal (
additional_error))
goto failure;

}
/* Decoder for common secondary structure prediction. */
else if (strcmp (long_options[option_index].name, "fold-decoder") == 0)
{


if (update_arg( (void *)&(args_info->fold_decoder_arg),
&(args_info->fold_decoder_orig), &(args_info->fold_decoder_given),
&(local_args_info.fold_decoder_given), optarg, cmdline_parser_fold_decoder_values, "Nussinov", ARG_STRING,
check_ambiguity, override, 0, 0,
"fold-decoder", '-',
additional_error))
goto failure;

}
/* No use of RNAalifold for calculating base-pairing probabilities. */
else if (strcmp (long_options[option_index].name, "no-alifold") == 0)
Expand All @@ -1342,7 +1367,7 @@ cmdline_parser_internal (
goto failure;

}
/* Use IPknot decoding. */
/* Set optimized parameters for IPknot decoding (--fold-decoder=IPknot -g4,8 -G2,4 --bp-update1). */
else if (strcmp (long_options[option_index].name, "ipknot") == 0)
{

Expand Down
9 changes: 7 additions & 2 deletions src/cmdline.h
View file
Original file line number Diff line number Diff line change
Expand Up @@ -77,6 +77,9 @@ struct gengetopt_args_info
char * fold_model_arg; /**< @brief Folding model for calculating base-pairing probablities (default='Boltzmann'). */
char * fold_model_orig; /**< @brief Folding model for calculating base-pairing probablities original value given at command line. */
const char *fold_model_help; /**< @brief Folding model for calculating base-pairing probablities help description. */
char * fold_decoder_arg; /**< @brief Decoder for common secondary structure prediction (default='Nussinov'). */
char * fold_decoder_orig; /**< @brief Decoder for common secondary structure prediction original value given at command line. */
const char *fold_decoder_help; /**< @brief Decoder for common secondary structure prediction help description. */
float fold_pct_arg; /**< @brief Weight of PCT for base-pairing probabilities (default='0.25'). */
char * fold_pct_orig; /**< @brief Weight of PCT for base-pairing probabilities original value given at command line. */
const char *fold_pct_help; /**< @brief Weight of PCT for base-pairing probabilities help description. */
Expand All @@ -102,8 +105,8 @@ struct gengetopt_args_info
unsigned int gamma1_min; /**< @brief Specify the threshold for base-pairing probabilities of the conclusive common secondary structuresby 1/(gamma+1))'s minimum occurreces */
unsigned int gamma1_max; /**< @brief Specify the threshold for base-pairing probabilities of the conclusive common secondary structuresby 1/(gamma+1))'s maximum occurreces */
const char *gamma1_help; /**< @brief Specify the threshold for base-pairing probabilities of the conclusive common secondary structuresby 1/(gamma+1)) help description. */
int ipknot_flag; /**< @brief Use IPknot decoding (default=off). */
const char *ipknot_help; /**< @brief Use IPknot decoding help description. */
int ipknot_flag; /**< @brief Set optimized parameters for IPknot decoding (--fold-decoder=IPknot -g4,8 -G2,4 --bp-update1) (default=off). */
const char *ipknot_help; /**< @brief Set optimized parameters for IPknot decoding (--fold-decoder=IPknot -g4,8 -G2,4 --bp-update1) help description. */
int bp_update_flag; /**< @brief Use the iterative update of BPs (default=off). */
const char *bp_update_help; /**< @brief Use the iterative update of BPs help description. */
int bp_update1_flag; /**< @brief Use the iterative update of BPs for the final prediction (default=off). */
Expand All @@ -126,6 +129,7 @@ struct gengetopt_args_info
unsigned int align_th_given ; /**< @brief Whether align-th was given. */
unsigned int align_aux_given ; /**< @brief Whether align-aux was given. */
unsigned int fold_model_given ; /**< @brief Whether fold-model was given. */
unsigned int fold_decoder_given ; /**< @brief Whether fold-decoder was given. */
unsigned int fold_pct_given ; /**< @brief Whether fold-pct was given. */
unsigned int fold_th_given ; /**< @brief Whether fold-th was given. */
unsigned int gamma_given ; /**< @brief Whether gamma was given. */
Expand Down Expand Up @@ -268,6 +272,7 @@ int cmdline_parser_required (struct gengetopt_args_info *args_info,

extern const char *cmdline_parser_align_model_values[]; /**< @brief Possible values for align-model. */
extern const char *cmdline_parser_fold_model_values[]; /**< @brief Possible values for fold-model. */
extern const char *cmdline_parser_fold_decoder_values[]; /**< @brief Possible values for fold-decoder. */


#ifdef __cplusplus
Expand Down
76 changes: 42 additions & 34 deletions src/dafs.cpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -1545,58 +1545,66 @@ parse_options(int& argc, char**& argv)
s_model_ = new CONTRAfold(CUTOFF);
assert(s_model_!=NULL);

if (args_info.fold_th_given==0)
{
th_s_.resize(1);
th_s_[0] = args_info.fold_th_arg[0];
}
else
VF th_s1;
if (args_info.fold_th_given)
{
th_s_.resize(args_info.fold_th_given);
std::copy(args_info.fold_th_arg, args_info.fold_th_arg+th_s_.size(), th_s_.begin());
}
if (args_info.gamma_given!=0)
else if (args_info.gamma_given)
{
th_s_.resize(args_info.gamma_given);
for (uint i=0; i!=th_s_.size(); ++i)
th_s_[i] = 1.0/(1.0+args_info.gamma_arg[i]);
}
else if (args_info.ipknot_flag)
{
th_s_.resize(2);
th_s_[0] = 1.0/(1.0+4.0);
th_s_[1] = 1.0/(1.0+8.0);
}
else
{
th_s_.resize(1);
th_s_[0] = args_info.fold_th_arg[0];
}

if (args_info.ipknot_flag==0)
if (args_info.fold_th1_given)
{
s_decoder_ = new SparseNussinov(w_, th_s_[0]);
if (args_info.fold_th1_given)
s_decoder1_ = new SparseNussinov(w_, args_info.fold_th1_arg[0]);
else if (args_info.gamma1_given)
s_decoder1_ = new SparseNussinov(w_, 1.0/(1.0+args_info.gamma1_arg[0]));
else
s_decoder1_ = new SparseNussinov(w_, th_s_[0]);
th_s1.resize(args_info.fold_th1_given);
std::copy(args_info.fold_th1_arg, args_info.fold_th1_arg+args_info.fold_th1_given, th_s1.begin());
}
else if (args_info.gamma1_given)
{
th_s1.resize(args_info.gamma1_given);
for (uint i=0; i!=th_s1.size(); ++i)
th_s1[i] = 1.0/(1.0+args_info.gamma1_arg[i]);
}
else if (args_info.ipknot_flag)
{
th_s1.resize(2);
th_s1[0] = 1.0/(1.0+2.0);
th_s1[1] = 1.0/(1.0+4.0);
}
else
{
th_s1=th_s_;
}

if (strcasecmp(args_info.fold_decoder_arg, "IPknot")==0 || args_info.ipknot_flag)
{
s_decoder_ = new IPknot(w_, th_s_);
if (args_info.fold_th1_given)
{
VF th(args_info.fold_th1_given);
std::copy(args_info.fold_th1_arg, args_info.fold_th1_arg+args_info.fold_th1_given, th.begin());
s_decoder1_ = new IPknot(w_, th);
}
else if (args_info.gamma1_given)
{
VF th(args_info.gamma1_given);
for (uint i=0; i!=th.size(); ++i)
th[i] = 1.0/(1.0+args_info.gamma1_arg[i]);
s_decoder1_ = new IPknot(w_, th);
}
else
s_decoder1_ = new IPknot(w_, th_s_);
s_decoder1_ = new IPknot(w_, th_s1);
}
else if (strcasecmp(args_info.fold_decoder_arg, "Nussinov")==0)
{
s_decoder_ = new SparseNussinov(w_, th_s_[0]);
s_decoder1_ = new SparseNussinov(w_, th_s1[0]);
}
assert(s_decoder_!=NULL);

use_bp_update_ = args_info.bp_update_flag!=0;
if (args_info.bp_update1_given)
use_bp_update1_ = args_info.bp_update1_flag!=0;
else
use_bp_update1_ = use_bp_update_;
use_bp_update1_ = args_info.bp_update1_flag!=0 ^ args_info.ipknot_flag!=0;

if (args_info.inputs_num==0)
{
Expand Down
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