| /dports/biology/iqtree/IQ-TREE-2.0.6/alignment/ |
| H A D | alignmentpairwise.cpp | 26 pair_freq = NULL; in AlignmentPairwise()
35 pair_freq = NULL; in AlignmentPairwise()
43 pair_freq = new double[total_size]; in AlignmentPairwise()
44 memset(pair_freq, 0, sizeof(double)*total_size); in AlignmentPairwise()
57 pair_freq = new double[num_states * num_states]; in AlignmentPairwise()
72 double *pair_pos = pair_freq + (cat*num_states*num_states); in addPattern()
143 double *pair_pos = pair_freq + cat*trans_size; in computeFunction()
166 lh -= pair_freq[i] * log(sum_trans_mat[i]); in computeFunction()
234 double *pair_pos = pair_freq + cat*trans_size; in computeFuncDerv()
286 df -= pair_freq[i] * d1; in computeFuncDerv()
[all …]
|
| H A D | alignmentpairwise.h | 93 double *pair_freq; variable
|
| H A D | superalignment.h | 125 …virtual void computeDivergenceMatrix(double *pair_freq, double *state_freq, bool normalize = true);
|
| H A D | alignment.cpp | 4532 ASSERT(pair_freq); in computeDivergenceMatrix()
4534 memset(pair_freq, 0, sizeof(double)*num_states*num_states); in computeDivergenceMatrix()
4548 double *pair_freq_ptr = pair_freq + (i*num_states); in computeDivergenceMatrix()
4558 pair_freq[j*num_states+i] = pair_freq[i*num_states+j]; in computeDivergenceMatrix()
4569 double *pair_freq_ptr = pair_freq + (i*num_states); in computeDivergenceMatrix()
4656 MatrixXd pair_freq = MatrixXd::Zero(num_states, num_states); in doSymTest() local
4660 pair_freq(it->at(seq1), it->at(seq2))++; in doSymTest()
4669 double divergence = pair_freq.sum() - pair_freq.diagonal().sum(); in doSymTest()
4683 MatrixXd sum = (pair_freq + pair_freq.transpose()); in doSymTest()
4684 ArrayXXd res = (pair_freq - pair_freq.transpose()).array().square() / sum.array(); in doSymTest()
[all …]
|
| H A D | alignment.h | 703 …virtual void computeDivergenceMatrix(double *pair_freq, double *state_freq, bool normalize = true);
|
| H A D | superalignment.cpp | 1080 void SuperAlignment::computeDivergenceMatrix(double *pair_freq, double *state_freq, bool normalize)… in computeDivergenceMatrix() argument
1083 memset(pair_freq, 0, sizeof(double)*nstates2); in computeDivergenceMatrix()
1093 pair_freq[i] += part_pair_freq[i]; in computeDivergenceMatrix()
1106 double *pair_freq_ptr = pair_freq + (i*nstates); in computeDivergenceMatrix()
|
| /dports/biology/iqtree/IQ-TREE-2.0.6/obsolete/ |
| H A D | ngs.cpp | 45 pair_freq = new double[total_size]; in NGSAlignment()
52 pair_freq = new double[nstate*nstate]; in NGSAlignment()
89 pair_freq = new double[total_size]; in readFritzFile()
94 pair_freq[i] = count; in readFritzFile()
117 state_count[i] += pair_freq[id]; in computeStateFreq()
118 state_count[j] += pair_freq[id]; in computeStateFreq()
536 df -= pair_freq[i] * d1; in computeFuncDerv()
761 while (id >= pair_freq.size()) { in processReadWhileParsing()
764 pair_freq.push_back(pair_pos); in processReadWhileParsing()
766 pair_pos = pair_freq[id]; in processReadWhileParsing()
[all …]
|
| H A D | ngs.h | 417 vector<double*> pair_freq; variable
|
| /dports/biology/iqtree/IQ-TREE-2.0.6/model/ |
| H A D | ratemeyerdiscrete.cpp | 289 int *pair_freq = new int[trans_size]; in computeFunction() local
293 memset(pair_freq, 0, trans_size * sizeof(int)); in computeFunction()
301 for (k = 0; k < trans_size; k++) if (pair_freq[k]) in computeFunction()
302 lh -= pair_freq[k] * log(trans_mat[k]); in computeFunction()
304 delete [] pair_freq; in computeFunction()
326 int *pair_freq = new int[trans_size]; in computeFuncDerv() local
330 memset(pair_freq, 0, trans_size * sizeof(int)); in computeFuncDerv()
340 for (k = 0; k < trans_size; k++) if (pair_freq[k]) { in computeFuncDerv()
346 derv1 += trans_derv1[k] * pair_freq[k]; in computeFuncDerv()
347 derv2 += trans_derv2[k] * pair_freq[k]; in computeFuncDerv()
[all …]
|
| H A D | partitionmodel.cpp | 88 double *pair_freq = new double[nstates * nstates]; in PartitionModel() local
90 tree->aln->computeDivergenceMatrix(pair_freq, state_freq); in PartitionModel()
100 ((ModelMarkov*)linked_models.begin()->second)->setFullRateMatrix(pair_freq, state_freq); in PartitionModel()
103 delete [] pair_freq; in PartitionModel()
|
| /dports/databases/mariadb104-server/mariadb-10.4.24/storage/mroonga/vendor/groonga/plugins/suggest/ |
| H A D | suggest.c | 163 grn_obj post, pair_freq, item_freq, item_freq2, item_boost; in cooccurrence_search() local
165 GRN_INT32_INIT(&pair_freq, 0); in cooccurrence_search()
174 GRN_BULK_REWIND(&pair_freq); in cooccurrence_search()
179 grn_obj_get_value(ctx, pairs_freq, p->rid, &pair_freq); in cooccurrence_search()
184 pfreq = GRN_INT32_VALUE(&pair_freq); in cooccurrence_search()
213 GRN_OBJ_FIN(ctx, &pair_freq); in cooccurrence_search()
|
| /dports/databases/mariadb104-client/mariadb-10.4.24/storage/mroonga/vendor/groonga/plugins/suggest/ |
| H A D | suggest.c | 163 grn_obj post, pair_freq, item_freq, item_freq2, item_boost; in cooccurrence_search() local
165 GRN_INT32_INIT(&pair_freq, 0); in cooccurrence_search()
174 GRN_BULK_REWIND(&pair_freq); in cooccurrence_search()
179 grn_obj_get_value(ctx, pairs_freq, p->rid, &pair_freq); in cooccurrence_search()
184 pfreq = GRN_INT32_VALUE(&pair_freq); in cooccurrence_search()
213 GRN_OBJ_FIN(ctx, &pair_freq); in cooccurrence_search()
|
| /dports/databases/mariadb103-client/mariadb-10.3.34/storage/mroonga/vendor/groonga/plugins/suggest/ |
| H A D | suggest.c | 163 grn_obj post, pair_freq, item_freq, item_freq2, item_boost; in cooccurrence_search() local
165 GRN_INT32_INIT(&pair_freq, 0); in cooccurrence_search()
174 GRN_BULK_REWIND(&pair_freq); in cooccurrence_search()
179 grn_obj_get_value(ctx, pairs_freq, p->rid, &pair_freq); in cooccurrence_search()
184 pfreq = GRN_INT32_VALUE(&pair_freq); in cooccurrence_search()
213 GRN_OBJ_FIN(ctx, &pair_freq); in cooccurrence_search()
|
| /dports/databases/mariadb105-client/mariadb-10.5.15/storage/mroonga/vendor/groonga/plugins/suggest/ |
| H A D | suggest.c | 163 grn_obj post, pair_freq, item_freq, item_freq2, item_boost; in cooccurrence_search() local
165 GRN_INT32_INIT(&pair_freq, 0); in cooccurrence_search()
174 GRN_BULK_REWIND(&pair_freq); in cooccurrence_search()
179 grn_obj_get_value(ctx, pairs_freq, p->rid, &pair_freq); in cooccurrence_search()
184 pfreq = GRN_INT32_VALUE(&pair_freq); in cooccurrence_search()
213 GRN_OBJ_FIN(ctx, &pair_freq); in cooccurrence_search()
|
| /dports/databases/mariadb103-server/mariadb-10.3.34/storage/mroonga/vendor/groonga/plugins/suggest/ |
| H A D | suggest.c | 163 grn_obj post, pair_freq, item_freq, item_freq2, item_boost; in cooccurrence_search() local
165 GRN_INT32_INIT(&pair_freq, 0); in cooccurrence_search()
174 GRN_BULK_REWIND(&pair_freq); in cooccurrence_search()
179 grn_obj_get_value(ctx, pairs_freq, p->rid, &pair_freq); in cooccurrence_search()
184 pfreq = GRN_INT32_VALUE(&pair_freq); in cooccurrence_search()
213 GRN_OBJ_FIN(ctx, &pair_freq); in cooccurrence_search()
|
| /dports/databases/mariadb105-server/mariadb-10.5.15/storage/mroonga/vendor/groonga/plugins/suggest/ |
| H A D | suggest.c | 163 grn_obj post, pair_freq, item_freq, item_freq2, item_boost; in cooccurrence_search() local
165 GRN_INT32_INIT(&pair_freq, 0); in cooccurrence_search()
174 GRN_BULK_REWIND(&pair_freq); in cooccurrence_search()
179 grn_obj_get_value(ctx, pairs_freq, p->rid, &pair_freq); in cooccurrence_search()
184 pfreq = GRN_INT32_VALUE(&pair_freq); in cooccurrence_search()
213 GRN_OBJ_FIN(ctx, &pair_freq); in cooccurrence_search()
|