/dports/biology/abyss/abyss-2.3.1/dialign/ |
H A D | alig.c | 103 algn->algn[i][j].predFPos = -1; in create_empty_alignment() 106 algn->algn[i][j].eqcParent= &(algn->algn[i][j]); in create_empty_alignment() 108 algn->algn[i][j].eqcRank= 0; in create_empty_alignment() 114 *algn->algn[i][j].proceed = 0; in create_empty_alignment() 116 algn->algn[i][j].predF = NULL; in create_empty_alignment() 117 algn->algn[i][j].succF = NULL; in create_empty_alignment() 119 algn->algn[i][j].row = i; in create_empty_alignment() 120 algn->algn[i][j].col = j; in create_empty_alignment() 156 apos = &(algn->algn[i][j]); in free_alignment() 184 free(algn->algn[i]); in free_alignment() [all …]
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H A D | museq.c | 55 extern void free_alignment(struct alignment *algn); 61 struct alignment *algn, int round); 151 struct alignment *algn= NULL; in main() local 153 algn = create_empty_alignment(in_seq_col); in main() 280 if(! para->FAST_MODE) free_alignment(algn); in main() 281 algn = salgn; in main() 290 simple_print_alignment_dna_retranslate(algn); in main() 292 simple_print_alignment_default(algn); in main() 295 simple_print_alignment_default(algn); in main() 303 fasta_print_alignment_default(algn, para->out_file); in main() [all …]
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H A D | io.c | 563 struct algn_pos **ap = algn->algn; in simple_print_alignment_default() 572 prepare_alignment(algn); in simple_print_alignment_default() 573 max = algn->max_pos; in simple_print_alignment_default() 641 struct algn_pos **ap = algn->algn; in simple_print_alignment_dna_retranslate() 650 max = algn->max_pos; in simple_print_alignment_dna_retranslate() 719 struct algn_pos **ap = algn->algn; in fasta_print_alignment_default() 722 max = algn->max_pos; in fasta_print_alignment_default() 730 max = algn->max_pos; in fasta_print_alignment_default() 767 struct algn_pos **ap = algn->algn; in fasta_print_alignment_dna_retranslate() 770 max = algn->max_pos; in fasta_print_alignment_dna_retranslate() [all …]
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H A D | assemble.c | 29 struct alignment *algn, 99 char o1 = algn->seq_is_orphane[s1]; in fit_fpos_diag() 100 char o2 = algn->seq_is_orphane[s2]; in fit_fpos_diag() 109 struct algn_pos **ap=algn->algn; in fit_fpos_diag() 176 char o1 = algn->seq_is_orphane[s1]; in adapt_diag() 177 char o2 = algn->seq_is_orphane[s2]; in adapt_diag() 186 struct algn_pos **ap=algn->algn; in adapt_diag() 664 ap1_1 = find_eqc(algn->algn, s1_1, p1_1); in confl_diag() 665 ap1_2 = find_eqc(algn->algn, s1_2, p1_2); in confl_diag() 758 ap2_1 = find_eqc(algn->algn, s2_1, p2_1); in confl_diag() [all …]
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H A D | io.h | 34 void simple_print_alignment_default(struct alignment *algn); 35 void simple_print_alignment_dna_retranslate(struct alignment *algn); 37 void fasta_print_alignment_default(struct alignment *algn, char *filename); 38 void fasta_print_alignment_dna_retranslate(struct alignment *algn, char *filename);
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/dports/biology/sra-tools/sra-tools-2.11.0/tools/cg-load/ |
H A D | writer-evidence-dnbs.c | 82 TableWriterAlgnData algn; member 107 self->algn.seq_spot_id.elements = 1; in CGWriterEvdDnbs_Make() 109 self->algn.seq_read_id.elements = 1; in CGWriterEvdDnbs_Make() 116 self->algn.ref_id.buffer = &self->match.ref_id; in CGWriterEvdDnbs_Make() 117 self->algn.ref_id.elements = 1; in CGWriterEvdDnbs_Make() 119 self->algn.ref_start.elements = 1; in CGWriterEvdDnbs_Make() 123 self->algn.ref_orientation.elements = 1; in CGWriterEvdDnbs_Make() 125 self->algn.ref_ploidy.elements = 1; in CGWriterEvdDnbs_Make() 126 self->algn.mapq.buffer = &self->match.mapq; in CGWriterEvdDnbs_Make() 127 self->algn.mapq.elements = 1; in CGWriterEvdDnbs_Make() [all …]
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H A D | writer-evidence-intervals.c | 69 TableWriterAlgnData algn; member 97 self->algn.ref_id.buffer = &self->match.ref_id; in CGWriterEvdInt_Make() 98 self->algn.ref_id.elements = 1; in CGWriterEvdInt_Make() 100 self->algn.ref_start.elements = 1; in CGWriterEvdInt_Make() 103 self->algn.ref_orientation.elements = 1; in CGWriterEvdInt_Make() 104 self->algn.mapq.buffer = &self->match.mapq; in CGWriterEvdInt_Make() 105 self->algn.mapq.elements = 1; in CGWriterEvdInt_Make() 153 self->algn.ploidy = 0; in CGWriterEvdInt_Write() 176 self->algn.ploidy = 0; in CGWriterEvdInt_Write() 211 self->algn.ploidy = 0; in CGWriterEvdInt_Write() [all …]
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H A D | writer-algn.c | 75 TableWriterAlgnData algn[CG_MAPPINGS_MAX]; member 111 self->algn[i].seq_spot_id.elements = 1; in CGWriterAlgn_Make() 114 self->algn[i].seq_read_id.elements = 1; in CGWriterAlgn_Make() 135 self->algn[i].ref_orientation.elements = 1; in CGWriterAlgn_Make() 138 self->algn[i].mapq.elements = 1; in CGWriterAlgn_Make() 144 self->algn[i].mate_ref_id.elements = 1; in CGWriterAlgn_Make() 147 self->algn[i].mate_ref_pos.elements = 1; in CGWriterAlgn_Make() 150 self->algn[i].template_len.elements = 1; in CGWriterAlgn_Make() 198 TableWriterAlgnData *const algn = &self->algn[mate]; in CGWriterAlgn_Save() local 260 algn->ploidy = 0; in CGWriterAlgn_Save() [all …]
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/dports/devel/binutils/binutils-2.37/gas/testsuite/gas/ppc/ |
H A D | test1xcoff32.d | 23 AUX val 8 prmhsh 0 snhsh 0 typ 1 algn 2 clss 1 stb 0 snstb 0 25 AUX val 96 prmhsh 0 snhsh 0 typ 1 algn 2 clss 0 stb 0 snstb 0 27 AUX indx 4 prmhsh 0 snhsh 0 typ 2 algn 0 clss 0 stb 0 snstb 0 29 AUX indx 4 prmhsh 0 snhsh 0 typ 2 algn 0 clss 0 stb 0 snstb 0 31 AUX indx 4 prmhsh 0 snhsh 0 typ 2 algn 0 clss 0 stb 0 snstb 0 33 AUX indx 4 prmhsh 0 snhsh 0 typ 2 algn 0 clss 0 stb 0 snstb 0 35 AUX indx 4 prmhsh 0 snhsh 0 typ 2 algn 0 clss 0 stb 0 snstb 0 37 AUX val 12 prmhsh 0 snhsh 0 typ 1 algn 2 clss 5 stb 0 snstb 0 41 AUX val 4 prmhsh 0 snhsh 0 typ 1 algn 2 clss 3 stb 0 snstb 0 43 AUX val 4 prmhsh 0 snhsh 0 typ 1 algn 2 clss 3 stb 0 snstb 0 [all …]
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/dports/lang/gnatdroid-binutils-x86/binutils-2.27/gas/testsuite/gas/ppc/ |
H A D | test1xcoff32.d | 23 AUX val 8 prmhsh 0 snhsh 0 typ 1 algn 2 clss 1 stb 0 snstb 0 25 AUX val 96 prmhsh 0 snhsh 0 typ 1 algn 2 clss 0 stb 0 snstb 0 27 AUX indx 4 prmhsh 0 snhsh 0 typ 2 algn 0 clss 0 stb 0 snstb 0 29 AUX indx 4 prmhsh 0 snhsh 0 typ 2 algn 0 clss 0 stb 0 snstb 0 31 AUX indx 4 prmhsh 0 snhsh 0 typ 2 algn 0 clss 0 stb 0 snstb 0 33 AUX indx 4 prmhsh 0 snhsh 0 typ 2 algn 0 clss 0 stb 0 snstb 0 35 AUX indx 4 prmhsh 0 snhsh 0 typ 2 algn 0 clss 0 stb 0 snstb 0 37 AUX val 12 prmhsh 0 snhsh 0 typ 1 algn 2 clss 5 stb 0 snstb 0 41 AUX val 4 prmhsh 0 snhsh 0 typ 1 algn 2 clss 3 stb 0 snstb 0 43 AUX val 4 prmhsh 0 snhsh 0 typ 1 algn 2 clss 3 stb 0 snstb 0 [all …]
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/dports/devel/arm-elf-binutils/binutils-2.37/gas/testsuite/gas/ppc/ |
H A D | test1xcoff32.d | 23 AUX val 8 prmhsh 0 snhsh 0 typ 1 algn 2 clss 1 stb 0 snstb 0 25 AUX val 96 prmhsh 0 snhsh 0 typ 1 algn 2 clss 0 stb 0 snstb 0 27 AUX indx 4 prmhsh 0 snhsh 0 typ 2 algn 0 clss 0 stb 0 snstb 0 29 AUX indx 4 prmhsh 0 snhsh 0 typ 2 algn 0 clss 0 stb 0 snstb 0 31 AUX indx 4 prmhsh 0 snhsh 0 typ 2 algn 0 clss 0 stb 0 snstb 0 33 AUX indx 4 prmhsh 0 snhsh 0 typ 2 algn 0 clss 0 stb 0 snstb 0 35 AUX indx 4 prmhsh 0 snhsh 0 typ 2 algn 0 clss 0 stb 0 snstb 0 37 AUX val 12 prmhsh 0 snhsh 0 typ 1 algn 2 clss 5 stb 0 snstb 0 41 AUX val 4 prmhsh 0 snhsh 0 typ 1 algn 2 clss 3 stb 0 snstb 0 43 AUX val 4 prmhsh 0 snhsh 0 typ 1 algn 2 clss 3 stb 0 snstb 0 [all …]
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/dports/devel/gnulibiberty/binutils-2.37/gas/testsuite/gas/ppc/ |
H A D | test1xcoff32.d | 23 AUX val 8 prmhsh 0 snhsh 0 typ 1 algn 2 clss 1 stb 0 snstb 0 25 AUX val 96 prmhsh 0 snhsh 0 typ 1 algn 2 clss 0 stb 0 snstb 0 27 AUX indx 4 prmhsh 0 snhsh 0 typ 2 algn 0 clss 0 stb 0 snstb 0 29 AUX indx 4 prmhsh 0 snhsh 0 typ 2 algn 0 clss 0 stb 0 snstb 0 31 AUX indx 4 prmhsh 0 snhsh 0 typ 2 algn 0 clss 0 stb 0 snstb 0 33 AUX indx 4 prmhsh 0 snhsh 0 typ 2 algn 0 clss 0 stb 0 snstb 0 35 AUX indx 4 prmhsh 0 snhsh 0 typ 2 algn 0 clss 0 stb 0 snstb 0 37 AUX val 12 prmhsh 0 snhsh 0 typ 1 algn 2 clss 5 stb 0 snstb 0 41 AUX val 4 prmhsh 0 snhsh 0 typ 1 algn 2 clss 3 stb 0 snstb 0 43 AUX val 4 prmhsh 0 snhsh 0 typ 1 algn 2 clss 3 stb 0 snstb 0 [all …]
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/dports/devel/zpu-gcc/zpu-toolchain-1.0/toolchain/binutils/gas/testsuite/gas/ppc/ |
H A D | test1xcoff32.d | 23 AUX val 8 prmhsh 0 snhsh 0 typ 1 algn 2 clss 1 stb 0 snstb 0 25 AUX val 96 prmhsh 0 snhsh 0 typ 1 algn 2 clss 0 stb 0 snstb 0 27 AUX indx 4 prmhsh 0 snhsh 0 typ 2 algn 0 clss 0 stb 0 snstb 0 29 AUX indx 4 prmhsh 0 snhsh 0 typ 2 algn 0 clss 0 stb 0 snstb 0 31 AUX indx 4 prmhsh 0 snhsh 0 typ 2 algn 0 clss 0 stb 0 snstb 0 33 AUX indx 4 prmhsh 0 snhsh 0 typ 2 algn 0 clss 0 stb 0 snstb 0 35 AUX indx 4 prmhsh 0 snhsh 0 typ 2 algn 0 clss 0 stb 0 snstb 0 37 AUX val 12 prmhsh 0 snhsh 0 typ 1 algn 2 clss 5 stb 0 snstb 0 41 AUX val 4 prmhsh 0 snhsh 0 typ 1 algn 2 clss 3 stb 0 snstb 0 43 AUX val 4 prmhsh 0 snhsh 0 typ 1 algn 2 clss 3 stb 0 snstb 0 [all …]
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/dports/lang/gnatdroid-binutils/binutils-2.27/gas/testsuite/gas/ppc/ |
H A D | test1xcoff32.d | 23 AUX val 8 prmhsh 0 snhsh 0 typ 1 algn 2 clss 1 stb 0 snstb 0 25 AUX val 96 prmhsh 0 snhsh 0 typ 1 algn 2 clss 0 stb 0 snstb 0 27 AUX indx 4 prmhsh 0 snhsh 0 typ 2 algn 0 clss 0 stb 0 snstb 0 29 AUX indx 4 prmhsh 0 snhsh 0 typ 2 algn 0 clss 0 stb 0 snstb 0 31 AUX indx 4 prmhsh 0 snhsh 0 typ 2 algn 0 clss 0 stb 0 snstb 0 33 AUX indx 4 prmhsh 0 snhsh 0 typ 2 algn 0 clss 0 stb 0 snstb 0 35 AUX indx 4 prmhsh 0 snhsh 0 typ 2 algn 0 clss 0 stb 0 snstb 0 37 AUX val 12 prmhsh 0 snhsh 0 typ 1 algn 2 clss 5 stb 0 snstb 0 41 AUX val 4 prmhsh 0 snhsh 0 typ 1 algn 2 clss 3 stb 0 snstb 0 43 AUX val 4 prmhsh 0 snhsh 0 typ 1 algn 2 clss 3 stb 0 snstb 0 [all …]
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/dports/devel/tigcc/tigcc-0.96.b8_10/gnu/binutils-2.16.1/gas/testsuite/gas/ppc/ |
H A D | test1xcoff32.d | 23 AUX val 8 prmhsh 0 snhsh 0 typ 1 algn 2 clss 1 stb 0 snstb 0 25 AUX val 96 prmhsh 0 snhsh 0 typ 1 algn 2 clss 0 stb 0 snstb 0 27 AUX indx 4 prmhsh 0 snhsh 0 typ 2 algn 0 clss 0 stb 0 snstb 0 29 AUX indx 4 prmhsh 0 snhsh 0 typ 2 algn 0 clss 0 stb 0 snstb 0 31 AUX indx 4 prmhsh 0 snhsh 0 typ 2 algn 0 clss 0 stb 0 snstb 0 33 AUX indx 4 prmhsh 0 snhsh 0 typ 2 algn 0 clss 0 stb 0 snstb 0 35 AUX indx 4 prmhsh 0 snhsh 0 typ 2 algn 0 clss 0 stb 0 snstb 0 37 AUX val 12 prmhsh 0 snhsh 0 typ 1 algn 2 clss 5 stb 0 snstb 0 41 AUX val 4 prmhsh 0 snhsh 0 typ 1 algn 2 clss 3 stb 0 snstb 0 43 AUX val 4 prmhsh 0 snhsh 0 typ 1 algn 2 clss 3 stb 0 snstb 0 [all …]
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/dports/devel/zpu-binutils/zpu-toolchain-1.0/toolchain/binutils/gas/testsuite/gas/ppc/ |
H A D | test1xcoff32.d | 23 AUX val 8 prmhsh 0 snhsh 0 typ 1 algn 2 clss 1 stb 0 snstb 0 25 AUX val 96 prmhsh 0 snhsh 0 typ 1 algn 2 clss 0 stb 0 snstb 0 27 AUX indx 4 prmhsh 0 snhsh 0 typ 2 algn 0 clss 0 stb 0 snstb 0 29 AUX indx 4 prmhsh 0 snhsh 0 typ 2 algn 0 clss 0 stb 0 snstb 0 31 AUX indx 4 prmhsh 0 snhsh 0 typ 2 algn 0 clss 0 stb 0 snstb 0 33 AUX indx 4 prmhsh 0 snhsh 0 typ 2 algn 0 clss 0 stb 0 snstb 0 35 AUX indx 4 prmhsh 0 snhsh 0 typ 2 algn 0 clss 0 stb 0 snstb 0 37 AUX val 12 prmhsh 0 snhsh 0 typ 1 algn 2 clss 5 stb 0 snstb 0 41 AUX val 4 prmhsh 0 snhsh 0 typ 1 algn 2 clss 3 stb 0 snstb 0 43 AUX val 4 prmhsh 0 snhsh 0 typ 1 algn 2 clss 3 stb 0 snstb 0 [all …]
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/dports/devel/djgpp-binutils/binutils-2.17/gas/testsuite/gas/ppc/ |
H A D | test1xcoff32.d | 23 AUX val 8 prmhsh 0 snhsh 0 typ 1 algn 2 clss 1 stb 0 snstb 0 25 AUX val 96 prmhsh 0 snhsh 0 typ 1 algn 2 clss 0 stb 0 snstb 0 27 AUX indx 4 prmhsh 0 snhsh 0 typ 2 algn 0 clss 0 stb 0 snstb 0 29 AUX indx 4 prmhsh 0 snhsh 0 typ 2 algn 0 clss 0 stb 0 snstb 0 31 AUX indx 4 prmhsh 0 snhsh 0 typ 2 algn 0 clss 0 stb 0 snstb 0 33 AUX indx 4 prmhsh 0 snhsh 0 typ 2 algn 0 clss 0 stb 0 snstb 0 35 AUX indx 4 prmhsh 0 snhsh 0 typ 2 algn 0 clss 0 stb 0 snstb 0 37 AUX val 12 prmhsh 0 snhsh 0 typ 1 algn 2 clss 5 stb 0 snstb 0 41 AUX val 4 prmhsh 0 snhsh 0 typ 1 algn 2 clss 3 stb 0 snstb 0 43 AUX val 4 prmhsh 0 snhsh 0 typ 1 algn 2 clss 3 stb 0 snstb 0 [all …]
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/dports/biology/abyss/abyss-2.3.1/Align/ |
H A D | dialign.cpp | 137 algn_pos **ap = o.algn; in print() 170 algn_pos **ap = o.algn; in countMatches() 236 struct algn_pos **ap = algn->algn; in get_alignment_consensus() 238 prepare_alignment(algn); in get_alignment_consensus() 239 max = algn->max_pos; in get_alignment_consensus() 243 max = algn->max_pos; in get_alignment_consensus() 291 struct alignment *algn = NULL; in dialign() local 400 free_alignment(algn); in dialign() 401 algn = salgn; in dialign() 411 print(ss, *algn, consensus); in dialign() [all …]
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H A D | dialign.h | 16 struct seq_col *in_seq_col, struct alignment *algn, int round); 26 struct alignment *algn, int round); 27 void prepare_alignment(struct alignment *algn); 29 void free_alignment(struct alignment* algn);
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/gnomon/ |
H A D | score.cpp | 632 int strand = algn.Strand(); in Init() 673 if(algn.Exons()[k-1].m_ssplice && algn.Exons()[k].m_fsplice) in Init() 786 int strand = algn.Strand(); in Init() 944 int strand = algn.Strand(); in Init() 957 if(algn.Exons().back().m_fsplice_sig == "XX" || algn.Exons().back().m_ssplice_sig == "XX") { in Init() 975 int strand = algn.Strand(); in Init() 980 if(algn.Exons()[k-1].m_ssplice && algn.Exons()[k].m_fsplice) continue; in Init() 1005 if(!algn.HasStart() && algn.Exons().front().m_ssplice_sig != "XX") in Init() 1031 if(!algn.HasStop() && algn.Exons().back().m_fsplice_sig != "XX") in Init() 1059 if(!algn.HasStart() && algn.Exons().back().m_fsplice_sig != "XX") in Init() [all …]
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/dports/lang/racket/racket-8.3/src/bc/src/ |
H A D | jitalloc.c | 35 intptr_t avail, algn; in prepare_retry_alloc() local 37 algn = GC_alloc_alignment(); in prepare_retry_alloc() 38 avail = algn - (GC_gen0_alloc_page_ptr & (algn - 1)); in prepare_retry_alloc() 42 else if (avail == algn) in prepare_retry_alloc() 111 intptr_t a_word, sz, algn; in scheme_inline_alloc() local 114 algn = GC_alloc_alignment(); in scheme_inline_alloc() 123 jit_andi_l(JIT_R2, JIT_R2, (algn - 1)); in scheme_inline_alloc() 124 ref = jit_blti_l(jit_forward(), JIT_R2, (algn - sz)); in scheme_inline_alloc()
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/dports/lang/racket-minimal/racket-8.3/src/bc/src/ |
H A D | jitalloc.c | 35 intptr_t avail, algn; in prepare_retry_alloc() local 37 algn = GC_alloc_alignment(); in prepare_retry_alloc() 38 avail = algn - (GC_gen0_alloc_page_ptr & (algn - 1)); in prepare_retry_alloc() 42 else if (avail == algn) in prepare_retry_alloc() 111 intptr_t a_word, sz, algn; in scheme_inline_alloc() local 114 algn = GC_alloc_alignment(); in scheme_inline_alloc() 123 jit_andi_l(JIT_R2, JIT_R2, (algn - 1)); in scheme_inline_alloc() 124 ref = jit_blti_l(jit_forward(), JIT_R2, (algn - sz)); in scheme_inline_alloc()
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/dports/shells/ast-ksh/ast-ksh93v/src/lib/libvcodex/Vcrdb/ |
H A D | vcrdformat.c | 415 static ssize_t fldpartition(fldz, mark, nc, algn) in fldpartition() 419 ssize_t algn; /* alignment */ 455 k = k >= nc ? nc : k <= c+algn ? c+algn : (k/algn)*algn; 561 ssize_t algn; 591 if(algn > 0 && (nc%algn) == 0 ) 592 { nf = fldpartition(fldz, mark, nc, algn); 599 else for(algn = 4; algn >= 1; algn /= 2) 600 { if((nc%algn) != 0 ) 602 nt = fldpartition(tmpz, mark, nc, algn); 636 ssize_t algn; /* alignment for fixed fields */ [all …]
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/dports/devel/isa-l/isa-l-2.30.0/include/ |
H A D | types.h | 58 # define posix_memalign(p, algn, len) (NULL == (*((char**)(p)) = (void*) _aligned_malloc(len, alg… 62 # define posix_memalign(p, algn, len) (NULL == (*((char**)(p)) = (void*) _aligned_malloc(len, alg…
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/dports/devel/dbus-java/dbus-java-2.7/org/freedesktop/dbus/ |
H A D | Message.java | 584 int algn = getAlignment(sigb[i]); in appendone() local 593 primbuf = new byte[len*algn]; in appendone() 598 primbuf = new byte[len*algn]; in appendone() 603 primbuf = new byte[len*algn]; in appendone() 607 primbuf, k, algn); in appendone() local 611 primbuf, k, algn); in appendone() local 614 primbuf = new byte[len*algn]; in appendone() 618 primbuf, k, algn); in appendone() local 866 byte algn = (byte) getAlignment(sigb[++ofs[0]]); in extractone() 868 int length = (int) (size / algn); in extractone() [all …]
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