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/dports/biology/abyss/abyss-2.3.1/dialign/
H A Dalig.c103 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 …]
H A Dmuseq.c55 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 …]
H A Dio.c563 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 …]
H A Dassemble.c29 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 …]
H A Dio.h34 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);
/dports/biology/sra-tools/sra-tools-2.11.0/tools/cg-load/
H A Dwriter-evidence-dnbs.c82 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 …]
H A Dwriter-evidence-intervals.c69 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 …]
H A Dwriter-algn.c75 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 …]
/dports/devel/binutils/binutils-2.37/gas/testsuite/gas/ppc/
H A Dtest1xcoff32.d23 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 …]
/dports/lang/gnatdroid-binutils-x86/binutils-2.27/gas/testsuite/gas/ppc/
H A Dtest1xcoff32.d23 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 …]
/dports/devel/arm-elf-binutils/binutils-2.37/gas/testsuite/gas/ppc/
H A Dtest1xcoff32.d23 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 …]
/dports/devel/gnulibiberty/binutils-2.37/gas/testsuite/gas/ppc/
H A Dtest1xcoff32.d23 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 …]
/dports/devel/zpu-gcc/zpu-toolchain-1.0/toolchain/binutils/gas/testsuite/gas/ppc/
H A Dtest1xcoff32.d23 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 …]
/dports/lang/gnatdroid-binutils/binutils-2.27/gas/testsuite/gas/ppc/
H A Dtest1xcoff32.d23 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 …]
/dports/devel/tigcc/tigcc-0.96.b8_10/gnu/binutils-2.16.1/gas/testsuite/gas/ppc/
H A Dtest1xcoff32.d23 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 …]
/dports/devel/zpu-binutils/zpu-toolchain-1.0/toolchain/binutils/gas/testsuite/gas/ppc/
H A Dtest1xcoff32.d23 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 …]
/dports/devel/djgpp-binutils/binutils-2.17/gas/testsuite/gas/ppc/
H A Dtest1xcoff32.d23 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 …]
/dports/biology/abyss/abyss-2.3.1/Align/
H A Ddialign.cpp137 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 …]
H A Ddialign.h16 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);
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/gnomon/
H A Dscore.cpp632 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 …]
/dports/lang/racket/racket-8.3/src/bc/src/
H A Djitalloc.c35 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()
/dports/lang/racket-minimal/racket-8.3/src/bc/src/
H A Djitalloc.c35 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()
/dports/shells/ast-ksh/ast-ksh93v/src/lib/libvcodex/Vcrdb/
H A Dvcrdformat.c415 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 …]
/dports/devel/isa-l/isa-l-2.30.0/include/
H A Dtypes.h58 # 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…
/dports/devel/dbus-java/dbus-java-2.7/org/freedesktop/dbus/
H A DMessage.java584 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()
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