2 #================ common .o files
4 doinit.o : doinit.c defs.h param.h upam.h structs.h uascii.h
5 $(CC) $(THR_CC) $(CFLAGS) -c doinit.c
7 init_sw.o : initfa.c defs.h param.h upam.h structs.h
8 $(CC) $(THR_CC) $(CFLAGS) -c -DSSEARCH initfa.c -o init_sw.o
10 init_ssw.o : initfa.c defs.h param.h upam.h structs.h
11 $(CC) $(THR_CC) $(CFLAGS) -c -DOSEARCH initfa.c -o init_ssw.o
13 init_rss.o : initfa.c defs.h param.h upam.h structs.h
14 $(CC) $(THR_CC) $(CFLAGS) -c -DPRSS initfa.c -o init_rss.o
16 init_rfx.o : initfa.c defs.h param.h upam.h structs.h
17 $(CC) $(THR_CC) $(CFLAGS) -c -DPRSS -DFASTX initfa.c -o init_rfx.o
19 init_fa.o : initfa.c defs.h param.h upam.h structs.h
20 $(CC) $(THR_CC) $(CFLAGS) -c -DFASTA initfa.c -o init_fa.o
22 init_ff.o : initfa.c defs.h param.h upam.h structs.h
23 $(CC) $(THR_CC) $(CFLAGS) -c -DFASTF initfa.c -o init_ff.o
25 init_tf.o : initfa.c defs.h param.h upam.h structs.h
26 $(CC) $(THR_CC) $(CFLAGS) -c -DFASTF -DTFAST initfa.c -o init_tf.o
28 init_fs.o : initfa.c defs.h param.h upam.h structs.h
29 $(CC) $(THR_CC) $(CFLAGS) -c -DFASTS initfa.c -o init_fs.o
31 init_fm.o : initfa.c defs.h param.h upam.h structs.h
32 $(CC) $(THR_CC) $(CFLAGS) -c -DFASTM initfa.c -o init_fm.o
34 init_tfs.o : initfa.c defs.h param.h upam.h structs.h
35 $(CC) $(THR_CC) $(CFLAGS) -c -DFASTS -DTFAST initfa.c -o init_tfs.o
37 init_tfm.o : initfa.c defs.h param.h upam.h structs.h
38 $(CC) $(THR_CC) $(CFLAGS) -c -DFASTM -DTFAST initfa.c -o init_tfm.o
40 init_tfa.o : initfa.c defs.h param.h upam.h structs.h
41 $(CC) $(THR_CC) $(CFLAGS) -c -DFASTA -DTFAST initfa.c -o init_tfa.o
43 init_fx.o : initfa.c defs.h param.h upam.h structs.h
44 $(CC) $(THR_CC) $(CFLAGS) -c -DFASTX initfa.c -o init_fx.o
46 init_tfx.o : initfa.c defs.h param.h upam.h structs.h
47 $(CC) $(THR_CC) $(CFLAGS) -c -DFASTX -DTFAST initfa.c -o init_tfx.o
49 init_fy.o : initfa.c defs.h param.h upam.h structs.h
50 $(CC) $(THR_CC) $(CFLAGS) -c -DFASTY initfa.c -o init_fy.o
52 init_tfy.o : initfa.c defs.h param.h upam.h structs.h
53 $(CC) $(THR_CC) $(CFLAGS) -c -DFASTY -DTFAST initfa.c -o init_tfy.o
55 #================ miscellaneous
58 $(CC) $(THR_CC) $(CFLAGS) -c htime.c
60 compacc.o : compacc.c upam.h uascii.h param.h structs.h $(MWH) defs.h
61 $(CC) $(THR_CC) $(CFLAGS) -c compacc.c
63 pssm_asn_subs.o : pssm_asn_subs.c defs.h
64 $(CC) $(THR_CC) $(CFLAGS) -c pssm_asn_subs.c
66 #================ display list of best hits / alignments
68 showbest.o : $(SHOWBESTC) $(MWH) defs.h param.h structs.h aln_structs.h drop_func.h
69 $(CC) $(THR_CC) $(CFLAGS) -c $(SHOWBESTC) -o showbest.o
71 showrss.o : showrss.c $(MWH) defs.h param.h structs.h aln_structs.h drop_func.h
72 $(CC) $(THR_CC) $(CFLAGS) -c showrss.c
74 showun.o : mshowbest.c $(MWH) defs.h aln_structs.h drop_func.h
75 $(CC) $(THR_CC) $(CFLAGS) -c -DSHOWUN mshowbest.c -o showun.o
77 showrel.o : $(SHOWBESTC) $(MWH) defs.h aln_structs.h drop_func.h
78 $(CC) $(THR_CC) $(CFLAGS) -c -DSHOWREL $(SHOWBESTC) -o showrel.o
80 showsum.o : showsum.c $(MWH) defs.h drop_func.h
81 $(CC) $(THR_CC) $(CFLAGS) -c showsum.c
83 $(SHOWALIGN).o : $(SHOWALIGN).c $(MWHP) defs.h structs.h param.h aln_structs.h drop_func.h
84 $(CC) $(THR_CC) $(CFLAGS) -c $(SHOWALIGN).c -o $(SHOWALIGN).o
86 $(SHOWALIGN)_u.o : $(SHOWALIGN).c $(MWHP) defs.h structs.h param.h aln_structs.h drop_func.h
87 $(CC) $(THR_CC) $(CFLAGS) -DSHOWUN -c -o $(SHOWALIGN)_u.o $(SHOWALIGN).c
88 re_getlib.o : re_getlib.c mw.h mm_file.h
89 $(CC) $(THR_CC) $(CFLAGS) -c re_getlib.c
91 lib_sel.o : lib_sel.c defs.h structs.h
92 $(CC) $(THR_CC) $(CFLAGS) -c lib_sel.c
94 c_dispn.o : c_dispn.c defs.h structs.h param.h
95 $(CC) $(THR_CC) $(CFLAGS) -c c_dispn.c
97 #================ statistical functions
99 karlin.o : karlin.c param.h
100 $(CC) $(THR_CC) $(CFLAGS) -c karlin.c
102 scaleswn.o : scaleswn.c defs.h param.h structs.h $(MWH) alt_parms.h
103 $(CC) $(THR_CC) $(CFLAGS) -c scaleswn.c
105 scaleswtf.o : scaleswt.c defs.h param.h structs.h $(MWH) alt_parms.h
106 $(CC) $(THR_CC) $(CFLAGS) -DFASTF -c scaleswt.c -o scaleswtf.o
108 scaleswts.o : scaleswt.c defs.h param.h structs.h $(MWH) alt_parms.h
109 $(CC) $(THR_CC) $(CFLAGS) -c scaleswt.c -o scaleswts.o
111 tatstats_fs.o : tatstats.c tatstats.h
112 $(CC) $(THR_CC) $(CFLAGS) -c -DFASTS tatstats.c -o tatstats_fs.o
114 tatstats_ff.o : tatstats.c tatstats.h
115 $(CC) $(THR_CC) $(CFLAGS) -c -DFASTF tatstats.c -o tatstats_ff.o
117 tatstats_fm.o : tatstats.c tatstats.h
118 $(CC) $(THR_CC) $(CFLAGS) -c -DFASTM tatstats.c -o tatstats_fm.o
120 last_tat.o : last_tat.c defs.h mm_file.h structs.h param.h
121 $(CC) $(THR_CC) $(CFLAGS) -c last_tat.c
123 #================ drop functions - actual scores/alignments
125 drop_nfa.o : dropnfa.c dropnfa.h param.h defs.h drop_func.h
126 $(CC) $(THR_CC) $(CFLAGS) -c dropnfa.c -o drop_nfa.o
128 # drop_ff, _fs, _fm must define FASTF, FASTS, and FASTM to ensure
129 # that tatstats.h is built appropriately
131 drop_ff.o : dropff2.c param.h defs.h tatstats.h drop_func.h
132 $(CC) $(THR_CC) $(CFLAGS) -DFASTF -c dropff2.c -o drop_ff.o
134 drop_tff.o : dropff2.c param.h defs.h tatstats.h drop_func.h
135 $(CC) $(THR_CC) $(CFLAGS) -DFASTF -DTFAST -c dropff2.c -o drop_tff.o
137 drop_ff2.o : dropff2.c param.h defs.h tatstats.h drop_func.h
138 $(CC) $(THR_CC) $(CFLAGS) -c -DFASTF dropff2.c -o drop_ff2.o
140 drop_tff2.o : dropff2.c param.h defs.h tatstats.h drop_func.h
141 $(CC) $(THR_CC) $(CFLAGS) -c -DFASTF -DTFAST dropff2.c -o drop_tff.o
143 drop_fs.o : dropfs2.c param.h defs.h tatstats.h drop_func.h
144 $(CC) $(THR_CC) $(CFLAGS) -DFASTS -c dropfs2.c -o drop_fs.o
146 drop_tfs.o : dropfs2.c param.h defs.h drop_func.h
147 $(CC) $(THR_CC) $(CFLAGS) -c -DTFAST -DFASTS dropfs2.c -o drop_tfs.o
149 drop_fm.o : dropfs2.c param.h defs.h drop_func.h
150 $(CC) $(THR_CC) $(CFLAGS) -c -DFASTM dropfs2.c -o drop_fm.o
152 drop_tfm.o : dropfs2.c param.h defs.h drop_func.h
153 $(CC) $(THR_CC) $(CFLAGS) -c -DTFAST -DFASTM dropfs2.c -o drop_tfm.o
155 drop_tfa.o : dropnfa.c dropnfa.h upam.h param.h defs.h
156 $(CC) $(THR_CC) $(CFLAGS) -c -DTFASTA dropnfa.c -o drop_tfa.o
158 drop_fx.o : dropfx.c upam.h param.h defs.h drop_func.h
159 $(CC) $(THR_CC) $(CFLAGS) -c dropfx.c -o drop_fx.o
161 drop_tfx.o : dropfx.c upam.h param.h defs.h drop_func.h
162 $(CC) $(THR_CC) $(CFLAGS) -c -DTFAST dropfx.c -o drop_tfx.o
164 drop_fz.o : dropfz2.c upam.h param.h defs.h aamap.h drop_func.h
165 $(CC) $(THR_CC) $(CFLAGS) -c dropfz2.c -o drop_fz.o
167 drop_tfz.o : dropfz2.c upam.h param.h defs.h aamap.h drop_func.h
168 $(CC) $(THR_CC) $(CFLAGS) -c -DTFAST dropfz2.c -o drop_tfz.o
170 dropnsw.o : dropnsw.c upam.h param.h structs.h drop_func.h
171 $(CC) $(THR_CC) $(CFLAGS) -c dropnsw.c
173 dropgsw.o : dropgsw.c dropgsw.h upam.h param.h structs.h drop_func.h
174 $(CC) $(THR_CC) $(CFLAGS) -c dropgsw.c
176 smith_waterman_altivec.o : smith_waterman_altivec.c smith_waterman_altivec.h dropgsw.h defs.h param.h
177 $(CC) $(THR_CC) $(CFLAGS) -c smith_waterman_altivec.c
179 smith_waterman_sse2.o : smith_waterman_sse2.c smith_waterman_sse2.h dropgsw.h defs.h param.h
180 $(CC) $(THR_CC) $(CFLAGS) -c smith_waterman_sse2.c
182 dropnw.o : dropnw.c upam.h param.h structs.h drop_func.h
183 $(CC) $(THR_CC) $(CFLAGS) -c dropnw.c
185 #================ reading query, libraries
187 getseq.o : getseq.c defs.h uascii.h structs.h upam.h mm_file.h
188 $(CC) $(THR_CC) $(CFLAGS) -c getseq.c
190 llgetaa.o : llgetaa.c upam.h uascii.h mm_file.h
191 $(CC) $(THR_CC) $(CFLAGS) -c -DNOLIB llgetaa.c
193 lgetlib.o : $(NGETLIB).c altlib.h upam.h uascii.h mm_file.h
194 $(CC) $(THR_CC) $(CFLAGS) -c $(NGETLIB).c -o lgetlib.o
196 lgetaa_m.o : mmgetaa.c altlib.h ncbl2_head.h upam.h uascii.h mm_file.h
197 $(CC) $(THR_CC) $(CFLAGS) -c mmgetaa.c -o lgetaa_m.o
199 ncbl_lib.o : ncbl_lib.c ncbl_head.h
200 $(CC) $(THR_CC) $(CFLAGS) -c ncbl_lib.c
202 ncbl2_mlib.o : ncbl2_mlib.c ncbl2_head.h mm_file.h
203 $(CC) $(THR_CC) $(CFLAGS) -c ncbl2_mlib.c
205 mysql_lib.o : mysql_lib.c mm_file.h
206 $(CC) $(THR_CC) $(CFLAGS) -c mysql_lib.c
208 pgsql_lib.o : pgsql_lib.c mm_file.h
209 $(CC) $(THR_CC) $(CFLAGS) -c pgsql_lib.c
211 #================ threading functions
213 pthr_subs2.o : pthr_subs2.c thr.h pthr_subs.h
214 $(CC) $(THR_CC) $(CFLAGS) -c pthr_subs2.c
216 uthr_subs.o : uthr_subs.c thr.h uthr_subs.h
217 $(CC) $(THR_CC) $(CFLAGS) -c uthr_subs.c
219 #================ translation
221 faatran.o : faatran.c upam.h uascii.h
222 $(CC) $(THR_CC) $(CFLAGS) -c faatran.c
224 url_subs.o : url_subs.c structs.h param.h
225 $(CC) $(THR_CC) $(CFLAGS) -c url_subs.c
227 $(NRAND).o : $(NRAND).c
228 $(CC) $(THR_CC) $(CFLAGS) -c $(NRAND).c
229 #================ pvm/mpi specific functions
231 hostacc.o : hostacc.c upam.h uascii.h
232 $(CC) $(THR_CC) $(CFLAGS) hostacc.c
234 workacc.o : workacc.c upam.h uascii.h param.h
235 $(NCC) $(THR_CC) $(CFLAGS) workacc.c -o workacc.o