1 AlignmentOutput.o AlignmentOutput.o: alignment/AlignmentOutput.cpp \
2 config.h alignment/AlignmentOutput.h /usr/include/c++/4.2.1/string \
3 /usr/include/c++/4.2.1/i686-apple-darwin10/bits/c++config.h \
4 /usr/include/c++/4.2.1/i686-apple-darwin10/bits/os_defines.h \
5 /usr/include/unistd.h /usr/include/_types.h /usr/include/sys/_types.h \
6 /usr/include/sys/cdefs.h /usr/include/machine/_types.h \
7 /usr/include/i386/_types.h /usr/include/sys/unistd.h \
8 /usr/include/sys/select.h /usr/include/sys/appleapiopts.h \
9 /usr/include/sys/_structs.h /usr/include/sys/_select.h \
10 /usr/include/c++/4.2.1/i686-apple-darwin10/bits/cpu_defines.h \
11 /usr/include/c++/4.2.1/bits/stringfwd.h \
12 /usr/include/c++/4.2.1/bits/char_traits.h \
13 /usr/include/c++/4.2.1/cstring /usr/include/c++/4.2.1/cstddef \
14 /usr/lib/gcc/i686-apple-darwin10/4.2.1/include/stddef.h \
15 /usr/include/string.h /usr/include/c++/4.2.1/bits/stl_algobase.h \
16 /usr/include/c++/4.2.1/climits \
17 /usr/lib/gcc/i686-apple-darwin10/4.2.1/include/limits.h \
18 /usr/lib/gcc/i686-apple-darwin10/4.2.1/include/syslimits.h \
19 /usr/include/limits.h /usr/include/machine/limits.h \
20 /usr/include/i386/limits.h /usr/include/i386/_limits.h \
21 /usr/include/sys/syslimits.h /usr/include/c++/4.2.1/cstdlib \
22 /usr/include/stdlib.h /usr/include/Availability.h \
23 /usr/include/AvailabilityInternal.h /usr/include/sys/wait.h \
24 /usr/include/sys/signal.h /usr/include/machine/signal.h \
25 /usr/include/i386/signal.h /usr/include/i386/_structs.h \
26 /usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
27 /usr/include/sys/resource.h /usr/include/machine/endian.h \
28 /usr/include/i386/endian.h /usr/include/sys/_endian.h \
29 /usr/include/libkern/_OSByteOrder.h \
30 /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
31 /usr/include/machine/types.h /usr/include/i386/types.h \
32 /usr/include/i386/_types.h /usr/include/c++/4.2.1/iosfwd \
33 /usr/include/c++/4.2.1/i686-apple-darwin10/bits/c++locale.h \
34 /usr/include/c++/4.2.1/clocale /usr/include/locale.h \
35 /usr/include/_locale.h /usr/include/c++/4.2.1/cstdio \
36 /usr/include/stdio.h /usr/include/c++/4.2.1/cstdarg \
37 /usr/lib/gcc/i686-apple-darwin10/4.2.1/include/stdarg.h \
38 /usr/include/c++/4.2.1/i686-apple-darwin10/bits/c++io.h \
39 /usr/include/c++/4.2.1/i686-apple-darwin10/bits/gthr.h \
40 /usr/include/c++/4.2.1/i686-apple-darwin10/bits/gthr-default.h \
41 /usr/include/pthread.h /usr/include/pthread_impl.h /usr/include/sched.h \
42 /usr/include/time.h /usr/include/_structs.h \
43 /usr/include/c++/4.2.1/cctype /usr/include/ctype.h \
44 /usr/include/runetype.h /usr/include/c++/4.2.1/bits/postypes.h \
45 /usr/include/c++/4.2.1/cwchar /usr/include/c++/4.2.1/ctime \
46 /usr/include/wchar.h /usr/include/_wctype.h \
47 /usr/lib/gcc/i686-apple-darwin10/4.2.1/include/stdint.h \
48 /usr/include/c++/4.2.1/bits/functexcept.h \
49 /usr/include/c++/4.2.1/exception_defines.h \
50 /usr/include/c++/4.2.1/bits/stl_pair.h \
51 /usr/include/c++/4.2.1/bits/cpp_type_traits.h \
52 /usr/include/c++/4.2.1/ext/type_traits.h /usr/include/c++/4.2.1/utility \
53 /usr/include/c++/4.2.1/bits/stl_relops.h \
54 /usr/include/c++/4.2.1/bits/stl_iterator_base_types.h \
55 /usr/include/c++/4.2.1/bits/stl_iterator_base_funcs.h \
56 /usr/include/c++/4.2.1/bits/concept_check.h \
57 /usr/include/c++/4.2.1/bits/stl_iterator.h \
58 /usr/include/c++/4.2.1/debug/debug.h /usr/include/c++/4.2.1/memory \
59 /usr/include/c++/4.2.1/bits/allocator.h \
60 /usr/include/c++/4.2.1/i686-apple-darwin10/bits/c++allocator.h \
61 /usr/include/c++/4.2.1/ext/new_allocator.h /usr/include/c++/4.2.1/new \
62 /usr/include/c++/4.2.1/exception \
63 /usr/include/c++/4.2.1/bits/stl_construct.h \
64 /usr/include/c++/4.2.1/bits/stl_uninitialized.h \
65 /usr/include/c++/4.2.1/bits/stl_raw_storage_iter.h \
66 /usr/include/c++/4.2.1/limits \
67 /usr/include/c++/4.2.1/bits/ostream_insert.h \
68 /usr/include/c++/4.2.1/bits/stl_function.h \
69 /usr/include/c++/4.2.1/bits/basic_string.h \
70 /usr/include/c++/4.2.1/ext/atomicity.h \
71 /usr/include/c++/4.2.1/i686-apple-darwin10/bits/atomic_word.h \
72 /usr/include/c++/4.2.1/algorithm /usr/include/c++/4.2.1/bits/stl_algo.h \
73 /usr/include/c++/4.2.1/bits/stl_heap.h \
74 /usr/include/c++/4.2.1/bits/stl_tempbuf.h \
75 /usr/include/c++/4.2.1/bits/basic_string.tcc \
76 /usr/include/c++/4.2.1/vector /usr/include/c++/4.2.1/bits/stl_vector.h \
77 /usr/include/c++/4.2.1/bits/stl_bvector.h \
78 /usr/include/c++/4.2.1/bits/vector.tcc /usr/include/c++/4.2.1/fstream \
79 /usr/include/c++/4.2.1/istream /usr/include/c++/4.2.1/ios \
80 /usr/include/c++/4.2.1/bits/localefwd.h \
81 /usr/include/c++/4.2.1/bits/ios_base.h \
82 /usr/include/c++/4.2.1/bits/locale_classes.h \
83 /usr/include/c++/4.2.1/streambuf \
84 /usr/include/c++/4.2.1/bits/streambuf.tcc \
85 /usr/include/c++/4.2.1/bits/basic_ios.h \
86 /usr/include/c++/4.2.1/bits/streambuf_iterator.h \
87 /usr/include/c++/4.2.1/bits/locale_facets.h \
88 /usr/include/c++/4.2.1/cwctype /usr/include/wctype.h \
89 /usr/include/c++/4.2.1/i686-apple-darwin10/bits/ctype_base.h \
90 /usr/include/c++/4.2.1/i686-apple-darwin10/bits/ctype_inline.h \
91 /usr/include/c++/4.2.1/bits/codecvt.h \
92 /usr/include/c++/4.2.1/i686-apple-darwin10/bits/time_members.h \
93 /usr/include/c++/4.2.1/i686-apple-darwin10/bits/messages_members.h \
94 /usr/include/c++/4.2.1/bits/basic_ios.tcc \
95 /usr/include/c++/4.2.1/bits/istream.tcc /usr/include/c++/4.2.1/locale \
96 /usr/include/c++/4.2.1/bits/locale_facets.tcc \
97 /usr/include/c++/4.2.1/typeinfo /usr/include/c++/4.2.1/ostream \
98 /usr/include/c++/4.2.1/bits/ostream.tcc \
99 /usr/include/c++/4.2.1/i686-apple-darwin10/bits/basic_file.h \
100 /usr/include/c++/4.2.1/bits/fstream.tcc /usr/include/c++/4.2.1/sstream \
101 /usr/include/c++/4.2.1/bits/sstream.tcc /usr/include/c++/4.2.1/cassert \
102 /usr/include/assert.h alignment/Alignment.h \
103 /usr/include/c++/4.2.1/iomanip /usr/include/c++/4.2.1/functional \
104 /usr/include/c++/4.2.1/stdexcept alignment/Sequence.h \
105 alignment/../general/userparams.h alignment/../general/UserParameters.h \
106 /usr/include/c++/4.2.1/iostream alignment/../general/utils.h \
107 alignment/../general/Utility.h /usr/include/errno.h \
108 /usr/include/sys/errno.h alignment/../general/clustalw.h \
109 alignment/../general/general.h alignment/../general/Array2D.h \
110 alignment/../general/SquareMat.h alignment/../general/SymMatrix.h \
111 /usr/include/c++/4.2.1/cmath /usr/include/math.h \
112 /usr/include/architecture/i386/math.h \
113 /usr/include/c++/4.2.1/bits/cmath.tcc alignment/../general/utils.h \
114 alignment/../substitutionMatrix/globalmatrix.h \
115 alignment/../substitutionMatrix/SubMatrix.h \
116 alignment/../substitutionMatrix/../general/clustalw.h \
117 alignment/../substitutionMatrix/../general/userparams.h \
118 alignment/../substitutionMatrix/../general/utils.h \
119 alignment/../substitutionMatrix/../general/Array2D.h \
120 alignment/../general/VectorOutOfRange.h \
121 alignment/../general/SequenceNotFoundException.h
125 alignment/AlignmentOutput.h:
127 /usr/include/c++/4.2.1/string:
129 /usr/include/c++/4.2.1/i686-apple-darwin10/bits/c++config.h:
131 /usr/include/c++/4.2.1/i686-apple-darwin10/bits/os_defines.h:
133 /usr/include/unistd.h:
135 /usr/include/_types.h:
137 /usr/include/sys/_types.h:
139 /usr/include/sys/cdefs.h:
141 /usr/include/machine/_types.h:
143 /usr/include/i386/_types.h:
145 /usr/include/sys/unistd.h:
147 /usr/include/sys/select.h:
149 /usr/include/sys/appleapiopts.h:
151 /usr/include/sys/_structs.h:
153 /usr/include/sys/_select.h:
155 /usr/include/c++/4.2.1/i686-apple-darwin10/bits/cpu_defines.h:
157 /usr/include/c++/4.2.1/bits/stringfwd.h:
159 /usr/include/c++/4.2.1/bits/char_traits.h:
161 /usr/include/c++/4.2.1/cstring:
163 /usr/include/c++/4.2.1/cstddef:
165 /usr/lib/gcc/i686-apple-darwin10/4.2.1/include/stddef.h:
167 /usr/include/string.h:
169 /usr/include/c++/4.2.1/bits/stl_algobase.h:
171 /usr/include/c++/4.2.1/climits:
173 /usr/lib/gcc/i686-apple-darwin10/4.2.1/include/limits.h:
175 /usr/lib/gcc/i686-apple-darwin10/4.2.1/include/syslimits.h:
177 /usr/include/limits.h:
179 /usr/include/machine/limits.h:
181 /usr/include/i386/limits.h:
183 /usr/include/i386/_limits.h:
185 /usr/include/sys/syslimits.h:
187 /usr/include/c++/4.2.1/cstdlib:
189 /usr/include/stdlib.h:
191 /usr/include/Availability.h:
193 /usr/include/AvailabilityInternal.h:
195 /usr/include/sys/wait.h:
197 /usr/include/sys/signal.h:
199 /usr/include/machine/signal.h:
201 /usr/include/i386/signal.h:
203 /usr/include/i386/_structs.h:
205 /usr/include/machine/_structs.h:
207 /usr/include/mach/i386/_structs.h:
209 /usr/include/sys/resource.h:
211 /usr/include/machine/endian.h:
213 /usr/include/i386/endian.h:
215 /usr/include/sys/_endian.h:
217 /usr/include/libkern/_OSByteOrder.h:
219 /usr/include/libkern/i386/_OSByteOrder.h:
221 /usr/include/alloca.h:
223 /usr/include/machine/types.h:
225 /usr/include/i386/types.h:
227 /usr/include/i386/_types.h:
229 /usr/include/c++/4.2.1/iosfwd:
231 /usr/include/c++/4.2.1/i686-apple-darwin10/bits/c++locale.h:
233 /usr/include/c++/4.2.1/clocale:
235 /usr/include/locale.h:
237 /usr/include/_locale.h:
239 /usr/include/c++/4.2.1/cstdio:
241 /usr/include/stdio.h:
243 /usr/include/c++/4.2.1/cstdarg:
245 /usr/lib/gcc/i686-apple-darwin10/4.2.1/include/stdarg.h:
247 /usr/include/c++/4.2.1/i686-apple-darwin10/bits/c++io.h:
249 /usr/include/c++/4.2.1/i686-apple-darwin10/bits/gthr.h:
251 /usr/include/c++/4.2.1/i686-apple-darwin10/bits/gthr-default.h:
253 /usr/include/pthread.h:
255 /usr/include/pthread_impl.h:
257 /usr/include/sched.h:
261 /usr/include/_structs.h:
263 /usr/include/c++/4.2.1/cctype:
265 /usr/include/ctype.h:
267 /usr/include/runetype.h:
269 /usr/include/c++/4.2.1/bits/postypes.h:
271 /usr/include/c++/4.2.1/cwchar:
273 /usr/include/c++/4.2.1/ctime:
275 /usr/include/wchar.h:
277 /usr/include/_wctype.h:
279 /usr/lib/gcc/i686-apple-darwin10/4.2.1/include/stdint.h:
281 /usr/include/c++/4.2.1/bits/functexcept.h:
283 /usr/include/c++/4.2.1/exception_defines.h:
285 /usr/include/c++/4.2.1/bits/stl_pair.h:
287 /usr/include/c++/4.2.1/bits/cpp_type_traits.h:
289 /usr/include/c++/4.2.1/ext/type_traits.h:
291 /usr/include/c++/4.2.1/utility:
293 /usr/include/c++/4.2.1/bits/stl_relops.h:
295 /usr/include/c++/4.2.1/bits/stl_iterator_base_types.h:
297 /usr/include/c++/4.2.1/bits/stl_iterator_base_funcs.h:
299 /usr/include/c++/4.2.1/bits/concept_check.h:
301 /usr/include/c++/4.2.1/bits/stl_iterator.h:
303 /usr/include/c++/4.2.1/debug/debug.h:
305 /usr/include/c++/4.2.1/memory:
307 /usr/include/c++/4.2.1/bits/allocator.h:
309 /usr/include/c++/4.2.1/i686-apple-darwin10/bits/c++allocator.h:
311 /usr/include/c++/4.2.1/ext/new_allocator.h:
313 /usr/include/c++/4.2.1/new:
315 /usr/include/c++/4.2.1/exception:
317 /usr/include/c++/4.2.1/bits/stl_construct.h:
319 /usr/include/c++/4.2.1/bits/stl_uninitialized.h:
321 /usr/include/c++/4.2.1/bits/stl_raw_storage_iter.h:
323 /usr/include/c++/4.2.1/limits:
325 /usr/include/c++/4.2.1/bits/ostream_insert.h:
327 /usr/include/c++/4.2.1/bits/stl_function.h:
329 /usr/include/c++/4.2.1/bits/basic_string.h:
331 /usr/include/c++/4.2.1/ext/atomicity.h:
333 /usr/include/c++/4.2.1/i686-apple-darwin10/bits/atomic_word.h:
335 /usr/include/c++/4.2.1/algorithm:
337 /usr/include/c++/4.2.1/bits/stl_algo.h:
339 /usr/include/c++/4.2.1/bits/stl_heap.h:
341 /usr/include/c++/4.2.1/bits/stl_tempbuf.h:
343 /usr/include/c++/4.2.1/bits/basic_string.tcc:
345 /usr/include/c++/4.2.1/vector:
347 /usr/include/c++/4.2.1/bits/stl_vector.h:
349 /usr/include/c++/4.2.1/bits/stl_bvector.h:
351 /usr/include/c++/4.2.1/bits/vector.tcc:
353 /usr/include/c++/4.2.1/fstream:
355 /usr/include/c++/4.2.1/istream:
357 /usr/include/c++/4.2.1/ios:
359 /usr/include/c++/4.2.1/bits/localefwd.h:
361 /usr/include/c++/4.2.1/bits/ios_base.h:
363 /usr/include/c++/4.2.1/bits/locale_classes.h:
365 /usr/include/c++/4.2.1/streambuf:
367 /usr/include/c++/4.2.1/bits/streambuf.tcc:
369 /usr/include/c++/4.2.1/bits/basic_ios.h:
371 /usr/include/c++/4.2.1/bits/streambuf_iterator.h:
373 /usr/include/c++/4.2.1/bits/locale_facets.h:
375 /usr/include/c++/4.2.1/cwctype:
377 /usr/include/wctype.h:
379 /usr/include/c++/4.2.1/i686-apple-darwin10/bits/ctype_base.h:
381 /usr/include/c++/4.2.1/i686-apple-darwin10/bits/ctype_inline.h:
383 /usr/include/c++/4.2.1/bits/codecvt.h:
385 /usr/include/c++/4.2.1/i686-apple-darwin10/bits/time_members.h:
387 /usr/include/c++/4.2.1/i686-apple-darwin10/bits/messages_members.h:
389 /usr/include/c++/4.2.1/bits/basic_ios.tcc:
391 /usr/include/c++/4.2.1/bits/istream.tcc:
393 /usr/include/c++/4.2.1/locale:
395 /usr/include/c++/4.2.1/bits/locale_facets.tcc:
397 /usr/include/c++/4.2.1/typeinfo:
399 /usr/include/c++/4.2.1/ostream:
401 /usr/include/c++/4.2.1/bits/ostream.tcc:
403 /usr/include/c++/4.2.1/i686-apple-darwin10/bits/basic_file.h:
405 /usr/include/c++/4.2.1/bits/fstream.tcc:
407 /usr/include/c++/4.2.1/sstream:
409 /usr/include/c++/4.2.1/bits/sstream.tcc:
411 /usr/include/c++/4.2.1/cassert:
413 /usr/include/assert.h:
415 alignment/Alignment.h:
417 /usr/include/c++/4.2.1/iomanip:
419 /usr/include/c++/4.2.1/functional:
421 /usr/include/c++/4.2.1/stdexcept:
423 alignment/Sequence.h:
425 alignment/../general/userparams.h:
427 alignment/../general/UserParameters.h:
429 /usr/include/c++/4.2.1/iostream:
431 alignment/../general/utils.h:
433 alignment/../general/Utility.h:
435 /usr/include/errno.h:
437 /usr/include/sys/errno.h:
439 alignment/../general/clustalw.h:
441 alignment/../general/general.h:
443 alignment/../general/Array2D.h:
445 alignment/../general/SquareMat.h:
447 alignment/../general/SymMatrix.h:
449 /usr/include/c++/4.2.1/cmath:
453 /usr/include/architecture/i386/math.h:
455 /usr/include/c++/4.2.1/bits/cmath.tcc:
457 alignment/../general/utils.h:
459 alignment/../substitutionMatrix/globalmatrix.h:
461 alignment/../substitutionMatrix/SubMatrix.h:
463 alignment/../substitutionMatrix/../general/clustalw.h:
465 alignment/../substitutionMatrix/../general/userparams.h:
467 alignment/../substitutionMatrix/../general/utils.h:
469 alignment/../substitutionMatrix/../general/Array2D.h:
471 alignment/../general/VectorOutOfRange.h:
473 alignment/../general/SequenceNotFoundException.h: