1 ObjectiveScore.o: alignment/ObjectiveScore.cpp config.h \
2 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/sstream \
3 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/istream \
4 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ios \
5 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iosfwd \
6 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h \
7 /usr/include/bits/wordsize.h \
8 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h \
9 /usr/include/features.h /usr/include/sys/cdefs.h \
10 /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
11 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h \
12 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stringfwd.h \
13 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/postypes.h \
14 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwchar \
15 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef \
16 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
17 /usr/include/wchar.h /usr/include/stdio.h \
18 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
19 /usr/include/bits/wchar.h /usr/include/xlocale.h \
20 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception \
21 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/char_traits.h \
22 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algobase.h \
23 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/functexcept.h \
24 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception_defines.h \
25 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h \
26 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h \
27 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/numeric_traits.h \
28 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_pair.h \
29 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/move.h \
30 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/concept_check.h \
31 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_types.h \
32 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_funcs.h \
33 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator.h \
34 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/debug/debug.h \
35 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/localefwd.h \
36 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++locale.h \
37 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/clocale \
38 /usr/include/locale.h /usr/include/bits/locale.h \
39 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cctype \
40 /usr/include/ctype.h /usr/include/bits/types.h \
41 /usr/include/bits/typesizes.h /usr/include/endian.h \
42 /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
43 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ios_base.h \
44 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/atomicity.h \
45 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr.h \
46 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr-default.h \
47 /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
48 /usr/include/bits/sched.h /usr/include/bits/time.h \
49 /usr/include/bits/pthreadtypes.h /usr/include/bits/setjmp.h \
50 /usr/include/unistd.h /usr/include/bits/posix_opt.h \
51 /usr/include/bits/environments.h /usr/include/bits/confname.h \
52 /usr/include/getopt.h \
53 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/atomic_word.h \
54 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.h \
55 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string \
56 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/allocator.h \
57 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++allocator.h \
58 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/new_allocator.h \
59 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/new \
60 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream_insert.h \
61 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cxxabi-forced.h \
62 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_function.h \
63 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/binders.h \
64 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.h \
65 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/initializer_list \
66 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.tcc \
67 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.tcc \
68 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/streambuf \
69 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf.tcc \
70 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.h \
71 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.h \
72 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwctype \
73 /usr/include/wctype.h \
74 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_base.h \
75 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf_iterator.h \
76 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_inline.h \
77 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.tcc \
78 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.tcc \
79 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ostream \
80 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream.tcc \
81 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/istream.tcc \
82 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/sstream.tcc \
83 alignment/ObjectiveScore.h alignment/../general/clustalw.h \
84 alignment/../general/general.h alignment/../general/Array2D.h \
85 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream \
86 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/vector \
87 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_construct.h \
88 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_uninitialized.h \
89 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h \
90 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_bvector.h \
91 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/vector.tcc \
92 alignment/../general/SquareMat.h \
93 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iomanip \
94 alignment/../general/SymMatrix.h \
95 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath \
96 /usr/include/math.h /usr/include/bits/huge_val.h \
97 /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \
98 /usr/include/bits/inf.h /usr/include/bits/nan.h \
99 /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \
100 /usr/include/bits/mathinline.h \
101 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc \
102 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/stdexcept \
103 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib \
104 /usr/include/stdlib.h /usr/include/bits/waitflags.h \
105 /usr/include/bits/waitstatus.h /usr/include/sys/types.h \
106 /usr/include/sys/select.h /usr/include/bits/select.h \
107 /usr/include/bits/sigset.h /usr/include/sys/sysmacros.h \
108 /usr/include/alloca.h alignment/../substitutionMatrix/globalmatrix.h \
109 alignment/../substitutionMatrix/SubMatrix.h \
110 alignment/../substitutionMatrix/../general/clustalw.h \
111 alignment/../substitutionMatrix/../general/userparams.h \
112 alignment/../substitutionMatrix/../general/UserParameters.h \
113 alignment/../substitutionMatrix/../general/utils.h \
114 alignment/../substitutionMatrix/../general/Utility.h \
115 /usr/include/libio.h /usr/include/_G_config.h \
116 /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
117 /usr/include/bits/stdio.h /usr/include/string.h /usr/include/errno.h \
118 /usr/include/bits/errno.h /usr/include/linux/errno.h \
119 /usr/include/asm/errno.h /usr/include/asm-generic/errno.h \
120 /usr/include/asm-generic/errno-base.h \
121 alignment/../substitutionMatrix/../general/clustalw.h \
122 alignment/../substitutionMatrix/../general/general.h \
123 alignment/../substitutionMatrix/../general/utils.h \
124 alignment/../substitutionMatrix/../general/Array2D.h \
125 alignment/Alignment.h alignment/Sequence.h \
126 alignment/../general/userparams.h alignment/../general/utils.h \
127 alignment/../general/VectorOutOfRange.h \
128 alignment/../general/SequenceNotFoundException.h \
129 alignment/../general/debuglogObject.h alignment/../general/DebugLog.h \
130 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/fstream \
131 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/codecvt.h \
132 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdio \
133 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/basic_file.h \
134 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++io.h \
135 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/fstream.tcc
139 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/sstream:
141 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/istream:
143 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ios:
145 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iosfwd:
147 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h:
149 /usr/include/bits/wordsize.h:
151 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h:
153 /usr/include/features.h:
155 /usr/include/sys/cdefs.h:
157 /usr/include/gnu/stubs.h:
159 /usr/include/gnu/stubs-64.h:
161 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h:
163 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stringfwd.h:
165 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/postypes.h:
167 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwchar:
169 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef:
171 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h:
173 /usr/include/wchar.h:
175 /usr/include/stdio.h:
177 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h:
179 /usr/include/bits/wchar.h:
181 /usr/include/xlocale.h:
183 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception:
185 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/char_traits.h:
187 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algobase.h:
189 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/functexcept.h:
191 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception_defines.h:
193 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h:
195 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h:
197 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/numeric_traits.h:
199 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_pair.h:
201 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/move.h:
203 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/concept_check.h:
205 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_types.h:
207 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_funcs.h:
209 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator.h:
211 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/debug/debug.h:
213 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/localefwd.h:
215 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++locale.h:
217 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/clocale:
219 /usr/include/locale.h:
221 /usr/include/bits/locale.h:
223 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cctype:
225 /usr/include/ctype.h:
227 /usr/include/bits/types.h:
229 /usr/include/bits/typesizes.h:
231 /usr/include/endian.h:
233 /usr/include/bits/endian.h:
235 /usr/include/bits/byteswap.h:
237 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ios_base.h:
239 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/atomicity.h:
241 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr.h:
243 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr-default.h:
245 /usr/include/pthread.h:
247 /usr/include/sched.h:
251 /usr/include/bits/sched.h:
253 /usr/include/bits/time.h:
255 /usr/include/bits/pthreadtypes.h:
257 /usr/include/bits/setjmp.h:
259 /usr/include/unistd.h:
261 /usr/include/bits/posix_opt.h:
263 /usr/include/bits/environments.h:
265 /usr/include/bits/confname.h:
267 /usr/include/getopt.h:
269 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/atomic_word.h:
271 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.h:
273 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string:
275 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/allocator.h:
277 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++allocator.h:
279 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/new_allocator.h:
281 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/new:
283 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream_insert.h:
285 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cxxabi-forced.h:
287 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_function.h:
289 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/binders.h:
291 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.h:
293 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/initializer_list:
295 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.tcc:
297 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.tcc:
299 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/streambuf:
301 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf.tcc:
303 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.h:
305 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.h:
307 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwctype:
309 /usr/include/wctype.h:
311 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_base.h:
313 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf_iterator.h:
315 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_inline.h:
317 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.tcc:
319 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.tcc:
321 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ostream:
323 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream.tcc:
325 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/istream.tcc:
327 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/sstream.tcc:
329 alignment/ObjectiveScore.h:
331 alignment/../general/clustalw.h:
333 alignment/../general/general.h:
335 alignment/../general/Array2D.h:
337 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream:
339 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/vector:
341 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_construct.h:
343 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_uninitialized.h:
345 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h:
347 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_bvector.h:
349 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/vector.tcc:
351 alignment/../general/SquareMat.h:
353 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iomanip:
355 alignment/../general/SymMatrix.h:
357 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath:
361 /usr/include/bits/huge_val.h:
363 /usr/include/bits/huge_valf.h:
365 /usr/include/bits/huge_vall.h:
367 /usr/include/bits/inf.h:
369 /usr/include/bits/nan.h:
371 /usr/include/bits/mathdef.h:
373 /usr/include/bits/mathcalls.h:
375 /usr/include/bits/mathinline.h:
377 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc:
379 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/stdexcept:
381 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib:
383 /usr/include/stdlib.h:
385 /usr/include/bits/waitflags.h:
387 /usr/include/bits/waitstatus.h:
389 /usr/include/sys/types.h:
391 /usr/include/sys/select.h:
393 /usr/include/bits/select.h:
395 /usr/include/bits/sigset.h:
397 /usr/include/sys/sysmacros.h:
399 /usr/include/alloca.h:
401 alignment/../substitutionMatrix/globalmatrix.h:
403 alignment/../substitutionMatrix/SubMatrix.h:
405 alignment/../substitutionMatrix/../general/clustalw.h:
407 alignment/../substitutionMatrix/../general/userparams.h:
409 alignment/../substitutionMatrix/../general/UserParameters.h:
411 alignment/../substitutionMatrix/../general/utils.h:
413 alignment/../substitutionMatrix/../general/Utility.h:
415 /usr/include/libio.h:
417 /usr/include/_G_config.h:
419 /usr/include/bits/stdio_lim.h:
421 /usr/include/bits/sys_errlist.h:
423 /usr/include/bits/stdio.h:
425 /usr/include/string.h:
427 /usr/include/errno.h:
429 /usr/include/bits/errno.h:
431 /usr/include/linux/errno.h:
433 /usr/include/asm/errno.h:
435 /usr/include/asm-generic/errno.h:
437 /usr/include/asm-generic/errno-base.h:
439 alignment/../substitutionMatrix/../general/clustalw.h:
441 alignment/../substitutionMatrix/../general/general.h:
443 alignment/../substitutionMatrix/../general/utils.h:
445 alignment/../substitutionMatrix/../general/Array2D.h:
447 alignment/Alignment.h:
449 alignment/Sequence.h:
451 alignment/../general/userparams.h:
453 alignment/../general/utils.h:
455 alignment/../general/VectorOutOfRange.h:
457 alignment/../general/SequenceNotFoundException.h:
459 alignment/../general/debuglogObject.h:
461 alignment/../general/DebugLog.h:
463 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/fstream:
465 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/codecvt.h:
467 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdio:
469 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/basic_file.h:
471 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++io.h:
473 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/fstream.tcc: