1 FileParser.o FileParser.o: fileInput/FileParser.cpp config.h \
2 fileInput/FileParser.h /usr/include/ctype.h /usr/include/features.h \
3 /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
4 /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
5 /usr/include/bits/types.h \
6 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stddef.h \
7 /usr/include/bits/typesizes.h /usr/include/endian.h \
8 /usr/include/bits/endian.h /usr/include/xlocale.h \
9 fileInput/../alignment/Sequence.h \
10 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector \
11 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/functexcept.h \
12 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception_defines.h \
13 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algobase.h \
14 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h \
15 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h \
16 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h \
17 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstring \
18 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstddef \
19 /usr/include/string.h \
20 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/climits \
21 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/limits.h \
22 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/syslimits.h \
23 /usr/include/limits.h /usr/include/bits/posix1_lim.h \
24 /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
25 /usr/include/bits/posix2_lim.h /usr/include/bits/xopen_lim.h \
26 /usr/include/bits/stdio_lim.h \
27 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdlib \
28 /usr/include/stdlib.h /usr/include/bits/waitflags.h \
29 /usr/include/bits/waitstatus.h /usr/include/sys/types.h \
30 /usr/include/time.h /usr/include/sys/select.h \
31 /usr/include/bits/select.h /usr/include/bits/sigset.h \
32 /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
33 /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \
34 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iosfwd \
35 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++locale.h \
36 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdio \
37 /usr/include/stdio.h /usr/include/libio.h /usr/include/_G_config.h \
38 /usr/include/wchar.h /usr/include/bits/wchar.h /usr/include/gconv.h \
39 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stdarg.h \
40 /usr/include/bits/sys_errlist.h /usr/include/bits/stdio.h \
41 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/clocale \
42 /usr/include/locale.h /usr/include/bits/locale.h \
43 /usr/include/langinfo.h /usr/include/nl_types.h /usr/include/iconv.h \
44 /usr/include/libintl.h \
45 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++io.h \
46 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr.h \
47 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr-default.h \
48 /usr/include/pthread.h /usr/include/sched.h /usr/include/bits/sched.h \
49 /usr/include/signal.h /usr/include/bits/setjmp.h /usr/include/unistd.h \
50 /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \
51 /usr/include/bits/confname.h /usr/include/getopt.h \
52 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cctype \
53 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stringfwd.h \
54 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/postypes.h \
55 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwchar \
56 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ctime \
57 /usr/include/stdint.h \
58 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_pair.h \
59 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cpp_type_traits.h \
60 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_types.h \
61 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_funcs.h \
62 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/concept_check.h \
63 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator.h \
64 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/debug/debug.h \
65 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/allocator.h \
66 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++allocator.h \
67 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ext/new_allocator.h \
68 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/new \
69 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception \
70 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_construct.h \
71 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_uninitialized.h \
72 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_vector.h \
73 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_bvector.h \
74 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/vector.tcc \
75 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/string \
76 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/char_traits.h \
77 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/memory \
78 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_raw_storage_iter.h \
79 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/limits \
80 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_function.h \
81 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.h \
82 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/atomicity.h \
83 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/atomic_word.h \
84 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/algorithm \
85 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algo.h \
86 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_heap.h \
87 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_tempbuf.h \
88 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.tcc \
89 fileInput/../alignment/../general/userparams.h \
90 fileInput/../alignment/../general/UserParameters.h \
91 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream \
92 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ostream \
93 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ios \
94 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/localefwd.h \
95 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ios_base.h \
96 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_classes.h \
97 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/streambuf \
98 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf.tcc \
99 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.h \
100 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf_iterator.h \
101 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.h \
102 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwctype \
103 /usr/include/wctype.h \
104 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_base.h \
105 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_inline.h \
106 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/codecvt.h \
107 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/time_members.h \
108 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/messages_members.h \
109 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc \
110 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc \
111 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale \
112 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc \
113 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo \
114 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream \
115 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc \
116 fileInput/../alignment/../general/utils.h \
117 fileInput/../alignment/../general/Utility.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-x86_64/errno.h \
120 /usr/include/asm-generic/errno.h /usr/include/asm-generic/errno-base.h \
121 fileInput/../alignment/../general/clustalw.h \
122 fileInput/../alignment/../general/general.h \
123 fileInput/../alignment/../general/Array2D.h \
124 fileInput/../alignment/../general/SquareMat.h \
125 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip \
126 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional \
127 fileInput/../alignment/../general/SymMatrix.h \
128 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath \
129 /usr/include/math.h /usr/include/bits/huge_val.h \
130 /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \
131 /usr/include/bits/inf.h /usr/include/bits/nan.h \
132 /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \
133 /usr/include/bits/mathinline.h \
134 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc \
135 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept \
136 fileInput/../alignment/../general/utils.h \
137 fileInput/../general/userparams.h fileInput/InFileStream.h \
138 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/fstream \
139 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/basic_file.h \
140 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/fstream.tcc
144 fileInput/FileParser.h:
146 /usr/include/ctype.h:
148 /usr/include/features.h:
150 /usr/include/sys/cdefs.h:
152 /usr/include/bits/wordsize.h:
154 /usr/include/gnu/stubs.h:
156 /usr/include/gnu/stubs-64.h:
158 /usr/include/bits/types.h:
160 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stddef.h:
162 /usr/include/bits/typesizes.h:
164 /usr/include/endian.h:
166 /usr/include/bits/endian.h:
168 /usr/include/xlocale.h:
170 fileInput/../alignment/Sequence.h:
172 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector:
174 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/functexcept.h:
176 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception_defines.h:
178 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algobase.h:
180 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h:
182 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/os_defines.h:
184 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h:
186 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstring:
188 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstddef:
190 /usr/include/string.h:
192 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/climits:
194 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/limits.h:
196 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/syslimits.h:
198 /usr/include/limits.h:
200 /usr/include/bits/posix1_lim.h:
202 /usr/include/bits/local_lim.h:
204 /usr/include/linux/limits.h:
206 /usr/include/bits/posix2_lim.h:
208 /usr/include/bits/xopen_lim.h:
210 /usr/include/bits/stdio_lim.h:
212 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdlib:
214 /usr/include/stdlib.h:
216 /usr/include/bits/waitflags.h:
218 /usr/include/bits/waitstatus.h:
220 /usr/include/sys/types.h:
224 /usr/include/sys/select.h:
226 /usr/include/bits/select.h:
228 /usr/include/bits/sigset.h:
230 /usr/include/bits/time.h:
232 /usr/include/sys/sysmacros.h:
234 /usr/include/bits/pthreadtypes.h:
236 /usr/include/alloca.h:
238 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iosfwd:
240 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++locale.h:
242 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdio:
244 /usr/include/stdio.h:
246 /usr/include/libio.h:
248 /usr/include/_G_config.h:
250 /usr/include/wchar.h:
252 /usr/include/bits/wchar.h:
254 /usr/include/gconv.h:
256 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stdarg.h:
258 /usr/include/bits/sys_errlist.h:
260 /usr/include/bits/stdio.h:
262 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/clocale:
264 /usr/include/locale.h:
266 /usr/include/bits/locale.h:
268 /usr/include/langinfo.h:
270 /usr/include/nl_types.h:
272 /usr/include/iconv.h:
274 /usr/include/libintl.h:
276 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++io.h:
278 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr.h:
280 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr-default.h:
282 /usr/include/pthread.h:
284 /usr/include/sched.h:
286 /usr/include/bits/sched.h:
288 /usr/include/signal.h:
290 /usr/include/bits/setjmp.h:
292 /usr/include/unistd.h:
294 /usr/include/bits/posix_opt.h:
296 /usr/include/bits/environments.h:
298 /usr/include/bits/confname.h:
300 /usr/include/getopt.h:
302 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cctype:
304 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stringfwd.h:
306 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/postypes.h:
308 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwchar:
310 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ctime:
312 /usr/include/stdint.h:
314 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_pair.h:
316 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cpp_type_traits.h:
318 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_types.h:
320 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_funcs.h:
322 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/concept_check.h:
324 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator.h:
326 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/debug/debug.h:
328 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/allocator.h:
330 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++allocator.h:
332 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ext/new_allocator.h:
334 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/new:
336 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception:
338 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_construct.h:
340 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_uninitialized.h:
342 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_vector.h:
344 /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_bvector.h:
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