hops.o: hops.cc /usr/include/c++/4.6/fstream /usr/include/c++/4.6/istream \
 /usr/include/c++/4.6/ios /usr/include/c++/4.6/iosfwd \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/c++config.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/os_defines.h \
 /usr/include/features.h /usr/include/x86_64-linux-gnu/bits/predefs.h \
 /usr/include/x86_64-linux-gnu/sys/cdefs.h \
 /usr/include/x86_64-linux-gnu/bits/wordsize.h \
 /usr/include/x86_64-linux-gnu/gnu/stubs.h \
 /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/cpu_defines.h \
 /usr/include/c++/4.6/bits/stringfwd.h \
 /usr/include/c++/4.6/bits/postypes.h /usr/include/c++/4.6/cwchar \
 /usr/include/wchar.h /usr/include/stdio.h \
 /usr/lib/gcc/x86_64-linux-gnu/4.6/include/stdarg.h \
 /usr/include/x86_64-linux-gnu/bits/wchar.h \
 /usr/lib/gcc/x86_64-linux-gnu/4.6/include/stddef.h \
 /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \
 /usr/include/c++/4.6/exception /usr/include/c++/4.6/bits/char_traits.h \
 /usr/include/c++/4.6/bits/stl_algobase.h \
 /usr/include/c++/4.6/bits/functexcept.h \
 /usr/include/c++/4.6/bits/exception_defines.h \
 /usr/include/c++/4.6/bits/cpp_type_traits.h \
 /usr/include/c++/4.6/ext/type_traits.h \
 /usr/include/c++/4.6/ext/numeric_traits.h \
 /usr/include/c++/4.6/bits/stl_pair.h /usr/include/c++/4.6/bits/move.h \
 /usr/include/c++/4.6/bits/concept_check.h \
 /usr/include/c++/4.6/bits/stl_iterator_base_types.h \
 /usr/include/c++/4.6/bits/stl_iterator_base_funcs.h \
 /usr/include/c++/4.6/bits/stl_iterator.h \
 /usr/include/c++/4.6/debug/debug.h /usr/include/c++/4.6/bits/localefwd.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/c++locale.h \
 /usr/include/c++/4.6/clocale /usr/include/locale.h \
 /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.6/cctype \
 /usr/include/ctype.h /usr/include/x86_64-linux-gnu/bits/types.h \
 /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \
 /usr/include/x86_64-linux-gnu/bits/endian.h \
 /usr/include/x86_64-linux-gnu/bits/byteswap.h \
 /usr/include/c++/4.6/bits/ios_base.h \
 /usr/include/c++/4.6/ext/atomicity.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/gthr.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/gthr-default.h \
 /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
 /usr/include/x86_64-linux-gnu/bits/sched.h \
 /usr/include/x86_64-linux-gnu/bits/time.h \
 /usr/include/x86_64-linux-gnu/bits/timex.h \
 /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \
 /usr/include/x86_64-linux-gnu/bits/setjmp.h /usr/include/unistd.h \
 /usr/include/x86_64-linux-gnu/bits/posix_opt.h \
 /usr/include/x86_64-linux-gnu/bits/environments.h \
 /usr/include/x86_64-linux-gnu/bits/confname.h /usr/include/getopt.h \
 /usr/include/x86_64-linux-gnu/bits/unistd.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/atomic_word.h \
 /usr/include/c++/4.6/bits/locale_classes.h /usr/include/c++/4.6/string \
 /usr/include/c++/4.6/bits/allocator.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/c++allocator.h \
 /usr/include/c++/4.6/ext/new_allocator.h /usr/include/c++/4.6/new \
 /usr/include/c++/4.6/bits/ostream_insert.h \
 /usr/include/c++/4.6/bits/cxxabi_forced.h \
 /usr/include/c++/4.6/bits/stl_function.h \
 /usr/include/c++/4.6/backward/binders.h \
 /usr/include/c++/4.6/bits/range_access.h \
 /usr/include/c++/4.6/bits/basic_string.h \
 /usr/include/c++/4.6/initializer_list \
 /usr/include/c++/4.6/bits/basic_string.tcc \
 /usr/include/c++/4.6/bits/locale_classes.tcc \
 /usr/include/c++/4.6/streambuf /usr/include/c++/4.6/bits/streambuf.tcc \
 /usr/include/c++/4.6/bits/basic_ios.h \
 /usr/include/c++/4.6/bits/locale_facets.h /usr/include/c++/4.6/cwctype \
 /usr/include/wctype.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/ctype_base.h \
 /usr/include/c++/4.6/bits/streambuf_iterator.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/ctype_inline.h \
 /usr/include/c++/4.6/bits/locale_facets.tcc \
 /usr/include/c++/4.6/bits/basic_ios.tcc /usr/include/c++/4.6/ostream \
 /usr/include/c++/4.6/bits/ostream.tcc \
 /usr/include/c++/4.6/bits/istream.tcc \
 /usr/include/c++/4.6/bits/codecvt.h /usr/include/c++/4.6/cstdio \
 /usr/include/libio.h /usr/include/_G_config.h \
 /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
 /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
 /usr/include/x86_64-linux-gnu/bits/stdio.h \
 /usr/include/x86_64-linux-gnu/bits/stdio2.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/basic_file.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/c++io.h \
 /usr/include/c++/4.6/bits/fstream.tcc Hops.h ../tools2/debug.h \
 /usr/include/stdlib.h /usr/include/x86_64-linux-gnu/bits/waitflags.h \
 /usr/include/x86_64-linux-gnu/bits/waitstatus.h \
 /usr/include/x86_64-linux-gnu/sys/types.h \
 /usr/include/x86_64-linux-gnu/sys/select.h \
 /usr/include/x86_64-linux-gnu/bits/select.h \
 /usr/include/x86_64-linux-gnu/bits/sigset.h \
 /usr/include/x86_64-linux-gnu/bits/select2.h \
 /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \
 /usr/include/x86_64-linux-gnu/bits/stdlib.h \
 /usr/include/c++/4.6/iostream /usr/include/assert.h ../tools2/Vec.h \
 /usr/include/libintl.h /usr/include/c++/4.6/vector \
 /usr/include/c++/4.6/bits/stl_construct.h \
 /usr/include/c++/4.6/bits/stl_uninitialized.h \
 /usr/include/c++/4.6/bits/stl_vector.h \
 /usr/include/c++/4.6/bits/stl_bvector.h \
 /usr/include/c++/4.6/bits/vector.tcc RnaSecondaryStructure.h \
 /usr/include/c++/4.6/set /usr/include/c++/4.6/bits/stl_tree.h \
 /usr/include/c++/4.6/bits/stl_set.h \
 /usr/include/c++/4.6/bits/stl_multiset.h Stem.h /usr/include/math.h \
 /usr/include/x86_64-linux-gnu/bits/huge_val.h \
 /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
 /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
 /usr/include/x86_64-linux-gnu/bits/inf.h \
 /usr/include/x86_64-linux-gnu/bits/nan.h \
 /usr/include/x86_64-linux-gnu/bits/mathdef.h \
 /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
 /usr/include/x86_64-linux-gnu/bits/mathinline.h \
 /usr/include/x86_64-linux-gnu/bits/math-finite.h \
 AbstractSecondaryStructure.h RnaInteractionType.h ../tools2/GetArg.h \
 /usr/include/string.h /usr/include/x86_64-linux-gnu/bits/string3.h \
 /usr/include/c++/4.6/cstdarg ../tools2/StringTools.h \
 /usr/include/c++/4.6/sstream /usr/include/c++/4.6/bits/sstream.tcc \
 /usr/include/c++/4.6/cstdlib /usr/include/malloc.h \
 RnaSecondaryStructureTools.h stemhelp.h ../numerics/RankedSolution5.h \
 /usr/include/c++/4.6/stack /usr/include/c++/4.6/deque \
 /usr/include/c++/4.6/bits/stl_deque.h \
 /usr/include/c++/4.6/bits/deque.tcc \
 /usr/include/c++/4.6/bits/stl_stack.h ../numerics/vectornumerics.h \
 /usr/lib/gcc/x86_64-linux-gnu/4.6/include-fixed/limits.h \
 /usr/lib/gcc/x86_64-linux-gnu/4.6/include-fixed/syslimits.h \
 /usr/include/limits.h /usr/include/x86_64-linux-gnu/bits/posix1_lim.h \
 /usr/include/x86_64-linux-gnu/bits/local_lim.h \
 /usr/include/linux/limits.h \
 /usr/include/x86_64-linux-gnu/bits/posix2_lim.h \
 /usr/include/x86_64-linux-gnu/bits/xopen_lim.h /usr/include/c++/4.6/list \
 /usr/include/c++/4.6/bits/stl_list.h /usr/include/c++/4.6/bits/list.tcc \
 /usr/include/c++/4.6/algorithm /usr/include/c++/4.6/utility \
 /usr/include/c++/4.6/bits/stl_relops.h \
 /usr/include/c++/4.6/bits/stl_algo.h \
 /usr/include/c++/4.6/bits/algorithmfwd.h \
 /usr/include/c++/4.6/bits/stl_heap.h \
 /usr/include/c++/4.6/bits/stl_tempbuf.h ../numerics/Matrix3D.h \
 ../numerics/Vector3D.h ../numerics/Limits.h \
 ../numerics/RankedSolution4.h ../numerics/generalNumerics.h \
 ../sequence/SimpleSequenceAlignment.h ../sequence/SequenceAlignment.h \
 /usr/include/c++/4.6/map /usr/include/c++/4.6/bits/stl_map.h \
 /usr/include/c++/4.6/bits/stl_multimap.h
stemhelptest.o: stemhelptest.cc stemhelp.h /usr/include/c++/4.6/iostream \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/c++config.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/os_defines.h \
 /usr/include/features.h /usr/include/x86_64-linux-gnu/bits/predefs.h \
 /usr/include/x86_64-linux-gnu/sys/cdefs.h \
 /usr/include/x86_64-linux-gnu/bits/wordsize.h \
 /usr/include/x86_64-linux-gnu/gnu/stubs.h \
 /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/cpu_defines.h \
 /usr/include/c++/4.6/ostream /usr/include/c++/4.6/ios \
 /usr/include/c++/4.6/iosfwd /usr/include/c++/4.6/bits/stringfwd.h \
 /usr/include/c++/4.6/bits/postypes.h /usr/include/c++/4.6/cwchar \
 /usr/include/wchar.h /usr/include/stdio.h \
 /usr/lib/gcc/x86_64-linux-gnu/4.6/include/stdarg.h \
 /usr/include/x86_64-linux-gnu/bits/wchar.h \
 /usr/lib/gcc/x86_64-linux-gnu/4.6/include/stddef.h \
 /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \
 /usr/include/c++/4.6/exception /usr/include/c++/4.6/bits/char_traits.h \
 /usr/include/c++/4.6/bits/stl_algobase.h \
 /usr/include/c++/4.6/bits/functexcept.h \
 /usr/include/c++/4.6/bits/exception_defines.h \
 /usr/include/c++/4.6/bits/cpp_type_traits.h \
 /usr/include/c++/4.6/ext/type_traits.h \
 /usr/include/c++/4.6/ext/numeric_traits.h \
 /usr/include/c++/4.6/bits/stl_pair.h /usr/include/c++/4.6/bits/move.h \
 /usr/include/c++/4.6/bits/concept_check.h \
 /usr/include/c++/4.6/bits/stl_iterator_base_types.h \
 /usr/include/c++/4.6/bits/stl_iterator_base_funcs.h \
 /usr/include/c++/4.6/bits/stl_iterator.h \
 /usr/include/c++/4.6/debug/debug.h /usr/include/c++/4.6/bits/localefwd.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/c++locale.h \
 /usr/include/c++/4.6/clocale /usr/include/locale.h \
 /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.6/cctype \
 /usr/include/ctype.h /usr/include/x86_64-linux-gnu/bits/types.h \
 /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \
 /usr/include/x86_64-linux-gnu/bits/endian.h \
 /usr/include/x86_64-linux-gnu/bits/byteswap.h \
 /usr/include/c++/4.6/bits/ios_base.h \
 /usr/include/c++/4.6/ext/atomicity.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/gthr.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/gthr-default.h \
 /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
 /usr/include/x86_64-linux-gnu/bits/sched.h \
 /usr/include/x86_64-linux-gnu/bits/time.h \
 /usr/include/x86_64-linux-gnu/bits/timex.h \
 /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \
 /usr/include/x86_64-linux-gnu/bits/setjmp.h /usr/include/unistd.h \
 /usr/include/x86_64-linux-gnu/bits/posix_opt.h \
 /usr/include/x86_64-linux-gnu/bits/environments.h \
 /usr/include/x86_64-linux-gnu/bits/confname.h /usr/include/getopt.h \
 /usr/include/x86_64-linux-gnu/bits/unistd.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/atomic_word.h \
 /usr/include/c++/4.6/bits/locale_classes.h /usr/include/c++/4.6/string \
 /usr/include/c++/4.6/bits/allocator.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/c++allocator.h \
 /usr/include/c++/4.6/ext/new_allocator.h /usr/include/c++/4.6/new \
 /usr/include/c++/4.6/bits/ostream_insert.h \
 /usr/include/c++/4.6/bits/cxxabi_forced.h \
 /usr/include/c++/4.6/bits/stl_function.h \
 /usr/include/c++/4.6/backward/binders.h \
 /usr/include/c++/4.6/bits/range_access.h \
 /usr/include/c++/4.6/bits/basic_string.h \
 /usr/include/c++/4.6/initializer_list \
 /usr/include/c++/4.6/bits/basic_string.tcc \
 /usr/include/c++/4.6/bits/locale_classes.tcc \
 /usr/include/c++/4.6/streambuf /usr/include/c++/4.6/bits/streambuf.tcc \
 /usr/include/c++/4.6/bits/basic_ios.h \
 /usr/include/c++/4.6/bits/locale_facets.h /usr/include/c++/4.6/cwctype \
 /usr/include/wctype.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/ctype_base.h \
 /usr/include/c++/4.6/bits/streambuf_iterator.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/ctype_inline.h \
 /usr/include/c++/4.6/bits/locale_facets.tcc \
 /usr/include/c++/4.6/bits/basic_ios.tcc \
 /usr/include/c++/4.6/bits/ostream.tcc /usr/include/c++/4.6/istream \
 /usr/include/c++/4.6/bits/istream.tcc ../tools2/Vec.h \
 /usr/include/libintl.h /usr/include/c++/4.6/vector \
 /usr/include/c++/4.6/bits/stl_construct.h \
 /usr/include/c++/4.6/bits/stl_uninitialized.h \
 /usr/include/c++/4.6/bits/stl_vector.h \
 /usr/include/c++/4.6/bits/stl_bvector.h \
 /usr/include/c++/4.6/bits/vector.tcc ../tools2/debug.h \
 /usr/include/stdlib.h /usr/include/x86_64-linux-gnu/bits/waitflags.h \
 /usr/include/x86_64-linux-gnu/bits/waitstatus.h \
 /usr/include/x86_64-linux-gnu/sys/types.h \
 /usr/include/x86_64-linux-gnu/sys/select.h \
 /usr/include/x86_64-linux-gnu/bits/select.h \
 /usr/include/x86_64-linux-gnu/bits/sigset.h \
 /usr/include/x86_64-linux-gnu/bits/select2.h \
 /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \
 /usr/include/x86_64-linux-gnu/bits/stdlib.h /usr/include/assert.h Stem.h \
 /usr/include/math.h /usr/include/x86_64-linux-gnu/bits/huge_val.h \
 /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
 /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
 /usr/include/x86_64-linux-gnu/bits/inf.h \
 /usr/include/x86_64-linux-gnu/bits/nan.h \
 /usr/include/x86_64-linux-gnu/bits/mathdef.h \
 /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
 /usr/include/x86_64-linux-gnu/bits/mathinline.h \
 /usr/include/x86_64-linux-gnu/bits/math-finite.h \
 ../numerics/RankedSolution5.h /usr/include/c++/4.6/stack \
 /usr/include/c++/4.6/deque /usr/include/c++/4.6/bits/stl_deque.h \
 /usr/include/c++/4.6/bits/deque.tcc \
 /usr/include/c++/4.6/bits/stl_stack.h RnaSecondaryStructure.h \
 /usr/include/c++/4.6/set /usr/include/c++/4.6/bits/stl_tree.h \
 /usr/include/c++/4.6/bits/stl_set.h \
 /usr/include/c++/4.6/bits/stl_multiset.h AbstractSecondaryStructure.h \
 RnaInteractionType.h
alidisc.o: alidisc.cc /usr/include/c++/4.6/iostream \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/c++config.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/os_defines.h \
 /usr/include/features.h /usr/include/x86_64-linux-gnu/bits/predefs.h \
 /usr/include/x86_64-linux-gnu/sys/cdefs.h \
 /usr/include/x86_64-linux-gnu/bits/wordsize.h \
 /usr/include/x86_64-linux-gnu/gnu/stubs.h \
 /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/cpu_defines.h \
 /usr/include/c++/4.6/ostream /usr/include/c++/4.6/ios \
 /usr/include/c++/4.6/iosfwd /usr/include/c++/4.6/bits/stringfwd.h \
 /usr/include/c++/4.6/bits/postypes.h /usr/include/c++/4.6/cwchar \
 /usr/include/wchar.h /usr/include/stdio.h \
 /usr/lib/gcc/x86_64-linux-gnu/4.6/include/stdarg.h \
 /usr/include/x86_64-linux-gnu/bits/wchar.h \
 /usr/lib/gcc/x86_64-linux-gnu/4.6/include/stddef.h \
 /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \
 /usr/include/c++/4.6/exception /usr/include/c++/4.6/bits/char_traits.h \
 /usr/include/c++/4.6/bits/stl_algobase.h \
 /usr/include/c++/4.6/bits/functexcept.h \
 /usr/include/c++/4.6/bits/exception_defines.h \
 /usr/include/c++/4.6/bits/cpp_type_traits.h \
 /usr/include/c++/4.6/ext/type_traits.h \
 /usr/include/c++/4.6/ext/numeric_traits.h \
 /usr/include/c++/4.6/bits/stl_pair.h /usr/include/c++/4.6/bits/move.h \
 /usr/include/c++/4.6/bits/concept_check.h \
 /usr/include/c++/4.6/bits/stl_iterator_base_types.h \
 /usr/include/c++/4.6/bits/stl_iterator_base_funcs.h \
 /usr/include/c++/4.6/bits/stl_iterator.h \
 /usr/include/c++/4.6/debug/debug.h /usr/include/c++/4.6/bits/localefwd.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/c++locale.h \
 /usr/include/c++/4.6/clocale /usr/include/locale.h \
 /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.6/cctype \
 /usr/include/ctype.h /usr/include/x86_64-linux-gnu/bits/types.h \
 /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \
 /usr/include/x86_64-linux-gnu/bits/endian.h \
 /usr/include/x86_64-linux-gnu/bits/byteswap.h \
 /usr/include/c++/4.6/bits/ios_base.h \
 /usr/include/c++/4.6/ext/atomicity.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/gthr.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/gthr-default.h \
 /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
 /usr/include/x86_64-linux-gnu/bits/sched.h \
 /usr/include/x86_64-linux-gnu/bits/time.h \
 /usr/include/x86_64-linux-gnu/bits/timex.h \
 /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \
 /usr/include/x86_64-linux-gnu/bits/setjmp.h /usr/include/unistd.h \
 /usr/include/x86_64-linux-gnu/bits/posix_opt.h \
 /usr/include/x86_64-linux-gnu/bits/environments.h \
 /usr/include/x86_64-linux-gnu/bits/confname.h /usr/include/getopt.h \
 /usr/include/x86_64-linux-gnu/bits/unistd.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/atomic_word.h \
 /usr/include/c++/4.6/bits/locale_classes.h /usr/include/c++/4.6/string \
 /usr/include/c++/4.6/bits/allocator.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/c++allocator.h \
 /usr/include/c++/4.6/ext/new_allocator.h /usr/include/c++/4.6/new \
 /usr/include/c++/4.6/bits/ostream_insert.h \
 /usr/include/c++/4.6/bits/cxxabi_forced.h \
 /usr/include/c++/4.6/bits/stl_function.h \
 /usr/include/c++/4.6/backward/binders.h \
 /usr/include/c++/4.6/bits/range_access.h \
 /usr/include/c++/4.6/bits/basic_string.h \
 /usr/include/c++/4.6/initializer_list \
 /usr/include/c++/4.6/bits/basic_string.tcc \
 /usr/include/c++/4.6/bits/locale_classes.tcc \
 /usr/include/c++/4.6/streambuf /usr/include/c++/4.6/bits/streambuf.tcc \
 /usr/include/c++/4.6/bits/basic_ios.h \
 /usr/include/c++/4.6/bits/locale_facets.h /usr/include/c++/4.6/cwctype \
 /usr/include/wctype.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/ctype_base.h \
 /usr/include/c++/4.6/bits/streambuf_iterator.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/ctype_inline.h \
 /usr/include/c++/4.6/bits/locale_facets.tcc \
 /usr/include/c++/4.6/bits/basic_ios.tcc \
 /usr/include/c++/4.6/bits/ostream.tcc /usr/include/c++/4.6/istream \
 /usr/include/c++/4.6/bits/istream.tcc /usr/include/c++/4.6/fstream \
 /usr/include/c++/4.6/bits/codecvt.h /usr/include/c++/4.6/cstdio \
 /usr/include/libio.h /usr/include/_G_config.h \
 /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
 /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
 /usr/include/x86_64-linux-gnu/bits/stdio.h \
 /usr/include/x86_64-linux-gnu/bits/stdio2.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/basic_file.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/c++io.h \
 /usr/include/c++/4.6/bits/fstream.tcc ../tools2/Vec.h \
 /usr/include/libintl.h /usr/include/c++/4.6/vector \
 /usr/include/c++/4.6/bits/stl_construct.h \
 /usr/include/c++/4.6/bits/stl_uninitialized.h \
 /usr/include/c++/4.6/bits/stl_vector.h \
 /usr/include/c++/4.6/bits/stl_bvector.h \
 /usr/include/c++/4.6/bits/vector.tcc ../tools2/debug.h \
 /usr/include/stdlib.h /usr/include/x86_64-linux-gnu/bits/waitflags.h \
 /usr/include/x86_64-linux-gnu/bits/waitstatus.h \
 /usr/include/x86_64-linux-gnu/sys/types.h \
 /usr/include/x86_64-linux-gnu/sys/select.h \
 /usr/include/x86_64-linux-gnu/bits/select.h \
 /usr/include/x86_64-linux-gnu/bits/sigset.h \
 /usr/include/x86_64-linux-gnu/bits/select2.h \
 /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \
 /usr/include/x86_64-linux-gnu/bits/stdlib.h /usr/include/assert.h \
 ../tools2/GetArg.h /usr/include/string.h \
 /usr/include/x86_64-linux-gnu/bits/string3.h \
 /usr/include/c++/4.6/cstdarg ../tools2/StringTools.h \
 /usr/include/c++/4.6/sstream /usr/include/c++/4.6/bits/sstream.tcc \
 /usr/include/c++/4.6/cstdlib /usr/include/malloc.h ../tools2/FileName.h \
 CompensationScorer.h ../numerics/generalNumerics.h /usr/include/math.h \
 /usr/include/x86_64-linux-gnu/bits/huge_val.h \
 /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
 /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
 /usr/include/x86_64-linux-gnu/bits/inf.h \
 /usr/include/x86_64-linux-gnu/bits/nan.h \
 /usr/include/x86_64-linux-gnu/bits/mathdef.h \
 /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
 /usr/include/x86_64-linux-gnu/bits/mathinline.h \
 /usr/include/x86_64-linux-gnu/bits/math-finite.h ../tools2/Random.h \
 /usr/include/c++/4.6/utility /usr/include/c++/4.6/bits/stl_relops.h \
 ../sequence/SequenceAlignment.h /usr/include/c++/4.6/map \
 /usr/include/c++/4.6/bits/stl_tree.h /usr/include/c++/4.6/bits/stl_map.h \
 /usr/include/c++/4.6/bits/stl_multimap.h \
 ../sequence/SimpleSequenceAlignment.h /usr/include/c++/4.6/iomanip \
 ../numerics/vectornumerics.h \
 /usr/lib/gcc/x86_64-linux-gnu/4.6/include-fixed/limits.h \
 /usr/lib/gcc/x86_64-linux-gnu/4.6/include-fixed/syslimits.h \
 /usr/include/limits.h /usr/include/x86_64-linux-gnu/bits/posix1_lim.h \
 /usr/include/x86_64-linux-gnu/bits/local_lim.h \
 /usr/include/linux/limits.h \
 /usr/include/x86_64-linux-gnu/bits/posix2_lim.h \
 /usr/include/x86_64-linux-gnu/bits/xopen_lim.h /usr/include/c++/4.6/list \
 /usr/include/c++/4.6/bits/stl_list.h /usr/include/c++/4.6/bits/list.tcc \
 /usr/include/c++/4.6/set /usr/include/c++/4.6/bits/stl_set.h \
 /usr/include/c++/4.6/bits/stl_multiset.h /usr/include/c++/4.6/algorithm \
 /usr/include/c++/4.6/bits/stl_algo.h \
 /usr/include/c++/4.6/bits/algorithmfwd.h \
 /usr/include/c++/4.6/bits/stl_heap.h \
 /usr/include/c++/4.6/bits/stl_tempbuf.h ../numerics/Matrix3D.h \
 ../numerics/Vector3D.h ../numerics/Limits.h \
 ../numerics/RankedSolution4.h
ranksec.o: ranksec.cc /usr/include/c++/4.6/iostream \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/c++config.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/os_defines.h \
 /usr/include/features.h /usr/include/x86_64-linux-gnu/bits/predefs.h \
 /usr/include/x86_64-linux-gnu/sys/cdefs.h \
 /usr/include/x86_64-linux-gnu/bits/wordsize.h \
 /usr/include/x86_64-linux-gnu/gnu/stubs.h \
 /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/cpu_defines.h \
 /usr/include/c++/4.6/ostream /usr/include/c++/4.6/ios \
 /usr/include/c++/4.6/iosfwd /usr/include/c++/4.6/bits/stringfwd.h \
 /usr/include/c++/4.6/bits/postypes.h /usr/include/c++/4.6/cwchar \
 /usr/include/wchar.h /usr/include/stdio.h \
 /usr/lib/gcc/x86_64-linux-gnu/4.6/include/stdarg.h \
 /usr/include/x86_64-linux-gnu/bits/wchar.h \
 /usr/lib/gcc/x86_64-linux-gnu/4.6/include/stddef.h \
 /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \
 /usr/include/c++/4.6/exception /usr/include/c++/4.6/bits/char_traits.h \
 /usr/include/c++/4.6/bits/stl_algobase.h \
 /usr/include/c++/4.6/bits/functexcept.h \
 /usr/include/c++/4.6/bits/exception_defines.h \
 /usr/include/c++/4.6/bits/cpp_type_traits.h \
 /usr/include/c++/4.6/ext/type_traits.h \
 /usr/include/c++/4.6/ext/numeric_traits.h \
 /usr/include/c++/4.6/bits/stl_pair.h /usr/include/c++/4.6/bits/move.h \
 /usr/include/c++/4.6/bits/concept_check.h \
 /usr/include/c++/4.6/bits/stl_iterator_base_types.h \
 /usr/include/c++/4.6/bits/stl_iterator_base_funcs.h \
 /usr/include/c++/4.6/bits/stl_iterator.h \
 /usr/include/c++/4.6/debug/debug.h /usr/include/c++/4.6/bits/localefwd.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/c++locale.h \
 /usr/include/c++/4.6/clocale /usr/include/locale.h \
 /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.6/cctype \
 /usr/include/ctype.h /usr/include/x86_64-linux-gnu/bits/types.h \
 /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \
 /usr/include/x86_64-linux-gnu/bits/endian.h \
 /usr/include/x86_64-linux-gnu/bits/byteswap.h \
 /usr/include/c++/4.6/bits/ios_base.h \
 /usr/include/c++/4.6/ext/atomicity.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/gthr.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/gthr-default.h \
 /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
 /usr/include/x86_64-linux-gnu/bits/sched.h \
 /usr/include/x86_64-linux-gnu/bits/time.h \
 /usr/include/x86_64-linux-gnu/bits/timex.h \
 /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \
 /usr/include/x86_64-linux-gnu/bits/setjmp.h /usr/include/unistd.h \
 /usr/include/x86_64-linux-gnu/bits/posix_opt.h \
 /usr/include/x86_64-linux-gnu/bits/environments.h \
 /usr/include/x86_64-linux-gnu/bits/confname.h /usr/include/getopt.h \
 /usr/include/x86_64-linux-gnu/bits/unistd.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/atomic_word.h \
 /usr/include/c++/4.6/bits/locale_classes.h /usr/include/c++/4.6/string \
 /usr/include/c++/4.6/bits/allocator.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/c++allocator.h \
 /usr/include/c++/4.6/ext/new_allocator.h /usr/include/c++/4.6/new \
 /usr/include/c++/4.6/bits/ostream_insert.h \
 /usr/include/c++/4.6/bits/cxxabi_forced.h \
 /usr/include/c++/4.6/bits/stl_function.h \
 /usr/include/c++/4.6/backward/binders.h \
 /usr/include/c++/4.6/bits/range_access.h \
 /usr/include/c++/4.6/bits/basic_string.h \
 /usr/include/c++/4.6/initializer_list \
 /usr/include/c++/4.6/bits/basic_string.tcc \
 /usr/include/c++/4.6/bits/locale_classes.tcc \
 /usr/include/c++/4.6/streambuf /usr/include/c++/4.6/bits/streambuf.tcc \
 /usr/include/c++/4.6/bits/basic_ios.h \
 /usr/include/c++/4.6/bits/locale_facets.h /usr/include/c++/4.6/cwctype \
 /usr/include/wctype.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/ctype_base.h \
 /usr/include/c++/4.6/bits/streambuf_iterator.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/ctype_inline.h \
 /usr/include/c++/4.6/bits/locale_facets.tcc \
 /usr/include/c++/4.6/bits/basic_ios.tcc \
 /usr/include/c++/4.6/bits/ostream.tcc /usr/include/c++/4.6/istream \
 /usr/include/c++/4.6/bits/istream.tcc /usr/include/c++/4.6/fstream \
 /usr/include/c++/4.6/bits/codecvt.h /usr/include/c++/4.6/cstdio \
 /usr/include/libio.h /usr/include/_G_config.h \
 /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
 /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
 /usr/include/x86_64-linux-gnu/bits/stdio.h \
 /usr/include/x86_64-linux-gnu/bits/stdio2.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/basic_file.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/c++io.h \
 /usr/include/c++/4.6/bits/fstream.tcc ../tools2/Vec.h \
 /usr/include/libintl.h /usr/include/c++/4.6/vector \
 /usr/include/c++/4.6/bits/stl_construct.h \
 /usr/include/c++/4.6/bits/stl_uninitialized.h \
 /usr/include/c++/4.6/bits/stl_vector.h \
 /usr/include/c++/4.6/bits/stl_bvector.h \
 /usr/include/c++/4.6/bits/vector.tcc ../tools2/debug.h \
 /usr/include/stdlib.h /usr/include/x86_64-linux-gnu/bits/waitflags.h \
 /usr/include/x86_64-linux-gnu/bits/waitstatus.h \
 /usr/include/x86_64-linux-gnu/sys/types.h \
 /usr/include/x86_64-linux-gnu/sys/select.h \
 /usr/include/x86_64-linux-gnu/bits/select.h \
 /usr/include/x86_64-linux-gnu/bits/sigset.h \
 /usr/include/x86_64-linux-gnu/bits/select2.h \
 /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \
 /usr/include/x86_64-linux-gnu/bits/stdlib.h /usr/include/assert.h \
 ../tools2/GetArg.h /usr/include/string.h \
 /usr/include/x86_64-linux-gnu/bits/string3.h \
 /usr/include/c++/4.6/cstdarg ../tools2/StringTools.h \
 /usr/include/c++/4.6/sstream /usr/include/c++/4.6/bits/sstream.tcc \
 /usr/include/c++/4.6/cstdlib /usr/include/malloc.h ../tools2/FileName.h \
 Stem.h /usr/include/math.h /usr/include/x86_64-linux-gnu/bits/huge_val.h \
 /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
 /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
 /usr/include/x86_64-linux-gnu/bits/inf.h \
 /usr/include/x86_64-linux-gnu/bits/nan.h \
 /usr/include/x86_64-linux-gnu/bits/mathdef.h \
 /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
 /usr/include/x86_64-linux-gnu/bits/mathinline.h \
 /usr/include/x86_64-linux-gnu/bits/math-finite.h stemhelp.h \
 ../numerics/RankedSolution5.h /usr/include/c++/4.6/stack \
 /usr/include/c++/4.6/deque /usr/include/c++/4.6/bits/stl_deque.h \
 /usr/include/c++/4.6/bits/deque.tcc \
 /usr/include/c++/4.6/bits/stl_stack.h RnaSecondaryStructure.h \
 /usr/include/c++/4.6/set /usr/include/c++/4.6/bits/stl_tree.h \
 /usr/include/c++/4.6/bits/stl_set.h \
 /usr/include/c++/4.6/bits/stl_multiset.h AbstractSecondaryStructure.h \
 RnaInteractionType.h ../numerics/vectornumerics.h \
 /usr/lib/gcc/x86_64-linux-gnu/4.6/include-fixed/limits.h \
 /usr/lib/gcc/x86_64-linux-gnu/4.6/include-fixed/syslimits.h \
 /usr/include/limits.h /usr/include/x86_64-linux-gnu/bits/posix1_lim.h \
 /usr/include/x86_64-linux-gnu/bits/local_lim.h \
 /usr/include/linux/limits.h \
 /usr/include/x86_64-linux-gnu/bits/posix2_lim.h \
 /usr/include/x86_64-linux-gnu/bits/xopen_lim.h /usr/include/c++/4.6/list \
 /usr/include/c++/4.6/bits/stl_list.h /usr/include/c++/4.6/bits/list.tcc \
 /usr/include/c++/4.6/algorithm /usr/include/c++/4.6/utility \
 /usr/include/c++/4.6/bits/stl_relops.h \
 /usr/include/c++/4.6/bits/stl_algo.h \
 /usr/include/c++/4.6/bits/algorithmfwd.h \
 /usr/include/c++/4.6/bits/stl_heap.h \
 /usr/include/c++/4.6/bits/stl_tempbuf.h ../numerics/Matrix3D.h \
 ../numerics/Vector3D.h ../numerics/Limits.h \
 ../numerics/RankedSolution4.h ../numerics/generalNumerics.h \
 ../sequence/SequenceAlignment.h /usr/include/c++/4.6/map \
 /usr/include/c++/4.6/bits/stl_map.h \
 /usr/include/c++/4.6/bits/stl_multimap.h \
 ../sequence/SimpleSequenceAlignment.h
rescalescores.o: rescalescores.cc /usr/include/c++/4.6/iostream \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/c++config.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/os_defines.h \
 /usr/include/features.h /usr/include/x86_64-linux-gnu/bits/predefs.h \
 /usr/include/x86_64-linux-gnu/sys/cdefs.h \
 /usr/include/x86_64-linux-gnu/bits/wordsize.h \
 /usr/include/x86_64-linux-gnu/gnu/stubs.h \
 /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/cpu_defines.h \
 /usr/include/c++/4.6/ostream /usr/include/c++/4.6/ios \
 /usr/include/c++/4.6/iosfwd /usr/include/c++/4.6/bits/stringfwd.h \
 /usr/include/c++/4.6/bits/postypes.h /usr/include/c++/4.6/cwchar \
 /usr/include/wchar.h /usr/include/stdio.h \
 /usr/lib/gcc/x86_64-linux-gnu/4.6/include/stdarg.h \
 /usr/include/x86_64-linux-gnu/bits/wchar.h \
 /usr/lib/gcc/x86_64-linux-gnu/4.6/include/stddef.h \
 /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \
 /usr/include/c++/4.6/exception /usr/include/c++/4.6/bits/char_traits.h \
 /usr/include/c++/4.6/bits/stl_algobase.h \
 /usr/include/c++/4.6/bits/functexcept.h \
 /usr/include/c++/4.6/bits/exception_defines.h \
 /usr/include/c++/4.6/bits/cpp_type_traits.h \
 /usr/include/c++/4.6/ext/type_traits.h \
 /usr/include/c++/4.6/ext/numeric_traits.h \
 /usr/include/c++/4.6/bits/stl_pair.h /usr/include/c++/4.6/bits/move.h \
 /usr/include/c++/4.6/bits/concept_check.h \
 /usr/include/c++/4.6/bits/stl_iterator_base_types.h \
 /usr/include/c++/4.6/bits/stl_iterator_base_funcs.h \
 /usr/include/c++/4.6/bits/stl_iterator.h \
 /usr/include/c++/4.6/debug/debug.h /usr/include/c++/4.6/bits/localefwd.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/c++locale.h \
 /usr/include/c++/4.6/clocale /usr/include/locale.h \
 /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.6/cctype \
 /usr/include/ctype.h /usr/include/x86_64-linux-gnu/bits/types.h \
 /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \
 /usr/include/x86_64-linux-gnu/bits/endian.h \
 /usr/include/x86_64-linux-gnu/bits/byteswap.h \
 /usr/include/c++/4.6/bits/ios_base.h \
 /usr/include/c++/4.6/ext/atomicity.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/gthr.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/gthr-default.h \
 /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
 /usr/include/x86_64-linux-gnu/bits/sched.h \
 /usr/include/x86_64-linux-gnu/bits/time.h \
 /usr/include/x86_64-linux-gnu/bits/timex.h \
 /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \
 /usr/include/x86_64-linux-gnu/bits/setjmp.h /usr/include/unistd.h \
 /usr/include/x86_64-linux-gnu/bits/posix_opt.h \
 /usr/include/x86_64-linux-gnu/bits/environments.h \
 /usr/include/x86_64-linux-gnu/bits/confname.h /usr/include/getopt.h \
 /usr/include/x86_64-linux-gnu/bits/unistd.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/atomic_word.h \
 /usr/include/c++/4.6/bits/locale_classes.h /usr/include/c++/4.6/string \
 /usr/include/c++/4.6/bits/allocator.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/c++allocator.h \
 /usr/include/c++/4.6/ext/new_allocator.h /usr/include/c++/4.6/new \
 /usr/include/c++/4.6/bits/ostream_insert.h \
 /usr/include/c++/4.6/bits/cxxabi_forced.h \
 /usr/include/c++/4.6/bits/stl_function.h \
 /usr/include/c++/4.6/backward/binders.h \
 /usr/include/c++/4.6/bits/range_access.h \
 /usr/include/c++/4.6/bits/basic_string.h \
 /usr/include/c++/4.6/initializer_list \
 /usr/include/c++/4.6/bits/basic_string.tcc \
 /usr/include/c++/4.6/bits/locale_classes.tcc \
 /usr/include/c++/4.6/streambuf /usr/include/c++/4.6/bits/streambuf.tcc \
 /usr/include/c++/4.6/bits/basic_ios.h \
 /usr/include/c++/4.6/bits/locale_facets.h /usr/include/c++/4.6/cwctype \
 /usr/include/wctype.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/ctype_base.h \
 /usr/include/c++/4.6/bits/streambuf_iterator.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/ctype_inline.h \
 /usr/include/c++/4.6/bits/locale_facets.tcc \
 /usr/include/c++/4.6/bits/basic_ios.tcc \
 /usr/include/c++/4.6/bits/ostream.tcc /usr/include/c++/4.6/istream \
 /usr/include/c++/4.6/bits/istream.tcc /usr/include/c++/4.6/fstream \
 /usr/include/c++/4.6/bits/codecvt.h /usr/include/c++/4.6/cstdio \
 /usr/include/libio.h /usr/include/_G_config.h \
 /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
 /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
 /usr/include/x86_64-linux-gnu/bits/stdio.h \
 /usr/include/x86_64-linux-gnu/bits/stdio2.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/basic_file.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/c++io.h \
 /usr/include/c++/4.6/bits/fstream.tcc ../tools2/Vec.h \
 /usr/include/libintl.h /usr/include/c++/4.6/vector \
 /usr/include/c++/4.6/bits/stl_construct.h \
 /usr/include/c++/4.6/bits/stl_uninitialized.h \
 /usr/include/c++/4.6/bits/stl_vector.h \
 /usr/include/c++/4.6/bits/stl_bvector.h \
 /usr/include/c++/4.6/bits/vector.tcc ../tools2/debug.h \
 /usr/include/stdlib.h /usr/include/x86_64-linux-gnu/bits/waitflags.h \
 /usr/include/x86_64-linux-gnu/bits/waitstatus.h \
 /usr/include/x86_64-linux-gnu/sys/types.h \
 /usr/include/x86_64-linux-gnu/sys/select.h \
 /usr/include/x86_64-linux-gnu/bits/select.h \
 /usr/include/x86_64-linux-gnu/bits/sigset.h \
 /usr/include/x86_64-linux-gnu/bits/select2.h \
 /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \
 /usr/include/x86_64-linux-gnu/bits/stdlib.h /usr/include/assert.h \
 ../tools2/GetArg.h /usr/include/string.h \
 /usr/include/x86_64-linux-gnu/bits/string3.h \
 /usr/include/c++/4.6/cstdarg ../tools2/StringTools.h \
 /usr/include/c++/4.6/sstream /usr/include/c++/4.6/bits/sstream.tcc \
 /usr/include/c++/4.6/cstdlib /usr/include/malloc.h ../tools2/FileName.h \
 ../sequence/SequenceAlignment.h /usr/include/c++/4.6/map \
 /usr/include/c++/4.6/bits/stl_tree.h /usr/include/c++/4.6/bits/stl_map.h \
 /usr/include/c++/4.6/bits/stl_multimap.h \
 ../sequence/SimpleSequenceAlignment.h sequencestat.h \
 /usr/include/c++/4.6/algorithm /usr/include/c++/4.6/utility \
 /usr/include/c++/4.6/bits/stl_relops.h \
 /usr/include/c++/4.6/bits/stl_algo.h \
 /usr/include/c++/4.6/bits/algorithmfwd.h \
 /usr/include/c++/4.6/bits/stl_heap.h \
 /usr/include/c++/4.6/bits/stl_tempbuf.h ../numerics/vectornumerics.h \
 /usr/include/math.h /usr/include/x86_64-linux-gnu/bits/huge_val.h \
 /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
 /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
 /usr/include/x86_64-linux-gnu/bits/inf.h \
 /usr/include/x86_64-linux-gnu/bits/nan.h \
 /usr/include/x86_64-linux-gnu/bits/mathdef.h \
 /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
 /usr/include/x86_64-linux-gnu/bits/mathinline.h \
 /usr/include/x86_64-linux-gnu/bits/math-finite.h \
 /usr/lib/gcc/x86_64-linux-gnu/4.6/include-fixed/limits.h \
 /usr/lib/gcc/x86_64-linux-gnu/4.6/include-fixed/syslimits.h \
 /usr/include/limits.h /usr/include/x86_64-linux-gnu/bits/posix1_lim.h \
 /usr/include/x86_64-linux-gnu/bits/local_lim.h \
 /usr/include/linux/limits.h \
 /usr/include/x86_64-linux-gnu/bits/posix2_lim.h \
 /usr/include/x86_64-linux-gnu/bits/xopen_lim.h /usr/include/c++/4.6/list \
 /usr/include/c++/4.6/bits/stl_list.h /usr/include/c++/4.6/bits/list.tcc \
 /usr/include/c++/4.6/set /usr/include/c++/4.6/bits/stl_set.h \
 /usr/include/c++/4.6/bits/stl_multiset.h ../numerics/Matrix3D.h \
 ../numerics/Vector3D.h ../numerics/Limits.h \
 ../numerics/RankedSolution4.h ../numerics/generalNumerics.h \
 CompensationScorer.h ../tools2/Random.h compass_help.h \
 ../numerics/RankedSolution5.h Stem.h ../tools2/ClassificationResult.h \
 ../numerics/Histogram.h stemhelp.h /usr/include/c++/4.6/stack \
 /usr/include/c++/4.6/deque /usr/include/c++/4.6/bits/stl_deque.h \
 /usr/include/c++/4.6/bits/deque.tcc \
 /usr/include/c++/4.6/bits/stl_stack.h RnaSecondaryStructure.h \
 AbstractSecondaryStructure.h RnaInteractionType.h
alignedit2.o: alignedit2.cc /usr/include/c++/4.6/iostream \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/c++config.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/os_defines.h \
 /usr/include/features.h /usr/include/x86_64-linux-gnu/bits/predefs.h \
 /usr/include/x86_64-linux-gnu/sys/cdefs.h \
 /usr/include/x86_64-linux-gnu/bits/wordsize.h \
 /usr/include/x86_64-linux-gnu/gnu/stubs.h \
 /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/cpu_defines.h \
 /usr/include/c++/4.6/ostream /usr/include/c++/4.6/ios \
 /usr/include/c++/4.6/iosfwd /usr/include/c++/4.6/bits/stringfwd.h \
 /usr/include/c++/4.6/bits/postypes.h /usr/include/c++/4.6/cwchar \
 /usr/include/wchar.h /usr/include/stdio.h \
 /usr/lib/gcc/x86_64-linux-gnu/4.6/include/stdarg.h \
 /usr/include/x86_64-linux-gnu/bits/wchar.h \
 /usr/lib/gcc/x86_64-linux-gnu/4.6/include/stddef.h \
 /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \
 /usr/include/c++/4.6/exception /usr/include/c++/4.6/bits/char_traits.h \
 /usr/include/c++/4.6/bits/stl_algobase.h \
 /usr/include/c++/4.6/bits/functexcept.h \
 /usr/include/c++/4.6/bits/exception_defines.h \
 /usr/include/c++/4.6/bits/cpp_type_traits.h \
 /usr/include/c++/4.6/ext/type_traits.h \
 /usr/include/c++/4.6/ext/numeric_traits.h \
 /usr/include/c++/4.6/bits/stl_pair.h /usr/include/c++/4.6/bits/move.h \
 /usr/include/c++/4.6/bits/concept_check.h \
 /usr/include/c++/4.6/bits/stl_iterator_base_types.h \
 /usr/include/c++/4.6/bits/stl_iterator_base_funcs.h \
 /usr/include/c++/4.6/bits/stl_iterator.h \
 /usr/include/c++/4.6/debug/debug.h /usr/include/c++/4.6/bits/localefwd.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/c++locale.h \
 /usr/include/c++/4.6/clocale /usr/include/locale.h \
 /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.6/cctype \
 /usr/include/ctype.h /usr/include/x86_64-linux-gnu/bits/types.h \
 /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \
 /usr/include/x86_64-linux-gnu/bits/endian.h \
 /usr/include/x86_64-linux-gnu/bits/byteswap.h \
 /usr/include/c++/4.6/bits/ios_base.h \
 /usr/include/c++/4.6/ext/atomicity.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/gthr.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/gthr-default.h \
 /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
 /usr/include/x86_64-linux-gnu/bits/sched.h \
 /usr/include/x86_64-linux-gnu/bits/time.h \
 /usr/include/x86_64-linux-gnu/bits/timex.h \
 /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \
 /usr/include/x86_64-linux-gnu/bits/setjmp.h /usr/include/unistd.h \
 /usr/include/x86_64-linux-gnu/bits/posix_opt.h \
 /usr/include/x86_64-linux-gnu/bits/environments.h \
 /usr/include/x86_64-linux-gnu/bits/confname.h /usr/include/getopt.h \
 /usr/include/x86_64-linux-gnu/bits/unistd.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/atomic_word.h \
 /usr/include/c++/4.6/bits/locale_classes.h /usr/include/c++/4.6/string \
 /usr/include/c++/4.6/bits/allocator.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/c++allocator.h \
 /usr/include/c++/4.6/ext/new_allocator.h /usr/include/c++/4.6/new \
 /usr/include/c++/4.6/bits/ostream_insert.h \
 /usr/include/c++/4.6/bits/cxxabi_forced.h \
 /usr/include/c++/4.6/bits/stl_function.h \
 /usr/include/c++/4.6/backward/binders.h \
 /usr/include/c++/4.6/bits/range_access.h \
 /usr/include/c++/4.6/bits/basic_string.h \
 /usr/include/c++/4.6/initializer_list \
 /usr/include/c++/4.6/bits/basic_string.tcc \
 /usr/include/c++/4.6/bits/locale_classes.tcc \
 /usr/include/c++/4.6/streambuf /usr/include/c++/4.6/bits/streambuf.tcc \
 /usr/include/c++/4.6/bits/basic_ios.h \
 /usr/include/c++/4.6/bits/locale_facets.h /usr/include/c++/4.6/cwctype \
 /usr/include/wctype.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/ctype_base.h \
 /usr/include/c++/4.6/bits/streambuf_iterator.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/ctype_inline.h \
 /usr/include/c++/4.6/bits/locale_facets.tcc \
 /usr/include/c++/4.6/bits/basic_ios.tcc \
 /usr/include/c++/4.6/bits/ostream.tcc /usr/include/c++/4.6/istream \
 /usr/include/c++/4.6/bits/istream.tcc /usr/include/c++/4.6/fstream \
 /usr/include/c++/4.6/bits/codecvt.h /usr/include/c++/4.6/cstdio \
 /usr/include/libio.h /usr/include/_G_config.h \
 /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
 /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
 /usr/include/x86_64-linux-gnu/bits/stdio.h \
 /usr/include/x86_64-linux-gnu/bits/stdio2.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/basic_file.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/c++io.h \
 /usr/include/c++/4.6/bits/fstream.tcc ../tools2/Vec.h \
 /usr/include/libintl.h /usr/include/c++/4.6/vector \
 /usr/include/c++/4.6/bits/stl_construct.h \
 /usr/include/c++/4.6/bits/stl_uninitialized.h \
 /usr/include/c++/4.6/bits/stl_vector.h \
 /usr/include/c++/4.6/bits/stl_bvector.h \
 /usr/include/c++/4.6/bits/vector.tcc ../tools2/debug.h \
 /usr/include/stdlib.h /usr/include/x86_64-linux-gnu/bits/waitflags.h \
 /usr/include/x86_64-linux-gnu/bits/waitstatus.h \
 /usr/include/x86_64-linux-gnu/sys/types.h \
 /usr/include/x86_64-linux-gnu/sys/select.h \
 /usr/include/x86_64-linux-gnu/bits/select.h \
 /usr/include/x86_64-linux-gnu/bits/sigset.h \
 /usr/include/x86_64-linux-gnu/bits/select2.h \
 /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \
 /usr/include/x86_64-linux-gnu/bits/stdlib.h /usr/include/assert.h \
 ../tools2/GetArg.h /usr/include/string.h \
 /usr/include/x86_64-linux-gnu/bits/string3.h \
 /usr/include/c++/4.6/cstdarg ../tools2/StringTools.h \
 /usr/include/c++/4.6/sstream /usr/include/c++/4.6/bits/sstream.tcc \
 /usr/include/c++/4.6/cstdlib /usr/include/malloc.h ../tools2/FileName.h \
 ../sequence/SequenceAlignment.h /usr/include/c++/4.6/map \
 /usr/include/c++/4.6/bits/stl_tree.h /usr/include/c++/4.6/bits/stl_map.h \
 /usr/include/c++/4.6/bits/stl_multimap.h \
 ../sequence/SequenceAlignmentTools.h /usr/include/c++/4.6/algorithm \
 /usr/include/c++/4.6/utility /usr/include/c++/4.6/bits/stl_relops.h \
 /usr/include/c++/4.6/bits/stl_algo.h \
 /usr/include/c++/4.6/bits/algorithmfwd.h \
 /usr/include/c++/4.6/bits/stl_heap.h \
 /usr/include/c++/4.6/bits/stl_tempbuf.h ../tools2/Random.h \
 ../sequence/SimpleSequenceAlignment.h ../numerics/vectornumerics.h \
 /usr/include/math.h /usr/include/x86_64-linux-gnu/bits/huge_val.h \
 /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
 /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
 /usr/include/x86_64-linux-gnu/bits/inf.h \
 /usr/include/x86_64-linux-gnu/bits/nan.h \
 /usr/include/x86_64-linux-gnu/bits/mathdef.h \
 /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
 /usr/include/x86_64-linux-gnu/bits/mathinline.h \
 /usr/include/x86_64-linux-gnu/bits/math-finite.h \
 /usr/lib/gcc/x86_64-linux-gnu/4.6/include-fixed/limits.h \
 /usr/lib/gcc/x86_64-linux-gnu/4.6/include-fixed/syslimits.h \
 /usr/include/limits.h /usr/include/x86_64-linux-gnu/bits/posix1_lim.h \
 /usr/include/x86_64-linux-gnu/bits/local_lim.h \
 /usr/include/linux/limits.h \
 /usr/include/x86_64-linux-gnu/bits/posix2_lim.h \
 /usr/include/x86_64-linux-gnu/bits/xopen_lim.h /usr/include/c++/4.6/list \
 /usr/include/c++/4.6/bits/stl_list.h /usr/include/c++/4.6/bits/list.tcc \
 /usr/include/c++/4.6/set /usr/include/c++/4.6/bits/stl_set.h \
 /usr/include/c++/4.6/bits/stl_multiset.h ../numerics/Matrix3D.h \
 ../numerics/Vector3D.h ../numerics/Limits.h \
 ../numerics/RankedSolution4.h ../numerics/generalNumerics.h \
 sequencestat.h CompensationScorer.h ../sequence/SequenceMutator.h Stem.h \
 stemhelp.h ../numerics/RankedSolution5.h /usr/include/c++/4.6/stack \
 /usr/include/c++/4.6/deque /usr/include/c++/4.6/bits/stl_deque.h \
 /usr/include/c++/4.6/bits/deque.tcc \
 /usr/include/c++/4.6/bits/stl_stack.h RnaSecondaryStructure.h \
 AbstractSecondaryStructure.h RnaInteractionType.h \
 ../sequence/SequenceAlignmentIOTools.h ../sequence/NucleotideTools.h
compass.o: compass.cc /usr/include/c++/4.6/iostream \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/c++config.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/os_defines.h \
 /usr/include/features.h /usr/include/x86_64-linux-gnu/bits/predefs.h \
 /usr/include/x86_64-linux-gnu/sys/cdefs.h \
 /usr/include/x86_64-linux-gnu/bits/wordsize.h \
 /usr/include/x86_64-linux-gnu/gnu/stubs.h \
 /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/cpu_defines.h \
 /usr/include/c++/4.6/ostream /usr/include/c++/4.6/ios \
 /usr/include/c++/4.6/iosfwd /usr/include/c++/4.6/bits/stringfwd.h \
 /usr/include/c++/4.6/bits/postypes.h /usr/include/c++/4.6/cwchar \
 /usr/include/wchar.h /usr/include/stdio.h \
 /usr/lib/gcc/x86_64-linux-gnu/4.6/include/stdarg.h \
 /usr/include/x86_64-linux-gnu/bits/wchar.h \
 /usr/lib/gcc/x86_64-linux-gnu/4.6/include/stddef.h \
 /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \
 /usr/include/c++/4.6/exception /usr/include/c++/4.6/bits/char_traits.h \
 /usr/include/c++/4.6/bits/stl_algobase.h \
 /usr/include/c++/4.6/bits/functexcept.h \
 /usr/include/c++/4.6/bits/exception_defines.h \
 /usr/include/c++/4.6/bits/cpp_type_traits.h \
 /usr/include/c++/4.6/ext/type_traits.h \
 /usr/include/c++/4.6/ext/numeric_traits.h \
 /usr/include/c++/4.6/bits/stl_pair.h /usr/include/c++/4.6/bits/move.h \
 /usr/include/c++/4.6/bits/concept_check.h \
 /usr/include/c++/4.6/bits/stl_iterator_base_types.h \
 /usr/include/c++/4.6/bits/stl_iterator_base_funcs.h \
 /usr/include/c++/4.6/bits/stl_iterator.h \
 /usr/include/c++/4.6/debug/debug.h /usr/include/c++/4.6/bits/localefwd.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/c++locale.h \
 /usr/include/c++/4.6/clocale /usr/include/locale.h \
 /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.6/cctype \
 /usr/include/ctype.h /usr/include/x86_64-linux-gnu/bits/types.h \
 /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \
 /usr/include/x86_64-linux-gnu/bits/endian.h \
 /usr/include/x86_64-linux-gnu/bits/byteswap.h \
 /usr/include/c++/4.6/bits/ios_base.h \
 /usr/include/c++/4.6/ext/atomicity.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/gthr.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/gthr-default.h \
 /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
 /usr/include/x86_64-linux-gnu/bits/sched.h \
 /usr/include/x86_64-linux-gnu/bits/time.h \
 /usr/include/x86_64-linux-gnu/bits/timex.h \
 /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \
 /usr/include/x86_64-linux-gnu/bits/setjmp.h /usr/include/unistd.h \
 /usr/include/x86_64-linux-gnu/bits/posix_opt.h \
 /usr/include/x86_64-linux-gnu/bits/environments.h \
 /usr/include/x86_64-linux-gnu/bits/confname.h /usr/include/getopt.h \
 /usr/include/x86_64-linux-gnu/bits/unistd.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/atomic_word.h \
 /usr/include/c++/4.6/bits/locale_classes.h /usr/include/c++/4.6/string \
 /usr/include/c++/4.6/bits/allocator.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/c++allocator.h \
 /usr/include/c++/4.6/ext/new_allocator.h /usr/include/c++/4.6/new \
 /usr/include/c++/4.6/bits/ostream_insert.h \
 /usr/include/c++/4.6/bits/cxxabi_forced.h \
 /usr/include/c++/4.6/bits/stl_function.h \
 /usr/include/c++/4.6/backward/binders.h \
 /usr/include/c++/4.6/bits/range_access.h \
 /usr/include/c++/4.6/bits/basic_string.h \
 /usr/include/c++/4.6/initializer_list \
 /usr/include/c++/4.6/bits/basic_string.tcc \
 /usr/include/c++/4.6/bits/locale_classes.tcc \
 /usr/include/c++/4.6/streambuf /usr/include/c++/4.6/bits/streambuf.tcc \
 /usr/include/c++/4.6/bits/basic_ios.h \
 /usr/include/c++/4.6/bits/locale_facets.h /usr/include/c++/4.6/cwctype \
 /usr/include/wctype.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/ctype_base.h \
 /usr/include/c++/4.6/bits/streambuf_iterator.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/ctype_inline.h \
 /usr/include/c++/4.6/bits/locale_facets.tcc \
 /usr/include/c++/4.6/bits/basic_ios.tcc \
 /usr/include/c++/4.6/bits/ostream.tcc /usr/include/c++/4.6/istream \
 /usr/include/c++/4.6/bits/istream.tcc /usr/include/c++/4.6/fstream \
 /usr/include/c++/4.6/bits/codecvt.h /usr/include/c++/4.6/cstdio \
 /usr/include/libio.h /usr/include/_G_config.h \
 /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
 /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
 /usr/include/x86_64-linux-gnu/bits/stdio.h \
 /usr/include/x86_64-linux-gnu/bits/stdio2.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/basic_file.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/c++io.h \
 /usr/include/c++/4.6/bits/fstream.tcc ../tools2/Vec.h \
 /usr/include/libintl.h /usr/include/c++/4.6/vector \
 /usr/include/c++/4.6/bits/stl_construct.h \
 /usr/include/c++/4.6/bits/stl_uninitialized.h \
 /usr/include/c++/4.6/bits/stl_vector.h \
 /usr/include/c++/4.6/bits/stl_bvector.h \
 /usr/include/c++/4.6/bits/vector.tcc ../tools2/debug.h \
 /usr/include/stdlib.h /usr/include/x86_64-linux-gnu/bits/waitflags.h \
 /usr/include/x86_64-linux-gnu/bits/waitstatus.h \
 /usr/include/x86_64-linux-gnu/sys/types.h \
 /usr/include/x86_64-linux-gnu/sys/select.h \
 /usr/include/x86_64-linux-gnu/bits/select.h \
 /usr/include/x86_64-linux-gnu/bits/sigset.h \
 /usr/include/x86_64-linux-gnu/bits/select2.h \
 /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \
 /usr/include/x86_64-linux-gnu/bits/stdlib.h /usr/include/assert.h \
 ../tools2/GetArg.h /usr/include/string.h \
 /usr/include/x86_64-linux-gnu/bits/string3.h \
 /usr/include/c++/4.6/cstdarg ../tools2/StringTools.h \
 /usr/include/c++/4.6/sstream /usr/include/c++/4.6/bits/sstream.tcc \
 /usr/include/c++/4.6/cstdlib /usr/include/malloc.h ../tools2/FileName.h \
 ../sequence/SequenceAlignment.h /usr/include/c++/4.6/map \
 /usr/include/c++/4.6/bits/stl_tree.h /usr/include/c++/4.6/bits/stl_map.h \
 /usr/include/c++/4.6/bits/stl_multimap.h \
 ../sequence/SimpleSequenceAlignment.h CompensationScorer.h \
 ../numerics/generalNumerics.h /usr/include/math.h \
 /usr/include/x86_64-linux-gnu/bits/huge_val.h \
 /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
 /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
 /usr/include/x86_64-linux-gnu/bits/inf.h \
 /usr/include/x86_64-linux-gnu/bits/nan.h \
 /usr/include/x86_64-linux-gnu/bits/mathdef.h \
 /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
 /usr/include/x86_64-linux-gnu/bits/mathinline.h \
 /usr/include/x86_64-linux-gnu/bits/math-finite.h ../tools2/Random.h \
 /usr/include/c++/4.6/utility /usr/include/c++/4.6/bits/stl_relops.h \
 ../numerics/vectornumerics.h \
 /usr/lib/gcc/x86_64-linux-gnu/4.6/include-fixed/limits.h \
 /usr/lib/gcc/x86_64-linux-gnu/4.6/include-fixed/syslimits.h \
 /usr/include/limits.h /usr/include/x86_64-linux-gnu/bits/posix1_lim.h \
 /usr/include/x86_64-linux-gnu/bits/local_lim.h \
 /usr/include/linux/limits.h \
 /usr/include/x86_64-linux-gnu/bits/posix2_lim.h \
 /usr/include/x86_64-linux-gnu/bits/xopen_lim.h /usr/include/c++/4.6/list \
 /usr/include/c++/4.6/bits/stl_list.h /usr/include/c++/4.6/bits/list.tcc \
 /usr/include/c++/4.6/set /usr/include/c++/4.6/bits/stl_set.h \
 /usr/include/c++/4.6/bits/stl_multiset.h /usr/include/c++/4.6/algorithm \
 /usr/include/c++/4.6/bits/stl_algo.h \
 /usr/include/c++/4.6/bits/algorithmfwd.h \
 /usr/include/c++/4.6/bits/stl_heap.h \
 /usr/include/c++/4.6/bits/stl_tempbuf.h ../numerics/Matrix3D.h \
 ../numerics/Vector3D.h ../numerics/Limits.h \
 ../numerics/RankedSolution4.h Stem.h ../numerics/Gaussian1D.h \
 sequencestat.h stemhelp.h ../numerics/RankedSolution5.h \
 /usr/include/c++/4.6/stack /usr/include/c++/4.6/deque \
 /usr/include/c++/4.6/bits/stl_deque.h \
 /usr/include/c++/4.6/bits/deque.tcc \
 /usr/include/c++/4.6/bits/stl_stack.h RnaSecondaryStructure.h \
 AbstractSecondaryStructure.h RnaInteractionType.h \
 ../numerics/ClassifierBase.h ../numerics/KnnNet2.h \
 ../numerics/KnnNode2.h ../numerics/ANN.h /usr/include/values.h \
 /usr/lib/gcc/x86_64-linux-gnu/4.6/include/float.h \
 ../numerics/KnnNetTrainer.h compass_help.h \
 ../tools2/ClassificationResult.h ../numerics/Histogram.h
compass_help.o: compass_help.cc compass_help.h \
 ../sequence/SequenceAlignment.h /usr/include/c++/4.6/iostream \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/c++config.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/os_defines.h \
 /usr/include/features.h /usr/include/x86_64-linux-gnu/bits/predefs.h \
 /usr/include/x86_64-linux-gnu/sys/cdefs.h \
 /usr/include/x86_64-linux-gnu/bits/wordsize.h \
 /usr/include/x86_64-linux-gnu/gnu/stubs.h \
 /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/cpu_defines.h \
 /usr/include/c++/4.6/ostream /usr/include/c++/4.6/ios \
 /usr/include/c++/4.6/iosfwd /usr/include/c++/4.6/bits/stringfwd.h \
 /usr/include/c++/4.6/bits/postypes.h /usr/include/c++/4.6/cwchar \
 /usr/include/wchar.h /usr/include/stdio.h \
 /usr/lib/gcc/x86_64-linux-gnu/4.6/include/stdarg.h \
 /usr/include/x86_64-linux-gnu/bits/wchar.h \
 /usr/lib/gcc/x86_64-linux-gnu/4.6/include/stddef.h \
 /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \
 /usr/include/c++/4.6/exception /usr/include/c++/4.6/bits/char_traits.h \
 /usr/include/c++/4.6/bits/stl_algobase.h \
 /usr/include/c++/4.6/bits/functexcept.h \
 /usr/include/c++/4.6/bits/exception_defines.h \
 /usr/include/c++/4.6/bits/cpp_type_traits.h \
 /usr/include/c++/4.6/ext/type_traits.h \
 /usr/include/c++/4.6/ext/numeric_traits.h \
 /usr/include/c++/4.6/bits/stl_pair.h /usr/include/c++/4.6/bits/move.h \
 /usr/include/c++/4.6/bits/concept_check.h \
 /usr/include/c++/4.6/bits/stl_iterator_base_types.h \
 /usr/include/c++/4.6/bits/stl_iterator_base_funcs.h \
 /usr/include/c++/4.6/bits/stl_iterator.h \
 /usr/include/c++/4.6/debug/debug.h /usr/include/c++/4.6/bits/localefwd.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/c++locale.h \
 /usr/include/c++/4.6/clocale /usr/include/locale.h \
 /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.6/cctype \
 /usr/include/ctype.h /usr/include/x86_64-linux-gnu/bits/types.h \
 /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \
 /usr/include/x86_64-linux-gnu/bits/endian.h \
 /usr/include/x86_64-linux-gnu/bits/byteswap.h \
 /usr/include/c++/4.6/bits/ios_base.h \
 /usr/include/c++/4.6/ext/atomicity.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/gthr.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/gthr-default.h \
 /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
 /usr/include/x86_64-linux-gnu/bits/sched.h \
 /usr/include/x86_64-linux-gnu/bits/time.h \
 /usr/include/x86_64-linux-gnu/bits/timex.h \
 /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \
 /usr/include/x86_64-linux-gnu/bits/setjmp.h /usr/include/unistd.h \
 /usr/include/x86_64-linux-gnu/bits/posix_opt.h \
 /usr/include/x86_64-linux-gnu/bits/environments.h \
 /usr/include/x86_64-linux-gnu/bits/confname.h /usr/include/getopt.h \
 /usr/include/x86_64-linux-gnu/bits/unistd.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/atomic_word.h \
 /usr/include/c++/4.6/bits/locale_classes.h /usr/include/c++/4.6/string \
 /usr/include/c++/4.6/bits/allocator.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/c++allocator.h \
 /usr/include/c++/4.6/ext/new_allocator.h /usr/include/c++/4.6/new \
 /usr/include/c++/4.6/bits/ostream_insert.h \
 /usr/include/c++/4.6/bits/cxxabi_forced.h \
 /usr/include/c++/4.6/bits/stl_function.h \
 /usr/include/c++/4.6/backward/binders.h \
 /usr/include/c++/4.6/bits/range_access.h \
 /usr/include/c++/4.6/bits/basic_string.h \
 /usr/include/c++/4.6/initializer_list \
 /usr/include/c++/4.6/bits/basic_string.tcc \
 /usr/include/c++/4.6/bits/locale_classes.tcc \
 /usr/include/c++/4.6/streambuf /usr/include/c++/4.6/bits/streambuf.tcc \
 /usr/include/c++/4.6/bits/basic_ios.h \
 /usr/include/c++/4.6/bits/locale_facets.h /usr/include/c++/4.6/cwctype \
 /usr/include/wctype.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/ctype_base.h \
 /usr/include/c++/4.6/bits/streambuf_iterator.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/ctype_inline.h \
 /usr/include/c++/4.6/bits/locale_facets.tcc \
 /usr/include/c++/4.6/bits/basic_ios.tcc \
 /usr/include/c++/4.6/bits/ostream.tcc /usr/include/c++/4.6/istream \
 /usr/include/c++/4.6/bits/istream.tcc ../tools2/Vec.h \
 /usr/include/libintl.h /usr/include/c++/4.6/vector \
 /usr/include/c++/4.6/bits/stl_construct.h \
 /usr/include/c++/4.6/bits/stl_uninitialized.h \
 /usr/include/c++/4.6/bits/stl_vector.h \
 /usr/include/c++/4.6/bits/stl_bvector.h \
 /usr/include/c++/4.6/bits/vector.tcc ../tools2/debug.h \
 /usr/include/stdlib.h /usr/include/x86_64-linux-gnu/bits/waitflags.h \
 /usr/include/x86_64-linux-gnu/bits/waitstatus.h \
 /usr/include/x86_64-linux-gnu/sys/types.h \
 /usr/include/x86_64-linux-gnu/sys/select.h \
 /usr/include/x86_64-linux-gnu/bits/select.h \
 /usr/include/x86_64-linux-gnu/bits/sigset.h \
 /usr/include/x86_64-linux-gnu/bits/select2.h \
 /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \
 /usr/include/x86_64-linux-gnu/bits/stdlib.h /usr/include/assert.h \
 /usr/include/c++/4.6/map /usr/include/c++/4.6/bits/stl_tree.h \
 /usr/include/c++/4.6/bits/stl_map.h \
 /usr/include/c++/4.6/bits/stl_multimap.h \
 ../sequence/SimpleSequenceAlignment.h ../tools2/StringTools.h \
 /usr/include/c++/4.6/sstream /usr/include/c++/4.6/bits/sstream.tcc \
 /usr/include/c++/4.6/cstdlib CompensationScorer.h \
 ../numerics/generalNumerics.h /usr/include/math.h \
 /usr/include/x86_64-linux-gnu/bits/huge_val.h \
 /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
 /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
 /usr/include/x86_64-linux-gnu/bits/inf.h \
 /usr/include/x86_64-linux-gnu/bits/nan.h \
 /usr/include/x86_64-linux-gnu/bits/mathdef.h \
 /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
 /usr/include/x86_64-linux-gnu/bits/mathinline.h \
 /usr/include/x86_64-linux-gnu/bits/math-finite.h ../tools2/Random.h \
 /usr/include/c++/4.6/utility /usr/include/c++/4.6/bits/stl_relops.h \
 ../numerics/RankedSolution5.h Stem.h ../tools2/ClassificationResult.h \
 ../numerics/Histogram.h ../numerics/vectornumerics.h \
 /usr/lib/gcc/x86_64-linux-gnu/4.6/include-fixed/limits.h \
 /usr/lib/gcc/x86_64-linux-gnu/4.6/include-fixed/syslimits.h \
 /usr/include/limits.h /usr/include/x86_64-linux-gnu/bits/posix1_lim.h \
 /usr/include/x86_64-linux-gnu/bits/local_lim.h \
 /usr/include/linux/limits.h \
 /usr/include/x86_64-linux-gnu/bits/posix2_lim.h \
 /usr/include/x86_64-linux-gnu/bits/xopen_lim.h \
 /usr/include/x86_64-linux-gnu/bits/stdio_lim.h /usr/include/c++/4.6/list \
 /usr/include/c++/4.6/bits/stl_list.h /usr/include/c++/4.6/bits/list.tcc \
 /usr/include/c++/4.6/set /usr/include/c++/4.6/bits/stl_set.h \
 /usr/include/c++/4.6/bits/stl_multiset.h /usr/include/c++/4.6/algorithm \
 /usr/include/c++/4.6/bits/stl_algo.h \
 /usr/include/c++/4.6/bits/algorithmfwd.h \
 /usr/include/c++/4.6/bits/stl_heap.h \
 /usr/include/c++/4.6/bits/stl_tempbuf.h ../numerics/Matrix3D.h \
 ../numerics/Vector3D.h ../numerics/Limits.h \
 ../numerics/RankedSolution4.h stemhelp.h /usr/include/c++/4.6/stack \
 /usr/include/c++/4.6/deque /usr/include/c++/4.6/bits/stl_deque.h \
 /usr/include/c++/4.6/bits/deque.tcc \
 /usr/include/c++/4.6/bits/stl_stack.h RnaSecondaryStructure.h \
 AbstractSecondaryStructure.h RnaInteractionType.h
CompensationScorer.o: CompensationScorer.cc CompensationScorer.h \
 /usr/include/c++/4.6/iostream \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/c++config.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/os_defines.h \
 /usr/include/features.h /usr/include/x86_64-linux-gnu/bits/predefs.h \
 /usr/include/x86_64-linux-gnu/sys/cdefs.h \
 /usr/include/x86_64-linux-gnu/bits/wordsize.h \
 /usr/include/x86_64-linux-gnu/gnu/stubs.h \
 /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/cpu_defines.h \
 /usr/include/c++/4.6/ostream /usr/include/c++/4.6/ios \
 /usr/include/c++/4.6/iosfwd /usr/include/c++/4.6/bits/stringfwd.h \
 /usr/include/c++/4.6/bits/postypes.h /usr/include/c++/4.6/cwchar \
 /usr/include/wchar.h /usr/include/stdio.h \
 /usr/lib/gcc/x86_64-linux-gnu/4.6/include/stdarg.h \
 /usr/include/x86_64-linux-gnu/bits/wchar.h \
 /usr/lib/gcc/x86_64-linux-gnu/4.6/include/stddef.h \
 /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \
 /usr/include/c++/4.6/exception /usr/include/c++/4.6/bits/char_traits.h \
 /usr/include/c++/4.6/bits/stl_algobase.h \
 /usr/include/c++/4.6/bits/functexcept.h \
 /usr/include/c++/4.6/bits/exception_defines.h \
 /usr/include/c++/4.6/bits/cpp_type_traits.h \
 /usr/include/c++/4.6/ext/type_traits.h \
 /usr/include/c++/4.6/ext/numeric_traits.h \
 /usr/include/c++/4.6/bits/stl_pair.h /usr/include/c++/4.6/bits/move.h \
 /usr/include/c++/4.6/bits/concept_check.h \
 /usr/include/c++/4.6/bits/stl_iterator_base_types.h \
 /usr/include/c++/4.6/bits/stl_iterator_base_funcs.h \
 /usr/include/c++/4.6/bits/stl_iterator.h \
 /usr/include/c++/4.6/debug/debug.h /usr/include/c++/4.6/bits/localefwd.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/c++locale.h \
 /usr/include/c++/4.6/clocale /usr/include/locale.h \
 /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.6/cctype \
 /usr/include/ctype.h /usr/include/x86_64-linux-gnu/bits/types.h \
 /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \
 /usr/include/x86_64-linux-gnu/bits/endian.h \
 /usr/include/x86_64-linux-gnu/bits/byteswap.h \
 /usr/include/c++/4.6/bits/ios_base.h \
 /usr/include/c++/4.6/ext/atomicity.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/gthr.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/gthr-default.h \
 /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
 /usr/include/x86_64-linux-gnu/bits/sched.h \
 /usr/include/x86_64-linux-gnu/bits/time.h \
 /usr/include/x86_64-linux-gnu/bits/timex.h \
 /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \
 /usr/include/x86_64-linux-gnu/bits/setjmp.h /usr/include/unistd.h \
 /usr/include/x86_64-linux-gnu/bits/posix_opt.h \
 /usr/include/x86_64-linux-gnu/bits/environments.h \
 /usr/include/x86_64-linux-gnu/bits/confname.h /usr/include/getopt.h \
 /usr/include/x86_64-linux-gnu/bits/unistd.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/atomic_word.h \
 /usr/include/c++/4.6/bits/locale_classes.h /usr/include/c++/4.6/string \
 /usr/include/c++/4.6/bits/allocator.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/c++allocator.h \
 /usr/include/c++/4.6/ext/new_allocator.h /usr/include/c++/4.6/new \
 /usr/include/c++/4.6/bits/ostream_insert.h \
 /usr/include/c++/4.6/bits/cxxabi_forced.h \
 /usr/include/c++/4.6/bits/stl_function.h \
 /usr/include/c++/4.6/backward/binders.h \
 /usr/include/c++/4.6/bits/range_access.h \
 /usr/include/c++/4.6/bits/basic_string.h \
 /usr/include/c++/4.6/initializer_list \
 /usr/include/c++/4.6/bits/basic_string.tcc \
 /usr/include/c++/4.6/bits/locale_classes.tcc \
 /usr/include/c++/4.6/streambuf /usr/include/c++/4.6/bits/streambuf.tcc \
 /usr/include/c++/4.6/bits/basic_ios.h \
 /usr/include/c++/4.6/bits/locale_facets.h /usr/include/c++/4.6/cwctype \
 /usr/include/wctype.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/ctype_base.h \
 /usr/include/c++/4.6/bits/streambuf_iterator.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/ctype_inline.h \
 /usr/include/c++/4.6/bits/locale_facets.tcc \
 /usr/include/c++/4.6/bits/basic_ios.tcc \
 /usr/include/c++/4.6/bits/ostream.tcc /usr/include/c++/4.6/istream \
 /usr/include/c++/4.6/bits/istream.tcc ../tools2/Vec.h \
 /usr/include/libintl.h /usr/include/c++/4.6/vector \
 /usr/include/c++/4.6/bits/stl_construct.h \
 /usr/include/c++/4.6/bits/stl_uninitialized.h \
 /usr/include/c++/4.6/bits/stl_vector.h \
 /usr/include/c++/4.6/bits/stl_bvector.h \
 /usr/include/c++/4.6/bits/vector.tcc ../tools2/debug.h \
 /usr/include/stdlib.h /usr/include/x86_64-linux-gnu/bits/waitflags.h \
 /usr/include/x86_64-linux-gnu/bits/waitstatus.h \
 /usr/include/x86_64-linux-gnu/sys/types.h \
 /usr/include/x86_64-linux-gnu/sys/select.h \
 /usr/include/x86_64-linux-gnu/bits/select.h \
 /usr/include/x86_64-linux-gnu/bits/sigset.h \
 /usr/include/x86_64-linux-gnu/bits/select2.h \
 /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \
 /usr/include/x86_64-linux-gnu/bits/stdlib.h /usr/include/assert.h \
 ../numerics/generalNumerics.h /usr/include/math.h \
 /usr/include/x86_64-linux-gnu/bits/huge_val.h \
 /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
 /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
 /usr/include/x86_64-linux-gnu/bits/inf.h \
 /usr/include/x86_64-linux-gnu/bits/nan.h \
 /usr/include/x86_64-linux-gnu/bits/mathdef.h \
 /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
 /usr/include/x86_64-linux-gnu/bits/mathinline.h \
 /usr/include/x86_64-linux-gnu/bits/math-finite.h ../tools2/Random.h \
 /usr/include/c++/4.6/utility /usr/include/c++/4.6/bits/stl_relops.h \
 ../numerics/vectornumerics.h \
 /usr/lib/gcc/x86_64-linux-gnu/4.6/include-fixed/limits.h \
 /usr/lib/gcc/x86_64-linux-gnu/4.6/include-fixed/syslimits.h \
 /usr/include/limits.h /usr/include/x86_64-linux-gnu/bits/posix1_lim.h \
 /usr/include/x86_64-linux-gnu/bits/local_lim.h \
 /usr/include/linux/limits.h \
 /usr/include/x86_64-linux-gnu/bits/posix2_lim.h \
 /usr/include/x86_64-linux-gnu/bits/xopen_lim.h \
 /usr/include/x86_64-linux-gnu/bits/stdio_lim.h /usr/include/c++/4.6/list \
 /usr/include/c++/4.6/bits/stl_list.h /usr/include/c++/4.6/bits/list.tcc \
 /usr/include/c++/4.6/set /usr/include/c++/4.6/bits/stl_tree.h \
 /usr/include/c++/4.6/bits/stl_set.h \
 /usr/include/c++/4.6/bits/stl_multiset.h /usr/include/c++/4.6/algorithm \
 /usr/include/c++/4.6/bits/stl_algo.h /usr/include/c++/4.6/cstdlib \
 /usr/include/c++/4.6/bits/algorithmfwd.h \
 /usr/include/c++/4.6/bits/stl_heap.h \
 /usr/include/c++/4.6/bits/stl_tempbuf.h ../numerics/Matrix3D.h \
 ../numerics/Vector3D.h ../numerics/Limits.h \
 ../numerics/RankedSolution4.h ../tools2/StringTools.h \
 /usr/include/c++/4.6/sstream /usr/include/c++/4.6/bits/sstream.tcc \
 /usr/include/libio.h /usr/include/_G_config.h \
 /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
 /usr/include/x86_64-linux-gnu/bits/stdio.h \
 /usr/include/x86_64-linux-gnu/bits/stdio2.h
sequencestat.o: sequencestat.cc sequencestat.h ../tools2/Vec.h \
 /usr/include/libintl.h /usr/include/features.h \
 /usr/include/x86_64-linux-gnu/bits/predefs.h \
 /usr/include/x86_64-linux-gnu/sys/cdefs.h \
 /usr/include/x86_64-linux-gnu/bits/wordsize.h \
 /usr/include/x86_64-linux-gnu/gnu/stubs.h \
 /usr/include/x86_64-linux-gnu/gnu/stubs-64.h /usr/include/c++/4.6/vector \
 /usr/include/c++/4.6/bits/stl_algobase.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/c++config.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/os_defines.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/cpu_defines.h \
 /usr/include/c++/4.6/bits/functexcept.h \
 /usr/include/c++/4.6/bits/exception_defines.h \
 /usr/include/c++/4.6/bits/cpp_type_traits.h \
 /usr/include/c++/4.6/ext/type_traits.h \
 /usr/include/c++/4.6/ext/numeric_traits.h \
 /usr/include/c++/4.6/bits/stl_pair.h /usr/include/c++/4.6/bits/move.h \
 /usr/include/c++/4.6/bits/concept_check.h \
 /usr/include/c++/4.6/bits/stl_iterator_base_types.h \
 /usr/include/c++/4.6/bits/stl_iterator_base_funcs.h \
 /usr/include/c++/4.6/bits/stl_iterator.h \
 /usr/include/c++/4.6/debug/debug.h /usr/include/c++/4.6/bits/allocator.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/c++allocator.h \
 /usr/include/c++/4.6/ext/new_allocator.h /usr/include/c++/4.6/new \
 /usr/include/c++/4.6/exception /usr/include/c++/4.6/bits/stl_construct.h \
 /usr/include/c++/4.6/bits/stl_uninitialized.h \
 /usr/include/c++/4.6/bits/stl_vector.h \
 /usr/include/c++/4.6/initializer_list \
 /usr/include/c++/4.6/bits/stl_bvector.h \
 /usr/include/c++/4.6/bits/range_access.h \
 /usr/include/c++/4.6/bits/vector.tcc ../tools2/debug.h \
 /usr/include/stdlib.h /usr/lib/gcc/x86_64-linux-gnu/4.6/include/stddef.h \
 /usr/include/x86_64-linux-gnu/bits/waitflags.h \
 /usr/include/x86_64-linux-gnu/bits/waitstatus.h /usr/include/endian.h \
 /usr/include/x86_64-linux-gnu/bits/endian.h \
 /usr/include/x86_64-linux-gnu/bits/byteswap.h /usr/include/xlocale.h \
 /usr/include/x86_64-linux-gnu/sys/types.h \
 /usr/include/x86_64-linux-gnu/bits/types.h \
 /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/time.h \
 /usr/include/x86_64-linux-gnu/sys/select.h \
 /usr/include/x86_64-linux-gnu/bits/select.h \
 /usr/include/x86_64-linux-gnu/bits/sigset.h \
 /usr/include/x86_64-linux-gnu/bits/time.h \
 /usr/include/x86_64-linux-gnu/bits/select2.h \
 /usr/include/x86_64-linux-gnu/sys/sysmacros.h \
 /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h /usr/include/alloca.h \
 /usr/include/x86_64-linux-gnu/bits/stdlib.h \
 /usr/include/c++/4.6/iostream /usr/include/c++/4.6/ostream \
 /usr/include/c++/4.6/ios /usr/include/c++/4.6/iosfwd \
 /usr/include/c++/4.6/bits/stringfwd.h \
 /usr/include/c++/4.6/bits/postypes.h /usr/include/c++/4.6/cwchar \
 /usr/include/wchar.h /usr/include/stdio.h \
 /usr/lib/gcc/x86_64-linux-gnu/4.6/include/stdarg.h \
 /usr/include/x86_64-linux-gnu/bits/wchar.h \
 /usr/include/x86_64-linux-gnu/bits/wchar2.h \
 /usr/include/c++/4.6/bits/char_traits.h \
 /usr/include/c++/4.6/bits/localefwd.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/c++locale.h \
 /usr/include/c++/4.6/clocale /usr/include/locale.h \
 /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.6/cctype \
 /usr/include/ctype.h /usr/include/c++/4.6/bits/ios_base.h \
 /usr/include/c++/4.6/ext/atomicity.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/gthr.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/gthr-default.h \
 /usr/include/pthread.h /usr/include/sched.h \
 /usr/include/x86_64-linux-gnu/bits/sched.h \
 /usr/include/x86_64-linux-gnu/bits/timex.h \
 /usr/include/x86_64-linux-gnu/bits/setjmp.h /usr/include/unistd.h \
 /usr/include/x86_64-linux-gnu/bits/posix_opt.h \
 /usr/include/x86_64-linux-gnu/bits/environments.h \
 /usr/include/x86_64-linux-gnu/bits/confname.h /usr/include/getopt.h \
 /usr/include/x86_64-linux-gnu/bits/unistd.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/atomic_word.h \
 /usr/include/c++/4.6/bits/locale_classes.h /usr/include/c++/4.6/string \
 /usr/include/c++/4.6/bits/ostream_insert.h \
 /usr/include/c++/4.6/bits/cxxabi_forced.h \
 /usr/include/c++/4.6/bits/stl_function.h \
 /usr/include/c++/4.6/backward/binders.h \
 /usr/include/c++/4.6/bits/basic_string.h \
 /usr/include/c++/4.6/bits/basic_string.tcc \
 /usr/include/c++/4.6/bits/locale_classes.tcc \
 /usr/include/c++/4.6/streambuf /usr/include/c++/4.6/bits/streambuf.tcc \
 /usr/include/c++/4.6/bits/basic_ios.h \
 /usr/include/c++/4.6/bits/locale_facets.h /usr/include/c++/4.6/cwctype \
 /usr/include/wctype.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/ctype_base.h \
 /usr/include/c++/4.6/bits/streambuf_iterator.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/ctype_inline.h \
 /usr/include/c++/4.6/bits/locale_facets.tcc \
 /usr/include/c++/4.6/bits/basic_ios.tcc \
 /usr/include/c++/4.6/bits/ostream.tcc /usr/include/c++/4.6/istream \
 /usr/include/c++/4.6/bits/istream.tcc /usr/include/assert.h \
 /usr/include/c++/4.6/algorithm /usr/include/c++/4.6/utility \
 /usr/include/c++/4.6/bits/stl_relops.h \
 /usr/include/c++/4.6/bits/stl_algo.h /usr/include/c++/4.6/cstdlib \
 /usr/include/c++/4.6/bits/algorithmfwd.h \
 /usr/include/c++/4.6/bits/stl_heap.h \
 /usr/include/c++/4.6/bits/stl_tempbuf.h ../sequence/SequenceAlignment.h \
 /usr/include/c++/4.6/map /usr/include/c++/4.6/bits/stl_tree.h \
 /usr/include/c++/4.6/bits/stl_map.h \
 /usr/include/c++/4.6/bits/stl_multimap.h /usr/include/math.h \
 /usr/include/x86_64-linux-gnu/bits/huge_val.h \
 /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
 /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
 /usr/include/x86_64-linux-gnu/bits/inf.h \
 /usr/include/x86_64-linux-gnu/bits/nan.h \
 /usr/include/x86_64-linux-gnu/bits/mathdef.h \
 /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
 /usr/include/x86_64-linux-gnu/bits/mathinline.h \
 /usr/include/x86_64-linux-gnu/bits/math-finite.h ../numerics/Limits.h
stemconvert.o: stemconvert.cc /usr/include/c++/4.6/iostream \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/c++config.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/os_defines.h \
 /usr/include/features.h /usr/include/x86_64-linux-gnu/bits/predefs.h \
 /usr/include/x86_64-linux-gnu/sys/cdefs.h \
 /usr/include/x86_64-linux-gnu/bits/wordsize.h \
 /usr/include/x86_64-linux-gnu/gnu/stubs.h \
 /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/cpu_defines.h \
 /usr/include/c++/4.6/ostream /usr/include/c++/4.6/ios \
 /usr/include/c++/4.6/iosfwd /usr/include/c++/4.6/bits/stringfwd.h \
 /usr/include/c++/4.6/bits/postypes.h /usr/include/c++/4.6/cwchar \
 /usr/include/wchar.h /usr/include/stdio.h \
 /usr/lib/gcc/x86_64-linux-gnu/4.6/include/stdarg.h \
 /usr/include/x86_64-linux-gnu/bits/wchar.h \
 /usr/lib/gcc/x86_64-linux-gnu/4.6/include/stddef.h \
 /usr/include/xlocale.h /usr/include/x86_64-linux-gnu/bits/wchar2.h \
 /usr/include/c++/4.6/exception /usr/include/c++/4.6/bits/char_traits.h \
 /usr/include/c++/4.6/bits/stl_algobase.h \
 /usr/include/c++/4.6/bits/functexcept.h \
 /usr/include/c++/4.6/bits/exception_defines.h \
 /usr/include/c++/4.6/bits/cpp_type_traits.h \
 /usr/include/c++/4.6/ext/type_traits.h \
 /usr/include/c++/4.6/ext/numeric_traits.h \
 /usr/include/c++/4.6/bits/stl_pair.h /usr/include/c++/4.6/bits/move.h \
 /usr/include/c++/4.6/bits/concept_check.h \
 /usr/include/c++/4.6/bits/stl_iterator_base_types.h \
 /usr/include/c++/4.6/bits/stl_iterator_base_funcs.h \
 /usr/include/c++/4.6/bits/stl_iterator.h \
 /usr/include/c++/4.6/debug/debug.h /usr/include/c++/4.6/bits/localefwd.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/c++locale.h \
 /usr/include/c++/4.6/clocale /usr/include/locale.h \
 /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.6/cctype \
 /usr/include/ctype.h /usr/include/x86_64-linux-gnu/bits/types.h \
 /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \
 /usr/include/x86_64-linux-gnu/bits/endian.h \
 /usr/include/x86_64-linux-gnu/bits/byteswap.h \
 /usr/include/c++/4.6/bits/ios_base.h \
 /usr/include/c++/4.6/ext/atomicity.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/gthr.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/gthr-default.h \
 /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
 /usr/include/x86_64-linux-gnu/bits/sched.h \
 /usr/include/x86_64-linux-gnu/bits/time.h \
 /usr/include/x86_64-linux-gnu/bits/timex.h \
 /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \
 /usr/include/x86_64-linux-gnu/bits/setjmp.h /usr/include/unistd.h \
 /usr/include/x86_64-linux-gnu/bits/posix_opt.h \
 /usr/include/x86_64-linux-gnu/bits/environments.h \
 /usr/include/x86_64-linux-gnu/bits/confname.h /usr/include/getopt.h \
 /usr/include/x86_64-linux-gnu/bits/unistd.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/atomic_word.h \
 /usr/include/c++/4.6/bits/locale_classes.h /usr/include/c++/4.6/string \
 /usr/include/c++/4.6/bits/allocator.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/c++allocator.h \
 /usr/include/c++/4.6/ext/new_allocator.h /usr/include/c++/4.6/new \
 /usr/include/c++/4.6/bits/ostream_insert.h \
 /usr/include/c++/4.6/bits/cxxabi_forced.h \
 /usr/include/c++/4.6/bits/stl_function.h \
 /usr/include/c++/4.6/backward/binders.h \
 /usr/include/c++/4.6/bits/range_access.h \
 /usr/include/c++/4.6/bits/basic_string.h \
 /usr/include/c++/4.6/initializer_list \
 /usr/include/c++/4.6/bits/basic_string.tcc \
 /usr/include/c++/4.6/bits/locale_classes.tcc \
 /usr/include/c++/4.6/streambuf /usr/include/c++/4.6/bits/streambuf.tcc \
 /usr/include/c++/4.6/bits/basic_ios.h \
 /usr/include/c++/4.6/bits/locale_facets.h /usr/include/c++/4.6/cwctype \
 /usr/include/wctype.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/ctype_base.h \
 /usr/include/c++/4.6/bits/streambuf_iterator.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/ctype_inline.h \
 /usr/include/c++/4.6/bits/locale_facets.tcc \
 /usr/include/c++/4.6/bits/basic_ios.tcc \
 /usr/include/c++/4.6/bits/ostream.tcc /usr/include/c++/4.6/istream \
 /usr/include/c++/4.6/bits/istream.tcc /usr/include/c++/4.6/fstream \
 /usr/include/c++/4.6/bits/codecvt.h /usr/include/c++/4.6/cstdio \
 /usr/include/libio.h /usr/include/_G_config.h \
 /usr/include/x86_64-linux-gnu/bits/stdio_lim.h \
 /usr/include/x86_64-linux-gnu/bits/sys_errlist.h \
 /usr/include/x86_64-linux-gnu/bits/stdio.h \
 /usr/include/x86_64-linux-gnu/bits/stdio2.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/basic_file.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/c++io.h \
 /usr/include/c++/4.6/bits/fstream.tcc ../tools2/Vec.h \
 /usr/include/libintl.h /usr/include/c++/4.6/vector \
 /usr/include/c++/4.6/bits/stl_construct.h \
 /usr/include/c++/4.6/bits/stl_uninitialized.h \
 /usr/include/c++/4.6/bits/stl_vector.h \
 /usr/include/c++/4.6/bits/stl_bvector.h \
 /usr/include/c++/4.6/bits/vector.tcc ../tools2/debug.h \
 /usr/include/stdlib.h /usr/include/x86_64-linux-gnu/bits/waitflags.h \
 /usr/include/x86_64-linux-gnu/bits/waitstatus.h \
 /usr/include/x86_64-linux-gnu/sys/types.h \
 /usr/include/x86_64-linux-gnu/sys/select.h \
 /usr/include/x86_64-linux-gnu/bits/select.h \
 /usr/include/x86_64-linux-gnu/bits/sigset.h \
 /usr/include/x86_64-linux-gnu/bits/select2.h \
 /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \
 /usr/include/x86_64-linux-gnu/bits/stdlib.h /usr/include/assert.h \
 ../tools2/GetArg.h /usr/include/string.h \
 /usr/include/x86_64-linux-gnu/bits/string3.h \
 /usr/include/c++/4.6/cstdarg ../tools2/StringTools.h \
 /usr/include/c++/4.6/sstream /usr/include/c++/4.6/bits/sstream.tcc \
 /usr/include/c++/4.6/cstdlib /usr/include/malloc.h ../tools2/FileName.h \
 stemhelp.h Stem.h /usr/include/math.h \
 /usr/include/x86_64-linux-gnu/bits/huge_val.h \
 /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
 /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
 /usr/include/x86_64-linux-gnu/bits/inf.h \
 /usr/include/x86_64-linux-gnu/bits/nan.h \
 /usr/include/x86_64-linux-gnu/bits/mathdef.h \
 /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
 /usr/include/x86_64-linux-gnu/bits/mathinline.h \
 /usr/include/x86_64-linux-gnu/bits/math-finite.h \
 ../numerics/RankedSolution5.h /usr/include/c++/4.6/stack \
 /usr/include/c++/4.6/deque /usr/include/c++/4.6/bits/stl_deque.h \
 /usr/include/c++/4.6/bits/deque.tcc \
 /usr/include/c++/4.6/bits/stl_stack.h RnaSecondaryStructure.h \
 /usr/include/c++/4.6/set /usr/include/c++/4.6/bits/stl_tree.h \
 /usr/include/c++/4.6/bits/stl_set.h \
 /usr/include/c++/4.6/bits/stl_multiset.h AbstractSecondaryStructure.h \
 RnaInteractionType.h ../sequence/SequenceAlignment.h \
 /usr/include/c++/4.6/map /usr/include/c++/4.6/bits/stl_map.h \
 /usr/include/c++/4.6/bits/stl_multimap.h \
 ../sequence/SimpleSequenceAlignment.h \
 ../sequence/SequenceAlignmentTools.h /usr/include/c++/4.6/algorithm \
 /usr/include/c++/4.6/utility /usr/include/c++/4.6/bits/stl_relops.h \
 /usr/include/c++/4.6/bits/stl_algo.h \
 /usr/include/c++/4.6/bits/algorithmfwd.h \
 /usr/include/c++/4.6/bits/stl_heap.h \
 /usr/include/c++/4.6/bits/stl_tempbuf.h ../tools2/Random.h \
 ../numerics/vectornumerics.h \
 /usr/lib/gcc/x86_64-linux-gnu/4.6/include-fixed/limits.h \
 /usr/lib/gcc/x86_64-linux-gnu/4.6/include-fixed/syslimits.h \
 /usr/include/limits.h /usr/include/x86_64-linux-gnu/bits/posix1_lim.h \
 /usr/include/x86_64-linux-gnu/bits/local_lim.h \
 /usr/include/linux/limits.h \
 /usr/include/x86_64-linux-gnu/bits/posix2_lim.h \
 /usr/include/x86_64-linux-gnu/bits/xopen_lim.h /usr/include/c++/4.6/list \
 /usr/include/c++/4.6/bits/stl_list.h /usr/include/c++/4.6/bits/list.tcc \
 ../numerics/Matrix3D.h ../numerics/Vector3D.h ../numerics/Limits.h \
 ../numerics/RankedSolution4.h ../numerics/generalNumerics.h \
 compass_help.h CompensationScorer.h ../tools2/ClassificationResult.h \
 ../numerics/Histogram.h StemTools.h ProbeStemEnergyModel.h \
 StemEnergyModel.h RnaSecondaryStructureTools.h RnaFormats.h
stemhelp.o: stemhelp.cc /usr/include/ctype.h /usr/include/features.h \
 /usr/include/x86_64-linux-gnu/bits/predefs.h \
 /usr/include/x86_64-linux-gnu/sys/cdefs.h \
 /usr/include/x86_64-linux-gnu/bits/wordsize.h \
 /usr/include/x86_64-linux-gnu/gnu/stubs.h \
 /usr/include/x86_64-linux-gnu/gnu/stubs-64.h \
 /usr/include/x86_64-linux-gnu/bits/types.h \
 /usr/include/x86_64-linux-gnu/bits/typesizes.h /usr/include/endian.h \
 /usr/include/x86_64-linux-gnu/bits/endian.h \
 /usr/include/x86_64-linux-gnu/bits/byteswap.h /usr/include/xlocale.h \
 stemhelp.h /usr/include/c++/4.6/iostream \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/c++config.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/os_defines.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/cpu_defines.h \
 /usr/include/c++/4.6/ostream /usr/include/c++/4.6/ios \
 /usr/include/c++/4.6/iosfwd /usr/include/c++/4.6/bits/stringfwd.h \
 /usr/include/c++/4.6/bits/postypes.h /usr/include/c++/4.6/cwchar \
 /usr/include/wchar.h /usr/include/stdio.h \
 /usr/lib/gcc/x86_64-linux-gnu/4.6/include/stdarg.h \
 /usr/include/x86_64-linux-gnu/bits/wchar.h \
 /usr/lib/gcc/x86_64-linux-gnu/4.6/include/stddef.h \
 /usr/include/x86_64-linux-gnu/bits/wchar2.h \
 /usr/include/c++/4.6/exception /usr/include/c++/4.6/bits/char_traits.h \
 /usr/include/c++/4.6/bits/stl_algobase.h \
 /usr/include/c++/4.6/bits/functexcept.h \
 /usr/include/c++/4.6/bits/exception_defines.h \
 /usr/include/c++/4.6/bits/cpp_type_traits.h \
 /usr/include/c++/4.6/ext/type_traits.h \
 /usr/include/c++/4.6/ext/numeric_traits.h \
 /usr/include/c++/4.6/bits/stl_pair.h /usr/include/c++/4.6/bits/move.h \
 /usr/include/c++/4.6/bits/concept_check.h \
 /usr/include/c++/4.6/bits/stl_iterator_base_types.h \
 /usr/include/c++/4.6/bits/stl_iterator_base_funcs.h \
 /usr/include/c++/4.6/bits/stl_iterator.h \
 /usr/include/c++/4.6/debug/debug.h /usr/include/c++/4.6/bits/localefwd.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/c++locale.h \
 /usr/include/c++/4.6/clocale /usr/include/locale.h \
 /usr/include/x86_64-linux-gnu/bits/locale.h /usr/include/c++/4.6/cctype \
 /usr/include/c++/4.6/bits/ios_base.h \
 /usr/include/c++/4.6/ext/atomicity.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/gthr.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/gthr-default.h \
 /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
 /usr/include/x86_64-linux-gnu/bits/sched.h \
 /usr/include/x86_64-linux-gnu/bits/time.h \
 /usr/include/x86_64-linux-gnu/bits/timex.h \
 /usr/include/x86_64-linux-gnu/bits/pthreadtypes.h \
 /usr/include/x86_64-linux-gnu/bits/setjmp.h /usr/include/unistd.h \
 /usr/include/x86_64-linux-gnu/bits/posix_opt.h \
 /usr/include/x86_64-linux-gnu/bits/environments.h \
 /usr/include/x86_64-linux-gnu/bits/confname.h /usr/include/getopt.h \
 /usr/include/x86_64-linux-gnu/bits/unistd.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/atomic_word.h \
 /usr/include/c++/4.6/bits/locale_classes.h /usr/include/c++/4.6/string \
 /usr/include/c++/4.6/bits/allocator.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/c++allocator.h \
 /usr/include/c++/4.6/ext/new_allocator.h /usr/include/c++/4.6/new \
 /usr/include/c++/4.6/bits/ostream_insert.h \
 /usr/include/c++/4.6/bits/cxxabi_forced.h \
 /usr/include/c++/4.6/bits/stl_function.h \
 /usr/include/c++/4.6/backward/binders.h \
 /usr/include/c++/4.6/bits/range_access.h \
 /usr/include/c++/4.6/bits/basic_string.h \
 /usr/include/c++/4.6/initializer_list \
 /usr/include/c++/4.6/bits/basic_string.tcc \
 /usr/include/c++/4.6/bits/locale_classes.tcc \
 /usr/include/c++/4.6/streambuf /usr/include/c++/4.6/bits/streambuf.tcc \
 /usr/include/c++/4.6/bits/basic_ios.h \
 /usr/include/c++/4.6/bits/locale_facets.h /usr/include/c++/4.6/cwctype \
 /usr/include/wctype.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/ctype_base.h \
 /usr/include/c++/4.6/bits/streambuf_iterator.h \
 /usr/include/c++/4.6/x86_64-linux-gnu/./bits/ctype_inline.h \
 /usr/include/c++/4.6/bits/locale_facets.tcc \
 /usr/include/c++/4.6/bits/basic_ios.tcc \
 /usr/include/c++/4.6/bits/ostream.tcc /usr/include/c++/4.6/istream \
 /usr/include/c++/4.6/bits/istream.tcc ../tools2/Vec.h \
 /usr/include/libintl.h /usr/include/c++/4.6/vector \
 /usr/include/c++/4.6/bits/stl_construct.h \
 /usr/include/c++/4.6/bits/stl_uninitialized.h \
 /usr/include/c++/4.6/bits/stl_vector.h \
 /usr/include/c++/4.6/bits/stl_bvector.h \
 /usr/include/c++/4.6/bits/vector.tcc ../tools2/debug.h \
 /usr/include/stdlib.h /usr/include/x86_64-linux-gnu/bits/waitflags.h \
 /usr/include/x86_64-linux-gnu/bits/waitstatus.h \
 /usr/include/x86_64-linux-gnu/sys/types.h \
 /usr/include/x86_64-linux-gnu/sys/select.h \
 /usr/include/x86_64-linux-gnu/bits/select.h \
 /usr/include/x86_64-linux-gnu/bits/sigset.h \
 /usr/include/x86_64-linux-gnu/bits/select2.h \
 /usr/include/x86_64-linux-gnu/sys/sysmacros.h /usr/include/alloca.h \
 /usr/include/x86_64-linux-gnu/bits/stdlib.h /usr/include/assert.h Stem.h \
 /usr/include/math.h /usr/include/x86_64-linux-gnu/bits/huge_val.h \
 /usr/include/x86_64-linux-gnu/bits/huge_valf.h \
 /usr/include/x86_64-linux-gnu/bits/huge_vall.h \
 /usr/include/x86_64-linux-gnu/bits/inf.h \
 /usr/include/x86_64-linux-gnu/bits/nan.h \
 /usr/include/x86_64-linux-gnu/bits/mathdef.h \
 /usr/include/x86_64-linux-gnu/bits/mathcalls.h \
 /usr/include/x86_64-linux-gnu/bits/mathinline.h \
 /usr/include/x86_64-linux-gnu/bits/math-finite.h \
 ../numerics/RankedSolution5.h /usr/include/c++/4.6/stack \
 /usr/include/c++/4.6/deque /usr/include/c++/4.6/bits/stl_deque.h \
 /usr/include/c++/4.6/bits/deque.tcc \
 /usr/include/c++/4.6/bits/stl_stack.h RnaSecondaryStructure.h \
 /usr/include/c++/4.6/set /usr/include/c++/4.6/bits/stl_tree.h \
 /usr/include/c++/4.6/bits/stl_set.h \
 /usr/include/c++/4.6/bits/stl_multiset.h AbstractSecondaryStructure.h \
 RnaInteractionType.h ../tools2/StringTools.h \
 /usr/include/c++/4.6/sstream /usr/include/c++/4.6/bits/sstream.tcc \
 /usr/include/c++/4.6/cstdlib ../numerics/vectornumerics.h \
 /usr/lib/gcc/x86_64-linux-gnu/4.6/include-fixed/limits.h \
 /usr/lib/gcc/x86_64-linux-gnu/4.6/include-fixed/syslimits.h \
 /usr/include/limits.h /usr/include/x86_64-linux-gnu/bits/posix1_lim.h \
 /usr/include/x86_64-linux-gnu/bits/local_lim.h \
 /usr/include/linux/limits.h \
 /usr/include/x86_64-linux-gnu/bits/posix2_lim.h \
 /usr/include/x86_64-linux-gnu/bits/xopen_lim.h \
 /usr/include/x86_64-linux-gnu/bits/stdio_lim.h /usr/include/c++/4.6/list \
 /usr/include/c++/4.6/bits/stl_list.h /usr/include/c++/4.6/bits/list.tcc \
 /usr/include/c++/4.6/algorithm /usr/include/c++/4.6/utility \
 /usr/include/c++/4.6/bits/stl_relops.h \
 /usr/include/c++/4.6/bits/stl_algo.h \
 /usr/include/c++/4.6/bits/algorithmfwd.h \
 /usr/include/c++/4.6/bits/stl_heap.h \
 /usr/include/c++/4.6/bits/stl_tempbuf.h ../numerics/Matrix3D.h \
 ../numerics/Vector3D.h ../numerics/Limits.h \
 ../numerics/RankedSolution4.h ../numerics/generalNumerics.h
