1 # Makefile.in generated by automake 1.10.2 from Makefile.am.
2 # src/Makefile. Generated from Makefile.in by configure.
4 # Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
5 # 2003, 2004, 2005, 2006, 2007, 2008 Free Software Foundation, Inc.
6 # This Makefile.in is free software; the Free Software Foundation
7 # gives unlimited permission to copy and/or distribute it,
8 # with or without modifications, as long as this notice is preserved.
10 # This program is distributed in the hope that it will be useful,
11 # but WITHOUT ANY WARRANTY, to the extent permitted by law; without
12 # even the implied warranty of MERCHANTABILITY or FITNESS FOR A
17 # Andreas Wilm (UCD): 2007-12-10
18 # Generated using the following sites
19 # http://www.openismus.com/documents/linux/automake/automake.shtml
20 # http://www.bioinf.uni-freiburg.de/~mmann/HowTo/automake.html
23 pkgdatadir = $(datadir)/clustalw
24 pkglibdir = $(libdir)/clustalw
25 pkgincludedir = $(includedir)/clustalw
26 am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
27 install_sh_DATA = $(install_sh) -c -m 644
28 install_sh_PROGRAM = $(install_sh) -c
29 install_sh_SCRIPT = $(install_sh) -c
30 INSTALL_HEADER = $(INSTALL_DATA)
31 transform = $(program_transform_name)
38 build_triplet = x86_64-unknown-linux-gnu
39 host_triplet = x86_64-unknown-linux-gnu
40 target_triplet = x86_64-unknown-linux-gnu
41 bin_PROGRAMS = clustalw2$(EXEEXT)
43 DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in \
44 $(srcdir)/clustalw_version.h.in $(srcdir)/config.h.in
45 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
46 am__aclocal_m4_deps = $(top_srcdir)/configure.ac
47 am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
49 mkinstalldirs = $(install_sh) -d
50 CONFIG_HEADER = config.h
51 CONFIG_CLEAN_FILES = clustalw_version.h
52 am__installdirs = "$(DESTDIR)$(bindir)"
53 binPROGRAMS_INSTALL = $(INSTALL_PROGRAM)
54 PROGRAMS = $(bin_PROGRAMS)
55 am_clustalw2_OBJECTS = FullPairwiseAlign.$(OBJEXT) \
56 FastPairwiseAlign.$(OBJEXT) MSFFileParser.$(OBJEXT) \
57 FileReader.$(OBJEXT) PIRFileParser.$(OBJEXT) \
58 RSFFileParser.$(OBJEXT) GDEFileParser.$(OBJEXT) \
59 InFileStream.$(OBJEXT) ClustalFileParser.$(OBJEXT) \
60 PearsonFileParser.$(OBJEXT) FileParser.$(OBJEXT) \
61 EMBLFileParser.$(OBJEXT) RootedClusterTree.$(OBJEXT) \
62 UPGMAAlgorithm.$(OBJEXT) Node.$(OBJEXT) \
63 RootedGuideTree.$(OBJEXT) RootedTreeOutput.$(OBJEXT) \
64 Tree.$(OBJEXT) ClusterTree.$(OBJEXT) TreeInterface.$(OBJEXT) \
65 UnRootedClusterTree.$(OBJEXT) ClusterTreeOutput.$(OBJEXT) \
66 RandomGenerator.$(OBJEXT) NJTree.$(OBJEXT) \
67 AlignmentSteps.$(OBJEXT) InteractiveMenu.$(OBJEXT) \
68 CommandLineParser.$(OBJEXT) SubMatrix.$(OBJEXT) \
69 Iteration.$(OBJEXT) MSA.$(OBJEXT) \
70 MyersMillerProfileAlign.$(OBJEXT) ProfileStandard.$(OBJEXT) \
71 ProfileWithSub.$(OBJEXT) ProfileBase.$(OBJEXT) \
72 LowScoreSegProfile.$(OBJEXT) OutputFile.$(OBJEXT) \
73 UserParameters.$(OBJEXT) Utility.$(OBJEXT) \
74 InvalidCombination.$(OBJEXT) DebugLog.$(OBJEXT) \
75 ClustalWResources.$(OBJEXT) VectorOutOfRange.$(OBJEXT) \
76 SymMatrix.$(OBJEXT) Stats.$(OBJEXT) Help.$(OBJEXT) \
77 Alignment.$(OBJEXT) AlignmentOutput.$(OBJEXT) \
78 ObjectiveScore.$(OBJEXT) Sequence.$(OBJEXT) Clustal.$(OBJEXT) \
80 clustalw2_OBJECTS = $(am_clustalw2_OBJECTS)
81 clustalw2_LDADD = $(LDADD)
82 DEFAULT_INCLUDES = -I.
83 depcomp = $(SHELL) $(top_srcdir)/depcomp
84 am__depfiles_maybe = depfiles
85 CXXCOMPILE = $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \
86 $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS)
88 CXXLINK = $(CXXLD) $(AM_CXXFLAGS) $(CXXFLAGS) $(AM_LDFLAGS) $(LDFLAGS) \
90 COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \
91 $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
93 LINK = $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(AM_LDFLAGS) $(LDFLAGS) -o $@
94 SOURCES = $(clustalw2_SOURCES)
95 DIST_SOURCES = $(clustalw2_SOURCES)
96 RECURSIVE_TARGETS = all-recursive check-recursive dvi-recursive \
97 html-recursive info-recursive install-data-recursive \
98 install-dvi-recursive install-exec-recursive \
99 install-html-recursive install-info-recursive \
100 install-pdf-recursive install-ps-recursive install-recursive \
101 installcheck-recursive installdirs-recursive pdf-recursive \
102 ps-recursive uninstall-recursive
103 RECURSIVE_CLEAN_TARGETS = mostlyclean-recursive clean-recursive \
104 distclean-recursive maintainer-clean-recursive
107 DIST_SUBDIRS = $(SUBDIRS)
108 DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
109 ACLOCAL = ${SHELL} /homes/pvtroshin/workspace/clustengine/binaries/src/clustalw/missing --run aclocal-1.10
110 AMTAR = ${SHELL} /homes/pvtroshin/workspace/clustengine/binaries/src/clustalw/missing --run tar
111 AUTOCONF = ${SHELL} /homes/pvtroshin/workspace/clustengine/binaries/src/clustalw/missing --run autoconf
112 AUTOHEADER = ${SHELL} /homes/pvtroshin/workspace/clustengine/binaries/src/clustalw/missing --run autoheader
113 AUTOMAKE = ${SHELL} /homes/pvtroshin/workspace/clustengine/binaries/src/clustalw/missing --run automake-1.10
116 CCDEPMODE = depmode=gcc3
118 CLUSTALW_NAME = ClustalW
119 CLUSTALW_VERSION = 2.0.12
123 CXXDEPMODE = depmode=gcc3
126 DEFS = -DHAVE_CONFIG_H
134 INSTALL = /usr/bin/install -c
135 INSTALL_DATA = ${INSTALL} -m 644
136 INSTALL_PROGRAM = ${INSTALL}
137 INSTALL_SCRIPT = ${INSTALL}
138 INSTALL_STRIP_PROGRAM = $(install_sh) -c -s
143 MAKEINFO = ${SHELL} /homes/pvtroshin/workspace/clustengine/binaries/src/clustalw/missing --run makeinfo
144 MKDIR_P = /bin/mkdir -p
147 PACKAGE_BUGREPORT = clustalw@ucd.ie
148 PACKAGE_NAME = clustalw
149 PACKAGE_STRING = clustalw 2.0.12
150 PACKAGE_TARNAME = clustalw
151 PACKAGE_VERSION = 2.0.12
158 abs_builddir = /homes/pvtroshin/workspace/clustengine/binaries/src/clustalw/src
159 abs_srcdir = /homes/pvtroshin/workspace/clustengine/binaries/src/clustalw/src
160 abs_top_builddir = /homes/pvtroshin/workspace/clustengine/binaries/src/clustalw
161 abs_top_srcdir = /homes/pvtroshin/workspace/clustengine/binaries/src/clustalw
164 am__include = include
167 am__tar = ${AMTAR} chof - "$$tardir"
168 am__untar = ${AMTAR} xf -
169 bindir = ${exec_prefix}/bin
170 build = x86_64-unknown-linux-gnu
174 build_vendor = unknown
176 datadir = ${datarootdir}
177 datarootdir = ${prefix}/share
178 docdir = ${datarootdir}/doc/${PACKAGE_TARNAME}
180 exec_prefix = ${prefix}
181 host = x86_64-unknown-linux-gnu
185 host_vendor = unknown
187 includedir = ${prefix}/include
188 infodir = ${datarootdir}/info
189 install_sh = $(SHELL) /homes/pvtroshin/workspace/clustengine/binaries/src/clustalw/install-sh
190 libdir = ${exec_prefix}/lib
191 libexecdir = ${exec_prefix}/libexec
192 localedir = ${datarootdir}/locale
193 localstatedir = ${prefix}/var
194 mandir = ${datarootdir}/man
195 mkdir_p = /bin/mkdir -p
196 oldincludedir = /usr/include
199 program_transform_name = s,x,x,
201 sbindir = ${exec_prefix}/sbin
202 sharedstatedir = ${prefix}/com
204 sysconfdir = ${prefix}/etc
205 target = x86_64-unknown-linux-gnu
208 target_os = linux-gnu
209 target_vendor = unknown
210 top_build_prefix = ../
214 # we do not use GNU-style files: NEWS README AUTHORS ChangeLog
215 AUTOMAKE_OPTIONS = foreign
217 clustalw2_SOURCES = ./pairwise/PairwiseAlignBase.h \
218 ./pairwise/FastPairwiseAlign.h \
219 ./pairwise/FullPairwiseAlign.cpp \
220 ./pairwise/FullPairwiseAlign.h \
221 ./pairwise/FastPairwiseAlign.cpp \
222 ./fileInput/FileParser.h \
223 ./fileInput/EMBLFileParser.h \
224 ./fileInput/MSFFileParser.cpp \
225 ./fileInput/FileReader.cpp \
226 ./fileInput/PIRFileParser.cpp \
227 ./fileInput/MSFFileParser.h \
228 ./fileInput/FileReader.h \
229 ./fileInput/RSFFileParser.cpp \
230 ./fileInput/PIRFileParser.h \
231 ./fileInput/GDEFileParser.cpp \
232 ./fileInput/RSFFileParser.h \
233 ./fileInput/GDEFileParser.h \
234 ./fileInput/InFileStream.cpp \
235 ./fileInput/ClustalFileParser.cpp \
236 ./fileInput/PearsonFileParser.cpp \
237 ./fileInput/InFileStream.h \
238 ./fileInput/ClustalFileParser.h \
239 ./fileInput/PearsonFileParser.h \
240 ./fileInput/FileParser.cpp \
241 ./fileInput/EMBLFileParser.cpp \
242 ./tree/UPGMA/RootedClusterTree.cpp \
243 ./tree/UPGMA/RootedGuideTree.h \
244 ./tree/UPGMA/UPGMAAlgorithm.cpp \
245 ./tree/UPGMA/RootedTreeOutput.h \
246 ./tree/UPGMA/RootedClusterTree.h \
247 ./tree/UPGMA/Node.cpp \
248 ./tree/UPGMA/UPGMAAlgorithm.h \
249 ./tree/UPGMA/upgmadata.h \
250 ./tree/UPGMA/Node.h \
251 ./tree/UPGMA/RootedGuideTree.cpp \
252 ./tree/UPGMA/RootedTreeOutput.cpp \
254 ./tree/ClusterTree.cpp \
255 ./tree/AlignmentSteps.h \
257 ./tree/ClusterTree.h \
258 ./tree/ClusterTreeAlgorithm.h \
259 ./tree/TreeInterface.cpp \
260 ./tree/UnRootedClusterTree.cpp \
261 ./tree/ClusterTreeOutput.cpp \
262 ./tree/TreeInterface.h \
264 ./tree/UnRootedClusterTree.h \
265 ./tree/RandomGenerator.cpp \
267 ./tree/ClusterTreeOutput.h \
268 ./tree/RandomGenerator.h \
270 ./tree/AlignmentSteps.cpp \
271 ./interface/InteractiveMenu.cpp \
272 ./interface/CommandLineParser.cpp \
273 ./interface/InteractiveMenu.h \
274 ./interface/CommandLineParser.h \
275 ./substitutionMatrix/SubMatrix.cpp \
276 ./substitutionMatrix/SubMatrix.h \
277 ./substitutionMatrix/globalmatrix.h \
278 ./substitutionMatrix/matrices.h \
279 ./multipleAlign/Iteration.cpp \
280 ./multipleAlign/MSA.cpp \
281 ./multipleAlign/MyersMillerProfileAlign.cpp \
282 ./multipleAlign/ProfileBase.h \
283 ./multipleAlign/ProfileStandard.cpp \
284 ./multipleAlign/LowScoreSegProfile.h \
285 ./multipleAlign/Iteration.h \
286 ./multipleAlign/MSA.h \
287 ./multipleAlign/MyersMillerProfileAlign.h \
288 ./multipleAlign/ProfileStandard.h \
289 ./multipleAlign/ProfileWithSub.cpp \
290 ./multipleAlign/ProfileAlignAlgorithm.h \
291 ./multipleAlign/ProfileBase.cpp \
292 ./multipleAlign/ProfileWithSub.h \
293 ./multipleAlign/LowScoreSegProfile.cpp \
294 ./general/ClustalWResources.h \
295 ./general/OutputFile.cpp \
296 ./general/VectorOutOfRange.h \
297 ./general/UserParameters.cpp \
298 ./general/SymMatrix.h \
299 ./general/Utility.cpp \
300 ./general/clustalw.h \
301 ./general/OutputFile.h \
304 ./general/UserParameters.h \
305 ./general/SquareMat.h \
306 ./general/Utility.h \
307 ./general/SequenceNotFoundException.h \
308 ./general/InvalidCombination.cpp \
309 ./general/Array2D.h \
310 ./general/RandomAccessLList.h \
311 ./general/general.h \
312 ./general/debuglogObject.h \
313 ./general/statsObject.h \
314 ./general/userparams.h \
315 ./general/DebugLog.cpp \
316 ./general/ClustalWResources.cpp \
317 ./general/VectorUtility.h \
318 ./general/VectorOutOfRange.cpp \
319 ./general/SymMatrix.cpp \
320 ./general/DebugLog.h \
321 ./general/Stats.cpp \
325 ./alignment/Alignment.cpp \
326 ./alignment/AlignmentOutput.cpp \
327 ./alignment/Alignment.h \
328 ./alignment/AlignmentOutput.h \
329 ./alignment/ObjectiveScore.cpp \
330 ./alignment/Sequence.cpp \
331 ./alignment/ObjectiveScore.h \
332 ./alignment/Sequence.h \
335 ./clustalw_version.h \
339 $(MAKE) $(AM_MAKEFLAGS) all-recursive
342 .SUFFIXES: .cpp .o .obj
343 $(srcdir)/Makefile.in: $(srcdir)/Makefile.am $(am__configure_deps)
345 case '$(am__configure_deps)' in \
347 ( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \
348 && { if test -f $@; then exit 0; else break; fi; }; \
352 echo ' cd $(top_srcdir) && $(AUTOMAKE) --foreign src/Makefile'; \
353 cd $(top_srcdir) && \
354 $(AUTOMAKE) --foreign src/Makefile
356 Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
359 cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
361 echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
362 cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
365 $(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
366 cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
368 $(top_srcdir)/configure: $(am__configure_deps)
369 cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
370 $(ACLOCAL_M4): $(am__aclocal_m4_deps)
371 cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
374 @if test ! -f $@; then \
376 $(MAKE) $(AM_MAKEFLAGS) stamp-h1; \
379 stamp-h1: $(srcdir)/config.h.in $(top_builddir)/config.status
381 cd $(top_builddir) && $(SHELL) ./config.status src/config.h
382 $(srcdir)/config.h.in: $(am__configure_deps)
383 cd $(top_srcdir) && $(AUTOHEADER)
388 -rm -f config.h stamp-h1
389 clustalw_version.h: $(top_builddir)/config.status $(srcdir)/clustalw_version.h.in
390 cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@
391 install-binPROGRAMS: $(bin_PROGRAMS)
393 test -z "$(bindir)" || $(MKDIR_P) "$(DESTDIR)$(bindir)"
394 @list='$(bin_PROGRAMS)'; for p in $$list; do \
395 p1=`echo $$p|sed 's/$(EXEEXT)$$//'`; \
398 f=`echo "$$p1" | sed 's,^.*/,,;$(transform);s/$$/$(EXEEXT)/'`; \
399 echo " $(INSTALL_PROGRAM_ENV) $(binPROGRAMS_INSTALL) '$$p' '$(DESTDIR)$(bindir)/$$f'"; \
400 $(INSTALL_PROGRAM_ENV) $(binPROGRAMS_INSTALL) "$$p" "$(DESTDIR)$(bindir)/$$f" || exit 1; \
404 uninstall-binPROGRAMS:
406 @list='$(bin_PROGRAMS)'; for p in $$list; do \
407 f=`echo "$$p" | sed 's,^.*/,,;s/$(EXEEXT)$$//;$(transform);s/$$/$(EXEEXT)/'`; \
408 echo " rm -f '$(DESTDIR)$(bindir)/$$f'"; \
409 rm -f "$(DESTDIR)$(bindir)/$$f"; \
413 -test -z "$(bin_PROGRAMS)" || rm -f $(bin_PROGRAMS)
414 clustalw2$(EXEEXT): $(clustalw2_OBJECTS) $(clustalw2_DEPENDENCIES)
415 @rm -f clustalw2$(EXEEXT)
416 $(CXXLINK) $(clustalw2_OBJECTS) $(clustalw2_LDADD) $(LIBS)
424 include ./$(DEPDIR)/Alignment.Po
425 include ./$(DEPDIR)/AlignmentOutput.Po
426 include ./$(DEPDIR)/AlignmentSteps.Po
427 include ./$(DEPDIR)/Clustal.Po
428 include ./$(DEPDIR)/ClustalFileParser.Po
429 include ./$(DEPDIR)/ClustalWResources.Po
430 include ./$(DEPDIR)/ClusterTree.Po
431 include ./$(DEPDIR)/ClusterTreeOutput.Po
432 include ./$(DEPDIR)/CommandLineParser.Po
433 include ./$(DEPDIR)/DebugLog.Po
434 include ./$(DEPDIR)/EMBLFileParser.Po
435 include ./$(DEPDIR)/FastPairwiseAlign.Po
436 include ./$(DEPDIR)/FileParser.Po
437 include ./$(DEPDIR)/FileReader.Po
438 include ./$(DEPDIR)/FullPairwiseAlign.Po
439 include ./$(DEPDIR)/GDEFileParser.Po
440 include ./$(DEPDIR)/Help.Po
441 include ./$(DEPDIR)/InFileStream.Po
442 include ./$(DEPDIR)/InteractiveMenu.Po
443 include ./$(DEPDIR)/InvalidCombination.Po
444 include ./$(DEPDIR)/Iteration.Po
445 include ./$(DEPDIR)/LowScoreSegProfile.Po
446 include ./$(DEPDIR)/MSA.Po
447 include ./$(DEPDIR)/MSFFileParser.Po
448 include ./$(DEPDIR)/MyersMillerProfileAlign.Po
449 include ./$(DEPDIR)/NJTree.Po
450 include ./$(DEPDIR)/Node.Po
451 include ./$(DEPDIR)/ObjectiveScore.Po
452 include ./$(DEPDIR)/OutputFile.Po
453 include ./$(DEPDIR)/PIRFileParser.Po
454 include ./$(DEPDIR)/PearsonFileParser.Po
455 include ./$(DEPDIR)/ProfileBase.Po
456 include ./$(DEPDIR)/ProfileStandard.Po
457 include ./$(DEPDIR)/ProfileWithSub.Po
458 include ./$(DEPDIR)/RSFFileParser.Po
459 include ./$(DEPDIR)/RandomGenerator.Po
460 include ./$(DEPDIR)/RootedClusterTree.Po
461 include ./$(DEPDIR)/RootedGuideTree.Po
462 include ./$(DEPDIR)/RootedTreeOutput.Po
463 include ./$(DEPDIR)/Sequence.Po
464 include ./$(DEPDIR)/Stats.Po
465 include ./$(DEPDIR)/SubMatrix.Po
466 include ./$(DEPDIR)/SymMatrix.Po
467 include ./$(DEPDIR)/Tree.Po
468 include ./$(DEPDIR)/TreeInterface.Po
469 include ./$(DEPDIR)/UPGMAAlgorithm.Po
470 include ./$(DEPDIR)/UnRootedClusterTree.Po
471 include ./$(DEPDIR)/UserParameters.Po
472 include ./$(DEPDIR)/Utility.Po
473 include ./$(DEPDIR)/VectorOutOfRange.Po
474 include ./$(DEPDIR)/main.Po
477 $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
478 mv -f $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
479 # source='$<' object='$@' libtool=no \
480 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
481 # $(CXXCOMPILE) -c -o $@ $<
484 $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
485 mv -f $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
486 # source='$<' object='$@' libtool=no \
487 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
488 # $(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
490 FullPairwiseAlign.o: ./pairwise/FullPairwiseAlign.cpp
491 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT FullPairwiseAlign.o -MD -MP -MF $(DEPDIR)/FullPairwiseAlign.Tpo -c -o FullPairwiseAlign.o `test -f './pairwise/FullPairwiseAlign.cpp' || echo '$(srcdir)/'`./pairwise/FullPairwiseAlign.cpp
492 mv -f $(DEPDIR)/FullPairwiseAlign.Tpo $(DEPDIR)/FullPairwiseAlign.Po
493 # source='./pairwise/FullPairwiseAlign.cpp' object='FullPairwiseAlign.o' libtool=no \
494 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
495 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o FullPairwiseAlign.o `test -f './pairwise/FullPairwiseAlign.cpp' || echo '$(srcdir)/'`./pairwise/FullPairwiseAlign.cpp
497 FullPairwiseAlign.obj: ./pairwise/FullPairwiseAlign.cpp
498 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT FullPairwiseAlign.obj -MD -MP -MF $(DEPDIR)/FullPairwiseAlign.Tpo -c -o FullPairwiseAlign.obj `if test -f './pairwise/FullPairwiseAlign.cpp'; then $(CYGPATH_W) './pairwise/FullPairwiseAlign.cpp'; else $(CYGPATH_W) '$(srcdir)/./pairwise/FullPairwiseAlign.cpp'; fi`
499 mv -f $(DEPDIR)/FullPairwiseAlign.Tpo $(DEPDIR)/FullPairwiseAlign.Po
500 # source='./pairwise/FullPairwiseAlign.cpp' object='FullPairwiseAlign.obj' libtool=no \
501 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
502 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o FullPairwiseAlign.obj `if test -f './pairwise/FullPairwiseAlign.cpp'; then $(CYGPATH_W) './pairwise/FullPairwiseAlign.cpp'; else $(CYGPATH_W) '$(srcdir)/./pairwise/FullPairwiseAlign.cpp'; fi`
504 FastPairwiseAlign.o: ./pairwise/FastPairwiseAlign.cpp
505 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT FastPairwiseAlign.o -MD -MP -MF $(DEPDIR)/FastPairwiseAlign.Tpo -c -o FastPairwiseAlign.o `test -f './pairwise/FastPairwiseAlign.cpp' || echo '$(srcdir)/'`./pairwise/FastPairwiseAlign.cpp
506 mv -f $(DEPDIR)/FastPairwiseAlign.Tpo $(DEPDIR)/FastPairwiseAlign.Po
507 # source='./pairwise/FastPairwiseAlign.cpp' object='FastPairwiseAlign.o' libtool=no \
508 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
509 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o FastPairwiseAlign.o `test -f './pairwise/FastPairwiseAlign.cpp' || echo '$(srcdir)/'`./pairwise/FastPairwiseAlign.cpp
511 FastPairwiseAlign.obj: ./pairwise/FastPairwiseAlign.cpp
512 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT FastPairwiseAlign.obj -MD -MP -MF $(DEPDIR)/FastPairwiseAlign.Tpo -c -o FastPairwiseAlign.obj `if test -f './pairwise/FastPairwiseAlign.cpp'; then $(CYGPATH_W) './pairwise/FastPairwiseAlign.cpp'; else $(CYGPATH_W) '$(srcdir)/./pairwise/FastPairwiseAlign.cpp'; fi`
513 mv -f $(DEPDIR)/FastPairwiseAlign.Tpo $(DEPDIR)/FastPairwiseAlign.Po
514 # source='./pairwise/FastPairwiseAlign.cpp' object='FastPairwiseAlign.obj' libtool=no \
515 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
516 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o FastPairwiseAlign.obj `if test -f './pairwise/FastPairwiseAlign.cpp'; then $(CYGPATH_W) './pairwise/FastPairwiseAlign.cpp'; else $(CYGPATH_W) '$(srcdir)/./pairwise/FastPairwiseAlign.cpp'; fi`
518 MSFFileParser.o: ./fileInput/MSFFileParser.cpp
519 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT MSFFileParser.o -MD -MP -MF $(DEPDIR)/MSFFileParser.Tpo -c -o MSFFileParser.o `test -f './fileInput/MSFFileParser.cpp' || echo '$(srcdir)/'`./fileInput/MSFFileParser.cpp
520 mv -f $(DEPDIR)/MSFFileParser.Tpo $(DEPDIR)/MSFFileParser.Po
521 # source='./fileInput/MSFFileParser.cpp' object='MSFFileParser.o' libtool=no \
522 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
523 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o MSFFileParser.o `test -f './fileInput/MSFFileParser.cpp' || echo '$(srcdir)/'`./fileInput/MSFFileParser.cpp
525 MSFFileParser.obj: ./fileInput/MSFFileParser.cpp
526 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT MSFFileParser.obj -MD -MP -MF $(DEPDIR)/MSFFileParser.Tpo -c -o MSFFileParser.obj `if test -f './fileInput/MSFFileParser.cpp'; then $(CYGPATH_W) './fileInput/MSFFileParser.cpp'; else $(CYGPATH_W) '$(srcdir)/./fileInput/MSFFileParser.cpp'; fi`
527 mv -f $(DEPDIR)/MSFFileParser.Tpo $(DEPDIR)/MSFFileParser.Po
528 # source='./fileInput/MSFFileParser.cpp' object='MSFFileParser.obj' libtool=no \
529 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
530 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o MSFFileParser.obj `if test -f './fileInput/MSFFileParser.cpp'; then $(CYGPATH_W) './fileInput/MSFFileParser.cpp'; else $(CYGPATH_W) '$(srcdir)/./fileInput/MSFFileParser.cpp'; fi`
532 FileReader.o: ./fileInput/FileReader.cpp
533 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT FileReader.o -MD -MP -MF $(DEPDIR)/FileReader.Tpo -c -o FileReader.o `test -f './fileInput/FileReader.cpp' || echo '$(srcdir)/'`./fileInput/FileReader.cpp
534 mv -f $(DEPDIR)/FileReader.Tpo $(DEPDIR)/FileReader.Po
535 # source='./fileInput/FileReader.cpp' object='FileReader.o' libtool=no \
536 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
537 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o FileReader.o `test -f './fileInput/FileReader.cpp' || echo '$(srcdir)/'`./fileInput/FileReader.cpp
539 FileReader.obj: ./fileInput/FileReader.cpp
540 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT FileReader.obj -MD -MP -MF $(DEPDIR)/FileReader.Tpo -c -o FileReader.obj `if test -f './fileInput/FileReader.cpp'; then $(CYGPATH_W) './fileInput/FileReader.cpp'; else $(CYGPATH_W) '$(srcdir)/./fileInput/FileReader.cpp'; fi`
541 mv -f $(DEPDIR)/FileReader.Tpo $(DEPDIR)/FileReader.Po
542 # source='./fileInput/FileReader.cpp' object='FileReader.obj' libtool=no \
543 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
544 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o FileReader.obj `if test -f './fileInput/FileReader.cpp'; then $(CYGPATH_W) './fileInput/FileReader.cpp'; else $(CYGPATH_W) '$(srcdir)/./fileInput/FileReader.cpp'; fi`
546 PIRFileParser.o: ./fileInput/PIRFileParser.cpp
547 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT PIRFileParser.o -MD -MP -MF $(DEPDIR)/PIRFileParser.Tpo -c -o PIRFileParser.o `test -f './fileInput/PIRFileParser.cpp' || echo '$(srcdir)/'`./fileInput/PIRFileParser.cpp
548 mv -f $(DEPDIR)/PIRFileParser.Tpo $(DEPDIR)/PIRFileParser.Po
549 # source='./fileInput/PIRFileParser.cpp' object='PIRFileParser.o' libtool=no \
550 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
551 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o PIRFileParser.o `test -f './fileInput/PIRFileParser.cpp' || echo '$(srcdir)/'`./fileInput/PIRFileParser.cpp
553 PIRFileParser.obj: ./fileInput/PIRFileParser.cpp
554 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT PIRFileParser.obj -MD -MP -MF $(DEPDIR)/PIRFileParser.Tpo -c -o PIRFileParser.obj `if test -f './fileInput/PIRFileParser.cpp'; then $(CYGPATH_W) './fileInput/PIRFileParser.cpp'; else $(CYGPATH_W) '$(srcdir)/./fileInput/PIRFileParser.cpp'; fi`
555 mv -f $(DEPDIR)/PIRFileParser.Tpo $(DEPDIR)/PIRFileParser.Po
556 # source='./fileInput/PIRFileParser.cpp' object='PIRFileParser.obj' libtool=no \
557 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
558 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o PIRFileParser.obj `if test -f './fileInput/PIRFileParser.cpp'; then $(CYGPATH_W) './fileInput/PIRFileParser.cpp'; else $(CYGPATH_W) '$(srcdir)/./fileInput/PIRFileParser.cpp'; fi`
560 RSFFileParser.o: ./fileInput/RSFFileParser.cpp
561 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT RSFFileParser.o -MD -MP -MF $(DEPDIR)/RSFFileParser.Tpo -c -o RSFFileParser.o `test -f './fileInput/RSFFileParser.cpp' || echo '$(srcdir)/'`./fileInput/RSFFileParser.cpp
562 mv -f $(DEPDIR)/RSFFileParser.Tpo $(DEPDIR)/RSFFileParser.Po
563 # source='./fileInput/RSFFileParser.cpp' object='RSFFileParser.o' libtool=no \
564 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
565 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o RSFFileParser.o `test -f './fileInput/RSFFileParser.cpp' || echo '$(srcdir)/'`./fileInput/RSFFileParser.cpp
567 RSFFileParser.obj: ./fileInput/RSFFileParser.cpp
568 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT RSFFileParser.obj -MD -MP -MF $(DEPDIR)/RSFFileParser.Tpo -c -o RSFFileParser.obj `if test -f './fileInput/RSFFileParser.cpp'; then $(CYGPATH_W) './fileInput/RSFFileParser.cpp'; else $(CYGPATH_W) '$(srcdir)/./fileInput/RSFFileParser.cpp'; fi`
569 mv -f $(DEPDIR)/RSFFileParser.Tpo $(DEPDIR)/RSFFileParser.Po
570 # source='./fileInput/RSFFileParser.cpp' object='RSFFileParser.obj' libtool=no \
571 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
572 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o RSFFileParser.obj `if test -f './fileInput/RSFFileParser.cpp'; then $(CYGPATH_W) './fileInput/RSFFileParser.cpp'; else $(CYGPATH_W) '$(srcdir)/./fileInput/RSFFileParser.cpp'; fi`
574 GDEFileParser.o: ./fileInput/GDEFileParser.cpp
575 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT GDEFileParser.o -MD -MP -MF $(DEPDIR)/GDEFileParser.Tpo -c -o GDEFileParser.o `test -f './fileInput/GDEFileParser.cpp' || echo '$(srcdir)/'`./fileInput/GDEFileParser.cpp
576 mv -f $(DEPDIR)/GDEFileParser.Tpo $(DEPDIR)/GDEFileParser.Po
577 # source='./fileInput/GDEFileParser.cpp' object='GDEFileParser.o' libtool=no \
578 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
579 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o GDEFileParser.o `test -f './fileInput/GDEFileParser.cpp' || echo '$(srcdir)/'`./fileInput/GDEFileParser.cpp
581 GDEFileParser.obj: ./fileInput/GDEFileParser.cpp
582 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT GDEFileParser.obj -MD -MP -MF $(DEPDIR)/GDEFileParser.Tpo -c -o GDEFileParser.obj `if test -f './fileInput/GDEFileParser.cpp'; then $(CYGPATH_W) './fileInput/GDEFileParser.cpp'; else $(CYGPATH_W) '$(srcdir)/./fileInput/GDEFileParser.cpp'; fi`
583 mv -f $(DEPDIR)/GDEFileParser.Tpo $(DEPDIR)/GDEFileParser.Po
584 # source='./fileInput/GDEFileParser.cpp' object='GDEFileParser.obj' libtool=no \
585 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
586 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o GDEFileParser.obj `if test -f './fileInput/GDEFileParser.cpp'; then $(CYGPATH_W) './fileInput/GDEFileParser.cpp'; else $(CYGPATH_W) '$(srcdir)/./fileInput/GDEFileParser.cpp'; fi`
588 InFileStream.o: ./fileInput/InFileStream.cpp
589 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT InFileStream.o -MD -MP -MF $(DEPDIR)/InFileStream.Tpo -c -o InFileStream.o `test -f './fileInput/InFileStream.cpp' || echo '$(srcdir)/'`./fileInput/InFileStream.cpp
590 mv -f $(DEPDIR)/InFileStream.Tpo $(DEPDIR)/InFileStream.Po
591 # source='./fileInput/InFileStream.cpp' object='InFileStream.o' libtool=no \
592 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
593 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o InFileStream.o `test -f './fileInput/InFileStream.cpp' || echo '$(srcdir)/'`./fileInput/InFileStream.cpp
595 InFileStream.obj: ./fileInput/InFileStream.cpp
596 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT InFileStream.obj -MD -MP -MF $(DEPDIR)/InFileStream.Tpo -c -o InFileStream.obj `if test -f './fileInput/InFileStream.cpp'; then $(CYGPATH_W) './fileInput/InFileStream.cpp'; else $(CYGPATH_W) '$(srcdir)/./fileInput/InFileStream.cpp'; fi`
597 mv -f $(DEPDIR)/InFileStream.Tpo $(DEPDIR)/InFileStream.Po
598 # source='./fileInput/InFileStream.cpp' object='InFileStream.obj' libtool=no \
599 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
600 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o InFileStream.obj `if test -f './fileInput/InFileStream.cpp'; then $(CYGPATH_W) './fileInput/InFileStream.cpp'; else $(CYGPATH_W) '$(srcdir)/./fileInput/InFileStream.cpp'; fi`
602 ClustalFileParser.o: ./fileInput/ClustalFileParser.cpp
603 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT ClustalFileParser.o -MD -MP -MF $(DEPDIR)/ClustalFileParser.Tpo -c -o ClustalFileParser.o `test -f './fileInput/ClustalFileParser.cpp' || echo '$(srcdir)/'`./fileInput/ClustalFileParser.cpp
604 mv -f $(DEPDIR)/ClustalFileParser.Tpo $(DEPDIR)/ClustalFileParser.Po
605 # source='./fileInput/ClustalFileParser.cpp' object='ClustalFileParser.o' libtool=no \
606 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
607 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o ClustalFileParser.o `test -f './fileInput/ClustalFileParser.cpp' || echo '$(srcdir)/'`./fileInput/ClustalFileParser.cpp
609 ClustalFileParser.obj: ./fileInput/ClustalFileParser.cpp
610 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT ClustalFileParser.obj -MD -MP -MF $(DEPDIR)/ClustalFileParser.Tpo -c -o ClustalFileParser.obj `if test -f './fileInput/ClustalFileParser.cpp'; then $(CYGPATH_W) './fileInput/ClustalFileParser.cpp'; else $(CYGPATH_W) '$(srcdir)/./fileInput/ClustalFileParser.cpp'; fi`
611 mv -f $(DEPDIR)/ClustalFileParser.Tpo $(DEPDIR)/ClustalFileParser.Po
612 # source='./fileInput/ClustalFileParser.cpp' object='ClustalFileParser.obj' libtool=no \
613 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
614 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o ClustalFileParser.obj `if test -f './fileInput/ClustalFileParser.cpp'; then $(CYGPATH_W) './fileInput/ClustalFileParser.cpp'; else $(CYGPATH_W) '$(srcdir)/./fileInput/ClustalFileParser.cpp'; fi`
616 PearsonFileParser.o: ./fileInput/PearsonFileParser.cpp
617 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT PearsonFileParser.o -MD -MP -MF $(DEPDIR)/PearsonFileParser.Tpo -c -o PearsonFileParser.o `test -f './fileInput/PearsonFileParser.cpp' || echo '$(srcdir)/'`./fileInput/PearsonFileParser.cpp
618 mv -f $(DEPDIR)/PearsonFileParser.Tpo $(DEPDIR)/PearsonFileParser.Po
619 # source='./fileInput/PearsonFileParser.cpp' object='PearsonFileParser.o' libtool=no \
620 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
621 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o PearsonFileParser.o `test -f './fileInput/PearsonFileParser.cpp' || echo '$(srcdir)/'`./fileInput/PearsonFileParser.cpp
623 PearsonFileParser.obj: ./fileInput/PearsonFileParser.cpp
624 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT PearsonFileParser.obj -MD -MP -MF $(DEPDIR)/PearsonFileParser.Tpo -c -o PearsonFileParser.obj `if test -f './fileInput/PearsonFileParser.cpp'; then $(CYGPATH_W) './fileInput/PearsonFileParser.cpp'; else $(CYGPATH_W) '$(srcdir)/./fileInput/PearsonFileParser.cpp'; fi`
625 mv -f $(DEPDIR)/PearsonFileParser.Tpo $(DEPDIR)/PearsonFileParser.Po
626 # source='./fileInput/PearsonFileParser.cpp' object='PearsonFileParser.obj' libtool=no \
627 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
628 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o PearsonFileParser.obj `if test -f './fileInput/PearsonFileParser.cpp'; then $(CYGPATH_W) './fileInput/PearsonFileParser.cpp'; else $(CYGPATH_W) '$(srcdir)/./fileInput/PearsonFileParser.cpp'; fi`
630 FileParser.o: ./fileInput/FileParser.cpp
631 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT FileParser.o -MD -MP -MF $(DEPDIR)/FileParser.Tpo -c -o FileParser.o `test -f './fileInput/FileParser.cpp' || echo '$(srcdir)/'`./fileInput/FileParser.cpp
632 mv -f $(DEPDIR)/FileParser.Tpo $(DEPDIR)/FileParser.Po
633 # source='./fileInput/FileParser.cpp' object='FileParser.o' libtool=no \
634 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
635 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o FileParser.o `test -f './fileInput/FileParser.cpp' || echo '$(srcdir)/'`./fileInput/FileParser.cpp
637 FileParser.obj: ./fileInput/FileParser.cpp
638 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT FileParser.obj -MD -MP -MF $(DEPDIR)/FileParser.Tpo -c -o FileParser.obj `if test -f './fileInput/FileParser.cpp'; then $(CYGPATH_W) './fileInput/FileParser.cpp'; else $(CYGPATH_W) '$(srcdir)/./fileInput/FileParser.cpp'; fi`
639 mv -f $(DEPDIR)/FileParser.Tpo $(DEPDIR)/FileParser.Po
640 # source='./fileInput/FileParser.cpp' object='FileParser.obj' libtool=no \
641 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
642 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o FileParser.obj `if test -f './fileInput/FileParser.cpp'; then $(CYGPATH_W) './fileInput/FileParser.cpp'; else $(CYGPATH_W) '$(srcdir)/./fileInput/FileParser.cpp'; fi`
644 EMBLFileParser.o: ./fileInput/EMBLFileParser.cpp
645 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT EMBLFileParser.o -MD -MP -MF $(DEPDIR)/EMBLFileParser.Tpo -c -o EMBLFileParser.o `test -f './fileInput/EMBLFileParser.cpp' || echo '$(srcdir)/'`./fileInput/EMBLFileParser.cpp
646 mv -f $(DEPDIR)/EMBLFileParser.Tpo $(DEPDIR)/EMBLFileParser.Po
647 # source='./fileInput/EMBLFileParser.cpp' object='EMBLFileParser.o' libtool=no \
648 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
649 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o EMBLFileParser.o `test -f './fileInput/EMBLFileParser.cpp' || echo '$(srcdir)/'`./fileInput/EMBLFileParser.cpp
651 EMBLFileParser.obj: ./fileInput/EMBLFileParser.cpp
652 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT EMBLFileParser.obj -MD -MP -MF $(DEPDIR)/EMBLFileParser.Tpo -c -o EMBLFileParser.obj `if test -f './fileInput/EMBLFileParser.cpp'; then $(CYGPATH_W) './fileInput/EMBLFileParser.cpp'; else $(CYGPATH_W) '$(srcdir)/./fileInput/EMBLFileParser.cpp'; fi`
653 mv -f $(DEPDIR)/EMBLFileParser.Tpo $(DEPDIR)/EMBLFileParser.Po
654 # source='./fileInput/EMBLFileParser.cpp' object='EMBLFileParser.obj' libtool=no \
655 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
656 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o EMBLFileParser.obj `if test -f './fileInput/EMBLFileParser.cpp'; then $(CYGPATH_W) './fileInput/EMBLFileParser.cpp'; else $(CYGPATH_W) '$(srcdir)/./fileInput/EMBLFileParser.cpp'; fi`
658 RootedClusterTree.o: ./tree/UPGMA/RootedClusterTree.cpp
659 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT RootedClusterTree.o -MD -MP -MF $(DEPDIR)/RootedClusterTree.Tpo -c -o RootedClusterTree.o `test -f './tree/UPGMA/RootedClusterTree.cpp' || echo '$(srcdir)/'`./tree/UPGMA/RootedClusterTree.cpp
660 mv -f $(DEPDIR)/RootedClusterTree.Tpo $(DEPDIR)/RootedClusterTree.Po
661 # source='./tree/UPGMA/RootedClusterTree.cpp' object='RootedClusterTree.o' libtool=no \
662 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
663 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o RootedClusterTree.o `test -f './tree/UPGMA/RootedClusterTree.cpp' || echo '$(srcdir)/'`./tree/UPGMA/RootedClusterTree.cpp
665 RootedClusterTree.obj: ./tree/UPGMA/RootedClusterTree.cpp
666 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT RootedClusterTree.obj -MD -MP -MF $(DEPDIR)/RootedClusterTree.Tpo -c -o RootedClusterTree.obj `if test -f './tree/UPGMA/RootedClusterTree.cpp'; then $(CYGPATH_W) './tree/UPGMA/RootedClusterTree.cpp'; else $(CYGPATH_W) '$(srcdir)/./tree/UPGMA/RootedClusterTree.cpp'; fi`
667 mv -f $(DEPDIR)/RootedClusterTree.Tpo $(DEPDIR)/RootedClusterTree.Po
668 # source='./tree/UPGMA/RootedClusterTree.cpp' object='RootedClusterTree.obj' libtool=no \
669 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
670 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o RootedClusterTree.obj `if test -f './tree/UPGMA/RootedClusterTree.cpp'; then $(CYGPATH_W) './tree/UPGMA/RootedClusterTree.cpp'; else $(CYGPATH_W) '$(srcdir)/./tree/UPGMA/RootedClusterTree.cpp'; fi`
672 UPGMAAlgorithm.o: ./tree/UPGMA/UPGMAAlgorithm.cpp
673 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT UPGMAAlgorithm.o -MD -MP -MF $(DEPDIR)/UPGMAAlgorithm.Tpo -c -o UPGMAAlgorithm.o `test -f './tree/UPGMA/UPGMAAlgorithm.cpp' || echo '$(srcdir)/'`./tree/UPGMA/UPGMAAlgorithm.cpp
674 mv -f $(DEPDIR)/UPGMAAlgorithm.Tpo $(DEPDIR)/UPGMAAlgorithm.Po
675 # source='./tree/UPGMA/UPGMAAlgorithm.cpp' object='UPGMAAlgorithm.o' libtool=no \
676 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
677 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o UPGMAAlgorithm.o `test -f './tree/UPGMA/UPGMAAlgorithm.cpp' || echo '$(srcdir)/'`./tree/UPGMA/UPGMAAlgorithm.cpp
679 UPGMAAlgorithm.obj: ./tree/UPGMA/UPGMAAlgorithm.cpp
680 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT UPGMAAlgorithm.obj -MD -MP -MF $(DEPDIR)/UPGMAAlgorithm.Tpo -c -o UPGMAAlgorithm.obj `if test -f './tree/UPGMA/UPGMAAlgorithm.cpp'; then $(CYGPATH_W) './tree/UPGMA/UPGMAAlgorithm.cpp'; else $(CYGPATH_W) '$(srcdir)/./tree/UPGMA/UPGMAAlgorithm.cpp'; fi`
681 mv -f $(DEPDIR)/UPGMAAlgorithm.Tpo $(DEPDIR)/UPGMAAlgorithm.Po
682 # source='./tree/UPGMA/UPGMAAlgorithm.cpp' object='UPGMAAlgorithm.obj' libtool=no \
683 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
684 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o UPGMAAlgorithm.obj `if test -f './tree/UPGMA/UPGMAAlgorithm.cpp'; then $(CYGPATH_W) './tree/UPGMA/UPGMAAlgorithm.cpp'; else $(CYGPATH_W) '$(srcdir)/./tree/UPGMA/UPGMAAlgorithm.cpp'; fi`
686 Node.o: ./tree/UPGMA/Node.cpp
687 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT Node.o -MD -MP -MF $(DEPDIR)/Node.Tpo -c -o Node.o `test -f './tree/UPGMA/Node.cpp' || echo '$(srcdir)/'`./tree/UPGMA/Node.cpp
688 mv -f $(DEPDIR)/Node.Tpo $(DEPDIR)/Node.Po
689 # source='./tree/UPGMA/Node.cpp' object='Node.o' libtool=no \
690 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
691 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o Node.o `test -f './tree/UPGMA/Node.cpp' || echo '$(srcdir)/'`./tree/UPGMA/Node.cpp
693 Node.obj: ./tree/UPGMA/Node.cpp
694 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT Node.obj -MD -MP -MF $(DEPDIR)/Node.Tpo -c -o Node.obj `if test -f './tree/UPGMA/Node.cpp'; then $(CYGPATH_W) './tree/UPGMA/Node.cpp'; else $(CYGPATH_W) '$(srcdir)/./tree/UPGMA/Node.cpp'; fi`
695 mv -f $(DEPDIR)/Node.Tpo $(DEPDIR)/Node.Po
696 # source='./tree/UPGMA/Node.cpp' object='Node.obj' libtool=no \
697 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
698 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o Node.obj `if test -f './tree/UPGMA/Node.cpp'; then $(CYGPATH_W) './tree/UPGMA/Node.cpp'; else $(CYGPATH_W) '$(srcdir)/./tree/UPGMA/Node.cpp'; fi`
700 RootedGuideTree.o: ./tree/UPGMA/RootedGuideTree.cpp
701 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT RootedGuideTree.o -MD -MP -MF $(DEPDIR)/RootedGuideTree.Tpo -c -o RootedGuideTree.o `test -f './tree/UPGMA/RootedGuideTree.cpp' || echo '$(srcdir)/'`./tree/UPGMA/RootedGuideTree.cpp
702 mv -f $(DEPDIR)/RootedGuideTree.Tpo $(DEPDIR)/RootedGuideTree.Po
703 # source='./tree/UPGMA/RootedGuideTree.cpp' object='RootedGuideTree.o' libtool=no \
704 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
705 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o RootedGuideTree.o `test -f './tree/UPGMA/RootedGuideTree.cpp' || echo '$(srcdir)/'`./tree/UPGMA/RootedGuideTree.cpp
707 RootedGuideTree.obj: ./tree/UPGMA/RootedGuideTree.cpp
708 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT RootedGuideTree.obj -MD -MP -MF $(DEPDIR)/RootedGuideTree.Tpo -c -o RootedGuideTree.obj `if test -f './tree/UPGMA/RootedGuideTree.cpp'; then $(CYGPATH_W) './tree/UPGMA/RootedGuideTree.cpp'; else $(CYGPATH_W) '$(srcdir)/./tree/UPGMA/RootedGuideTree.cpp'; fi`
709 mv -f $(DEPDIR)/RootedGuideTree.Tpo $(DEPDIR)/RootedGuideTree.Po
710 # source='./tree/UPGMA/RootedGuideTree.cpp' object='RootedGuideTree.obj' libtool=no \
711 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
712 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o RootedGuideTree.obj `if test -f './tree/UPGMA/RootedGuideTree.cpp'; then $(CYGPATH_W) './tree/UPGMA/RootedGuideTree.cpp'; else $(CYGPATH_W) '$(srcdir)/./tree/UPGMA/RootedGuideTree.cpp'; fi`
714 RootedTreeOutput.o: ./tree/UPGMA/RootedTreeOutput.cpp
715 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT RootedTreeOutput.o -MD -MP -MF $(DEPDIR)/RootedTreeOutput.Tpo -c -o RootedTreeOutput.o `test -f './tree/UPGMA/RootedTreeOutput.cpp' || echo '$(srcdir)/'`./tree/UPGMA/RootedTreeOutput.cpp
716 mv -f $(DEPDIR)/RootedTreeOutput.Tpo $(DEPDIR)/RootedTreeOutput.Po
717 # source='./tree/UPGMA/RootedTreeOutput.cpp' object='RootedTreeOutput.o' libtool=no \
718 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
719 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o RootedTreeOutput.o `test -f './tree/UPGMA/RootedTreeOutput.cpp' || echo '$(srcdir)/'`./tree/UPGMA/RootedTreeOutput.cpp
721 RootedTreeOutput.obj: ./tree/UPGMA/RootedTreeOutput.cpp
722 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT RootedTreeOutput.obj -MD -MP -MF $(DEPDIR)/RootedTreeOutput.Tpo -c -o RootedTreeOutput.obj `if test -f './tree/UPGMA/RootedTreeOutput.cpp'; then $(CYGPATH_W) './tree/UPGMA/RootedTreeOutput.cpp'; else $(CYGPATH_W) '$(srcdir)/./tree/UPGMA/RootedTreeOutput.cpp'; fi`
723 mv -f $(DEPDIR)/RootedTreeOutput.Tpo $(DEPDIR)/RootedTreeOutput.Po
724 # source='./tree/UPGMA/RootedTreeOutput.cpp' object='RootedTreeOutput.obj' libtool=no \
725 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
726 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o RootedTreeOutput.obj `if test -f './tree/UPGMA/RootedTreeOutput.cpp'; then $(CYGPATH_W) './tree/UPGMA/RootedTreeOutput.cpp'; else $(CYGPATH_W) '$(srcdir)/./tree/UPGMA/RootedTreeOutput.cpp'; fi`
728 Tree.o: ./tree/Tree.cpp
729 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT Tree.o -MD -MP -MF $(DEPDIR)/Tree.Tpo -c -o Tree.o `test -f './tree/Tree.cpp' || echo '$(srcdir)/'`./tree/Tree.cpp
730 mv -f $(DEPDIR)/Tree.Tpo $(DEPDIR)/Tree.Po
731 # source='./tree/Tree.cpp' object='Tree.o' libtool=no \
732 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
733 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o Tree.o `test -f './tree/Tree.cpp' || echo '$(srcdir)/'`./tree/Tree.cpp
735 Tree.obj: ./tree/Tree.cpp
736 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT Tree.obj -MD -MP -MF $(DEPDIR)/Tree.Tpo -c -o Tree.obj `if test -f './tree/Tree.cpp'; then $(CYGPATH_W) './tree/Tree.cpp'; else $(CYGPATH_W) '$(srcdir)/./tree/Tree.cpp'; fi`
737 mv -f $(DEPDIR)/Tree.Tpo $(DEPDIR)/Tree.Po
738 # source='./tree/Tree.cpp' object='Tree.obj' libtool=no \
739 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
740 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o Tree.obj `if test -f './tree/Tree.cpp'; then $(CYGPATH_W) './tree/Tree.cpp'; else $(CYGPATH_W) '$(srcdir)/./tree/Tree.cpp'; fi`
742 ClusterTree.o: ./tree/ClusterTree.cpp
743 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT ClusterTree.o -MD -MP -MF $(DEPDIR)/ClusterTree.Tpo -c -o ClusterTree.o `test -f './tree/ClusterTree.cpp' || echo '$(srcdir)/'`./tree/ClusterTree.cpp
744 mv -f $(DEPDIR)/ClusterTree.Tpo $(DEPDIR)/ClusterTree.Po
745 # source='./tree/ClusterTree.cpp' object='ClusterTree.o' libtool=no \
746 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
747 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o ClusterTree.o `test -f './tree/ClusterTree.cpp' || echo '$(srcdir)/'`./tree/ClusterTree.cpp
749 ClusterTree.obj: ./tree/ClusterTree.cpp
750 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT ClusterTree.obj -MD -MP -MF $(DEPDIR)/ClusterTree.Tpo -c -o ClusterTree.obj `if test -f './tree/ClusterTree.cpp'; then $(CYGPATH_W) './tree/ClusterTree.cpp'; else $(CYGPATH_W) '$(srcdir)/./tree/ClusterTree.cpp'; fi`
751 mv -f $(DEPDIR)/ClusterTree.Tpo $(DEPDIR)/ClusterTree.Po
752 # source='./tree/ClusterTree.cpp' object='ClusterTree.obj' libtool=no \
753 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
754 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o ClusterTree.obj `if test -f './tree/ClusterTree.cpp'; then $(CYGPATH_W) './tree/ClusterTree.cpp'; else $(CYGPATH_W) '$(srcdir)/./tree/ClusterTree.cpp'; fi`
756 TreeInterface.o: ./tree/TreeInterface.cpp
757 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT TreeInterface.o -MD -MP -MF $(DEPDIR)/TreeInterface.Tpo -c -o TreeInterface.o `test -f './tree/TreeInterface.cpp' || echo '$(srcdir)/'`./tree/TreeInterface.cpp
758 mv -f $(DEPDIR)/TreeInterface.Tpo $(DEPDIR)/TreeInterface.Po
759 # source='./tree/TreeInterface.cpp' object='TreeInterface.o' libtool=no \
760 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
761 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o TreeInterface.o `test -f './tree/TreeInterface.cpp' || echo '$(srcdir)/'`./tree/TreeInterface.cpp
763 TreeInterface.obj: ./tree/TreeInterface.cpp
764 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT TreeInterface.obj -MD -MP -MF $(DEPDIR)/TreeInterface.Tpo -c -o TreeInterface.obj `if test -f './tree/TreeInterface.cpp'; then $(CYGPATH_W) './tree/TreeInterface.cpp'; else $(CYGPATH_W) '$(srcdir)/./tree/TreeInterface.cpp'; fi`
765 mv -f $(DEPDIR)/TreeInterface.Tpo $(DEPDIR)/TreeInterface.Po
766 # source='./tree/TreeInterface.cpp' object='TreeInterface.obj' libtool=no \
767 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
768 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o TreeInterface.obj `if test -f './tree/TreeInterface.cpp'; then $(CYGPATH_W) './tree/TreeInterface.cpp'; else $(CYGPATH_W) '$(srcdir)/./tree/TreeInterface.cpp'; fi`
770 UnRootedClusterTree.o: ./tree/UnRootedClusterTree.cpp
771 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT UnRootedClusterTree.o -MD -MP -MF $(DEPDIR)/UnRootedClusterTree.Tpo -c -o UnRootedClusterTree.o `test -f './tree/UnRootedClusterTree.cpp' || echo '$(srcdir)/'`./tree/UnRootedClusterTree.cpp
772 mv -f $(DEPDIR)/UnRootedClusterTree.Tpo $(DEPDIR)/UnRootedClusterTree.Po
773 # source='./tree/UnRootedClusterTree.cpp' object='UnRootedClusterTree.o' libtool=no \
774 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
775 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o UnRootedClusterTree.o `test -f './tree/UnRootedClusterTree.cpp' || echo '$(srcdir)/'`./tree/UnRootedClusterTree.cpp
777 UnRootedClusterTree.obj: ./tree/UnRootedClusterTree.cpp
778 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT UnRootedClusterTree.obj -MD -MP -MF $(DEPDIR)/UnRootedClusterTree.Tpo -c -o UnRootedClusterTree.obj `if test -f './tree/UnRootedClusterTree.cpp'; then $(CYGPATH_W) './tree/UnRootedClusterTree.cpp'; else $(CYGPATH_W) '$(srcdir)/./tree/UnRootedClusterTree.cpp'; fi`
779 mv -f $(DEPDIR)/UnRootedClusterTree.Tpo $(DEPDIR)/UnRootedClusterTree.Po
780 # source='./tree/UnRootedClusterTree.cpp' object='UnRootedClusterTree.obj' libtool=no \
781 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
782 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o UnRootedClusterTree.obj `if test -f './tree/UnRootedClusterTree.cpp'; then $(CYGPATH_W) './tree/UnRootedClusterTree.cpp'; else $(CYGPATH_W) '$(srcdir)/./tree/UnRootedClusterTree.cpp'; fi`
784 ClusterTreeOutput.o: ./tree/ClusterTreeOutput.cpp
785 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT ClusterTreeOutput.o -MD -MP -MF $(DEPDIR)/ClusterTreeOutput.Tpo -c -o ClusterTreeOutput.o `test -f './tree/ClusterTreeOutput.cpp' || echo '$(srcdir)/'`./tree/ClusterTreeOutput.cpp
786 mv -f $(DEPDIR)/ClusterTreeOutput.Tpo $(DEPDIR)/ClusterTreeOutput.Po
787 # source='./tree/ClusterTreeOutput.cpp' object='ClusterTreeOutput.o' libtool=no \
788 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
789 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o ClusterTreeOutput.o `test -f './tree/ClusterTreeOutput.cpp' || echo '$(srcdir)/'`./tree/ClusterTreeOutput.cpp
791 ClusterTreeOutput.obj: ./tree/ClusterTreeOutput.cpp
792 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT ClusterTreeOutput.obj -MD -MP -MF $(DEPDIR)/ClusterTreeOutput.Tpo -c -o ClusterTreeOutput.obj `if test -f './tree/ClusterTreeOutput.cpp'; then $(CYGPATH_W) './tree/ClusterTreeOutput.cpp'; else $(CYGPATH_W) '$(srcdir)/./tree/ClusterTreeOutput.cpp'; fi`
793 mv -f $(DEPDIR)/ClusterTreeOutput.Tpo $(DEPDIR)/ClusterTreeOutput.Po
794 # source='./tree/ClusterTreeOutput.cpp' object='ClusterTreeOutput.obj' libtool=no \
795 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
796 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o ClusterTreeOutput.obj `if test -f './tree/ClusterTreeOutput.cpp'; then $(CYGPATH_W) './tree/ClusterTreeOutput.cpp'; else $(CYGPATH_W) '$(srcdir)/./tree/ClusterTreeOutput.cpp'; fi`
798 RandomGenerator.o: ./tree/RandomGenerator.cpp
799 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT RandomGenerator.o -MD -MP -MF $(DEPDIR)/RandomGenerator.Tpo -c -o RandomGenerator.o `test -f './tree/RandomGenerator.cpp' || echo '$(srcdir)/'`./tree/RandomGenerator.cpp
800 mv -f $(DEPDIR)/RandomGenerator.Tpo $(DEPDIR)/RandomGenerator.Po
801 # source='./tree/RandomGenerator.cpp' object='RandomGenerator.o' libtool=no \
802 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
803 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o RandomGenerator.o `test -f './tree/RandomGenerator.cpp' || echo '$(srcdir)/'`./tree/RandomGenerator.cpp
805 RandomGenerator.obj: ./tree/RandomGenerator.cpp
806 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT RandomGenerator.obj -MD -MP -MF $(DEPDIR)/RandomGenerator.Tpo -c -o RandomGenerator.obj `if test -f './tree/RandomGenerator.cpp'; then $(CYGPATH_W) './tree/RandomGenerator.cpp'; else $(CYGPATH_W) '$(srcdir)/./tree/RandomGenerator.cpp'; fi`
807 mv -f $(DEPDIR)/RandomGenerator.Tpo $(DEPDIR)/RandomGenerator.Po
808 # source='./tree/RandomGenerator.cpp' object='RandomGenerator.obj' libtool=no \
809 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
810 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o RandomGenerator.obj `if test -f './tree/RandomGenerator.cpp'; then $(CYGPATH_W) './tree/RandomGenerator.cpp'; else $(CYGPATH_W) '$(srcdir)/./tree/RandomGenerator.cpp'; fi`
812 NJTree.o: ./tree/NJTree.cpp
813 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT NJTree.o -MD -MP -MF $(DEPDIR)/NJTree.Tpo -c -o NJTree.o `test -f './tree/NJTree.cpp' || echo '$(srcdir)/'`./tree/NJTree.cpp
814 mv -f $(DEPDIR)/NJTree.Tpo $(DEPDIR)/NJTree.Po
815 # source='./tree/NJTree.cpp' object='NJTree.o' libtool=no \
816 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
817 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o NJTree.o `test -f './tree/NJTree.cpp' || echo '$(srcdir)/'`./tree/NJTree.cpp
819 NJTree.obj: ./tree/NJTree.cpp
820 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT NJTree.obj -MD -MP -MF $(DEPDIR)/NJTree.Tpo -c -o NJTree.obj `if test -f './tree/NJTree.cpp'; then $(CYGPATH_W) './tree/NJTree.cpp'; else $(CYGPATH_W) '$(srcdir)/./tree/NJTree.cpp'; fi`
821 mv -f $(DEPDIR)/NJTree.Tpo $(DEPDIR)/NJTree.Po
822 # source='./tree/NJTree.cpp' object='NJTree.obj' libtool=no \
823 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
824 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o NJTree.obj `if test -f './tree/NJTree.cpp'; then $(CYGPATH_W) './tree/NJTree.cpp'; else $(CYGPATH_W) '$(srcdir)/./tree/NJTree.cpp'; fi`
826 AlignmentSteps.o: ./tree/AlignmentSteps.cpp
827 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT AlignmentSteps.o -MD -MP -MF $(DEPDIR)/AlignmentSteps.Tpo -c -o AlignmentSteps.o `test -f './tree/AlignmentSteps.cpp' || echo '$(srcdir)/'`./tree/AlignmentSteps.cpp
828 mv -f $(DEPDIR)/AlignmentSteps.Tpo $(DEPDIR)/AlignmentSteps.Po
829 # source='./tree/AlignmentSteps.cpp' object='AlignmentSteps.o' libtool=no \
830 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
831 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o AlignmentSteps.o `test -f './tree/AlignmentSteps.cpp' || echo '$(srcdir)/'`./tree/AlignmentSteps.cpp
833 AlignmentSteps.obj: ./tree/AlignmentSteps.cpp
834 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT AlignmentSteps.obj -MD -MP -MF $(DEPDIR)/AlignmentSteps.Tpo -c -o AlignmentSteps.obj `if test -f './tree/AlignmentSteps.cpp'; then $(CYGPATH_W) './tree/AlignmentSteps.cpp'; else $(CYGPATH_W) '$(srcdir)/./tree/AlignmentSteps.cpp'; fi`
835 mv -f $(DEPDIR)/AlignmentSteps.Tpo $(DEPDIR)/AlignmentSteps.Po
836 # source='./tree/AlignmentSteps.cpp' object='AlignmentSteps.obj' libtool=no \
837 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
838 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o AlignmentSteps.obj `if test -f './tree/AlignmentSteps.cpp'; then $(CYGPATH_W) './tree/AlignmentSteps.cpp'; else $(CYGPATH_W) '$(srcdir)/./tree/AlignmentSteps.cpp'; fi`
840 InteractiveMenu.o: ./interface/InteractiveMenu.cpp
841 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT InteractiveMenu.o -MD -MP -MF $(DEPDIR)/InteractiveMenu.Tpo -c -o InteractiveMenu.o `test -f './interface/InteractiveMenu.cpp' || echo '$(srcdir)/'`./interface/InteractiveMenu.cpp
842 mv -f $(DEPDIR)/InteractiveMenu.Tpo $(DEPDIR)/InteractiveMenu.Po
843 # source='./interface/InteractiveMenu.cpp' object='InteractiveMenu.o' libtool=no \
844 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
845 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o InteractiveMenu.o `test -f './interface/InteractiveMenu.cpp' || echo '$(srcdir)/'`./interface/InteractiveMenu.cpp
847 InteractiveMenu.obj: ./interface/InteractiveMenu.cpp
848 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT InteractiveMenu.obj -MD -MP -MF $(DEPDIR)/InteractiveMenu.Tpo -c -o InteractiveMenu.obj `if test -f './interface/InteractiveMenu.cpp'; then $(CYGPATH_W) './interface/InteractiveMenu.cpp'; else $(CYGPATH_W) '$(srcdir)/./interface/InteractiveMenu.cpp'; fi`
849 mv -f $(DEPDIR)/InteractiveMenu.Tpo $(DEPDIR)/InteractiveMenu.Po
850 # source='./interface/InteractiveMenu.cpp' object='InteractiveMenu.obj' libtool=no \
851 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
852 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o InteractiveMenu.obj `if test -f './interface/InteractiveMenu.cpp'; then $(CYGPATH_W) './interface/InteractiveMenu.cpp'; else $(CYGPATH_W) '$(srcdir)/./interface/InteractiveMenu.cpp'; fi`
854 CommandLineParser.o: ./interface/CommandLineParser.cpp
855 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT CommandLineParser.o -MD -MP -MF $(DEPDIR)/CommandLineParser.Tpo -c -o CommandLineParser.o `test -f './interface/CommandLineParser.cpp' || echo '$(srcdir)/'`./interface/CommandLineParser.cpp
856 mv -f $(DEPDIR)/CommandLineParser.Tpo $(DEPDIR)/CommandLineParser.Po
857 # source='./interface/CommandLineParser.cpp' object='CommandLineParser.o' libtool=no \
858 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
859 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o CommandLineParser.o `test -f './interface/CommandLineParser.cpp' || echo '$(srcdir)/'`./interface/CommandLineParser.cpp
861 CommandLineParser.obj: ./interface/CommandLineParser.cpp
862 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT CommandLineParser.obj -MD -MP -MF $(DEPDIR)/CommandLineParser.Tpo -c -o CommandLineParser.obj `if test -f './interface/CommandLineParser.cpp'; then $(CYGPATH_W) './interface/CommandLineParser.cpp'; else $(CYGPATH_W) '$(srcdir)/./interface/CommandLineParser.cpp'; fi`
863 mv -f $(DEPDIR)/CommandLineParser.Tpo $(DEPDIR)/CommandLineParser.Po
864 # source='./interface/CommandLineParser.cpp' object='CommandLineParser.obj' libtool=no \
865 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
866 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o CommandLineParser.obj `if test -f './interface/CommandLineParser.cpp'; then $(CYGPATH_W) './interface/CommandLineParser.cpp'; else $(CYGPATH_W) '$(srcdir)/./interface/CommandLineParser.cpp'; fi`
868 SubMatrix.o: ./substitutionMatrix/SubMatrix.cpp
869 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT SubMatrix.o -MD -MP -MF $(DEPDIR)/SubMatrix.Tpo -c -o SubMatrix.o `test -f './substitutionMatrix/SubMatrix.cpp' || echo '$(srcdir)/'`./substitutionMatrix/SubMatrix.cpp
870 mv -f $(DEPDIR)/SubMatrix.Tpo $(DEPDIR)/SubMatrix.Po
871 # source='./substitutionMatrix/SubMatrix.cpp' object='SubMatrix.o' libtool=no \
872 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
873 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o SubMatrix.o `test -f './substitutionMatrix/SubMatrix.cpp' || echo '$(srcdir)/'`./substitutionMatrix/SubMatrix.cpp
875 SubMatrix.obj: ./substitutionMatrix/SubMatrix.cpp
876 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT SubMatrix.obj -MD -MP -MF $(DEPDIR)/SubMatrix.Tpo -c -o SubMatrix.obj `if test -f './substitutionMatrix/SubMatrix.cpp'; then $(CYGPATH_W) './substitutionMatrix/SubMatrix.cpp'; else $(CYGPATH_W) '$(srcdir)/./substitutionMatrix/SubMatrix.cpp'; fi`
877 mv -f $(DEPDIR)/SubMatrix.Tpo $(DEPDIR)/SubMatrix.Po
878 # source='./substitutionMatrix/SubMatrix.cpp' object='SubMatrix.obj' libtool=no \
879 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
880 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o SubMatrix.obj `if test -f './substitutionMatrix/SubMatrix.cpp'; then $(CYGPATH_W) './substitutionMatrix/SubMatrix.cpp'; else $(CYGPATH_W) '$(srcdir)/./substitutionMatrix/SubMatrix.cpp'; fi`
882 Iteration.o: ./multipleAlign/Iteration.cpp
883 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT Iteration.o -MD -MP -MF $(DEPDIR)/Iteration.Tpo -c -o Iteration.o `test -f './multipleAlign/Iteration.cpp' || echo '$(srcdir)/'`./multipleAlign/Iteration.cpp
884 mv -f $(DEPDIR)/Iteration.Tpo $(DEPDIR)/Iteration.Po
885 # source='./multipleAlign/Iteration.cpp' object='Iteration.o' libtool=no \
886 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
887 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o Iteration.o `test -f './multipleAlign/Iteration.cpp' || echo '$(srcdir)/'`./multipleAlign/Iteration.cpp
889 Iteration.obj: ./multipleAlign/Iteration.cpp
890 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT Iteration.obj -MD -MP -MF $(DEPDIR)/Iteration.Tpo -c -o Iteration.obj `if test -f './multipleAlign/Iteration.cpp'; then $(CYGPATH_W) './multipleAlign/Iteration.cpp'; else $(CYGPATH_W) '$(srcdir)/./multipleAlign/Iteration.cpp'; fi`
891 mv -f $(DEPDIR)/Iteration.Tpo $(DEPDIR)/Iteration.Po
892 # source='./multipleAlign/Iteration.cpp' object='Iteration.obj' libtool=no \
893 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
894 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o Iteration.obj `if test -f './multipleAlign/Iteration.cpp'; then $(CYGPATH_W) './multipleAlign/Iteration.cpp'; else $(CYGPATH_W) '$(srcdir)/./multipleAlign/Iteration.cpp'; fi`
896 MSA.o: ./multipleAlign/MSA.cpp
897 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT MSA.o -MD -MP -MF $(DEPDIR)/MSA.Tpo -c -o MSA.o `test -f './multipleAlign/MSA.cpp' || echo '$(srcdir)/'`./multipleAlign/MSA.cpp
898 mv -f $(DEPDIR)/MSA.Tpo $(DEPDIR)/MSA.Po
899 # source='./multipleAlign/MSA.cpp' object='MSA.o' libtool=no \
900 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
901 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o MSA.o `test -f './multipleAlign/MSA.cpp' || echo '$(srcdir)/'`./multipleAlign/MSA.cpp
903 MSA.obj: ./multipleAlign/MSA.cpp
904 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT MSA.obj -MD -MP -MF $(DEPDIR)/MSA.Tpo -c -o MSA.obj `if test -f './multipleAlign/MSA.cpp'; then $(CYGPATH_W) './multipleAlign/MSA.cpp'; else $(CYGPATH_W) '$(srcdir)/./multipleAlign/MSA.cpp'; fi`
905 mv -f $(DEPDIR)/MSA.Tpo $(DEPDIR)/MSA.Po
906 # source='./multipleAlign/MSA.cpp' object='MSA.obj' libtool=no \
907 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
908 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o MSA.obj `if test -f './multipleAlign/MSA.cpp'; then $(CYGPATH_W) './multipleAlign/MSA.cpp'; else $(CYGPATH_W) '$(srcdir)/./multipleAlign/MSA.cpp'; fi`
910 MyersMillerProfileAlign.o: ./multipleAlign/MyersMillerProfileAlign.cpp
911 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT MyersMillerProfileAlign.o -MD -MP -MF $(DEPDIR)/MyersMillerProfileAlign.Tpo -c -o MyersMillerProfileAlign.o `test -f './multipleAlign/MyersMillerProfileAlign.cpp' || echo '$(srcdir)/'`./multipleAlign/MyersMillerProfileAlign.cpp
912 mv -f $(DEPDIR)/MyersMillerProfileAlign.Tpo $(DEPDIR)/MyersMillerProfileAlign.Po
913 # source='./multipleAlign/MyersMillerProfileAlign.cpp' object='MyersMillerProfileAlign.o' libtool=no \
914 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
915 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o MyersMillerProfileAlign.o `test -f './multipleAlign/MyersMillerProfileAlign.cpp' || echo '$(srcdir)/'`./multipleAlign/MyersMillerProfileAlign.cpp
917 MyersMillerProfileAlign.obj: ./multipleAlign/MyersMillerProfileAlign.cpp
918 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT MyersMillerProfileAlign.obj -MD -MP -MF $(DEPDIR)/MyersMillerProfileAlign.Tpo -c -o MyersMillerProfileAlign.obj `if test -f './multipleAlign/MyersMillerProfileAlign.cpp'; then $(CYGPATH_W) './multipleAlign/MyersMillerProfileAlign.cpp'; else $(CYGPATH_W) '$(srcdir)/./multipleAlign/MyersMillerProfileAlign.cpp'; fi`
919 mv -f $(DEPDIR)/MyersMillerProfileAlign.Tpo $(DEPDIR)/MyersMillerProfileAlign.Po
920 # source='./multipleAlign/MyersMillerProfileAlign.cpp' object='MyersMillerProfileAlign.obj' libtool=no \
921 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
922 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o MyersMillerProfileAlign.obj `if test -f './multipleAlign/MyersMillerProfileAlign.cpp'; then $(CYGPATH_W) './multipleAlign/MyersMillerProfileAlign.cpp'; else $(CYGPATH_W) '$(srcdir)/./multipleAlign/MyersMillerProfileAlign.cpp'; fi`
924 ProfileStandard.o: ./multipleAlign/ProfileStandard.cpp
925 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT ProfileStandard.o -MD -MP -MF $(DEPDIR)/ProfileStandard.Tpo -c -o ProfileStandard.o `test -f './multipleAlign/ProfileStandard.cpp' || echo '$(srcdir)/'`./multipleAlign/ProfileStandard.cpp
926 mv -f $(DEPDIR)/ProfileStandard.Tpo $(DEPDIR)/ProfileStandard.Po
927 # source='./multipleAlign/ProfileStandard.cpp' object='ProfileStandard.o' libtool=no \
928 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
929 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o ProfileStandard.o `test -f './multipleAlign/ProfileStandard.cpp' || echo '$(srcdir)/'`./multipleAlign/ProfileStandard.cpp
931 ProfileStandard.obj: ./multipleAlign/ProfileStandard.cpp
932 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT ProfileStandard.obj -MD -MP -MF $(DEPDIR)/ProfileStandard.Tpo -c -o ProfileStandard.obj `if test -f './multipleAlign/ProfileStandard.cpp'; then $(CYGPATH_W) './multipleAlign/ProfileStandard.cpp'; else $(CYGPATH_W) '$(srcdir)/./multipleAlign/ProfileStandard.cpp'; fi`
933 mv -f $(DEPDIR)/ProfileStandard.Tpo $(DEPDIR)/ProfileStandard.Po
934 # source='./multipleAlign/ProfileStandard.cpp' object='ProfileStandard.obj' libtool=no \
935 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
936 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o ProfileStandard.obj `if test -f './multipleAlign/ProfileStandard.cpp'; then $(CYGPATH_W) './multipleAlign/ProfileStandard.cpp'; else $(CYGPATH_W) '$(srcdir)/./multipleAlign/ProfileStandard.cpp'; fi`
938 ProfileWithSub.o: ./multipleAlign/ProfileWithSub.cpp
939 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT ProfileWithSub.o -MD -MP -MF $(DEPDIR)/ProfileWithSub.Tpo -c -o ProfileWithSub.o `test -f './multipleAlign/ProfileWithSub.cpp' || echo '$(srcdir)/'`./multipleAlign/ProfileWithSub.cpp
940 mv -f $(DEPDIR)/ProfileWithSub.Tpo $(DEPDIR)/ProfileWithSub.Po
941 # source='./multipleAlign/ProfileWithSub.cpp' object='ProfileWithSub.o' libtool=no \
942 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
943 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o ProfileWithSub.o `test -f './multipleAlign/ProfileWithSub.cpp' || echo '$(srcdir)/'`./multipleAlign/ProfileWithSub.cpp
945 ProfileWithSub.obj: ./multipleAlign/ProfileWithSub.cpp
946 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT ProfileWithSub.obj -MD -MP -MF $(DEPDIR)/ProfileWithSub.Tpo -c -o ProfileWithSub.obj `if test -f './multipleAlign/ProfileWithSub.cpp'; then $(CYGPATH_W) './multipleAlign/ProfileWithSub.cpp'; else $(CYGPATH_W) '$(srcdir)/./multipleAlign/ProfileWithSub.cpp'; fi`
947 mv -f $(DEPDIR)/ProfileWithSub.Tpo $(DEPDIR)/ProfileWithSub.Po
948 # source='./multipleAlign/ProfileWithSub.cpp' object='ProfileWithSub.obj' libtool=no \
949 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
950 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o ProfileWithSub.obj `if test -f './multipleAlign/ProfileWithSub.cpp'; then $(CYGPATH_W) './multipleAlign/ProfileWithSub.cpp'; else $(CYGPATH_W) '$(srcdir)/./multipleAlign/ProfileWithSub.cpp'; fi`
952 ProfileBase.o: ./multipleAlign/ProfileBase.cpp
953 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT ProfileBase.o -MD -MP -MF $(DEPDIR)/ProfileBase.Tpo -c -o ProfileBase.o `test -f './multipleAlign/ProfileBase.cpp' || echo '$(srcdir)/'`./multipleAlign/ProfileBase.cpp
954 mv -f $(DEPDIR)/ProfileBase.Tpo $(DEPDIR)/ProfileBase.Po
955 # source='./multipleAlign/ProfileBase.cpp' object='ProfileBase.o' libtool=no \
956 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
957 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o ProfileBase.o `test -f './multipleAlign/ProfileBase.cpp' || echo '$(srcdir)/'`./multipleAlign/ProfileBase.cpp
959 ProfileBase.obj: ./multipleAlign/ProfileBase.cpp
960 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT ProfileBase.obj -MD -MP -MF $(DEPDIR)/ProfileBase.Tpo -c -o ProfileBase.obj `if test -f './multipleAlign/ProfileBase.cpp'; then $(CYGPATH_W) './multipleAlign/ProfileBase.cpp'; else $(CYGPATH_W) '$(srcdir)/./multipleAlign/ProfileBase.cpp'; fi`
961 mv -f $(DEPDIR)/ProfileBase.Tpo $(DEPDIR)/ProfileBase.Po
962 # source='./multipleAlign/ProfileBase.cpp' object='ProfileBase.obj' libtool=no \
963 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
964 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o ProfileBase.obj `if test -f './multipleAlign/ProfileBase.cpp'; then $(CYGPATH_W) './multipleAlign/ProfileBase.cpp'; else $(CYGPATH_W) '$(srcdir)/./multipleAlign/ProfileBase.cpp'; fi`
966 LowScoreSegProfile.o: ./multipleAlign/LowScoreSegProfile.cpp
967 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT LowScoreSegProfile.o -MD -MP -MF $(DEPDIR)/LowScoreSegProfile.Tpo -c -o LowScoreSegProfile.o `test -f './multipleAlign/LowScoreSegProfile.cpp' || echo '$(srcdir)/'`./multipleAlign/LowScoreSegProfile.cpp
968 mv -f $(DEPDIR)/LowScoreSegProfile.Tpo $(DEPDIR)/LowScoreSegProfile.Po
969 # source='./multipleAlign/LowScoreSegProfile.cpp' object='LowScoreSegProfile.o' libtool=no \
970 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
971 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o LowScoreSegProfile.o `test -f './multipleAlign/LowScoreSegProfile.cpp' || echo '$(srcdir)/'`./multipleAlign/LowScoreSegProfile.cpp
973 LowScoreSegProfile.obj: ./multipleAlign/LowScoreSegProfile.cpp
974 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT LowScoreSegProfile.obj -MD -MP -MF $(DEPDIR)/LowScoreSegProfile.Tpo -c -o LowScoreSegProfile.obj `if test -f './multipleAlign/LowScoreSegProfile.cpp'; then $(CYGPATH_W) './multipleAlign/LowScoreSegProfile.cpp'; else $(CYGPATH_W) '$(srcdir)/./multipleAlign/LowScoreSegProfile.cpp'; fi`
975 mv -f $(DEPDIR)/LowScoreSegProfile.Tpo $(DEPDIR)/LowScoreSegProfile.Po
976 # source='./multipleAlign/LowScoreSegProfile.cpp' object='LowScoreSegProfile.obj' libtool=no \
977 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
978 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o LowScoreSegProfile.obj `if test -f './multipleAlign/LowScoreSegProfile.cpp'; then $(CYGPATH_W) './multipleAlign/LowScoreSegProfile.cpp'; else $(CYGPATH_W) '$(srcdir)/./multipleAlign/LowScoreSegProfile.cpp'; fi`
980 OutputFile.o: ./general/OutputFile.cpp
981 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT OutputFile.o -MD -MP -MF $(DEPDIR)/OutputFile.Tpo -c -o OutputFile.o `test -f './general/OutputFile.cpp' || echo '$(srcdir)/'`./general/OutputFile.cpp
982 mv -f $(DEPDIR)/OutputFile.Tpo $(DEPDIR)/OutputFile.Po
983 # source='./general/OutputFile.cpp' object='OutputFile.o' libtool=no \
984 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
985 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o OutputFile.o `test -f './general/OutputFile.cpp' || echo '$(srcdir)/'`./general/OutputFile.cpp
987 OutputFile.obj: ./general/OutputFile.cpp
988 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT OutputFile.obj -MD -MP -MF $(DEPDIR)/OutputFile.Tpo -c -o OutputFile.obj `if test -f './general/OutputFile.cpp'; then $(CYGPATH_W) './general/OutputFile.cpp'; else $(CYGPATH_W) '$(srcdir)/./general/OutputFile.cpp'; fi`
989 mv -f $(DEPDIR)/OutputFile.Tpo $(DEPDIR)/OutputFile.Po
990 # source='./general/OutputFile.cpp' object='OutputFile.obj' libtool=no \
991 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
992 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o OutputFile.obj `if test -f './general/OutputFile.cpp'; then $(CYGPATH_W) './general/OutputFile.cpp'; else $(CYGPATH_W) '$(srcdir)/./general/OutputFile.cpp'; fi`
994 UserParameters.o: ./general/UserParameters.cpp
995 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT UserParameters.o -MD -MP -MF $(DEPDIR)/UserParameters.Tpo -c -o UserParameters.o `test -f './general/UserParameters.cpp' || echo '$(srcdir)/'`./general/UserParameters.cpp
996 mv -f $(DEPDIR)/UserParameters.Tpo $(DEPDIR)/UserParameters.Po
997 # source='./general/UserParameters.cpp' object='UserParameters.o' libtool=no \
998 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
999 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o UserParameters.o `test -f './general/UserParameters.cpp' || echo '$(srcdir)/'`./general/UserParameters.cpp
1001 UserParameters.obj: ./general/UserParameters.cpp
1002 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT UserParameters.obj -MD -MP -MF $(DEPDIR)/UserParameters.Tpo -c -o UserParameters.obj `if test -f './general/UserParameters.cpp'; then $(CYGPATH_W) './general/UserParameters.cpp'; else $(CYGPATH_W) '$(srcdir)/./general/UserParameters.cpp'; fi`
1003 mv -f $(DEPDIR)/UserParameters.Tpo $(DEPDIR)/UserParameters.Po
1004 # source='./general/UserParameters.cpp' object='UserParameters.obj' libtool=no \
1005 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
1006 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o UserParameters.obj `if test -f './general/UserParameters.cpp'; then $(CYGPATH_W) './general/UserParameters.cpp'; else $(CYGPATH_W) '$(srcdir)/./general/UserParameters.cpp'; fi`
1008 Utility.o: ./general/Utility.cpp
1009 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT Utility.o -MD -MP -MF $(DEPDIR)/Utility.Tpo -c -o Utility.o `test -f './general/Utility.cpp' || echo '$(srcdir)/'`./general/Utility.cpp
1010 mv -f $(DEPDIR)/Utility.Tpo $(DEPDIR)/Utility.Po
1011 # source='./general/Utility.cpp' object='Utility.o' libtool=no \
1012 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
1013 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o Utility.o `test -f './general/Utility.cpp' || echo '$(srcdir)/'`./general/Utility.cpp
1015 Utility.obj: ./general/Utility.cpp
1016 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT Utility.obj -MD -MP -MF $(DEPDIR)/Utility.Tpo -c -o Utility.obj `if test -f './general/Utility.cpp'; then $(CYGPATH_W) './general/Utility.cpp'; else $(CYGPATH_W) '$(srcdir)/./general/Utility.cpp'; fi`
1017 mv -f $(DEPDIR)/Utility.Tpo $(DEPDIR)/Utility.Po
1018 # source='./general/Utility.cpp' object='Utility.obj' libtool=no \
1019 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
1020 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o Utility.obj `if test -f './general/Utility.cpp'; then $(CYGPATH_W) './general/Utility.cpp'; else $(CYGPATH_W) '$(srcdir)/./general/Utility.cpp'; fi`
1022 InvalidCombination.o: ./general/InvalidCombination.cpp
1023 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT InvalidCombination.o -MD -MP -MF $(DEPDIR)/InvalidCombination.Tpo -c -o InvalidCombination.o `test -f './general/InvalidCombination.cpp' || echo '$(srcdir)/'`./general/InvalidCombination.cpp
1024 mv -f $(DEPDIR)/InvalidCombination.Tpo $(DEPDIR)/InvalidCombination.Po
1025 # source='./general/InvalidCombination.cpp' object='InvalidCombination.o' libtool=no \
1026 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
1027 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o InvalidCombination.o `test -f './general/InvalidCombination.cpp' || echo '$(srcdir)/'`./general/InvalidCombination.cpp
1029 InvalidCombination.obj: ./general/InvalidCombination.cpp
1030 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT InvalidCombination.obj -MD -MP -MF $(DEPDIR)/InvalidCombination.Tpo -c -o InvalidCombination.obj `if test -f './general/InvalidCombination.cpp'; then $(CYGPATH_W) './general/InvalidCombination.cpp'; else $(CYGPATH_W) '$(srcdir)/./general/InvalidCombination.cpp'; fi`
1031 mv -f $(DEPDIR)/InvalidCombination.Tpo $(DEPDIR)/InvalidCombination.Po
1032 # source='./general/InvalidCombination.cpp' object='InvalidCombination.obj' libtool=no \
1033 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
1034 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o InvalidCombination.obj `if test -f './general/InvalidCombination.cpp'; then $(CYGPATH_W) './general/InvalidCombination.cpp'; else $(CYGPATH_W) '$(srcdir)/./general/InvalidCombination.cpp'; fi`
1036 DebugLog.o: ./general/DebugLog.cpp
1037 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT DebugLog.o -MD -MP -MF $(DEPDIR)/DebugLog.Tpo -c -o DebugLog.o `test -f './general/DebugLog.cpp' || echo '$(srcdir)/'`./general/DebugLog.cpp
1038 mv -f $(DEPDIR)/DebugLog.Tpo $(DEPDIR)/DebugLog.Po
1039 # source='./general/DebugLog.cpp' object='DebugLog.o' libtool=no \
1040 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
1041 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o DebugLog.o `test -f './general/DebugLog.cpp' || echo '$(srcdir)/'`./general/DebugLog.cpp
1043 DebugLog.obj: ./general/DebugLog.cpp
1044 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT DebugLog.obj -MD -MP -MF $(DEPDIR)/DebugLog.Tpo -c -o DebugLog.obj `if test -f './general/DebugLog.cpp'; then $(CYGPATH_W) './general/DebugLog.cpp'; else $(CYGPATH_W) '$(srcdir)/./general/DebugLog.cpp'; fi`
1045 mv -f $(DEPDIR)/DebugLog.Tpo $(DEPDIR)/DebugLog.Po
1046 # source='./general/DebugLog.cpp' object='DebugLog.obj' libtool=no \
1047 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
1048 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o DebugLog.obj `if test -f './general/DebugLog.cpp'; then $(CYGPATH_W) './general/DebugLog.cpp'; else $(CYGPATH_W) '$(srcdir)/./general/DebugLog.cpp'; fi`
1050 ClustalWResources.o: ./general/ClustalWResources.cpp
1051 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT ClustalWResources.o -MD -MP -MF $(DEPDIR)/ClustalWResources.Tpo -c -o ClustalWResources.o `test -f './general/ClustalWResources.cpp' || echo '$(srcdir)/'`./general/ClustalWResources.cpp
1052 mv -f $(DEPDIR)/ClustalWResources.Tpo $(DEPDIR)/ClustalWResources.Po
1053 # source='./general/ClustalWResources.cpp' object='ClustalWResources.o' libtool=no \
1054 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
1055 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o ClustalWResources.o `test -f './general/ClustalWResources.cpp' || echo '$(srcdir)/'`./general/ClustalWResources.cpp
1057 ClustalWResources.obj: ./general/ClustalWResources.cpp
1058 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT ClustalWResources.obj -MD -MP -MF $(DEPDIR)/ClustalWResources.Tpo -c -o ClustalWResources.obj `if test -f './general/ClustalWResources.cpp'; then $(CYGPATH_W) './general/ClustalWResources.cpp'; else $(CYGPATH_W) '$(srcdir)/./general/ClustalWResources.cpp'; fi`
1059 mv -f $(DEPDIR)/ClustalWResources.Tpo $(DEPDIR)/ClustalWResources.Po
1060 # source='./general/ClustalWResources.cpp' object='ClustalWResources.obj' libtool=no \
1061 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
1062 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o ClustalWResources.obj `if test -f './general/ClustalWResources.cpp'; then $(CYGPATH_W) './general/ClustalWResources.cpp'; else $(CYGPATH_W) '$(srcdir)/./general/ClustalWResources.cpp'; fi`
1064 VectorOutOfRange.o: ./general/VectorOutOfRange.cpp
1065 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT VectorOutOfRange.o -MD -MP -MF $(DEPDIR)/VectorOutOfRange.Tpo -c -o VectorOutOfRange.o `test -f './general/VectorOutOfRange.cpp' || echo '$(srcdir)/'`./general/VectorOutOfRange.cpp
1066 mv -f $(DEPDIR)/VectorOutOfRange.Tpo $(DEPDIR)/VectorOutOfRange.Po
1067 # source='./general/VectorOutOfRange.cpp' object='VectorOutOfRange.o' libtool=no \
1068 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
1069 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o VectorOutOfRange.o `test -f './general/VectorOutOfRange.cpp' || echo '$(srcdir)/'`./general/VectorOutOfRange.cpp
1071 VectorOutOfRange.obj: ./general/VectorOutOfRange.cpp
1072 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT VectorOutOfRange.obj -MD -MP -MF $(DEPDIR)/VectorOutOfRange.Tpo -c -o VectorOutOfRange.obj `if test -f './general/VectorOutOfRange.cpp'; then $(CYGPATH_W) './general/VectorOutOfRange.cpp'; else $(CYGPATH_W) '$(srcdir)/./general/VectorOutOfRange.cpp'; fi`
1073 mv -f $(DEPDIR)/VectorOutOfRange.Tpo $(DEPDIR)/VectorOutOfRange.Po
1074 # source='./general/VectorOutOfRange.cpp' object='VectorOutOfRange.obj' libtool=no \
1075 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
1076 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o VectorOutOfRange.obj `if test -f './general/VectorOutOfRange.cpp'; then $(CYGPATH_W) './general/VectorOutOfRange.cpp'; else $(CYGPATH_W) '$(srcdir)/./general/VectorOutOfRange.cpp'; fi`
1078 SymMatrix.o: ./general/SymMatrix.cpp
1079 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT SymMatrix.o -MD -MP -MF $(DEPDIR)/SymMatrix.Tpo -c -o SymMatrix.o `test -f './general/SymMatrix.cpp' || echo '$(srcdir)/'`./general/SymMatrix.cpp
1080 mv -f $(DEPDIR)/SymMatrix.Tpo $(DEPDIR)/SymMatrix.Po
1081 # source='./general/SymMatrix.cpp' object='SymMatrix.o' libtool=no \
1082 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
1083 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o SymMatrix.o `test -f './general/SymMatrix.cpp' || echo '$(srcdir)/'`./general/SymMatrix.cpp
1085 SymMatrix.obj: ./general/SymMatrix.cpp
1086 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT SymMatrix.obj -MD -MP -MF $(DEPDIR)/SymMatrix.Tpo -c -o SymMatrix.obj `if test -f './general/SymMatrix.cpp'; then $(CYGPATH_W) './general/SymMatrix.cpp'; else $(CYGPATH_W) '$(srcdir)/./general/SymMatrix.cpp'; fi`
1087 mv -f $(DEPDIR)/SymMatrix.Tpo $(DEPDIR)/SymMatrix.Po
1088 # source='./general/SymMatrix.cpp' object='SymMatrix.obj' libtool=no \
1089 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
1090 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o SymMatrix.obj `if test -f './general/SymMatrix.cpp'; then $(CYGPATH_W) './general/SymMatrix.cpp'; else $(CYGPATH_W) '$(srcdir)/./general/SymMatrix.cpp'; fi`
1092 Stats.o: ./general/Stats.cpp
1093 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT Stats.o -MD -MP -MF $(DEPDIR)/Stats.Tpo -c -o Stats.o `test -f './general/Stats.cpp' || echo '$(srcdir)/'`./general/Stats.cpp
1094 mv -f $(DEPDIR)/Stats.Tpo $(DEPDIR)/Stats.Po
1095 # source='./general/Stats.cpp' object='Stats.o' libtool=no \
1096 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
1097 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o Stats.o `test -f './general/Stats.cpp' || echo '$(srcdir)/'`./general/Stats.cpp
1099 Stats.obj: ./general/Stats.cpp
1100 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT Stats.obj -MD -MP -MF $(DEPDIR)/Stats.Tpo -c -o Stats.obj `if test -f './general/Stats.cpp'; then $(CYGPATH_W) './general/Stats.cpp'; else $(CYGPATH_W) '$(srcdir)/./general/Stats.cpp'; fi`
1101 mv -f $(DEPDIR)/Stats.Tpo $(DEPDIR)/Stats.Po
1102 # source='./general/Stats.cpp' object='Stats.obj' libtool=no \
1103 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
1104 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o Stats.obj `if test -f './general/Stats.cpp'; then $(CYGPATH_W) './general/Stats.cpp'; else $(CYGPATH_W) '$(srcdir)/./general/Stats.cpp'; fi`
1107 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT Help.o -MD -MP -MF $(DEPDIR)/Help.Tpo -c -o Help.o `test -f './Help.cpp' || echo '$(srcdir)/'`./Help.cpp
1108 mv -f $(DEPDIR)/Help.Tpo $(DEPDIR)/Help.Po
1109 # source='./Help.cpp' object='Help.o' libtool=no \
1110 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
1111 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o Help.o `test -f './Help.cpp' || echo '$(srcdir)/'`./Help.cpp
1113 Help.obj: ./Help.cpp
1114 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT Help.obj -MD -MP -MF $(DEPDIR)/Help.Tpo -c -o Help.obj `if test -f './Help.cpp'; then $(CYGPATH_W) './Help.cpp'; else $(CYGPATH_W) '$(srcdir)/./Help.cpp'; fi`
1115 mv -f $(DEPDIR)/Help.Tpo $(DEPDIR)/Help.Po
1116 # source='./Help.cpp' object='Help.obj' libtool=no \
1117 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
1118 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o Help.obj `if test -f './Help.cpp'; then $(CYGPATH_W) './Help.cpp'; else $(CYGPATH_W) '$(srcdir)/./Help.cpp'; fi`
1120 Alignment.o: ./alignment/Alignment.cpp
1121 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT Alignment.o -MD -MP -MF $(DEPDIR)/Alignment.Tpo -c -o Alignment.o `test -f './alignment/Alignment.cpp' || echo '$(srcdir)/'`./alignment/Alignment.cpp
1122 mv -f $(DEPDIR)/Alignment.Tpo $(DEPDIR)/Alignment.Po
1123 # source='./alignment/Alignment.cpp' object='Alignment.o' libtool=no \
1124 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
1125 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o Alignment.o `test -f './alignment/Alignment.cpp' || echo '$(srcdir)/'`./alignment/Alignment.cpp
1127 Alignment.obj: ./alignment/Alignment.cpp
1128 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT Alignment.obj -MD -MP -MF $(DEPDIR)/Alignment.Tpo -c -o Alignment.obj `if test -f './alignment/Alignment.cpp'; then $(CYGPATH_W) './alignment/Alignment.cpp'; else $(CYGPATH_W) '$(srcdir)/./alignment/Alignment.cpp'; fi`
1129 mv -f $(DEPDIR)/Alignment.Tpo $(DEPDIR)/Alignment.Po
1130 # source='./alignment/Alignment.cpp' object='Alignment.obj' libtool=no \
1131 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
1132 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o Alignment.obj `if test -f './alignment/Alignment.cpp'; then $(CYGPATH_W) './alignment/Alignment.cpp'; else $(CYGPATH_W) '$(srcdir)/./alignment/Alignment.cpp'; fi`
1134 AlignmentOutput.o: ./alignment/AlignmentOutput.cpp
1135 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT AlignmentOutput.o -MD -MP -MF $(DEPDIR)/AlignmentOutput.Tpo -c -o AlignmentOutput.o `test -f './alignment/AlignmentOutput.cpp' || echo '$(srcdir)/'`./alignment/AlignmentOutput.cpp
1136 mv -f $(DEPDIR)/AlignmentOutput.Tpo $(DEPDIR)/AlignmentOutput.Po
1137 # source='./alignment/AlignmentOutput.cpp' object='AlignmentOutput.o' libtool=no \
1138 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
1139 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o AlignmentOutput.o `test -f './alignment/AlignmentOutput.cpp' || echo '$(srcdir)/'`./alignment/AlignmentOutput.cpp
1141 AlignmentOutput.obj: ./alignment/AlignmentOutput.cpp
1142 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT AlignmentOutput.obj -MD -MP -MF $(DEPDIR)/AlignmentOutput.Tpo -c -o AlignmentOutput.obj `if test -f './alignment/AlignmentOutput.cpp'; then $(CYGPATH_W) './alignment/AlignmentOutput.cpp'; else $(CYGPATH_W) '$(srcdir)/./alignment/AlignmentOutput.cpp'; fi`
1143 mv -f $(DEPDIR)/AlignmentOutput.Tpo $(DEPDIR)/AlignmentOutput.Po
1144 # source='./alignment/AlignmentOutput.cpp' object='AlignmentOutput.obj' libtool=no \
1145 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
1146 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o AlignmentOutput.obj `if test -f './alignment/AlignmentOutput.cpp'; then $(CYGPATH_W) './alignment/AlignmentOutput.cpp'; else $(CYGPATH_W) '$(srcdir)/./alignment/AlignmentOutput.cpp'; fi`
1148 ObjectiveScore.o: ./alignment/ObjectiveScore.cpp
1149 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT ObjectiveScore.o -MD -MP -MF $(DEPDIR)/ObjectiveScore.Tpo -c -o ObjectiveScore.o `test -f './alignment/ObjectiveScore.cpp' || echo '$(srcdir)/'`./alignment/ObjectiveScore.cpp
1150 mv -f $(DEPDIR)/ObjectiveScore.Tpo $(DEPDIR)/ObjectiveScore.Po
1151 # source='./alignment/ObjectiveScore.cpp' object='ObjectiveScore.o' libtool=no \
1152 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
1153 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o ObjectiveScore.o `test -f './alignment/ObjectiveScore.cpp' || echo '$(srcdir)/'`./alignment/ObjectiveScore.cpp
1155 ObjectiveScore.obj: ./alignment/ObjectiveScore.cpp
1156 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT ObjectiveScore.obj -MD -MP -MF $(DEPDIR)/ObjectiveScore.Tpo -c -o ObjectiveScore.obj `if test -f './alignment/ObjectiveScore.cpp'; then $(CYGPATH_W) './alignment/ObjectiveScore.cpp'; else $(CYGPATH_W) '$(srcdir)/./alignment/ObjectiveScore.cpp'; fi`
1157 mv -f $(DEPDIR)/ObjectiveScore.Tpo $(DEPDIR)/ObjectiveScore.Po
1158 # source='./alignment/ObjectiveScore.cpp' object='ObjectiveScore.obj' libtool=no \
1159 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
1160 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o ObjectiveScore.obj `if test -f './alignment/ObjectiveScore.cpp'; then $(CYGPATH_W) './alignment/ObjectiveScore.cpp'; else $(CYGPATH_W) '$(srcdir)/./alignment/ObjectiveScore.cpp'; fi`
1162 Sequence.o: ./alignment/Sequence.cpp
1163 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT Sequence.o -MD -MP -MF $(DEPDIR)/Sequence.Tpo -c -o Sequence.o `test -f './alignment/Sequence.cpp' || echo '$(srcdir)/'`./alignment/Sequence.cpp
1164 mv -f $(DEPDIR)/Sequence.Tpo $(DEPDIR)/Sequence.Po
1165 # source='./alignment/Sequence.cpp' object='Sequence.o' libtool=no \
1166 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
1167 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o Sequence.o `test -f './alignment/Sequence.cpp' || echo '$(srcdir)/'`./alignment/Sequence.cpp
1169 Sequence.obj: ./alignment/Sequence.cpp
1170 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT Sequence.obj -MD -MP -MF $(DEPDIR)/Sequence.Tpo -c -o Sequence.obj `if test -f './alignment/Sequence.cpp'; then $(CYGPATH_W) './alignment/Sequence.cpp'; else $(CYGPATH_W) '$(srcdir)/./alignment/Sequence.cpp'; fi`
1171 mv -f $(DEPDIR)/Sequence.Tpo $(DEPDIR)/Sequence.Po
1172 # source='./alignment/Sequence.cpp' object='Sequence.obj' libtool=no \
1173 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
1174 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o Sequence.obj `if test -f './alignment/Sequence.cpp'; then $(CYGPATH_W) './alignment/Sequence.cpp'; else $(CYGPATH_W) '$(srcdir)/./alignment/Sequence.cpp'; fi`
1176 Clustal.o: ./Clustal.cpp
1177 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT Clustal.o -MD -MP -MF $(DEPDIR)/Clustal.Tpo -c -o Clustal.o `test -f './Clustal.cpp' || echo '$(srcdir)/'`./Clustal.cpp
1178 mv -f $(DEPDIR)/Clustal.Tpo $(DEPDIR)/Clustal.Po
1179 # source='./Clustal.cpp' object='Clustal.o' libtool=no \
1180 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
1181 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o Clustal.o `test -f './Clustal.cpp' || echo '$(srcdir)/'`./Clustal.cpp
1183 Clustal.obj: ./Clustal.cpp
1184 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT Clustal.obj -MD -MP -MF $(DEPDIR)/Clustal.Tpo -c -o Clustal.obj `if test -f './Clustal.cpp'; then $(CYGPATH_W) './Clustal.cpp'; else $(CYGPATH_W) '$(srcdir)/./Clustal.cpp'; fi`
1185 mv -f $(DEPDIR)/Clustal.Tpo $(DEPDIR)/Clustal.Po
1186 # source='./Clustal.cpp' object='Clustal.obj' libtool=no \
1187 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
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1191 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT main.o -MD -MP -MF $(DEPDIR)/main.Tpo -c -o main.o `test -f './main.cpp' || echo '$(srcdir)/'`./main.cpp
1192 mv -f $(DEPDIR)/main.Tpo $(DEPDIR)/main.Po
1193 # source='./main.cpp' object='main.o' libtool=no \
1194 # DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
1195 # $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o main.o `test -f './main.cpp' || echo '$(srcdir)/'`./main.cpp
1197 main.obj: ./main.cpp
1198 $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT main.obj -MD -MP -MF $(DEPDIR)/main.Tpo -c -o main.obj `if test -f './main.cpp'; then $(CYGPATH_W) './main.cpp'; else $(CYGPATH_W) '$(srcdir)/./main.cpp'; fi`
1199 mv -f $(DEPDIR)/main.Tpo $(DEPDIR)/main.Po
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1365 distdir=`$(am__cd) $(distdir) && pwd`; \
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1368 $(MAKE) $(AM_MAKEFLAGS) \
1369 top_distdir="$$top_distdir" \
1370 distdir="$$distdir/$$subdir" \
1371 am__remove_distdir=: \
1372 am__skip_length_check=: \
1378 check: check-recursive
1379 all-am: Makefile $(PROGRAMS) config.h
1380 installdirs: installdirs-recursive
1382 for dir in "$(DESTDIR)$(bindir)"; do \
1383 test -z "$$dir" || $(MKDIR_P) "$$dir"; \
1385 install: install-recursive
1386 install-exec: install-exec-recursive
1387 install-data: install-data-recursive
1388 uninstall: uninstall-recursive
1391 @$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
1393 installcheck: installcheck-recursive
1395 $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
1396 install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
1397 `test -z '$(STRIP)' || \
1398 echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
1399 mostlyclean-generic:
1404 -test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
1406 maintainer-clean-generic:
1407 @echo "This command is intended for maintainers to use"
1408 @echo "it deletes files that may require special tools to rebuild."
1409 clean: clean-recursive
1411 clean-am: clean-binPROGRAMS clean-generic mostlyclean-am
1413 distclean: distclean-recursive
1416 distclean-am: clean-am distclean-compile distclean-generic \
1417 distclean-hdr distclean-tags
1423 html: html-recursive
1425 info: info-recursive
1431 install-dvi: install-dvi-recursive
1433 install-exec-am: install-binPROGRAMS
1435 install-html: install-html-recursive
1437 install-info: install-info-recursive
1441 install-pdf: install-pdf-recursive
1443 install-ps: install-ps-recursive
1447 maintainer-clean: maintainer-clean-recursive
1450 maintainer-clean-am: distclean-am maintainer-clean-generic
1452 mostlyclean: mostlyclean-recursive
1454 mostlyclean-am: mostlyclean-compile mostlyclean-generic
1464 uninstall-am: uninstall-binPROGRAMS
1466 .MAKE: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) install-am \
1469 .PHONY: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) CTAGS GTAGS \
1470 all all-am check check-am clean clean-binPROGRAMS \
1471 clean-generic ctags ctags-recursive distclean \
1472 distclean-compile distclean-generic distclean-hdr \
1473 distclean-tags distdir dvi dvi-am html html-am info info-am \
1474 install install-am install-binPROGRAMS install-data \
1475 install-data-am install-dvi install-dvi-am install-exec \
1476 install-exec-am install-html install-html-am install-info \
1477 install-info-am install-man install-pdf install-pdf-am \
1478 install-ps install-ps-am install-strip installcheck \
1479 installcheck-am installdirs installdirs-am maintainer-clean \
1480 maintainer-clean-generic mostlyclean mostlyclean-compile \
1481 mostlyclean-generic pdf pdf-am ps ps-am tags tags-recursive \
1482 uninstall uninstall-am uninstall-binPROGRAMS
1484 # Tell versions [3.59,3.63) of GNU make to not export all variables.
1485 # Otherwise a system limit (for SysV at least) may be exceeded.