source: tags/arb-6.0/SL/NEIGHBOURJOIN/Makefile

Last change on this file was 11401, checked in by westram, 11 years ago
  • reintegrates 'tree' into 'trunk':
    • consensus trees:
      • support for merging partial trees ("worked" before, but results were crap; implements #65)
      • generated trees are automatically re-rooted and -ordered
      • always list source trees in consensus-tree-comment; show info about partial trees
      • fixed progress bar
    • made GBT_TREE a base class of other tree classes (implements #31)
    • save tree properties in properties (not in DB)
    • new functions 'Remove zombies/marked from ALL trees'
    • tree load/save: layout fixes
    • unit tests
      • added tests for basic tree modifications (PARSIMONY)
    • performance:
      • compute_tree updates tree information in one traversal
      • tree generators are now capable to generate any type of tree (w/o needing to copy it once)
    • bugfixes:
      • NNI (of marked species) was also always performed for colored species
      • centered beautify-order is stable now
      • improved 'search optimal root'
  • adds:
File size: 1.7 KB
Line 
1# for variables passed from parent makefile see ../../SOURCE_TOOLS/parent_make.txt
2
3.SUFFIXES: .o .c .cxx .depend
4
5C_OBJECTS = 
6CPP_OBJECTS = \
7        NJ.o \
8
9OBJECTS=$(C_OBJECTS) $(CPP_OBJECTS)
10
11$(MAIN): $(OBJECTS)
12        $(LINK_STATIC_LIB) $(MAIN) $(OBJECTS)
13
14.cxx.o:
15        $(A_CXX) $(cflags) $(cxxflags) -c $< $(CXX_INCLUDES) $(POST_COMPILE)
16
17.c.o:
18        $(A_CC) $(cflags) -c $< $(CC_INCLUDES) $(POST_COMPILE)
19
20clean:
21        rm -f $(OBJECTS) *.a
22
23DEPENDS = $(OBJECTS:.o=.depend)
24depends: $(DEPENDS)
25        @cat $(DEPENDS) | grep -v '^#' >>Makefile
26        @rm $(DEPENDS)
27$(DEPENDS): depend.init
28depend.init:
29        $(MAKEDEPEND) $(MAKEDEPENDFLAGS) 2>/dev/null # remove dependencies
30.c.depend:
31        $(MAKEDEPEND) -f- $(MAKEDEPENDFLAGS) $< 2>/dev/null >$@
32.cxx.depend:
33        $(MAKEDEPEND) -f- $(MAKEDEPENDFLAGS) $< 2>/dev/null >$@
34
35# DO NOT DELETE
36
37# Do not add dependencies manually - use 'make depend' in $ARBHOME
38# For formatting issues see SOURCE_TOOLS/fix_depends.pl (from SL)
39
40NJ.o: neighbourjoin.hxx
41NJ.o: NJ.hxx
42NJ.o: $(ARBHOME)/INCLUDE/ad_prot.h
43NJ.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
44NJ.o: $(ARBHOME)/INCLUDE/AP_matrix.hxx
45NJ.o: $(ARBHOME)/INCLUDE/arb_assert.h
46NJ.o: $(ARBHOME)/INCLUDE/arb_core.h
47NJ.o: $(ARBHOME)/INCLUDE/arb_diff.h
48NJ.o: $(ARBHOME)/INCLUDE/arb_error.h
49NJ.o: $(ARBHOME)/INCLUDE/arb_msg.h
50NJ.o: $(ARBHOME)/INCLUDE/arb_string.h
51NJ.o: $(ARBHOME)/INCLUDE/arbdb.h
52NJ.o: $(ARBHOME)/INCLUDE/arbdb_base.h
53NJ.o: $(ARBHOME)/INCLUDE/arbdbt.h
54NJ.o: $(ARBHOME)/INCLUDE/arbtools.h
55NJ.o: $(ARBHOME)/INCLUDE/attributes.h
56NJ.o: $(ARBHOME)/INCLUDE/cxxforward.h
57NJ.o: $(ARBHOME)/INCLUDE/downcast.h
58NJ.o: $(ARBHOME)/INCLUDE/dupstr.h
59NJ.o: $(ARBHOME)/INCLUDE/gccver.h
60NJ.o: $(ARBHOME)/INCLUDE/smartptr.h
61NJ.o: $(ARBHOME)/INCLUDE/static_assert.h
62NJ.o: $(ARBHOME)/INCLUDE/test_global.h
63NJ.o: $(ARBHOME)/INCLUDE/test_unit.h
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