source: branches/profile/SL/SEQUENCE/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: 5.6 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        AP_seq_dna.o \
8        AP_seq_protein.o \
9        AP_seq_simple_pro.o \
10        AP_sequence.o \
11
12OBJECTS=$(C_OBJECTS) $(CPP_OBJECTS)
13
14$(MAIN): $(OBJECTS)
15        $(LINK_STATIC_LIB) $(MAIN) $(OBJECTS)
16
17.cxx.o:
18        $(A_CXX) $(cflags) $(cxxflags) -c $< $(CXX_INCLUDES) $(POST_COMPILE)
19
20.c.o:
21        $(A_CC) $(cflags) -c $< $(CC_INCLUDES) $(POST_COMPILE)
22
23clean:
24        rm -f $(OBJECTS) *.a
25
26DEPENDS = $(OBJECTS:.o=.depend)
27depends: $(DEPENDS)
28        @cat $(DEPENDS) | grep -v '^#' >>Makefile
29        @rm $(DEPENDS)
30$(DEPENDS): depend.init
31depend.init:
32        $(MAKEDEPEND) $(MAKEDEPENDFLAGS) 2>/dev/null # remove dependencies
33.c.depend:
34        $(MAKEDEPEND) -f- $(MAKEDEPENDFLAGS) $< 2>/dev/null >$@
35.cxx.depend:
36        $(MAKEDEPEND) -f- $(MAKEDEPENDFLAGS) $< 2>/dev/null >$@
37
38# DO NOT DELETE
39
40# Do not add dependencies manually - use 'make depend' in $ARBHOME
41# For formatting issues see SOURCE_TOOLS/fix_depends.pl (from SL)
42
43AP_seq_dna.o: AP_parsimony_defaults.hxx
44AP_seq_dna.o: AP_seq_dna.hxx
45AP_seq_dna.o: AP_sequence.hxx
46AP_seq_dna.o: $(ARBHOME)/INCLUDE/ad_prot.h
47AP_seq_dna.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
48AP_seq_dna.o: $(ARBHOME)/INCLUDE/AliView.hxx
49AP_seq_dna.o: $(ARBHOME)/INCLUDE/AP_filter.hxx
50AP_seq_dna.o: $(ARBHOME)/INCLUDE/AP_pro_a_nucs.hxx
51AP_seq_dna.o: $(ARBHOME)/INCLUDE/arb_assert.h
52AP_seq_dna.o: $(ARBHOME)/INCLUDE/arb_core.h
53AP_seq_dna.o: $(ARBHOME)/INCLUDE/arb_error.h
54AP_seq_dna.o: $(ARBHOME)/INCLUDE/arb_msg.h
55AP_seq_dna.o: $(ARBHOME)/INCLUDE/arb_string.h
56AP_seq_dna.o: $(ARBHOME)/INCLUDE/ARB_Tree.hxx
57AP_seq_dna.o: $(ARBHOME)/INCLUDE/arbdb.h
58AP_seq_dna.o: $(ARBHOME)/INCLUDE/arbdb_base.h
59AP_seq_dna.o: $(ARBHOME)/INCLUDE/arbdbt.h
60AP_seq_dna.o: $(ARBHOME)/INCLUDE/arbtools.h
61AP_seq_dna.o: $(ARBHOME)/INCLUDE/attributes.h
62AP_seq_dna.o: $(ARBHOME)/INCLUDE/cxxforward.h
63AP_seq_dna.o: $(ARBHOME)/INCLUDE/downcast.h
64AP_seq_dna.o: $(ARBHOME)/INCLUDE/dupstr.h
65AP_seq_dna.o: $(ARBHOME)/INCLUDE/gccver.h
66AP_seq_dna.o: $(ARBHOME)/INCLUDE/RootedTree.h
67AP_seq_dna.o: $(ARBHOME)/INCLUDE/smartptr.h
68AP_seq_dna.o: $(ARBHOME)/INCLUDE/static_assert.h
69AP_seq_dna.o: $(ARBHOME)/INCLUDE/test_global.h
70
71AP_seq_protein.o: AP_parsimony_defaults.hxx
72AP_seq_protein.o: AP_seq_protein.hxx
73AP_seq_protein.o: AP_sequence.hxx
74AP_seq_protein.o: $(ARBHOME)/INCLUDE/ad_prot.h
75AP_seq_protein.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
76AP_seq_protein.o: $(ARBHOME)/INCLUDE/AliView.hxx
77AP_seq_protein.o: $(ARBHOME)/INCLUDE/AP_filter.hxx
78AP_seq_protein.o: $(ARBHOME)/INCLUDE/AP_pro_a_nucs.hxx
79AP_seq_protein.o: $(ARBHOME)/INCLUDE/arb_assert.h
80AP_seq_protein.o: $(ARBHOME)/INCLUDE/arb_core.h
81AP_seq_protein.o: $(ARBHOME)/INCLUDE/arb_error.h
82AP_seq_protein.o: $(ARBHOME)/INCLUDE/arb_msg.h
83AP_seq_protein.o: $(ARBHOME)/INCLUDE/arb_str.h
84AP_seq_protein.o: $(ARBHOME)/INCLUDE/arb_string.h
85AP_seq_protein.o: $(ARBHOME)/INCLUDE/ARB_Tree.hxx
86AP_seq_protein.o: $(ARBHOME)/INCLUDE/arbdb.h
87AP_seq_protein.o: $(ARBHOME)/INCLUDE/arbdb_base.h
88AP_seq_protein.o: $(ARBHOME)/INCLUDE/arbdbt.h
89AP_seq_protein.o: $(ARBHOME)/INCLUDE/arbtools.h
90AP_seq_protein.o: $(ARBHOME)/INCLUDE/attributes.h
91AP_seq_protein.o: $(ARBHOME)/INCLUDE/cxxforward.h
92AP_seq_protein.o: $(ARBHOME)/INCLUDE/downcast.h
93AP_seq_protein.o: $(ARBHOME)/INCLUDE/dupstr.h
94AP_seq_protein.o: $(ARBHOME)/INCLUDE/gccver.h
95AP_seq_protein.o: $(ARBHOME)/INCLUDE/RootedTree.h
96AP_seq_protein.o: $(ARBHOME)/INCLUDE/smartptr.h
97AP_seq_protein.o: $(ARBHOME)/INCLUDE/static_assert.h
98AP_seq_protein.o: $(ARBHOME)/INCLUDE/test_global.h
99
100AP_seq_simple_pro.o: AP_seq_simple_pro.hxx
101AP_seq_simple_pro.o: AP_sequence.hxx
102AP_seq_simple_pro.o: $(ARBHOME)/INCLUDE/ad_prot.h
103AP_seq_simple_pro.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
104AP_seq_simple_pro.o: $(ARBHOME)/INCLUDE/AliView.hxx
105AP_seq_simple_pro.o: $(ARBHOME)/INCLUDE/AP_filter.hxx
106AP_seq_simple_pro.o: $(ARBHOME)/INCLUDE/AP_pro_a_nucs.hxx
107AP_seq_simple_pro.o: $(ARBHOME)/INCLUDE/arb_assert.h
108AP_seq_simple_pro.o: $(ARBHOME)/INCLUDE/arb_core.h
109AP_seq_simple_pro.o: $(ARBHOME)/INCLUDE/arb_error.h
110AP_seq_simple_pro.o: $(ARBHOME)/INCLUDE/arb_msg.h
111AP_seq_simple_pro.o: $(ARBHOME)/INCLUDE/arb_string.h
112AP_seq_simple_pro.o: $(ARBHOME)/INCLUDE/ARB_Tree.hxx
113AP_seq_simple_pro.o: $(ARBHOME)/INCLUDE/arbdb.h
114AP_seq_simple_pro.o: $(ARBHOME)/INCLUDE/arbdb_base.h
115AP_seq_simple_pro.o: $(ARBHOME)/INCLUDE/arbdbt.h
116AP_seq_simple_pro.o: $(ARBHOME)/INCLUDE/arbtools.h
117AP_seq_simple_pro.o: $(ARBHOME)/INCLUDE/attributes.h
118AP_seq_simple_pro.o: $(ARBHOME)/INCLUDE/cxxforward.h
119AP_seq_simple_pro.o: $(ARBHOME)/INCLUDE/downcast.h
120AP_seq_simple_pro.o: $(ARBHOME)/INCLUDE/dupstr.h
121AP_seq_simple_pro.o: $(ARBHOME)/INCLUDE/gccver.h
122AP_seq_simple_pro.o: $(ARBHOME)/INCLUDE/RootedTree.h
123AP_seq_simple_pro.o: $(ARBHOME)/INCLUDE/smartptr.h
124AP_seq_simple_pro.o: $(ARBHOME)/INCLUDE/static_assert.h
125AP_seq_simple_pro.o: $(ARBHOME)/INCLUDE/test_global.h
126
127AP_sequence.o: AP_sequence.hxx
128AP_sequence.o: $(ARBHOME)/INCLUDE/ad_prot.h
129AP_sequence.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
130AP_sequence.o: $(ARBHOME)/INCLUDE/AliView.hxx
131AP_sequence.o: $(ARBHOME)/INCLUDE/arb_assert.h
132AP_sequence.o: $(ARBHOME)/INCLUDE/arb_core.h
133AP_sequence.o: $(ARBHOME)/INCLUDE/arb_error.h
134AP_sequence.o: $(ARBHOME)/INCLUDE/arb_msg.h
135AP_sequence.o: $(ARBHOME)/INCLUDE/arb_string.h
136AP_sequence.o: $(ARBHOME)/INCLUDE/arbdb.h
137AP_sequence.o: $(ARBHOME)/INCLUDE/arbdb_base.h
138AP_sequence.o: $(ARBHOME)/INCLUDE/arbdbt.h
139AP_sequence.o: $(ARBHOME)/INCLUDE/arbtools.h
140AP_sequence.o: $(ARBHOME)/INCLUDE/attributes.h
141AP_sequence.o: $(ARBHOME)/INCLUDE/cxxforward.h
142AP_sequence.o: $(ARBHOME)/INCLUDE/downcast.h
143AP_sequence.o: $(ARBHOME)/INCLUDE/dupstr.h
144AP_sequence.o: $(ARBHOME)/INCLUDE/gccver.h
145AP_sequence.o: $(ARBHOME)/INCLUDE/smartptr.h
146AP_sequence.o: $(ARBHOME)/INCLUDE/static_assert.h
147AP_sequence.o: $(ARBHOME)/INCLUDE/test_global.h
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