source: tags/arb-6.0/CONSENSUS_TREE/Makefile

Last change on this file was 11401, checked in by westram, 12 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:
  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 6.9 KB
Line 
1.SUFFIXES: .o .cxx .depend
2
3OBJS = CT_part.o CT_hash.o CT_ntree.o CT_rbtree.o CT_dtree.o CT_ctree.o CT_mem.o
4
5$(MAIN): $(OBJS)
6        $(LINK_STATIC_LIB) $(MAIN) $(OBJS)
7
8.cxx.o:
9        $(A_CXX) $(cflags) $(cxxflags) -c $< $(CXX_INCLUDES) $(POST_COMPILE)
10clean:
11        rm -f $(OBJS) *.a
12
13DEPENDS = $(OBJS:.o=.depend)
14depends: $(DEPENDS)
15        @cat $(DEPENDS) | grep -v '^#' >>Makefile
16        @rm $(DEPENDS)
17$(DEPENDS): depend.init
18depend.init:
19        $(MAKEDEPEND) $(MAKEDEPENDFLAGS) 2>/dev/null # remove dependencies
20.c.depend:
21        $(MAKEDEPEND) -f- $(MAKEDEPENDFLAGS) $< 2>/dev/null >$@
22.cxx.depend:
23        $(MAKEDEPEND) -f- $(MAKEDEPENDFLAGS) $< 2>/dev/null >$@
24
25# DO NOT DELETE THIS LINE -- make depend depends on it.
26
27# Do not add dependencies manually - use 'make depend' in $ARBHOME
28# For formatting issues see SOURCE_TOOLS/fix_depends.pl (from main)
29
30CT_ctree.o: CT_ctree.hxx
31CT_ctree.o: CT_def.hxx
32CT_ctree.o: CT_hash.hxx
33CT_ctree.o: CT_mem.hxx
34CT_ctree.o: CT_ntree.hxx
35CT_ctree.o: CT_part.hxx
36CT_ctree.o: $(ARBHOME)/INCLUDE/ad_prot.h
37CT_ctree.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
38CT_ctree.o: $(ARBHOME)/INCLUDE/arb_assert.h
39CT_ctree.o: $(ARBHOME)/INCLUDE/arb_core.h
40CT_ctree.o: $(ARBHOME)/INCLUDE/arb_error.h
41CT_ctree.o: $(ARBHOME)/INCLUDE/arb_msg.h
42CT_ctree.o: $(ARBHOME)/INCLUDE/arb_progress.h
43CT_ctree.o: $(ARBHOME)/INCLUDE/arb_strarray.h
44CT_ctree.o: $(ARBHOME)/INCLUDE/arb_strbuf.h
45CT_ctree.o: $(ARBHOME)/INCLUDE/arb_string.h
46CT_ctree.o: $(ARBHOME)/INCLUDE/arbdb.h
47CT_ctree.o: $(ARBHOME)/INCLUDE/arbdb_base.h
48CT_ctree.o: $(ARBHOME)/INCLUDE/arbdbt.h
49CT_ctree.o: $(ARBHOME)/INCLUDE/arbtools.h
50CT_ctree.o: $(ARBHOME)/INCLUDE/attributes.h
51CT_ctree.o: $(ARBHOME)/INCLUDE/cxxforward.h
52CT_ctree.o: $(ARBHOME)/INCLUDE/downcast.h
53CT_ctree.o: $(ARBHOME)/INCLUDE/dupstr.h
54CT_ctree.o: $(ARBHOME)/INCLUDE/gccver.h
55CT_ctree.o: $(ARBHOME)/INCLUDE/RootedTree.h
56CT_ctree.o: $(ARBHOME)/INCLUDE/smartptr.h
57CT_ctree.o: $(ARBHOME)/INCLUDE/static_assert.h
58CT_ctree.o: $(ARBHOME)/INCLUDE/test_global.h
59
60CT_dtree.o: CT_ctree.hxx
61CT_dtree.o: CT_def.hxx
62CT_dtree.o: CT_hash.hxx
63CT_dtree.o: CT_mem.hxx
64CT_dtree.o: CT_part.hxx
65CT_dtree.o: $(ARBHOME)/INCLUDE/ad_prot.h
66CT_dtree.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
67CT_dtree.o: $(ARBHOME)/INCLUDE/arb_assert.h
68CT_dtree.o: $(ARBHOME)/INCLUDE/arb_core.h
69CT_dtree.o: $(ARBHOME)/INCLUDE/arb_error.h
70CT_dtree.o: $(ARBHOME)/INCLUDE/arb_msg.h
71CT_dtree.o: $(ARBHOME)/INCLUDE/arb_progress.h
72CT_dtree.o: $(ARBHOME)/INCLUDE/arb_strarray.h
73CT_dtree.o: $(ARBHOME)/INCLUDE/arb_string.h
74CT_dtree.o: $(ARBHOME)/INCLUDE/arbdb.h
75CT_dtree.o: $(ARBHOME)/INCLUDE/arbdb_base.h
76CT_dtree.o: $(ARBHOME)/INCLUDE/arbdbt.h
77CT_dtree.o: $(ARBHOME)/INCLUDE/arbtools.h
78CT_dtree.o: $(ARBHOME)/INCLUDE/attributes.h
79CT_dtree.o: $(ARBHOME)/INCLUDE/cxxforward.h
80CT_dtree.o: $(ARBHOME)/INCLUDE/downcast.h
81CT_dtree.o: $(ARBHOME)/INCLUDE/dupstr.h
82CT_dtree.o: $(ARBHOME)/INCLUDE/gccver.h
83CT_dtree.o: $(ARBHOME)/INCLUDE/RootedTree.h
84CT_dtree.o: $(ARBHOME)/INCLUDE/smartptr.h
85CT_dtree.o: $(ARBHOME)/INCLUDE/static_assert.h
86CT_dtree.o: $(ARBHOME)/INCLUDE/test_global.h
87
88CT_hash.o: CT_ctree.hxx
89CT_hash.o: CT_def.hxx
90CT_hash.o: CT_hash.hxx
91CT_hash.o: CT_mem.hxx
92CT_hash.o: CT_ntree.hxx
93CT_hash.o: CT_part.hxx
94CT_hash.o: $(ARBHOME)/INCLUDE/ad_prot.h
95CT_hash.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
96CT_hash.o: $(ARBHOME)/INCLUDE/arb_assert.h
97CT_hash.o: $(ARBHOME)/INCLUDE/arb_core.h
98CT_hash.o: $(ARBHOME)/INCLUDE/arb_error.h
99CT_hash.o: $(ARBHOME)/INCLUDE/arb_msg.h
100CT_hash.o: $(ARBHOME)/INCLUDE/arb_progress.h
101CT_hash.o: $(ARBHOME)/INCLUDE/arb_sort.h
102CT_hash.o: $(ARBHOME)/INCLUDE/arb_strarray.h
103CT_hash.o: $(ARBHOME)/INCLUDE/arb_string.h
104CT_hash.o: $(ARBHOME)/INCLUDE/arbdb.h
105CT_hash.o: $(ARBHOME)/INCLUDE/arbdb_base.h
106CT_hash.o: $(ARBHOME)/INCLUDE/arbdbt.h
107CT_hash.o: $(ARBHOME)/INCLUDE/arbtools.h
108CT_hash.o: $(ARBHOME)/INCLUDE/attributes.h
109CT_hash.o: $(ARBHOME)/INCLUDE/cxxforward.h
110CT_hash.o: $(ARBHOME)/INCLUDE/downcast.h
111CT_hash.o: $(ARBHOME)/INCLUDE/dupstr.h
112CT_hash.o: $(ARBHOME)/INCLUDE/gccver.h
113CT_hash.o: $(ARBHOME)/INCLUDE/RootedTree.h
114CT_hash.o: $(ARBHOME)/INCLUDE/smartptr.h
115CT_hash.o: $(ARBHOME)/INCLUDE/static_assert.h
116CT_hash.o: $(ARBHOME)/INCLUDE/test_global.h
117
118CT_ntree.o: CT_def.hxx
119CT_ntree.o: CT_mem.hxx
120CT_ntree.o: CT_ntree.hxx
121CT_ntree.o: CT_part.hxx
122CT_ntree.o: $(ARBHOME)/INCLUDE/ad_prot.h
123CT_ntree.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
124CT_ntree.o: $(ARBHOME)/INCLUDE/arb_assert.h
125CT_ntree.o: $(ARBHOME)/INCLUDE/arb_core.h
126CT_ntree.o: $(ARBHOME)/INCLUDE/arb_error.h
127CT_ntree.o: $(ARBHOME)/INCLUDE/arb_msg.h
128CT_ntree.o: $(ARBHOME)/INCLUDE/arb_string.h
129CT_ntree.o: $(ARBHOME)/INCLUDE/arbdb.h
130CT_ntree.o: $(ARBHOME)/INCLUDE/arbdb_base.h
131CT_ntree.o: $(ARBHOME)/INCLUDE/arbdbt.h
132CT_ntree.o: $(ARBHOME)/INCLUDE/arbtools.h
133CT_ntree.o: $(ARBHOME)/INCLUDE/attributes.h
134CT_ntree.o: $(ARBHOME)/INCLUDE/cxxforward.h
135CT_ntree.o: $(ARBHOME)/INCLUDE/downcast.h
136CT_ntree.o: $(ARBHOME)/INCLUDE/dupstr.h
137CT_ntree.o: $(ARBHOME)/INCLUDE/gccver.h
138CT_ntree.o: $(ARBHOME)/INCLUDE/smartptr.h
139CT_ntree.o: $(ARBHOME)/INCLUDE/static_assert.h
140CT_ntree.o: $(ARBHOME)/INCLUDE/test_global.h
141
142CT_part.o: CT_def.hxx
143CT_part.o: CT_mem.hxx
144CT_part.o: CT_part.hxx
145CT_part.o: $(ARBHOME)/INCLUDE/ad_prot.h
146CT_part.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
147CT_part.o: $(ARBHOME)/INCLUDE/arb_assert.h
148CT_part.o: $(ARBHOME)/INCLUDE/arb_core.h
149CT_part.o: $(ARBHOME)/INCLUDE/arb_error.h
150CT_part.o: $(ARBHOME)/INCLUDE/arb_msg.h
151CT_part.o: $(ARBHOME)/INCLUDE/arb_strarray.h
152CT_part.o: $(ARBHOME)/INCLUDE/arb_string.h
153CT_part.o: $(ARBHOME)/INCLUDE/arbdb.h
154CT_part.o: $(ARBHOME)/INCLUDE/arbdb_base.h
155CT_part.o: $(ARBHOME)/INCLUDE/arbdbt.h
156CT_part.o: $(ARBHOME)/INCLUDE/arbtools.h
157CT_part.o: $(ARBHOME)/INCLUDE/attributes.h
158CT_part.o: $(ARBHOME)/INCLUDE/cxxforward.h
159CT_part.o: $(ARBHOME)/INCLUDE/downcast.h
160CT_part.o: $(ARBHOME)/INCLUDE/dupstr.h
161CT_part.o: $(ARBHOME)/INCLUDE/gccver.h
162CT_part.o: $(ARBHOME)/INCLUDE/smartptr.h
163CT_part.o: $(ARBHOME)/INCLUDE/static_assert.h
164CT_part.o: $(ARBHOME)/INCLUDE/test_global.h
165CT_part.o: $(ARBHOME)/INCLUDE/test_unit.h
166
167CT_rbtree.o: CT_ctree.hxx
168CT_rbtree.o: CT_def.hxx
169CT_rbtree.o: CT_mem.hxx
170CT_rbtree.o: CT_ntree.hxx
171CT_rbtree.o: CT_part.hxx
172CT_rbtree.o: $(ARBHOME)/INCLUDE/ad_prot.h
173CT_rbtree.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
174CT_rbtree.o: $(ARBHOME)/INCLUDE/arb_assert.h
175CT_rbtree.o: $(ARBHOME)/INCLUDE/arb_core.h
176CT_rbtree.o: $(ARBHOME)/INCLUDE/arb_error.h
177CT_rbtree.o: $(ARBHOME)/INCLUDE/arb_msg.h
178CT_rbtree.o: $(ARBHOME)/INCLUDE/arb_progress.h
179CT_rbtree.o: $(ARBHOME)/INCLUDE/arb_sort.h
180CT_rbtree.o: $(ARBHOME)/INCLUDE/arb_strarray.h
181CT_rbtree.o: $(ARBHOME)/INCLUDE/arb_string.h
182CT_rbtree.o: $(ARBHOME)/INCLUDE/arbdb.h
183CT_rbtree.o: $(ARBHOME)/INCLUDE/arbdb_base.h
184CT_rbtree.o: $(ARBHOME)/INCLUDE/arbdbt.h
185CT_rbtree.o: $(ARBHOME)/INCLUDE/arbtools.h
186CT_rbtree.o: $(ARBHOME)/INCLUDE/attributes.h
187CT_rbtree.o: $(ARBHOME)/INCLUDE/cxxforward.h
188CT_rbtree.o: $(ARBHOME)/INCLUDE/downcast.h
189CT_rbtree.o: $(ARBHOME)/INCLUDE/dupstr.h
190CT_rbtree.o: $(ARBHOME)/INCLUDE/gccver.h
191CT_rbtree.o: $(ARBHOME)/INCLUDE/RootedTree.h
192CT_rbtree.o: $(ARBHOME)/INCLUDE/smartptr.h
193CT_rbtree.o: $(ARBHOME)/INCLUDE/static_assert.h
194CT_rbtree.o: $(ARBHOME)/INCLUDE/test_global.h
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