source: tags/arb-6.0/STAT/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:
  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 5.5 KB
Line 
1# for variables passed from parent makefile see ../SOURCE_TOOLS/parent_make.txt
2
3.SUFFIXES: .o .cxx .depend
4
5CPP_OBJECTS = \
6        ST_ml.o \
7        ST_window.o \
8        ST_quality.o \
9
10$(MAIN): $(CPP_OBJECTS)
11        $(LINK_STATIC_LIB) $(MAIN) $(CPP_OBJECTS)
12
13.cxx.o:
14        $(A_CXX) $(cflags) $(cxxflags) -c $< $(CXX_INCLUDES) $(POST_COMPILE)
15
16clean:
17        rm -f $(CPP_OBJECTS) *.a
18
19DEPENDS = $(CPP_OBJECTS:.o=.depend)
20depends: $(DEPENDS)
21        @cat $(DEPENDS) | grep -v '^#' >>Makefile
22        @rm $(DEPENDS)
23$(DEPENDS): depend.init
24depend.init:
25        $(MAKEDEPEND) $(MAKEDEPENDFLAGS) 2>/dev/null # remove dependencies
26.c.depend:
27        $(MAKEDEPEND) -f- $(MAKEDEPENDFLAGS) $< 2>/dev/null >$@
28.cxx.depend:
29        $(MAKEDEPEND) -f- $(MAKEDEPENDFLAGS) $< 2>/dev/null >$@
30
31# DO NOT DELETE THIS LINE -- make depend depends on it.
32
33# Do not add dependencies manually - use 'make depend' in $ARBHOME
34# For formatting issues see SOURCE_TOOLS/fix_depends.pl (from main)
35
36ST_ml.o: MostLikelySeq.hxx
37ST_ml.o: st_ml.hxx
38ST_ml.o: $(ARBHOME)/INCLUDE/ad_cb.h
39ST_ml.o: $(ARBHOME)/INCLUDE/ad_cb_prot.h
40ST_ml.o: $(ARBHOME)/INCLUDE/ad_prot.h
41ST_ml.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
42ST_ml.o: $(ARBHOME)/INCLUDE/AliView.hxx
43ST_ml.o: $(ARBHOME)/INCLUDE/AP_filter.hxx
44ST_ml.o: $(ARBHOME)/INCLUDE/AP_sequence.hxx
45ST_ml.o: $(ARBHOME)/INCLUDE/AP_Tree.hxx
46ST_ml.o: $(ARBHOME)/INCLUDE/arb_assert.h
47ST_ml.o: $(ARBHOME)/INCLUDE/arb_core.h
48ST_ml.o: $(ARBHOME)/INCLUDE/arb_error.h
49ST_ml.o: $(ARBHOME)/INCLUDE/arb_msg.h
50ST_ml.o: $(ARBHOME)/INCLUDE/arb_progress.h
51ST_ml.o: $(ARBHOME)/INCLUDE/arb_string.h
52ST_ml.o: $(ARBHOME)/INCLUDE/ARB_Tree.hxx
53ST_ml.o: $(ARBHOME)/INCLUDE/arbdb.h
54ST_ml.o: $(ARBHOME)/INCLUDE/arbdb_base.h
55ST_ml.o: $(ARBHOME)/INCLUDE/arbdbt.h
56ST_ml.o: $(ARBHOME)/INCLUDE/arbtools.h
57ST_ml.o: $(ARBHOME)/INCLUDE/attributes.h
58ST_ml.o: $(ARBHOME)/INCLUDE/aw_base.hxx
59ST_ml.o: $(ARBHOME)/INCLUDE/aw_color_groups.hxx
60ST_ml.o: $(ARBHOME)/INCLUDE/cb.h
61ST_ml.o: $(ARBHOME)/INCLUDE/cb_base.h
62ST_ml.o: $(ARBHOME)/INCLUDE/cbtypes.h
63ST_ml.o: $(ARBHOME)/INCLUDE/ColumnStat.hxx
64ST_ml.o: $(ARBHOME)/INCLUDE/cxxforward.h
65ST_ml.o: $(ARBHOME)/INCLUDE/downcast.h
66ST_ml.o: $(ARBHOME)/INCLUDE/dupstr.h
67ST_ml.o: $(ARBHOME)/INCLUDE/gccver.h
68ST_ml.o: $(ARBHOME)/INCLUDE/gui_aliview.hxx
69ST_ml.o: $(ARBHOME)/INCLUDE/RootedTree.h
70ST_ml.o: $(ARBHOME)/INCLUDE/smartptr.h
71ST_ml.o: $(ARBHOME)/INCLUDE/static_assert.h
72ST_ml.o: $(ARBHOME)/INCLUDE/test_global.h
73ST_ml.o: $(ARBHOME)/INCLUDE/ttypes.h
74
75ST_quality.o: MostLikelySeq.hxx
76ST_quality.o: st_ml.hxx
77ST_quality.o: st_quality.hxx
78ST_quality.o: st_window.hxx
79ST_quality.o: $(ARBHOME)/INCLUDE/ad_prot.h
80ST_quality.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
81ST_quality.o: $(ARBHOME)/INCLUDE/AliView.hxx
82ST_quality.o: $(ARBHOME)/INCLUDE/AP_filter.hxx
83ST_quality.o: $(ARBHOME)/INCLUDE/AP_sequence.hxx
84ST_quality.o: $(ARBHOME)/INCLUDE/arb_assert.h
85ST_quality.o: $(ARBHOME)/INCLUDE/arb_core.h
86ST_quality.o: $(ARBHOME)/INCLUDE/arb_error.h
87ST_quality.o: $(ARBHOME)/INCLUDE/arb_msg.h
88ST_quality.o: $(ARBHOME)/INCLUDE/arb_progress.h
89ST_quality.o: $(ARBHOME)/INCLUDE/arb_strbuf.h
90ST_quality.o: $(ARBHOME)/INCLUDE/arb_string.h
91ST_quality.o: $(ARBHOME)/INCLUDE/arbdb.h
92ST_quality.o: $(ARBHOME)/INCLUDE/arbdb_base.h
93ST_quality.o: $(ARBHOME)/INCLUDE/arbdbt.h
94ST_quality.o: $(ARBHOME)/INCLUDE/arbtools.h
95ST_quality.o: $(ARBHOME)/INCLUDE/attributes.h
96ST_quality.o: $(ARBHOME)/INCLUDE/aw_base.hxx
97ST_quality.o: $(ARBHOME)/INCLUDE/aw_keysym.hxx
98ST_quality.o: $(ARBHOME)/INCLUDE/aw_window.hxx
99ST_quality.o: $(ARBHOME)/INCLUDE/BI_helix.hxx
100ST_quality.o: $(ARBHOME)/INCLUDE/cb.h
101ST_quality.o: $(ARBHOME)/INCLUDE/cb_base.h
102ST_quality.o: $(ARBHOME)/INCLUDE/cbtypes.h
103ST_quality.o: $(ARBHOME)/INCLUDE/ColumnStat.hxx
104ST_quality.o: $(ARBHOME)/INCLUDE/cxxforward.h
105ST_quality.o: $(ARBHOME)/INCLUDE/downcast.h
106ST_quality.o: $(ARBHOME)/INCLUDE/dupstr.h
107ST_quality.o: $(ARBHOME)/INCLUDE/gccver.h
108ST_quality.o: $(ARBHOME)/INCLUDE/smartptr.h
109ST_quality.o: $(ARBHOME)/INCLUDE/static_assert.h
110ST_quality.o: $(ARBHOME)/INCLUDE/test_global.h
111ST_quality.o: $(ARBHOME)/INCLUDE/ttypes.h
112
113ST_window.o: st_ml.hxx
114ST_window.o: st_quality.hxx
115ST_window.o: st_window.hxx
116ST_window.o: $(ARBHOME)/INCLUDE/ad_prot.h
117ST_window.o: $(ARBHOME)/INCLUDE/arb_assert.h
118ST_window.o: $(ARBHOME)/INCLUDE/arb_core.h
119ST_window.o: $(ARBHOME)/INCLUDE/arb_error.h
120ST_window.o: $(ARBHOME)/INCLUDE/arb_msg.h
121ST_window.o: $(ARBHOME)/INCLUDE/arb_string.h
122ST_window.o: $(ARBHOME)/INCLUDE/arbdb.h
123ST_window.o: $(ARBHOME)/INCLUDE/arbdb_base.h
124ST_window.o: $(ARBHOME)/INCLUDE/arbtools.h
125ST_window.o: $(ARBHOME)/INCLUDE/attributes.h
126ST_window.o: $(ARBHOME)/INCLUDE/aw_awar.hxx
127ST_window.o: $(ARBHOME)/INCLUDE/aw_awar_defs.hxx
128ST_window.o: $(ARBHOME)/INCLUDE/aw_awars.hxx
129ST_window.o: $(ARBHOME)/INCLUDE/aw_base.hxx
130ST_window.o: $(ARBHOME)/INCLUDE/aw_keysym.hxx
131ST_window.o: $(ARBHOME)/INCLUDE/aw_msg.hxx
132ST_window.o: $(ARBHOME)/INCLUDE/aw_root.hxx
133ST_window.o: $(ARBHOME)/INCLUDE/aw_scalar.hxx
134ST_window.o: $(ARBHOME)/INCLUDE/aw_select.hxx
135ST_window.o: $(ARBHOME)/INCLUDE/aw_window.hxx
136ST_window.o: $(ARBHOME)/INCLUDE/awt_filter.hxx
137ST_window.o: $(ARBHOME)/INCLUDE/cb.h
138ST_window.o: $(ARBHOME)/INCLUDE/cb_base.h
139ST_window.o: $(ARBHOME)/INCLUDE/cbtypes.h
140ST_window.o: $(ARBHOME)/INCLUDE/ColumnStat.hxx
141ST_window.o: $(ARBHOME)/INCLUDE/cxxforward.h
142ST_window.o: $(ARBHOME)/INCLUDE/dupstr.h
143ST_window.o: $(ARBHOME)/INCLUDE/gccver.h
144ST_window.o: $(ARBHOME)/INCLUDE/gui_aliview.hxx
145ST_window.o: $(ARBHOME)/INCLUDE/item_sel_list.h
146ST_window.o: $(ARBHOME)/INCLUDE/items.h
147ST_window.o: $(ARBHOME)/INCLUDE/smartptr.h
148ST_window.o: $(ARBHOME)/INCLUDE/static_assert.h
149ST_window.o: $(ARBHOME)/INCLUDE/test_global.h
150ST_window.o: $(ARBHOME)/INCLUDE/ttypes.h
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