source: branches/profile/SL/AP_TREE/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: 2.4 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 = AP_Tree.o
7OBJECTS=$(C_OBJECTS) $(CPP_OBJECTS)
8
9$(MAIN): $(OBJECTS)
10        $(LINK_STATIC_LIB) $(MAIN) $(OBJECTS)
11
12.cxx.o:
13        $(A_CXX) $(cflags) $(cxxflags) -c $< $(CXX_INCLUDES) $(POST_COMPILE)
14
15.c.o:
16        $(A_CC) $(cflags) -c $< $(CC_INCLUDES) $(POST_COMPILE)
17
18clean:
19        rm -f $(OBJECTS) *.a
20
21DEPENDS = $(OBJECTS:.o=.depend)
22depends: $(DEPENDS)
23        @cat $(DEPENDS) | grep -v '^#' >>Makefile
24        @rm $(DEPENDS)
25$(DEPENDS): depend.init
26depend.init:
27        $(MAKEDEPEND) $(MAKEDEPENDFLAGS) 2>/dev/null # remove dependencies
28.c.depend:
29        $(MAKEDEPEND) -f- $(MAKEDEPENDFLAGS) $< 2>/dev/null >$@
30.cxx.depend:
31        $(MAKEDEPEND) -f- $(MAKEDEPENDFLAGS) $< 2>/dev/null >$@
32
33# DO NOT DELETE
34
35# Do not add dependencies manually - use 'make depend' in $ARBHOME
36# For formatting issues see SOURCE_TOOLS/fix_depends.pl (from SL)
37
38AP_Tree.o: AP_Tree.hxx
39AP_Tree.o: $(ARBHOME)/INCLUDE/ad_cb.h
40AP_Tree.o: $(ARBHOME)/INCLUDE/ad_cb_prot.h
41AP_Tree.o: $(ARBHOME)/INCLUDE/ad_prot.h
42AP_Tree.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
43AP_Tree.o: $(ARBHOME)/INCLUDE/AliView.hxx
44AP_Tree.o: $(ARBHOME)/INCLUDE/AP_filter.hxx
45AP_Tree.o: $(ARBHOME)/INCLUDE/AP_sequence.hxx
46AP_Tree.o: $(ARBHOME)/INCLUDE/arb_assert.h
47AP_Tree.o: $(ARBHOME)/INCLUDE/arb_core.h
48AP_Tree.o: $(ARBHOME)/INCLUDE/arb_error.h
49AP_Tree.o: $(ARBHOME)/INCLUDE/arb_msg.h
50AP_Tree.o: $(ARBHOME)/INCLUDE/arb_progress.h
51AP_Tree.o: $(ARBHOME)/INCLUDE/arb_string.h
52AP_Tree.o: $(ARBHOME)/INCLUDE/ARB_Tree.hxx
53AP_Tree.o: $(ARBHOME)/INCLUDE/arbdb.h
54AP_Tree.o: $(ARBHOME)/INCLUDE/arbdb_base.h
55AP_Tree.o: $(ARBHOME)/INCLUDE/arbdbt.h
56AP_Tree.o: $(ARBHOME)/INCLUDE/arbtools.h
57AP_Tree.o: $(ARBHOME)/INCLUDE/attributes.h
58AP_Tree.o: $(ARBHOME)/INCLUDE/aw_base.hxx
59AP_Tree.o: $(ARBHOME)/INCLUDE/aw_color_groups.hxx
60AP_Tree.o: $(ARBHOME)/INCLUDE/aw_msg.hxx
61AP_Tree.o: $(ARBHOME)/INCLUDE/awt_attributes.hxx
62AP_Tree.o: $(ARBHOME)/INCLUDE/cb.h
63AP_Tree.o: $(ARBHOME)/INCLUDE/cb_base.h
64AP_Tree.o: $(ARBHOME)/INCLUDE/cbtypes.h
65AP_Tree.o: $(ARBHOME)/INCLUDE/cxxforward.h
66AP_Tree.o: $(ARBHOME)/INCLUDE/downcast.h
67AP_Tree.o: $(ARBHOME)/INCLUDE/dupstr.h
68AP_Tree.o: $(ARBHOME)/INCLUDE/gccver.h
69AP_Tree.o: $(ARBHOME)/INCLUDE/RootedTree.h
70AP_Tree.o: $(ARBHOME)/INCLUDE/smartptr.h
71AP_Tree.o: $(ARBHOME)/INCLUDE/static_assert.h
72AP_Tree.o: $(ARBHOME)/INCLUDE/test_global.h
73AP_Tree.o: $(ARBHOME)/INCLUDE/ttypes.h
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