source: tags/arb-6.0/PROBE_DESIGN/Makefile

Last change on this file was 11401, checked in by westram, 10 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: 7.4 KB
Line 
1# for variables passed from parent makefile see ../SOURCE_TOOLS/parent_make.txt
2.SUFFIXES: .o .cxx .depend
3CPP_OBJECTS = probe_design.o SaiProbeVisualization.o probe_match_parser.o
4$(MAIN): $(CPP_OBJECTS)
5        $(LINK_STATIC_LIB) $(MAIN) $(CPP_OBJECTS)
6.cxx.o:
7        $(A_CXX) $(cflags) $(cxxflags) -c -o $@ $(@:.o=.cxx)  $(CXX_INCLUDES) $(POST_COMPILE)
8
9clean:
10        rm -f $(CPP_OBJECTS) *.a
11
12DEPENDS = $(CPP_OBJECTS:.o=.depend)
13depends: $(DEPENDS)
14        @cat $(DEPENDS) | grep -v '^#' >>Makefile
15        @rm $(DEPENDS)
16$(DEPENDS): depend.init
17depend.init:
18        $(MAKEDEPEND) $(MAKEDEPENDFLAGS) 2>/dev/null # remove dependencies
19.c.depend:
20        $(MAKEDEPEND) -f- $(MAKEDEPENDFLAGS) $< 2>/dev/null >$@
21.cxx.depend:
22        $(MAKEDEPEND) -f- $(MAKEDEPENDFLAGS) $< 2>/dev/null >$@
23
24# DO NOT DELETE THIS LINE -- make depend depends on it.
25
26# Do not add dependencies manually - use 'make depend' in $ARBHOME
27# For formatting issues see SOURCE_TOOLS/fix_depends.pl (from main)
28
29probe_design.o: probe_design.hxx
30probe_design.o: probe_match_parser.hxx
31probe_design.o: SaiProbeVisualization.hxx
32probe_design.o: $(ARBHOME)/INCLUDE/ad_prot.h
33probe_design.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
34probe_design.o: $(ARBHOME)/INCLUDE/adGene.h
35probe_design.o: $(ARBHOME)/INCLUDE/aisc_global.h
36probe_design.o: $(ARBHOME)/INCLUDE/AliView.hxx
37probe_design.o: $(ARBHOME)/INCLUDE/AP_sequence.hxx
38probe_design.o: $(ARBHOME)/INCLUDE/AP_Tree.hxx
39probe_design.o: $(ARBHOME)/INCLUDE/arb_assert.h
40probe_design.o: $(ARBHOME)/INCLUDE/arb_core.h
41probe_design.o: $(ARBHOME)/INCLUDE/arb_error.h
42probe_design.o: $(ARBHOME)/INCLUDE/arb_file.h
43probe_design.o: $(ARBHOME)/INCLUDE/arb_msg.h
44probe_design.o: $(ARBHOME)/INCLUDE/arb_progress.h
45probe_design.o: $(ARBHOME)/INCLUDE/arb_strarray.h
46probe_design.o: $(ARBHOME)/INCLUDE/arb_strbuf.h
47probe_design.o: $(ARBHOME)/INCLUDE/arb_string.h
48probe_design.o: $(ARBHOME)/INCLUDE/ARB_Tree.hxx
49probe_design.o: $(ARBHOME)/INCLUDE/arbdb.h
50probe_design.o: $(ARBHOME)/INCLUDE/arbdb_base.h
51probe_design.o: $(ARBHOME)/INCLUDE/arbdbt.h
52probe_design.o: $(ARBHOME)/INCLUDE/arbtools.h
53probe_design.o: $(ARBHOME)/INCLUDE/attributes.h
54probe_design.o: $(ARBHOME)/INCLUDE/aw_awar.hxx
55probe_design.o: $(ARBHOME)/INCLUDE/aw_awar_defs.hxx
56probe_design.o: $(ARBHOME)/INCLUDE/aw_awars.hxx
57probe_design.o: $(ARBHOME)/INCLUDE/aw_base.hxx
58probe_design.o: $(ARBHOME)/INCLUDE/aw_color_groups.hxx
59probe_design.o: $(ARBHOME)/INCLUDE/aw_device.hxx
60probe_design.o: $(ARBHOME)/INCLUDE/aw_device_click.hxx
61probe_design.o: $(ARBHOME)/INCLUDE/aw_edit.hxx
62probe_design.o: $(ARBHOME)/INCLUDE/aw_keysym.hxx
63probe_design.o: $(ARBHOME)/INCLUDE/aw_msg.hxx
64probe_design.o: $(ARBHOME)/INCLUDE/aw_position.hxx
65probe_design.o: $(ARBHOME)/INCLUDE/aw_preset.hxx
66probe_design.o: $(ARBHOME)/INCLUDE/aw_question.hxx
67probe_design.o: $(ARBHOME)/INCLUDE/aw_root.hxx
68probe_design.o: $(ARBHOME)/INCLUDE/aw_scalar.hxx
69probe_design.o: $(ARBHOME)/INCLUDE/aw_select.hxx
70probe_design.o: $(ARBHOME)/INCLUDE/aw_window.hxx
71probe_design.o: $(ARBHOME)/INCLUDE/awt_canvas.hxx
72probe_design.o: $(ARBHOME)/INCLUDE/awt_config_manager.hxx
73probe_design.o: $(ARBHOME)/INCLUDE/awt_sel_boxes.hxx
74probe_design.o: $(ARBHOME)/INCLUDE/bytestring.h
75probe_design.o: $(ARBHOME)/INCLUDE/cb.h
76probe_design.o: $(ARBHOME)/INCLUDE/cb_base.h
77probe_design.o: $(ARBHOME)/INCLUDE/cbtypes.h
78probe_design.o: $(ARBHOME)/INCLUDE/client.h
79probe_design.o: $(ARBHOME)/INCLUDE/client_types.h
80probe_design.o: $(ARBHOME)/INCLUDE/cxxforward.h
81probe_design.o: $(ARBHOME)/INCLUDE/downcast.h
82probe_design.o: $(ARBHOME)/INCLUDE/dupstr.h
83probe_design.o: $(ARBHOME)/INCLUDE/gccver.h
84probe_design.o: $(ARBHOME)/INCLUDE/GEN.hxx
85probe_design.o: $(ARBHOME)/INCLUDE/items.h
86probe_design.o: $(ARBHOME)/INCLUDE/iupac.h
87probe_design.o: $(ARBHOME)/INCLUDE/PT_com.h
88probe_design.o: $(ARBHOME)/INCLUDE/PT_server.h
89probe_design.o: $(ARBHOME)/INCLUDE/RootedTree.h
90probe_design.o: $(ARBHOME)/INCLUDE/servercntrl.h
91probe_design.o: $(ARBHOME)/INCLUDE/smartptr.h
92probe_design.o: $(ARBHOME)/INCLUDE/static_assert.h
93probe_design.o: $(ARBHOME)/INCLUDE/test_global.h
94probe_design.o: $(ARBHOME)/INCLUDE/TreeCallbacks.hxx
95probe_design.o: $(ARBHOME)/INCLUDE/TreeDisplay.hxx
96probe_design.o: $(ARBHOME)/INCLUDE/ttypes.h
97
98probe_match_parser.o: probe_match_parser.hxx
99probe_match_parser.o: $(ARBHOME)/INCLUDE/ad_prot.h
100probe_match_parser.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
101probe_match_parser.o: $(ARBHOME)/INCLUDE/arb_assert.h
102probe_match_parser.o: $(ARBHOME)/INCLUDE/arb_core.h
103probe_match_parser.o: $(ARBHOME)/INCLUDE/arb_defs.h
104probe_match_parser.o: $(ARBHOME)/INCLUDE/arb_error.h
105probe_match_parser.o: $(ARBHOME)/INCLUDE/arb_msg.h
106probe_match_parser.o: $(ARBHOME)/INCLUDE/arb_string.h
107probe_match_parser.o: $(ARBHOME)/INCLUDE/arbdb.h
108probe_match_parser.o: $(ARBHOME)/INCLUDE/arbdb_base.h
109probe_match_parser.o: $(ARBHOME)/INCLUDE/arbdbt.h
110probe_match_parser.o: $(ARBHOME)/INCLUDE/arbtools.h
111probe_match_parser.o: $(ARBHOME)/INCLUDE/attributes.h
112probe_match_parser.o: $(ARBHOME)/INCLUDE/cxxforward.h
113probe_match_parser.o: $(ARBHOME)/INCLUDE/downcast.h
114probe_match_parser.o: $(ARBHOME)/INCLUDE/dupstr.h
115probe_match_parser.o: $(ARBHOME)/INCLUDE/gccver.h
116probe_match_parser.o: $(ARBHOME)/INCLUDE/smartptr.h
117probe_match_parser.o: $(ARBHOME)/INCLUDE/static_assert.h
118probe_match_parser.o: $(ARBHOME)/INCLUDE/test_global.h
119
120SaiProbeVisualization.o: probe_match_parser.hxx
121SaiProbeVisualization.o: SaiProbeVisualization.hxx
122SaiProbeVisualization.o: $(ARBHOME)/INCLUDE/ad_prot.h
123SaiProbeVisualization.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
124SaiProbeVisualization.o: $(ARBHOME)/INCLUDE/arb_assert.h
125SaiProbeVisualization.o: $(ARBHOME)/INCLUDE/arb_core.h
126SaiProbeVisualization.o: $(ARBHOME)/INCLUDE/arb_error.h
127SaiProbeVisualization.o: $(ARBHOME)/INCLUDE/arb_msg.h
128SaiProbeVisualization.o: $(ARBHOME)/INCLUDE/arb_string.h
129SaiProbeVisualization.o: $(ARBHOME)/INCLUDE/arbdb.h
130SaiProbeVisualization.o: $(ARBHOME)/INCLUDE/arbdb_base.h
131SaiProbeVisualization.o: $(ARBHOME)/INCLUDE/arbdbt.h
132SaiProbeVisualization.o: $(ARBHOME)/INCLUDE/arbtools.h
133SaiProbeVisualization.o: $(ARBHOME)/INCLUDE/attributes.h
134SaiProbeVisualization.o: $(ARBHOME)/INCLUDE/aw_awar.hxx
135SaiProbeVisualization.o: $(ARBHOME)/INCLUDE/aw_awar_defs.hxx
136SaiProbeVisualization.o: $(ARBHOME)/INCLUDE/aw_awars.hxx
137SaiProbeVisualization.o: $(ARBHOME)/INCLUDE/aw_base.hxx
138SaiProbeVisualization.o: $(ARBHOME)/INCLUDE/aw_device.hxx
139SaiProbeVisualization.o: $(ARBHOME)/INCLUDE/aw_device_click.hxx
140SaiProbeVisualization.o: $(ARBHOME)/INCLUDE/aw_keysym.hxx
141SaiProbeVisualization.o: $(ARBHOME)/INCLUDE/aw_msg.hxx
142SaiProbeVisualization.o: $(ARBHOME)/INCLUDE/aw_position.hxx
143SaiProbeVisualization.o: $(ARBHOME)/INCLUDE/aw_preset.hxx
144SaiProbeVisualization.o: $(ARBHOME)/INCLUDE/aw_root.hxx
145SaiProbeVisualization.o: $(ARBHOME)/INCLUDE/aw_window.hxx
146SaiProbeVisualization.o: $(ARBHOME)/INCLUDE/awt_canvas.hxx
147SaiProbeVisualization.o: $(ARBHOME)/INCLUDE/awt_config_manager.hxx
148SaiProbeVisualization.o: $(ARBHOME)/INCLUDE/awt_sel_boxes.hxx
149SaiProbeVisualization.o: $(ARBHOME)/INCLUDE/cb.h
150SaiProbeVisualization.o: $(ARBHOME)/INCLUDE/cb_base.h
151SaiProbeVisualization.o: $(ARBHOME)/INCLUDE/cbtypes.h
152SaiProbeVisualization.o: $(ARBHOME)/INCLUDE/cxxforward.h
153SaiProbeVisualization.o: $(ARBHOME)/INCLUDE/downcast.h
154SaiProbeVisualization.o: $(ARBHOME)/INCLUDE/dupstr.h
155SaiProbeVisualization.o: $(ARBHOME)/INCLUDE/gccver.h
156SaiProbeVisualization.o: $(ARBHOME)/INCLUDE/items.h
157SaiProbeVisualization.o: $(ARBHOME)/INCLUDE/nds.h
158SaiProbeVisualization.o: $(ARBHOME)/INCLUDE/smartptr.h
159SaiProbeVisualization.o: $(ARBHOME)/INCLUDE/static_assert.h
160SaiProbeVisualization.o: $(ARBHOME)/INCLUDE/test_global.h
161SaiProbeVisualization.o: $(ARBHOME)/INCLUDE/ttypes.h
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