ARB
ARB_Tree.hxx
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1 // =============================================================== //
2 // //
3 // File : ARB_Tree.hxx //
4 // Purpose : Tree types with sequence knowledge //
5 // //
6 // Coded by Ralf Westram (coder@reallysoft.de) in October 2009 //
7 // Institute of Microbiology (Technical University Munich) //
8 // http://www.arb-home.de/ //
9 // //
10 // =============================================================== //
11 
12 #ifndef ARB_TREE_HXX
13 #define ARB_TREE_HXX
14 
15 #ifndef ALIVIEW_HXX
16 #include <AliView.hxx>
17 #endif
18 #ifndef DOWNCAST_H
19 #include <downcast.h>
20 #endif
21 #ifndef TREENODE_H
22 #include <TreeNode.h>
23 #endif
24 #ifndef AP_SEQUENCE_HXX
25 #include <AP_sequence.hxx>
26 #endif
27 
28 
29 #define at_assert(cond) arb_assert(cond)
30 
31 typedef void (*ARB_tree_node_del_cb)(GBDATA*, class ARB_seqtree*);
32 
33 class ARB_seqtree_root;
34 class ARB_seqtree;
35 class ARB_edge;
36 class AP_weights;
37 class AliView;
38 
39 #ifdef GCC_TOO_SMART_FOR_USEFUL_FINAL_TYPE_SUGGESTION
40 # pragma GCC diagnostic push
41 # pragma GCC diagnostic ignored "-Wsuggest-final-types"
42 #endif
43 
44 class ARB_seqtree_root : public TreeRoot { // derived from Noncopyable
45  AliView *ali;
46 
47  AP_sequence *seqTemplate;
48 
49  // following variables are set, if the tree has been loaded from DB
50  char *tree_name; // name of the tree in DB
51  GBDATA *gb_tree; // tree container in DB
52 
53  bool isLinkedToDB;
54  bool addDeleteCallbacks;
55 
56 protected:
57  void set_gb_tree(GBDATA *gbTree) {
58  at_assert(implicated(gb_tree, gb_tree == gbTree));
59  at_assert(tree_name);
60  gb_tree = gbTree;
61  }
62  void set_gb_tree_and_name(GBDATA *gbTree, const char *name) {
63  at_assert(!gb_tree);
64  at_assert(!tree_name);
65  gb_tree = gbTree;
66  tree_name = ARB_strdup(name);
67  }
68 
69 public:
70  ARB_seqtree_root(AliView *aliView, AP_sequence *seqTempl, bool add_delete_callbacks);
72 
74 
75  const AliView *get_aliview() const { return ali; }
76 
77  const AP_filter *get_filter() const { return ali->get_filter(); }
78  const AP_weights *get_weights() const { return ali->get_weights(); }
79 
80  GBDATA *get_gb_main() const { return ali->get_gb_main(); }
81 
82  GBDATA *get_gb_tree() const { return gb_tree; } // NULp if no tree loaded (or tree disappeared from DB)
83  void tree_deleted_cb(GBDATA *gb_tree_del); // internal
84 
85  const char *get_tree_name() const { return tree_name; } // NULp if no tree loaded (or tree disappeared from DB)
86 
87  virtual GB_ERROR loadFromDB(const char *name) __ATTR__USERESULT;
88  virtual GB_ERROR saveToDB() __ATTR__USERESULT;
89 
90  const AP_sequence *get_seqTemplate() const { return seqTemplate; }
91 
92  GB_ERROR linkToDB(int *zombies, int *duplicates) __ATTR__USERESULT;
93  void unlinkFromDB(); // @@@ is (but should not be) unused
95 };
96 MARK_NONFINAL_CLASS(ARB_seqtree_root); // does not work for too smart gcc|s
97 #ifdef GCC_TOO_SMART_FOR_USEFUL_FINAL_TYPE_SUGGESTION
98 # pragma GCC diagnostic pop
99 #endif
100 
101 MARK_NONFINAL_FUNCTION(ARB_seqtree_root,GB_ERROR,loadFromDB,(const char*),NULp);
103 
105  size_t leafs;
106  size_t innerNodes;
107  size_t groups;
108  size_t unlinked; // unlinked leafs (same as 'leafs' if tree is unlinked)
109  size_t marked; // leafs linked to marked species
110  // size_t with_sequence; // @@@ add when AP_sequence is member of ARB_seqtree
111 
112  ARB_tree_info();
113 
114  size_t nodes() const { return innerNodes+leafs; }
115  size_t linked() const { return leafs-unlinked; }
116  size_t unmarked() const { return linked()-marked; }
117 };
118 
119 class ARB_seqtree : public TreeNode { // derived from Noncopyable
120  friend GB_ERROR ARB_seqtree_root::loadFromDB(const char *name);
121  friend GB_ERROR ARB_seqtree_root::linkToDB(int *zombies, int *duplicates);
122  friend void ARB_seqtree_root::unlinkFromDB();
123 
124  AP_sequence *seq; /* NULp if tree is unlinked
125  * otherwise automatically valid for leafs with gb_node!
126  * may be set manually for inner nodes
127  */
128 
129  // ------------------
130  // functions
131 
132  void unloadSequences();
133  GB_ERROR preloadLeafSequences();
134 
136  void remove_delete_cb_rec(ARB_tree_node_del_cb cb);
137 
138 protected:
139  AP_sequence *take_seq() { // afterwards not has no seq and caller is responsible for sequence
140  AP_sequence *result = seq;
141  seq = NULp;
142  return result;
143  }
144  void replace_seq(AP_sequence *sequence);
145 
147 
148 public:
150  TreeNode(root),
151  seq(NULp)
152  {}
153 
155 
157 
158  // order in dendogram:
159  bool is_upper_son() const { return is_leftson(); }
160  bool is_lower_son() const { return is_rightson(); }
161 
162  AP_sequence *get_seq() { return seq; }
163  const AP_sequence *get_seq() const { return seq; }
165  at_assert(!seq); // already set
166 #ifndef UNIT_TESTS // UT_DIFF
167  // unit tests are allowed to leave sequence undefined // @@@ better solution?
168  at_assert(sequence);
169 #endif
170  seq = sequence;
171  return seq;
172  }
173 
174  bool hasSequence() const { return seq && seq->hasSequence(); }
175 
176  void mark_subtree();
178 
179 };
180 
181 #define OVERRIDE_SEQ_ACCESSORS(SEQTYPE,BASETREETYPE) \
182  SEQTYPE *get_seq() { return DOWNCAST(SEQTYPE*,BASETREETYPE::get_seq()); } \
183  const SEQTYPE *get_seq() const { return DOWNCAST(const SEQTYPE*,BASETREETYPE::get_seq()); } \
184  SEQTYPE *set_seq(AP_sequence *sequence) { return DOWNCAST(SEQTYPE*, BASETREETYPE::set_seq(sequence)); } \
185 
187  virtual ~ARB_tree_predicate() {}
188  virtual bool selects(const ARB_seqtree& tree) const = 0;
189 };
190 
191 // ------------------------
192 // ARB_countedTree
193 // tree that knows its size
194 
195 class ARB_countedTree : public ARB_seqtree {
196 protected:
198 public:
199  explicit ARB_countedTree(ARB_seqtree_root *tree_root_)
200  : ARB_seqtree(tree_root_)
201  {}
203 
204  // @@@ TODO:
205  // - add debug code (checking init_tree() is called exactly once)
206  // - init_tree() might be called automatically via announce_tree_constructed()
207 
208  virtual void init_tree() = 0; /* impl. shall initialize the tree
209  * (including some kind of leaf counter)
210  * needs to be called manually */
211 
212  void compute_tree() OVERRIDE {} // ARB_countedTree always is informed about its subtrees
213 
214  size_t relative_position_in(const ARB_countedTree *upgroup) const;
215 };
216 
217 
218 
219 #else
220 #error ARB_Tree.hxx included twice
221 #endif // ARB_TREE_HXX
GBDATA * get_gb_main() const
Definition: ARB_Tree.hxx:80
const char * GB_ERROR
Definition: arb_core.h:25
bool is_rightson() const
Definition: TreeNode.h:193
const AliView * get_aliview() const
Definition: ARB_Tree.hxx:75
string result
void compute_tree() OVERRIDE
Definition: ARB_Tree.hxx:212
size_t marked
Definition: ARB_Tree.hxx:109
#define implicated(hypothesis, conclusion)
Definition: arb_assert.h:289
size_t nodes() const
Definition: ARB_Tree.hxx:114
bool is_upper_son() const
Definition: ARB_Tree.hxx:159
bool hasSequence() const
Definition: ARB_Tree.hxx:174
PREPARE_MARK_NONFINAL_CLASS(ARB_seqtree_root)
size_t groups
Definition: ARB_Tree.hxx:107
size_t unlinked
Definition: ARB_Tree.hxx:108
size_t unmarked() const
Definition: ARB_Tree.hxx:116
char * ARB_strdup(const char *str)
Definition: arb_string.h:27
void calcTreeInfo(ARB_tree_info &info)
Definition: ARB_Tree.cxx:163
ARB_seqtree_root(AliView *aliView, AP_sequence *seqTempl, bool add_delete_callbacks)
Definition: ARB_Tree.cxx:28
#define at_assert(cond)
Definition: ARB_Tree.hxx:29
const AP_weights * get_weights() const
Definition: AliView.hxx:45
#define cb(action)
const AP_filter * get_filter() const
Definition: ARB_Tree.hxx:77
size_t leafs
Definition: ARB_Tree.hxx:105
MARK_NONFINAL_FUNCTION(ARB_seqtree_root, GB_ERROR, loadFromDB,(const char *), NULp)
size_t relative_position_in(const ARB_countedTree *upgroup) const
Definition: ARB_Tree.cxx:267
void replace_seq(AP_sequence *sequence)
Definition: ARB_Tree.cxx:256
const char * get_tree_name() const
Definition: ARB_Tree.hxx:85
MARK_NONFINAL_CLASS(ARB_seqtree_root)
GBDATA * get_gb_tree() const
Definition: ARB_Tree.hxx:82
DEFINE_TREE_ACCESSORS(ARB_seqtree_root, ARB_seqtree)
const AP_weights * get_weights() const
Definition: ARB_Tree.hxx:78
virtual GB_ERROR saveToDB() __ATTR__USERESULT
Definition: ARB_Tree.cxx:107
bool is_leftson() const
Definition: TreeNode.h:188
virtual bool selects(const ARB_seqtree &tree) const =0
virtual GB_ERROR loadFromDB(const char *name) __ATTR__USERESULT
Definition: ARB_Tree.cxx:66
bool hasSequence() const
Definition: AP_sequence.hxx:75
~ARB_seqtree() OVERRIDE
Definition: ARB_Tree.cxx:184
void unlinkFromDB()
Definition: ARB_Tree.cxx:147
size_t innerNodes
Definition: ARB_Tree.hxx:106
DEFINE_TREE_ACCESSORS(ARB_seqtree_root, ARB_countedTree)
AP_sequence * get_seq()
Definition: ARB_Tree.hxx:162
const AP_sequence * get_seq() const
Definition: ARB_Tree.hxx:163
AP_sequence * set_seq(AP_sequence *sequence)
Definition: ARB_Tree.hxx:164
ARB_countedTree(ARB_seqtree_root *tree_root_)
Definition: ARB_Tree.hxx:199
const AP_filter * get_filter() const
Definition: AliView.hxx:42
DEFINE_TREE_ROOT_ACCESSORS(ARB_seqtree_root, ARB_seqtree)
~ARB_seqtree_root() OVERRIDE
Definition: ARB_Tree.cxx:49
~ARB_countedTree() OVERRIDE
Definition: ARB_Tree.hxx:197
virtual ~ARB_tree_predicate()
Definition: ARB_Tree.hxx:187
virtual void init_tree()=0
AP_sequence * take_seq()
Definition: ARB_Tree.hxx:139
GB_ERROR linkToDB(int *zombies, int *duplicates) __ATTR__USERESULT
Definition: ARB_Tree.cxx:130
#define OVERRIDE
Definition: cxxforward.h:93
#define __ATTR__USERESULT
Definition: attributes.h:58
char * name
Definition: TreeNode.h:134
bool contains_marked_species()
Definition: ARB_Tree.cxx:198
#define NULp
Definition: cxxforward.h:97
size_t linked() const
Definition: ARB_Tree.hxx:115
void(* ARB_tree_node_del_cb)(GBDATA *, class ARB_seqtree *)
Definition: ARB_Tree.hxx:31
void set_gb_tree_and_name(GBDATA *gbTree, const char *name)
Definition: ARB_Tree.hxx:62
const AP_sequence * get_seqTemplate() const
Definition: ARB_Tree.hxx:90
void mark_subtree()
Definition: ARB_Tree.cxx:188
static int info[maxsites+1]
bool is_lower_son() const
Definition: ARB_Tree.hxx:160
GBDATA * get_gb_main() const
Definition: AliView.hxx:46
void set_gb_tree(GBDATA *gbTree)
Definition: ARB_Tree.hxx:57
void tree_deleted_cb(GBDATA *gb_tree_del)
Definition: ARB_Tree.cxx:57