// =============================================================== // // // // File : ARB_Tree.hxx // // Purpose : Tree types with sequence knowledge // // // // Coded by Ralf Westram (coder@reallysoft.de) in October 2009 // // Institute of Microbiology (Technical University Munich) // // http://www.arb-home.de/ // // // // =============================================================== // #ifndef ARB_TREE_HXX #define ARB_TREE_HXX #ifndef ALIVIEW_HXX #include #endif #ifndef DOWNCAST_H #include #endif #ifndef TREENODE_H #include #endif #ifndef AP_SEQUENCE_HXX #include #endif #define at_assert(cond) arb_assert(cond) typedef void (*ARB_tree_node_del_cb)(GBDATA*, class ARB_seqtree*); class ARB_seqtree_root; class ARB_seqtree; class ARB_edge; class AP_weights; class AliView; #ifdef GCC_TOO_SMART_FOR_USEFUL_FINAL_TYPE_SUGGESTION # pragma GCC diagnostic push # pragma GCC diagnostic ignored "-Wsuggest-final-types" #endif class ARB_seqtree_root : public TreeRoot { // derived from Noncopyable AliView *ali; AP_sequence *seqTemplate; // following variables are set, if the tree has been loaded from DB char *tree_name; // name of the tree in DB GBDATA *gb_tree; // tree container in DB bool isLinkedToDB; bool addDeleteCallbacks; protected: void set_gb_tree(GBDATA *gbTree) { at_assert(implicated(gb_tree, gb_tree == gbTree)); at_assert(tree_name); gb_tree = gbTree; } void set_gb_tree_and_name(GBDATA *gbTree, const char *name) { at_assert(!gb_tree); at_assert(!tree_name); gb_tree = gbTree; tree_name = ARB_strdup(name); } public: ARB_seqtree_root(AliView *aliView, AP_sequence *seqTempl, bool add_delete_callbacks); ~ARB_seqtree_root() OVERRIDE; DEFINE_TREE_ROOT_ACCESSORS(ARB_seqtree_root, ARB_seqtree); const AliView *get_aliview() const { return ali; } const AP_filter *get_filter() const { return ali->get_filter(); } const AP_weights *get_weights() const { return ali->get_weights(); } GBDATA *get_gb_main() const { return ali->get_gb_main(); } GBDATA *get_gb_tree() const { return gb_tree; } // NULp if no tree loaded (or tree disappeared from DB) void tree_deleted_cb(GBDATA *gb_tree_del); // internal const char *get_tree_name() const { return tree_name; } // NULp if no tree loaded (or tree disappeared from DB) virtual GB_ERROR loadFromDB(const char *name) __ATTR__USERESULT; virtual GB_ERROR saveToDB() __ATTR__USERESULT; const AP_sequence *get_seqTemplate() const { return seqTemplate; } GB_ERROR linkToDB(int *zombies, int *duplicates) __ATTR__USERESULT; void unlinkFromDB(); // @@@ is (but should not be) unused PREPARE_MARK_NONFINAL_CLASS(ARB_seqtree_root); }; MARK_NONFINAL_CLASS(ARB_seqtree_root); // does not work for too smart gcc|s #ifdef GCC_TOO_SMART_FOR_USEFUL_FINAL_TYPE_SUGGESTION # pragma GCC diagnostic pop #endif MARK_NONFINAL_FUNCTION(ARB_seqtree_root,GB_ERROR,loadFromDB,(const char*),NULp); MARK_NONFINAL_FUNCTION(ARB_seqtree_root,GB_ERROR,saveToDB,(),NULp); struct ARB_tree_info { size_t leafs; size_t innerNodes; size_t groups; size_t unlinked; // unlinked leafs (same as 'leafs' if tree is unlinked) size_t marked; // leafs linked to marked species // size_t with_sequence; // @@@ add when AP_sequence is member of ARB_seqtree ARB_tree_info(); size_t nodes() const { return innerNodes+leafs; } size_t linked() const { return leafs-unlinked; } size_t unmarked() const { return linked()-marked; } }; class ARB_seqtree : public TreeNode { // derived from Noncopyable friend GB_ERROR ARB_seqtree_root::loadFromDB(const char *name); friend GB_ERROR ARB_seqtree_root::linkToDB(int *zombies, int *duplicates); friend void ARB_seqtree_root::unlinkFromDB(); AP_sequence *seq; /* NULp if tree is unlinked * otherwise automatically valid for leafs with gb_node! * may be set manually for inner nodes */ // ------------------ // functions void unloadSequences(); GB_ERROR preloadLeafSequences(); GB_ERROR add_delete_cb_rec(ARB_tree_node_del_cb cb) __ATTR__USERESULT; void remove_delete_cb_rec(ARB_tree_node_del_cb cb); protected: AP_sequence *take_seq() { // afterwards not has no seq and caller is responsible for sequence AP_sequence *result = seq; seq = NULp; return result; } void replace_seq(AP_sequence *sequence); ~ARB_seqtree() OVERRIDE; public: ARB_seqtree(ARB_seqtree_root *root) : TreeNode(root), seq(NULp) {} DEFINE_TREE_ACCESSORS(ARB_seqtree_root, ARB_seqtree); void calcTreeInfo(ARB_tree_info& info); // order in dendogram: bool is_upper_son() const { return is_leftson(); } bool is_lower_son() const { return is_rightson(); } AP_sequence *get_seq() { return seq; } const AP_sequence *get_seq() const { return seq; } AP_sequence *set_seq(AP_sequence *sequence) { at_assert(!seq); // already set #ifndef UNIT_TESTS // UT_DIFF // unit tests are allowed to leave sequence undefined // @@@ better solution? at_assert(sequence); #endif seq = sequence; return seq; } bool hasSequence() const { return seq && seq->hasSequence(); } void mark_subtree(); bool contains_marked_species(); }; #define OVERRIDE_SEQ_ACCESSORS(SEQTYPE,BASETREETYPE) \ SEQTYPE *get_seq() { return DOWNCAST(SEQTYPE*,BASETREETYPE::get_seq()); } \ const SEQTYPE *get_seq() const { return DOWNCAST(const SEQTYPE*,BASETREETYPE::get_seq()); } \ SEQTYPE *set_seq(AP_sequence *sequence) { return DOWNCAST(SEQTYPE*, BASETREETYPE::set_seq(sequence)); } \ struct ARB_tree_predicate { virtual ~ARB_tree_predicate() {} virtual bool selects(const ARB_seqtree& tree) const = 0; }; // ------------------------ // ARB_countedTree // tree that knows its size class ARB_countedTree : public ARB_seqtree { protected: ~ARB_countedTree() OVERRIDE {} public: explicit ARB_countedTree(ARB_seqtree_root *tree_root_) : ARB_seqtree(tree_root_) {} DEFINE_TREE_ACCESSORS(ARB_seqtree_root, ARB_countedTree); // @@@ TODO: // - add debug code (checking init_tree() is called exactly once) // - init_tree() might be called automatically via announce_tree_constructed() virtual void init_tree() = 0; /* impl. shall initialize the tree * (including some kind of leaf counter) * needs to be called manually */ void compute_tree() OVERRIDE {} // ARB_countedTree always is informed about its subtrees size_t relative_position_in(const ARB_countedTree *upgroup) const; }; #else #error ARB_Tree.hxx included twice #endif // ARB_TREE_HXX