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Classes | |
| class | TreeRoot |
| struct | TreeNode |
| struct | TreeNode::multifurc_limits |
| struct | SimpleRoot |
| class | FINAL_TYPE< SEQTYPE > |
| xml element More... | |
| class | ARB_edge |
Macros | |
| #define | rt_assert(cond) arb_assert(cond) |
| #define | DEFINE_READ_ACCESSORS(TYPE, ACCESS, MEMBER) |
| #define | KEELED_INDICATOR '!' |
| #define | DEFINE_TREE_ROOT_ACCESSORS(RootType, TreeType) DEFINE_DOWNCAST_ACCESSORS(TreeType, get_root_node, TreeRoot::get_root_node()) |
| #define | DEFINE_TREE_RELATIVES_ACCESSORS(TreeType) |
| #define | DEFINE_TREE_ACCESSORS(RootType, TreeType) |
| #define | ASSERT_VALID_TREE(tree) |
| #define | ASSERT_VALID_TREE_OR_NULL(tree) |
| #define | TEST_EXPECT_VALID_TREE(tree) |
| #define | TEST_EXPECT_VALID_TREE_OR_NULL(tree) |
| #define | TEST_EXPECT_VALID_TREE__BROKEN(tree) |
| #define | TEST_EXPECT_VALID_TREE_OR_NULL__BROKEN(tree) |
Enumerations | |
| enum | TreeOrder { ORDER_BIG_DOWN = 1, ORDER_BIG_TO_EDGE = 2, ORDER_BIG_TO_CENTER = 4, ORDER_ALTERNATING = 8, BIG_BRANCHES_TO_TOP = 0, BIG_BRANCHES_TO_BOTTOM = ORDER_BIG_DOWN, BIG_BRANCHES_TO_EDGE = ORDER_BIG_TO_EDGE, BIG_BRANCHES_TO_CENTER = ORDER_BIG_TO_CENTER, BIG_BRANCHES_ALTERNATING = ORDER_BIG_TO_CENTER|ORDER_ALTERNATING } |
| enum | ARB_edge_type { EDGE_TO_ROOT, EDGE_TO_LEAF, ROOT_EDGE } |
Functions | |
| MARK_NONFINAL_METHOD (TreeRoot, change_root,(TreeNode *, TreeNode *)) | |
| GBT_RemarkType | parse_remark (const char *remark, double &bootstrap) |
| bool | parse_treelabel (const char *&label, double &bootstrap) |
| MARK_NONFINAL_METHOD (TreeNode, swap_sons,()) | |
| MARK_NONFINAL_METHOD (TreeNode, set_root,()) | |
| void | destroy (TreeNode *that) |
| void | destroy (TreeNode *that, TreeRoot *root) |
| ARB_edge | parentEdge (TreeNode *son) |
| ARB_edge | leafEdge (TreeNode *leaf) |
| ARB_edge | rootEdge (TreeRoot *root) |
Macro Definition Documentation
| #define rt_assert | ( | cond | ) | arb_assert(cond) |
Definition at line 22 of file TreeNode.h.
Referenced by TreeNode::LengthCollector::add_parent_length(), ARB_edge::ARB_edge(), TreeNode::branchlen2bootstrap(), TreeRoot::change_root(), ARB_edge::counter_next(), ARB_edge::counter_previous(), TreeRoot::delete_by_node(), TreeNode::destroy(), TreeNode::LengthCollector::eliminate_parent_edge(), TreeNode::find_parent_clade(), TreeNode::fixKeeledOrientation(), TreeNode::get_brother(), NodeLeafDistance::get_downdist(), FINAL_TYPE< SEQTYPE >::get_leaf_count(), TreeNode::get_remark(), TreeNode::get_remark_ptr(), TreeNode::get_root_node(), NodeLeafDistance::get_updist(), TreeNode::has_group_info(), TreeNode::has_valid_root_remarks(), TreeNode::is_normal_group(), leafEdge(), TreeNode::markAsLeaf(), TreeNode::multifurcate(), ARB_edge::next(), parentEdge(), TreeNode::parse_bootstrap(), TreeRoot::predelete(), ARB_edge::previous(), TreeNode::set_branchlength_preserving(), TreeNode::set_root(), TreeNode::swap_sons(), TreeNode::unkeelGroup(), TreeNode::use_as_remark(), TreeNode::~TreeNode(), and TreeRoot::~TreeRoot().
| #define DEFINE_READ_ACCESSORS | ( | TYPE, | |
| ACCESS, | |||
| MEMBER | |||
| ) |
Definition at line 49 of file TreeNode.h.
| #define KEELED_INDICATOR '!' |
Definition at line 168 of file TreeNode.h.
Referenced by build_taxonomy_rek(), GBT_write_group_name(), get_downgroups(), QueriedGroups::get_group_display(), and tree2newick().
| #define DEFINE_TREE_ROOT_ACCESSORS | ( | RootType, | |
| TreeType | |||
| ) | DEFINE_DOWNCAST_ACCESSORS(TreeType, get_root_node, TreeRoot::get_root_node()) |
Definition at line 610 of file TreeNode.h.
| #define DEFINE_TREE_RELATIVES_ACCESSORS | ( | TreeType | ) |
Definition at line 613 of file TreeNode.h.
| #define DEFINE_TREE_ACCESSORS | ( | RootType, | |
| TreeType | |||
| ) |
Definition at line 621 of file TreeNode.h.
| #define ASSERT_VALID_TREE | ( | tree | ) |
Definition at line 647 of file TreeNode.h.
Referenced by AP_main::all_available_reverts_will_produce_valid_trees(), AP_tree::initial_insert(), AP_tree::insert(), insert_all_species_into_tree(), insert_species_into_tree(), PARSIMONY_testenv< SEQTYPE >::load_tree(), nt_add(), optimizeTree(), AP_tree::REMOVE(), AP_tree_root::remove_leafs(), and AP_main::revert_will_produce_valid_tree().
| #define ASSERT_VALID_TREE_OR_NULL | ( | tree | ) |
Definition at line 648 of file TreeNode.h.
Referenced by AP_tree::REMOVE(), and AP_tree_root::remove_leafs().
| #define TEST_EXPECT_VALID_TREE | ( | tree | ) |
Definition at line 660 of file TreeNode.h.
| #define TEST_EXPECT_VALID_TREE_OR_NULL | ( | tree | ) |
Definition at line 661 of file TreeNode.h.
| #define TEST_EXPECT_VALID_TREE__BROKEN | ( | tree | ) |
Definition at line 662 of file TreeNode.h.
| #define TEST_EXPECT_VALID_TREE_OR_NULL__BROKEN | ( | tree | ) |
Definition at line 663 of file TreeNode.h.
Enumeration Type Documentation
| enum TreeOrder |
| Enumerator | |
|---|---|
| ORDER_BIG_DOWN | |
| ORDER_BIG_TO_EDGE | |
| ORDER_BIG_TO_CENTER | |
| ORDER_ALTERNATING | |
| BIG_BRANCHES_TO_TOP | |
| BIG_BRANCHES_TO_BOTTOM | |
| BIG_BRANCHES_TO_EDGE | |
| BIG_BRANCHES_TO_CENTER | |
| BIG_BRANCHES_ALTERNATING | |
Definition at line 35 of file TreeNode.h.
| enum ARB_edge_type |
| Enumerator | |
|---|---|
| EDGE_TO_ROOT | |
| EDGE_TO_LEAF | |
| ROOT_EDGE | |
Definition at line 698 of file TreeNode.h.
Function Documentation
|
inline |
analyse 'remark' and return GBT_RemarkType. If result is REMARK_BOOTSTRAP, 'bootstrap' contains the bootstrap value
Definition at line 117 of file TreeNode.h.
References NULp, REMARK_BOOTSTRAP, REMARK_NONE, and REMARK_OTHER.
Referenced by BootstrapConfig::display_remark(), and TreeNode::parse_bootstrap().
|
inline |
analyse 'label' and report found bootstrap and/or/nor label.
If result is true, 'bootstrap' contains the bootstrap value.
Afterwards 'label' will point to the non-bootstrap part of the input (may become NULp if input is plain bootstrap)..
Interpretation of boostrap values: input result
66% 0.66 0.77 0.77 88 88.0
(Note: after importing trees the bootstrap values get scaled depending on the overall range of values found)
Definition at line 129 of file TreeNode.h.
Referenced by GBT_write_group_name().
| MARK_NONFINAL_METHOD | ( | TreeNode | , |
| swap_sons | , | ||
| () | |||
| ) |
| MARK_NONFINAL_METHOD | ( | TreeNode | , |
| set_root | , | ||
| () | |||
| ) |
|
inline |
Definition at line 600 of file TreeNode.h.
References TreeNode::destroy().
Referenced by ARB_main(), create_consense_tree_cb(), di_calculate_compressed_matrix_cb(), di_calculate_tree_cb(), DI_MATRIX::extract_from_tree(), GBT_commit_rename_session(), GBT_compress_sequence_tree2(), GBT_remove_leafs(), get_cached_taxonomy(), AWT_graphic_tree::load_from_DB(), main(), mark_action(), MatrixOrder::MatrixOrder(), nt_add_partial(), NT_alltree_remove_leafs(), PVP_calculate(), sort_tree_by_other_tree(), sq_calc_seq_quality_cb(), transform_gbd_to_leaf(), TREE_load(), TREE_load_to_db(), TREE_write_Newick(), AWT_graphic_tree::~AWT_graphic_tree(), and TreeContainer::~TreeContainer().
Definition at line 603 of file TreeNode.h.
References TreeNode::destroy().
returns edge to father (or to brother for sons of root). Cannot be called with root-node (but can be called with each end of any ARB_edge)
Definition at line 883 of file TreeNode.h.
References EDGE_TO_ROOT, TreeNode::get_brother(), TreeNode::is_root_node(), ROOT_EDGE, and rt_assert.
Referenced by TreeNode::LengthCollector::eliminate_parent_edge(), TreeNode::LengthCollector::independent_distribution(), leafEdge(), and TreeNode::multifurcate().
Definition at line 893 of file TreeNode.h.
References ARB_edge::inverse(), TreeNode::is_leaf(), parentEdge(), and rt_assert.
Definition at line 898 of file TreeNode.h.
References ROOT_EDGE.
Referenced by calc_branchlengths_and_reorder(), insert_all_species_into_tree(), insert_species_into_tree(), ArbParsimony::kernighan_optimize_tree(), PARSIMONY_testenv< SEQTYPE >::load_tree(), mixtree_and_calclengths(), AP_tree_edge::nni_rec(), nt_add(), NT_bootstrap(), GroupSearch::perform_search(), and recursiveNNI().
