source: branches/profile/SL/TREE_READ/TreeRead.h

Last change on this file was 11401, checked in by westram, 12 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: 1.2 KB
Line 
1// ============================================================ //
2//                                                              //
3//   File      : TreeRead.h                                     //
4//   Purpose   :                                                //
5//                                                              //
6//   Coded by Ralf Westram (coder@reallysoft.de) in June 2009   //
7//   Institute of Microbiology (Technical University Munich)    //
8//   www.arb-home.de                                            //
9//                                                              //
10// ============================================================ //
11
12#ifndef TREEREAD_H
13#define TREEREAD_H
14
15#ifndef ARBDBT_H
16#include <arbdbt.h>
17#endif
18
19#define DEFAULT_BRANCH_LENGTH_MARKER -1000.0 // tree-edges w/o length are marked with this value during read and corrected in TREE_scale
20
21inline bool is_marked_as_default_len(GBT_LEN len) { return len <= DEFAULT_BRANCH_LENGTH_MARKER; }
22
23GBT_TREE *TREE_load(const char *path, const TreeNodeFactory& nodeMaker, char **commentPtr, bool allow_length_scaling, char **warningPtr);
24void TREE_scale(GBT_TREE *tree, double length_scale, double bootstrap_scale);
25
26#else
27#error TreeRead.h included twice
28#endif // TREEREAD_H
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