Opened 23 months ago

Last modified 4 months ago

#701 accepted task

separate code for PosVarParsimony SAI calculation

Reported by: westram Owned by: westram
Priority: major Milestone: r18q1
Component: ARB_NTREE Version: SVN
Keywords: silva Cc: cquast@…

Description (last modified by westram)


  • needed by SILVA pipeline


  • code to calculate posvar-SAI shall move into its own library (separated from GUI code and ARB_NTREE)
  • functionality needed in pipeline:
    1. load tree from file
    2. calculate SAI from tree + sequences
    3. delete tree

Proposed interface:

  1. new function
    GB_ERROR TREE_load_to_db(GBDATA *gb_main, 
                             const char *treefile, 
                             const char *treename);
  2. new function
    GB_ERROR PVP_calculate(GBDATA *gb_main,
                           const char *ali_name,
                           const char *tree_name,
                           const char *target_SAI_name);
  3. to delete a tree from database simply use
    GB_ERROR error = NULL;
      GB_transaction ta(gb_main);
      GBDATA *gb_tree = GBT_find_tree(gb_main, name);
      if (gb_tree) error = GB_delete(gb_tree);

Put 1. into SL/TREE_READ and 2. into new library.

Change History (3)

comment:1 Changed 13 months ago by westram

  • Description modified (diff)
  • Milestone set to wishlist

comment:2 Changed 12 months ago by westram

  • Milestone changed from wishlist to r18q1
  • Status changed from new to assigned

comment:3 Changed 4 months ago by westram

  • Status changed from assigned to accepted
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