source: branches/profile/MERGE/MG_adapt_ali.hxx

Last change on this file was 7800, checked in by westram, 14 years ago

merge from dev [7687] [7692] [7693] [7694] [7695] [7697] [7706] [7707] [7708]

  • replaced 'char' (heap-array of heap-char*) by new class StrArray
    • added several tests for StrArray
    • removed function flavours using element result parameter (e.g. GBT_get_tree_names_and_count)
  • split StrArray into StrArray (heap), ConstStrArray (just pointers) and base class (CharPtrArray)
    • use ConstStrArray in several cases (e.g. config, tree and alignment names)
  • GBT_split_string
    • changed allocation: dups source and does destructive split (similar to strtok)
    • returns ConstStrArray instead of char
    • added destructive versions (GBT_splitNdestroy_string)
  • refactored parsePositions / parseCSV using ConstStrArray
File size: 1.2 KB
Line 
1// ============================================================= //
2//                                                               //
3//   File      : MG_adapt_ali.hxx                                //
4//   Purpose   :                                                 //
5//                                                               //
6//   Institute of Microbiology (Technical University Munich)     //
7//   http://www.arb-home.de/                                     //
8//                                                               //
9// ============================================================= //
10
11#ifndef MG_ADAPT_ALI_HXX
12#define MG_ADAPT_ALI_HXX
13
14#ifndef ARBDB_BASE_H
15#include <arbdb_base.h>
16#endif
17#ifndef ARB_STRARRAY_H
18#include <arb_strarray.h>
19#endif
20
21class MG_remap;
22
23struct MG_remaps : virtual Noncopyable {
24    int             n_remaps;
25    ConstStrArray   alignment_names;
26    MG_remap      **remaps;
27
28    MG_remaps(GBDATA *gb_left, GBDATA *gb_right, bool enable, const char *reference_species_names);
29    ~MG_remaps();
30};
31
32
33GB_ERROR MG_transfer_all_alignments(MG_remaps *remaps, GBDATA *source_species, GBDATA *destination_species);
34
35#else
36#error mg_adapt_ali.hxx included twice
37#endif // MG_ADAPT_ALI_HXX
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