source: trunk/SL/SEQUENCE/AP_seq_simple_pro.hxx

Last change on this file was 16880, checked in by westram, 8 years ago
  • reintegrates 'multicore' into 'trunk'
    • derive sequence classes able to be combined from new class AP_combinableSeq
      • elim dummy functions from rest of hierarchy
    • implements non-writing combine for add-species (speedup: 25-35%)
    • introduce type Mutations ⇒ uses long everywhere (before mostly, but not always used float)
    • allows use of futures
      • nucleotide combine is able to calculate async (disabled via define atm → NEVER_COMBINE_ASYNC; needs more work on calling algorithm)
  • adds: log:branches/multicore@16769:16879
  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 1.6 KB
Line 
1// =============================================================== //
2//                                                                 //
3//   File      : AP_seq_simple_pro.hxx                             //
4//   Purpose   :                                                   //
5//                                                                 //
6//   Institute of Microbiology (Technical University Munich)       //
7//   http://www.arb-home.de/                                       //
8//                                                                 //
9// =============================================================== //
10
11#ifndef AP_SEQ_SIMPLE_PRO_HXX
12#define AP_SEQ_SIMPLE_PRO_HXX
13
14#ifndef AP_SEQUENCE_HXX
15#include <AP_sequence.hxx>
16#endif
17#ifndef DOWNCAST_H
18#include <downcast.h>
19#endif
20
21enum aas {
22    ALA, ARG, ASN, ASP, CYS, GLN, GLU, GLY, HIS, ILEU, LEU, LYS, MET, PHE, PRO,
23    SER, THR, TRP, TYR, VAL, STOP, DEL, ASX, GLX, UNK, QUEST
24};
25
26typedef unsigned char ap_pro;   // aas but only one character used
27
28class AP_sequence_simple_protein : public AP_sequence { // derived from a Noncopyable
29    ap_pro *sequence;
30
31    void set(const char *sequence) OVERRIDE;
32    void unset() OVERRIDE;
33
34public:
35
36    AP_sequence_simple_protein(const AliView *aliview);
37    ~AP_sequence_simple_protein() OVERRIDE;
38
39    AP_sequence *dup() const OVERRIDE;                             // used to get the real new element
40
41    const ap_pro *get_sequence() const { return sequence; }
42    ap_pro *get_sequence() { return sequence; }
43};
44
45
46#else
47#error AP_seq_simple_pro.hxx included twice
48#endif // AP_SEQ_SIMPLE_PRO_HXX
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