ARB
ColumnStat.hxx
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1 // =============================================================== //
2 // //
3 // File : ColumnStat.hxx //
4 // Purpose : //
5 // //
6 // Institute of Microbiology (Technical University Munich) //
7 // http://www.arb-home.de/ //
8 // //
9 // =============================================================== //
10 
11 #ifndef COLUMNSTAT_HXX
12 #define COLUMNSTAT_HXX
13 
14 #ifndef ARBDB_BASE_H
15 #include <arbdb_base.h>
16 #endif
17 #ifndef ARBTOOLS_H
18 #include <arbtools.h>
19 #endif
20 #ifndef ARB_ASSERT_H
21 #include <arb_assert.h>
22 #endif
23 
24 /* Create a window, that allows you to select a column statistic and
25  * get the weights from the selected SAI
26  *
27  * 1. create ColumnStat
28  * 2. build button with callback COLSTAT_create_selection_window
29  * 3. call ColumnStat::go(second_filter)
30  * 4. use ColumnStat::get_weights()
31  */
32 
33 class AW_root;
34 class AW_window;
35 class AP_filter;
36 class AW_awar;
37 
38 #define DIST_MIN_SEQ(seq_anz) (seq_anz / 10)
39 
40 class ColumnStat : virtual Noncopyable {
41  GBDATA *gb_main;
42  AW_root *awr;
43 
44  char *awar_name;
45  char *awar_alignment;
46  char *awar_smooth;
47  char *awar_enable_helix;
48 
49  char *alignment_name;
50  char *type_path;
51 
52  class AW_DB_selection *saisel;
53 
54  // all members below are valid after calling calculate() only!
55  //
56  // @@@ they should be stored in a separate class and referenced by pointer here
57  // (e.g. rename this class into ColumnStatSelector and name the new class ColumnStat)
58 
59  size_t seq_len; // real length == 0 -> not valid
60  GB_UINT4 *weights; // helix = 1, non helix == 2
61  float *rates;
62  float *ttratio;
63  bool *is_helix;
64  GB_UINT4 *mut_sum;
65  GB_UINT4 *freq_sum;
66  char *desc;
67  float *frequency[256];
68 
69 public:
70  ColumnStat(GBDATA *gb_main_, AW_root *awr_, const char *awar_template, AW_awar *awar_used_alignment);
71  ~ColumnStat();
72 
74  void forget();
75 
76  GBDATA *get_gb_main() const { return gb_main; }
77 
78  bool has_valid_alignment() const { return !strchr(alignment_name, '?'); }
79 
80  const char *get_awar_smooth() const { return awar_smooth; }
81  const char *get_awar_enable_helix() const { return awar_enable_helix; }
82  const char *get_type_path() const { arb_assert(has_valid_alignment()); return type_path; }
83 
84  bool has_rates() const { return rates; }
85  void weight_by_inverseRates() const;
86 
87  size_t get_length() const { return seq_len; }
88 
89  const GB_UINT4 *get_weights() const { return weights; }
90  const float *get_rates() const { return rates; }
91  const float *get_ttratio() const { return ttratio; }
92  const bool *get_is_helix() const { return is_helix; }
93  const float *get_frequencies(unsigned char c) const { return frequency[c]; }
94 
97 
98  void print();
99 };
100 
102 void COLSTAT_create_selection_list(AW_window *aww, ColumnStat *column_stat);
103 
104 #else
105 #error ColumnStat.hxx included twice
106 #endif // COLUMNSTAT_HXX
const char * get_awar_smooth() const
Definition: ColumnStat.hxx:80
#define arb_assert(cond)
Definition: arb_assert.h:245
const float * get_frequencies(unsigned char c) const
Definition: ColumnStat.hxx:93
const char * get_type_path() const
Definition: ColumnStat.hxx:82
void print()
Definition: ColumnStat.cxx:313
AW_window * COLSTAT_create_selection_window(AW_root *root, ColumnStat *column_stat)
Definition: ColumnStat.cxx:373
const char * get_awar_enable_helix() const
Definition: ColumnStat.hxx:81
bool has_rates() const
Definition: ColumnStat.hxx:84
ColumnStat(GBDATA *gb_main_, AW_root *awr_, const char *awar_template, AW_awar *awar_used_alignment)
Definition: ColumnStat.cxx:44
unsigned int GB_UINT4
Definition: arbdb_base.h:37
void refresh_sai_selection_list()
Definition: ColumnStat.cxx:31
void COLSTAT_create_selection_list(AW_window *aww, ColumnStat *column_stat)
Definition: ColumnStat.cxx:369
const float * get_rates() const
Definition: ColumnStat.hxx:90
const float * get_ttratio() const
Definition: ColumnStat.hxx:91
void create_sai_selection_list(AW_window *aww)
Definition: ColumnStat.cxx:364
static int weights[MAX_BASETYPES][MAX_BASETYPES]
Definition: ClustalV.cxx:71
__ATTR__USERESULT GB_ERROR calculate(AP_filter *filter)
Definition: ColumnStat.cxx:107
void forget()
Definition: ColumnStat.cxx:83
bool has_valid_alignment() const
Definition: ColumnStat.hxx:78
GBDATA * get_gb_main() const
Definition: ColumnStat.hxx:76
const GB_UINT4 * get_weights() const
Definition: ColumnStat.hxx:89
static double ttratio
#define __ATTR__USERESULT
Definition: attributes.h:58
size_t get_length() const
Definition: ColumnStat.hxx:87
void weight_by_inverseRates() const
Definition: ColumnStat.cxx:303
GBDATA * gb_main
Definition: adname.cxx:33
const bool * get_is_helix() const
Definition: ColumnStat.hxx:92