ARB
SEC_abspos.cxx
Go to the documentation of this file.
1 // =============================================================== //
2 // //
3 // File : SEC_abspos.cxx //
4 // Purpose : Encapsulates helix position access //
5 // //
6 // Coded by Ralf Westram (coder@reallysoft.de) in July 2007 //
7 // Institute of Microbiology (Technical University Munich) //
8 // http://www.arb-home.de/ //
9 // //
10 // =============================================================== //
11 
12 #include "SEC_abspos.hxx"
13 
14 #include <arb_mem.h>
15 
16 #include <cstdlib>
17 #include <cstring>
18 
19 using namespace std;
20 
21 void XString::set_length(size_t len) {
22  if (number_found && x_string_len<len) freenull(number_found);
23  x_string_len = len;
24  initialized = false;
25 }
26 
27 XString::XString(size_t ali_length) :
28  abspos(NULp),
29  number_found(NULp)
30 {
31  int len = ali_length+1; // need one more (cause 'x's are written behind position)
32  ARB_alloc(x_string, len+1);
33  memset(x_string, '.', len);
34  x_string[len] = 0;
35  set_length(len);
36  initialize();
37 }
38 
39 XString::XString(const char *saved_x_string, size_t saved_length, size_t ali_length) :
40  abspos(NULp),
41  number_found(NULp)
42 {
43  size_t xlen = ali_length+1;
44 
45  sec_assert(saved_length == strlen(saved_x_string));
46  sec_assert(saved_length == xlen || saved_length == xlen-1);
47 
48  ARB_alloc(x_string, xlen+1);
49  memcpy(x_string, saved_x_string, saved_length+1);
50 
51  if (saved_length == xlen-1) { // normal case
52  x_string[xlen-1] = '.'; // additional position is a gap (SAI 'HELIX' should have a gap at end)
53  x_string[xlen] = 0; // (see also comments in get_x_string())
54  }
55 
56  set_length(xlen);
57  initialize();
58 }
59 
61  // detect number of 'x's in x_string :
62  {
63  size_t len = 0;
64  int x = 0;
65 
66  while (char c = x_string[len]) {
67  if (c == 'x') x++;
68  len++;
69  }
70 
71  sec_assert(len == x_string_len);
72 
73  if (abspos) { // re-initialization
74  if (x_count<x) freenull(abspos); // abspos array too small
75  }
76  x_count = x;
77  }
78 
79  if (!abspos) ARB_alloc(abspos, x_count);
80  if (!number_found) ARB_alloc(number_found, x_string_len);
81 
82  // init abspos and number_found :
83  {
84  int pos = 0;
85  int x = 0;
86 
87  while (char c = x_string[pos]) {
88  number_found[pos] = x;
89  if (c == 'x') {
90  abspos[x] = pos;
91  x++;
92  }
93  pos++;
94  }
95  }
96 
97  initialized = true;
98 }
99 
101  free(x_string);
102  free(abspos);
103  free(number_found);
104 }
105 
106 size_t XString::getAbsPos(int x) const {
107  sec_assert(initialized);
108  sec_assert(x >= 0 && x<x_count);
109  size_t pos = abspos[x];
110  sec_assert(pos<x_string_len);
111  return pos;
112 }
113 
114 int XString::getXleftOf(size_t pos) const {
115  sec_assert(initialized);
116  sec_assert(pos<x_string_len);
117  int x = number_found[pos];
118  sec_assert(x >= 0 && x<x_count);
119  return x;
120 }
121 
122 const char *XString::get_x_string() const {
123  sec_assert(initialized);
124 
125  static char *copy = NULp;
126  static size_t copy_alloc = 0;
127 
128  size_t bufsize = x_string_len+1;
129 
130  if (!copy || copy_alloc<bufsize) {
131  freeset(copy, ARB_alloc<char>(bufsize));
132  copy_alloc = bufsize;
133  }
134 
135  memcpy(copy, x_string, x_string_len+1);
136 
137  int add_pos = x_string_len-1;
138 
139  if (copy[add_pos] == '.') { // can be removed - added again after reload
140  copy[add_pos] = 0; // hide internal additional position
141  }
142  else {
143  // happens only if there's a helix on last alignment position.
144  // In this case we save the additional position to DB, which will
145  // lead the user to reformat his alignment (which will add a gap
146  // at end of SAI HELIX)
147  }
148  return copy;
149 }
150 
int getXleftOf(size_t abspos) const
Definition: SEC_abspos.cxx:114
STL namespace.
static bool initialized
Definition: AW_advice.cxx:36
TYPE * ARB_alloc(size_t nelem)
Definition: arb_mem.h:56
const char * get_x_string() const
Definition: SEC_abspos.cxx:122
size_t getAbsPos(int x) const
Definition: SEC_abspos.cxx:106
void initialize()
Definition: SEC_abspos.cxx:60
static void copy(double **i, double **j)
Definition: trnsprob.cxx:32
#define NULp
Definition: cxxforward.h:97
XString(size_t ali_length)
Definition: SEC_abspos.cxx:27
#define sec_assert(cond)
Definition: SEC_defs.hxx:19