ARB
SequenceBuffer.h
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1 // ================================================================ //
2 // //
3 // File : SequenceBuffer.h //
4 // Purpose : //
5 // //
6 // Coded by Ralf Westram (coder@reallysoft.de) in December 2006 //
7 // Institute of Microbiology (Technical University Munich) //
8 // http://www.arb-home.de/ //
9 // //
10 // ================================================================ //
11 #ifndef SEQUENCEBUFFER_H
12 #define SEQUENCEBUFFER_H
13 
14 #ifndef TYPES_H
15 #include "types.h"
16 #endif
17 #ifndef SMARTPTR_H
18 #include <smartptr.h>
19 #endif
20 
21 class CharCounter {
22  size_t count[256];
23  size_t all;
24 
25 public:
26  CharCounter() { clear(); }
27 
28  size_t getCount(unsigned char idx) const { return count[idx]; }
29  size_t getCount() const { return all; }
30  void countChars(const std::string& line);
31 
32  void clear();
33 };
34 
35 
37 
38 class BaseCounter {
39  std::string source; // where does information originate from
40  size_t count[BC_COUNTERS]; // number of occurrences of single bases
41 
42  SmartPtr<CharCounter> char_count; // character counter (used by addLine)
43 
44  void catchUpWithLineCounter() const;
45 
46 public:
47  BaseCounter(const std::string& Source)
48  : source(Source)
49  {
50  for (int i = 0; i<BC_COUNTERS; ++i) count[i] = 0;
51  }
52 
53  void addCount(Base base, size_t amount) { count[base] += amount; }
54  void checkOverallCounter() const;
55  void calcOverallCounter();
56 
57  void startLineCounter();
58  void addLine(const std::string& line) {
59  gi_assert(!char_count.isNull()); // call startLineCounter before!
60  char_count->countChars(line);
61  }
62 
63  void expectEqual(const BaseCounter& other) const;
64  size_t getCount(Base base) const {
65  catchUpWithLineCounter();
66  return count[base];
67  }
68 };
69 
70 class SequenceBuffer : virtual Noncopyable {
71  stringVector lines; // stores input lines
72  BaseCounter baseCounter;
73  mutable char *seq;
74 
75 public:
76  SequenceBuffer(size_t expectedSize) :
77  baseCounter("sequence data"),
78  seq(NULp)
79  {
80  lines.reserve(expectedSize/60+1); // flatfiles use 60 bases per sequence line
81  baseCounter.startLineCounter();
82  }
84 
85  void addLine(const std::string& line) {
86  lines.push_back(line);
87  baseCounter.addLine(line);
88  }
89 
90  const BaseCounter& getBaseCounter() const { return baseCounter; }
91  BaseCounter& getBaseCounter() { return baseCounter; }
92 
93  const char *getSequence() const;
94 };
95 
96 
97 #else
98 #error SequenceBuffer.h included twice
99 #endif // SEQUENCEBUFFER_H
100 
void calcOverallCounter()
return string(buffer, length)
#define gi_assert(cond)
Definition: defs.h:26
SequenceBuffer(size_t expectedSize)
std::vector< std::string > stringVector
Definition: types.h:30
void expectEqual(const BaseCounter &other) const
size_t getCount(Base base) const
bool isNull() const
test if SmartPtr is NULp
Definition: smartptr.h:248
size_t getCount(unsigned char idx) const
void addLine(const std::string &line)
void countChars(const std::string &line)
BaseCounter(const std::string &Source)
const BaseCounter & getBaseCounter() const
void startLineCounter()
void addLine(const std::string &line)
size_t getCount() const
void checkOverallCounter() const
static int line
Definition: arb_a2ps.c:296
#define NULp
Definition: cxxforward.h:97
const char * getSequence() const
void addCount(Base base, size_t amount)
BaseCounter & getBaseCounter()
Base