ARB
reader.h
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1 #ifndef READER_H
2 #define READER_H
3 
4 #ifndef BUFFEREDFILEREADER_H
5 #include <BufferedFileReader.h>
6 #endif
7 #ifndef DEFS_H
8 #include "defs.h"
9 #endif
10 #ifndef FUN_H
11 #include "fun.h"
12 #endif
13 #ifndef SEQ_H
14 #include "seq.h"
15 #endif
16 #ifndef INPUT_FORMAT_H
17 #include "input_format.h"
18 #endif
19 
20 
21 class Reader : virtual Noncopyable {
22  FILE *fp;
23  BufferedFileReader *file;
24  char linebuf[LINESIZE];
25  const char *curr; // NULp means "EOF reached"
26  bool failure;
27 
28  void reset() {
29  curr = linebuf;
30  failure = false;
31  }
32 
33  void read();
34 
35 public:
36  Reader(const char *inf);
37  virtual ~Reader();
38 
39  void rewind() { file->rewind(); reset(); read(); }
40 
41  Reader& operator++() { read(); return *this; }
42 
43  const char *line() const { return curr; }
44 
45  void set_line(const char *new_line) {
46  ca_assert(new_line);
47  ca_assert(strlen(new_line)<LINESIZE);
48  strcpy(linebuf, new_line);
49  }
50 
51  bool failed() const { return failure; }
52  bool ok() const { return !failure; }
53 
54  void abort() { failure = true; curr = NULp; }
55  void ignore_rest_of_file() { curr = NULp; }
56 
57  template<class PRED>
58  void skipOverLinesThat(const PRED& match_condition) {
59  while (line() && match_condition(line()))
60  ++(*this);
61  }
63 };
64 MARK_NONFINAL_DTOR(Reader); // silence weird suggestion to make Reader-dtor final
65 
66 inline const char *shorttimekeep(char *heapcopy) { RETURN_LOCAL_ALLOC(heapcopy); }
67 inline const char *shorttimecopy(const char *nocopy) { return shorttimekeep(nulldup(nocopy)); }
68 
69 struct FormatReader {
70  virtual ~FormatReader() {}
71  virtual bool read_one_entry(Seq& seq) __ATTR__USERESULT = 0;
72  virtual bool failed() const = 0;
73  virtual void ignore_rest_of_file() = 0;
74  virtual void rewind() = 0;
75  virtual InputFormat& get_data() = 0;
76 
78 };
79 
81 
82 struct SimpleFormatReader : public Reader, public FormatReader {
83  SimpleFormatReader(const char *inf) : Reader(inf) {}
84  bool failed() const OVERRIDE { return Reader::failed(); }
87 };
88 
89 // --------------------------------------------------------------------------------
90 
91 #if defined(ASSERTION_USED)
92 #define ENFORCE_CHECKED_WRITTEN
93 #endif
94 
95 struct Writer {
96  Writer() {}
97  virtual ~Writer() {}
98 
99  virtual bool ok() const = 0;
100  virtual void out(char ch) = 0;
101  virtual const char *name() const = 0;
102 
103  virtual void throw_write_error() const __ATTR__NORETURN;
104  virtual int out(const char *text) {
105  int i = 0;
106  while (text[i]) {
107  out(text[i++]);
108  }
109  return i;
110  }
111  virtual int outf(const char *format, ...) __ATTR__FORMAT_MEMBER(1);
112 
113  void repeated(char ch, int repeat) { while (repeat--) out(ch); }
114 };
115 
116 #ifdef GCC_TOO_SMART_FOR_USEFUL_FINAL_TYPE_SUGGESTION
117 # pragma GCC diagnostic push
118 # pragma GCC diagnostic ignored "-Wsuggest-final-types"
119 #endif
120 
121 class FileWriter : public Writer, virtual Noncopyable {
122  FILE *ofp;
123  char *filename;
124  int written; // count written sequences
125 
126 #if defined(ENFORCE_CHECKED_WRITTEN)
127  bool checked_written;
128 #endif
129 
130  bool is_fine() const { return ofp && !Convaln_exception::exception_thrown(); }
131 
132 public:
133  FileWriter(const char *outf);
135 
136  FILE *get_FILE() { return ofp; }
137 
138  bool ok() const OVERRIDE { return ofp; }
139  void out(char ch) FINAL_OVERRIDE {
140  if (fputc(ch, ofp) == EOF) throw_write_error();
141  }
142 
143  const char *name() const OVERRIDE { return filename; }
144 
145  int out(const char *text) OVERRIDE { return Writer::out(text); }
146  int outf(const char *format, ...) OVERRIDE __ATTR__FORMAT_MEMBER(1);
147 
148  void seq_done() { ++written; }
149  void seq_done(int count) { ca_assert(count >= 0); written += count; }
150 
151  void expect_written();
152 
154 };
155 MARK_NONFINAL_CLASS(FileWriter); // does not work for too smart gcc|s
156 #ifdef GCC_TOO_SMART_FOR_USEFUL_FINAL_TYPE_SUGGESTION
157 # pragma GCC diagnostic pop
158 #endif
159 
160 #else
161 #error reader.h included twice
162 #endif // READER_H
163 
int out(const char *text) OVERRIDE
Definition: reader.h:145
Reader(const char *inf)
Definition: reader.cxx:4
Definition: reader.h:21
FileWriter(const char *outf)
Definition: reader.cxx:69
void seq_done()
Definition: reader.h:148
bool failed() const
Definition: reader.h:51
virtual bool ok() const =0
AliDataPtr format(AliDataPtr data, const size_t wanted_len, GB_ERROR &error)
Definition: insdel.cxx:615
virtual void ignore_rest_of_file()=0
void out(char ch) FINAL_OVERRIDE
Definition: reader.h:139
Reader & operator++()
Definition: reader.h:41
void abort()
Definition: reader.h:54
#define ca_assert(cond)
Definition: global.h:33
virtual void rewind()=0
PREPARE_MARK_NONFINAL_CLASS(FileWriter)
void expect_written()
Definition: reader.cxx:97
void repeated(char ch, int repeat)
Definition: reader.h:113
SimpleFormatReader(const char *inf)
Definition: reader.h:83
bool failed() const OVERRIDE
Definition: reader.h:84
const char * shorttimekeep(char *heapcopy)
Definition: reader.h:66
virtual bool read_one_entry(Seq &seq) __ATTR__USERESULT=0
PREPARE_MARK_NONFINAL_CLASS(Reader)
Definition: reader.h:95
MARK_NONFINAL_CLASS(FileWriter)
FILE * seq
Definition: rns.c:46
virtual InputFormat & get_data()=0
#define FINAL_OVERRIDE
Definition: cxxforward.h:95
MARK_NONFINAL_DTOR(Reader)
Writer()
Definition: reader.h:96
const char * name() const OVERRIDE
Definition: reader.h:143
void ignore_rest_of_file() OVERRIDE
Definition: reader.h:85
#define __ATTR__FORMAT_MEMBER(pos)
Definition: attributes.h:62
bool ok() const
Definition: reader.h:52
static SmartPtr< FormatReader > create(const FormattedFile &in)
Definition: convert.cxx:13
Generic smart pointer.
Definition: smartptr.h:149
Definition: seq.h:43
virtual void out(char ch)=0
SmartPtr< FormatReader > FormatReaderPtr
Definition: reader.h:80
FILE * get_FILE()
Definition: reader.h:136
fputc('\n', stderr)
virtual int outf(const char *format,...) __ATTR__FORMAT_MEMBER(1)
Definition: reader.cxx:121
#define RETURN_LOCAL_ALLOC(mallocation)
Definition: smartptr.h:310
virtual ~Writer()
Definition: reader.h:97
void rewind()
Definition: reader.h:39
bool ok() const OVERRIDE
Definition: reader.h:138
virtual void throw_write_error() const __ATTR__NORETURN
Definition: reader.cxx:107
void ignore_rest_of_file()
Definition: reader.h:55
static const Convaln_exception * exception_thrown()
Definition: global.h:71
virtual ~Reader()
Definition: reader.cxx:26
#define OVERRIDE
Definition: cxxforward.h:93
#define __ATTR__USERESULT
Definition: attributes.h:58
virtual const char * name() const =0
const char * shorttimecopy(const char *nocopy)
Definition: reader.h:67
const char * line() const
Definition: reader.h:43
#define NULp
Definition: cxxforward.h:97
void seq_done(int count)
Definition: reader.h:149
virtual bool failed() const =0
#define __ATTR__NORETURN
Definition: attributes.h:56
int outf(const char *format,...) OVERRIDE __ATTR__FORMAT_MEMBER(1)
Definition: reader.cxx:112
void set_line(const char *new_line)
Definition: reader.h:45
~FileWriter() OVERRIDE
Definition: reader.cxx:83
#define LINESIZE
Definition: defs.h:16
virtual ~FormatReader()
Definition: reader.h:70
void rewind() OVERRIDE
Definition: reader.h:86
void skipOverLinesThat(const PRED &match_condition)
Definition: reader.h:58