Bug Summary

File:.Linux_CentOS6-x86_64-clang3.7.0/libraries/HDDM/hddm_mc_s++.cpp
Location:line 151, column 10
Description:Called C++ object pointer is null

Annotated Source Code

1/*
2 * hddm_mc_s.cpp - DO NOT EDIT THIS FILE
3 *
4 * This file was generated automatically by hddm-cpp from the file
5 * libraries/HDDM/mc.xml
6
7 * This c++ source implements the methods for the classes
8 * described in the data model (from libraries/HDDM/mc.xml).
9 *
10 * The hddm data model tool set was written by
11 * Richard Jones, University of Connecticut.
12 *
13 * For more information see the following web site
14 *
15 * http://zeus.phys.uconn.edu/halld/datamodel/doc
16 */
17
18#include <sstream>
19#include "hddm_mc_s.hpp"
20
21#ifndef _FILE_OFFSET_BITS64
22# define _FILE_OFFSET_BITS64 64
23#endif
24
25using namespace hddm_mc_s;
26
27static int tags_match(const std::string &a, const std::string &b)
28{
29 if (a == b) {
30 return true;
31 }
32 else {
33 int len = a.length();
34 int ia=0;
35 int ib=0;
36 for (; a[ia] == b[ib]; ++ia, ++ib, --len) {}
37 for (; a[ia] == ' '; ++ia, --len) {}
38 for (; a[ia] == '/'; ++ia, --len) {}
39 for (; b[ib] == ' '; ++ib) {}
40 for (; b[ib] == '/'; ++ib) {}
41 return (a.substr(ia) == b.substr(ib));
42 }
43}
44
45
46streamposition::streamposition()
47 : block_start(), block_offset(), block_status() {}
48
49streamposition::streamposition(uint64_t start, uint32_t offset, uint32_t status)
50 : block_start(start), block_offset(offset), block_status(status) {}
51
52istream::istream(std::istream &src)
53 : m_xstr(0),
54 m_istr(src),
55 m_xcmp(0),
56 m_xraw(0),
57 m_status_bits(0)
58{
59 char hdr[10];
60 src.getline(hdr,7);
61 m_documentString = hdr;
62 if (m_documentString != "<HDDM ") {
63 throw std::runtime_error("hddm_mc_s::istream::istream error - invalid hddm header");
64 }
65 src.clear();
66 std::string line;
67 while (std::getline(src,line).good()) {
68 m_documentString += line + "\n";
69 if (line == "</HDDM>") {
70 break;
71 }
72 }
73 if (src.bad()) {
74 throw std::runtime_error("hddm_mc_s::istream::istream error - invalid hddm header");
75 }
76 m_genome.m_tagname = "HDDM";
77 m_genome.m_sequence = synthesize(m_documentString,0,HDDM::DocumentString(),0);
78 m_event_buffer = new char[m_event_buffer_size = 100000];
79 m_sbuf = new istreambuffer(m_event_buffer,m_event_buffer_size);
80 configure_streambufs();
81 m_next_event_size = 0;
82 m_events_to_skip = 0;
83 m_records_read = 0;
84 m_bytes_read = 0;
85}
86
87istream::~istream() {
88 if (m_xraw) {
89 m_istr.rdbuf(m_xraw);
90 }
91 if (m_xcmp) {
92 delete m_xcmp;
93 }
94 if (m_xstr) {
95 delete m_xstr;
96 }
97 if (m_sbuf) {
98 delete m_sbuf;
99 }
100 delete [] m_event_buffer;
101}
102
103streamposition istream::getPosition() const {
104 streamposition pos;
105 pos.block_status = m_status_bits;
106 if (m_status_bits & (k_bz2_compression | k_z_compression)) {
107 if (m_status_bits & k_can_reposition) {
108 pos.block_start = m_xraw->pubseekoff(0,std::ios_base::cur,
109 std::ios_base::out);
110 if (m_status_bits & k_bz2_compression) {
111 pos.block_offset = dynamic_cast<xstream::bz::istreambuf*>(m_xcmp)
112 ->get_block_offset();
113 pos.block_start -= dynamic_cast<xstream::bz::istreambuf*>(m_xcmp)
114 ->get_block_buffered();
115 }
116 else {
117 pos.block_offset = dynamic_cast<xstream::z::istreambuf*>(m_xcmp)
118 ->get_block_offset();
119 pos.block_start -= dynamic_cast<xstream::z::istreambuf*>(m_xcmp)
120 ->get_block_buffered();
121 }
122 if (m_next_event_size > 0)
123 pos.block_offset -= std::streamoff(4);
124 }
125 else {
126 throw std::runtime_error("hddm_mc_s::istream::getPosition error - "
127 "old-format hddm input file does not support repositioning.");
128 }
129 }
130 else {
131 pos.block_start = m_istr.tellg();
132 if (m_next_event_size > 0)
133 pos.block_start -= std::streamoff(4);
134 pos.block_offset = 0;
135 }
136 return pos;
137}
138
139void istream::setPosition(const streamposition &pos) {
140 m_status_bits = pos.block_status;
141 if (m_status_bits & (k_bz2_compression | k_z_compression)) {
1
Taking true branch
→
142 if ((m_status_bits & k_can_reposition) == 0) {
2
←
Taking false branch
→
143 throw std::runtime_error("hddm_mc_s::istream::setPosition error - "
144 "old-format hddm input file does not support repositioning.");
145 }
146 if (m_xraw == 0 || pos.block_start != getPosition().block_start ||
147 pos.block_offset < getPosition().block_offset)
148 {
149 m_bytes_read = 0;
150 configure_streambufs();
3
←
Calling 'istream::configure_streambufs'
→
7
←
Returning from 'istream::configure_streambufs'
→
151 m_xraw->pubseekoff(pos.block_start,std::ios_base::beg,
8
←
Called C++ object pointer is null
152 std::ios_base::in);
153 m_next_event_size = 0;
154 }
155 int advance;
156 while ((advance = pos.block_offset - getPosition().block_offset)) {
157 char tmpbuf[advance];
158 m_xcmp->sgetn(tmpbuf, advance);
159 }
160 }
161 else if (pos.block_start != getPosition().block_start) {
162 m_istr.seekg(pos.block_start);
163 m_next_event_size = 0;
164 }
165}
166
167void istream::configure_streambufs() {
168 if (m_xstr == 0) {
4
←
Taking false branch
→
169 m_xstr = new xstream::xdr::istream(m_sbuf);
170 }
171 if (m_xraw == 0 && (m_status_bits & k_z_compression) != 0) {
172 //std::cerr << "input switched on z compression" << std::endl;
173 m_xraw = m_istr.rdbuf();
174 m_xcmp = new xstream::z::istreambuf(m_xraw);
175 m_istr.rdbuf(m_xcmp);
176 }
177 else if (m_xraw == 0 && (m_status_bits & k_bz2_compression) != 0) {
178 //std::cerr << "input switched on bz2 compression" << std::endl;
179 m_xraw = m_istr.rdbuf();
180 m_xcmp = new xstream::bz::istreambuf(m_xraw);
181 m_istr.rdbuf(m_xcmp);
182 }
183 else if (m_xraw == 0 && (m_status_bits & k_bits_compression) != 0) {
184 throw std::runtime_error("hddm_mc_s::istream::configure_streambufs error - "
185 "unrecognized compression flag requested.");
186 }
187 else if (m_xraw != 0) {
5
←
Taking true branch
→
188 m_istr.rdbuf(m_xraw);
189 delete m_xcmp;
190 m_xcmp = 0;
191 m_xraw = 0;
6
←
Null pointer value stored to field 'm_xraw'
→
192 configure_streambufs();
193 }
194}
195
196istream &istream::operator>>(HDDM &record) {
197 if (m_next_event_size == 0) {
198 m_istr.read(m_event_buffer,4);
199 m_bytes_read += m_istr.gcount();
200 if (!m_istr.good()) {
201 throw std::runtime_error("hddm_mc_s::istream::operator>> error - "
202 "attempt to read past end of file!");
203 }
204 m_sbuf->reset();
205 *m_xstr >> m_next_event_size;
206 return *this >> record;
207 }
208 else if (m_next_event_size == 1) {
209 m_istr.read(m_event_buffer+4,4);
210 m_bytes_read += m_istr.gcount();
211 if (!m_istr.good()) {
212 throw std::runtime_error("hddm_mc_s::istream::operator>> error -"
213 " read error on token input!");
214 }
215 int size;
216 *m_xstr >> size;
217 m_istr.read(m_event_buffer+8,size);
218 m_bytes_read += m_istr.gcount();
219 if (!m_istr.good()) {
220 throw std::runtime_error("hddm_mc_s::istream::operator>> error -"
221 " read error on token input!");
222 }
223 int format, flags;
224 *m_xstr >> format >> flags;
225 if (format != 0) {
226 throw std::runtime_error("hddm_mc_s::istream::operator>> error - "
227 "unsupported compression format!");
228 }
229 else if (flags != m_status_bits) {
230 int oldcmp = m_status_bits & k_bits_compression;
231 int newcmp = flags & k_bits_compression;
232 m_status_bits = flags;
233 if (oldcmp != newcmp) {
234 configure_streambufs();
235 }
236 }
237 m_next_event_size = 0;
238 return *this >> record;
239 }
240 else if (m_next_event_size+8 > m_event_buffer_size) {
241 delete m_xstr;
242 delete m_sbuf;
243 char *newbuf = new char[m_event_buffer_size = m_next_event_size+1000];
244 m_sbuf = new istreambuffer(newbuf, m_event_buffer_size);
245 m_xstr = new xstream::xdr::istream(m_sbuf);
246 memcpy(newbuf,m_event_buffer,4);
247 delete [] m_event_buffer;
248 m_event_buffer = newbuf;
249 }
250
251 m_istr.read(m_event_buffer+4,m_next_event_size);
252 m_bytes_read += m_istr.gcount();
253 m_records_read++;
254 if (!m_istr.good()) {
255 throw std::runtime_error("hddm_mc_s::istream::operator>> error -"
256 " read error in mid-record!");
257 }
258 if ((m_status_bits & k_crc32_integrity) != 0) {
259 unsigned int recorded_crc;
260 char crcbuf[10];
261 istreambuffer sbuf(crcbuf,10);
262 xstream::xdr::istream xstr(&sbuf);
263 m_istr.read(crcbuf,4);
264 m_bytes_read += m_istr.gcount();
265 xstr >> recorded_crc;
266 xstream::digest::crc32 crc;
267 std::ostream out(&crc);
268 out.write(m_event_buffer,m_next_event_size+4);
269 out.flush();
270 if (crc.digest() != recorded_crc) {
271 char errmsg[] =
272 "WARNING: crc data integrity check failed"
273 " on hddm_mc_s input stream!"
274 "\nThis may be the result of a bug in the"
275 " xstream library if you are analyzing a data"
276 " file that was generated by code prior to svn"
277 " rev 18530.\nIf this concerns you, regenerate"
278 " using a newer build of the sim-recon tools"
279 " and it should go away.\n";
280 if ((m_status_bits & 0x02) == 0) {
281 std::cerr << errmsg << std::endl;
282 m_status_bits |= 0x02;
283 }
284 //throw std::runtime_error("hddm_mc_s::istream::operator>> error -"
285 // " crc check error on input stream!");
286 }
287 }
288
289 if (m_events_to_skip) {
290 --m_events_to_skip;
291 m_next_event_size = 0;
292 return *this >> record;
293 }
294 m_sbuf->reset();
295 m_sequencing = 0;
296 m_codon = &m_genome;
297 *this >> (streamable&)record;
298 m_istr.read(m_event_buffer,4);
299 m_bytes_read += m_istr.gcount();
300 if (m_istr.eof()) {
301 m_next_event_size = 0;
302 }
303 else if (!m_istr.good()) {
304 throw std::runtime_error("hddm_mc_s::istream::operator>> error - "
305 "read error on event size!");
306 }
307 else {
308 m_sbuf->reset();
309 *m_xstr >> m_next_event_size;
310 }
311 return *this;
312}
313
314ostream::ostream(std::ostream &src)
315 : m_xstr(0),
316 m_ostr(src),
317 m_xcmp(0),
318 m_xraw(0),
319 m_status_bits(k_default_status)
320{
321 m_ostr << HDDM::DocumentString();
322 if (!m_ostr.good()) {
323 throw std::runtime_error("hddm_mc_s::ostream::ostream(ostream) "
324 "error - write error on header output!");
325 }
326 m_event_buffer = new char[m_event_buffer_size = 100000];
327 m_sbuf = new ostreambuffer(m_event_buffer,m_event_buffer_size);
328 configure_streambufs();
329 m_records_written = 0;
330 m_bytes_written = 0;
331}
332
333ostream::~ostream() {
334 if (m_xstr) {
335 delete m_xstr;
336 }
337 if (m_xraw) {
338 m_ostr.flush();
339 m_ostr.rdbuf(m_xraw);
340 }
341 if (m_xcmp) {
342 delete m_xcmp;
343 }
344 if (m_sbuf) {
345 delete m_sbuf;
346 }
347 delete [] m_event_buffer;
348}
349
350void ostream::setCompression(int flags) {
351 if ((flags ^ m_status_bits) & k_bits_compression) {
352 m_status_bits &= ~k_bits_compression;
353 m_status_bits |= flags;
354 m_status_bits |= k_can_reposition;
355 m_sbuf->reset();
356 *m_xstr << 1 << 8 << 0 << m_status_bits;
357 m_ostr.write(m_sbuf->getbuf(),m_sbuf->size());
358 if (!m_ostr.good()) {
359 throw std::runtime_error("hddm_mc_s::ostream::setCompression"
360 " error - write error on token output!");
361 }
362 configure_streambufs();
363 }
364}
365
366void ostream::setIntegrityChecks(int flags) {
367 if ((flags ^ m_status_bits) & k_bits_integrity) {
368 m_status_bits &= ~k_bits_integrity;
369 m_status_bits |= flags;
370 m_sbuf->reset();
371 *m_xstr << 1 << 8 << 0 << m_status_bits;
372 m_ostr.write(m_sbuf->getbuf(),m_sbuf->size());
373 if (!m_ostr.good()) {
374 throw std::runtime_error("hddm_mc_s::ostream::setIntegrityChecks error - "
375 "write error on token output!");
376 }
377 }
378}
379
380streamposition ostream::getPosition() const {
381 streamposition pos;
382 pos.block_status = m_status_bits;
383 if (m_status_bits & k_bz2_compression) {
384 pos.block_start = m_xraw->pubseekoff(0,std::ios_base::cur,
385 std::ios_base::out);
386 pos.block_offset = ((xstream::bz::istreambuf*)m_xcmp)->get_block_offset();
387 }
388 else if (m_status_bits & k_z_compression) {
389 pos.block_start = m_xraw->pubseekoff(0,std::ios_base::cur,
390 std::ios_base::out);
391 pos.block_offset = ((xstream::z::istreambuf*)m_xcmp)->get_block_offset();
392 }
393 else {
394 pos.block_start = m_ostr.tellp();
395 pos.block_offset = 0;
396 }
397 return pos;
398}
399
400void ostream::configure_streambufs() {
401 if (m_xstr == 0) {
402 m_xstr = new xstream::xdr::ostream(m_sbuf);
403 }
404 if (m_xraw == 0 && (m_status_bits & k_z_compression) != 0) {
405 //std::cerr << "output switched on z compression" << std::endl;
406 m_xraw = m_ostr.rdbuf();
407 m_xcmp = new xstream::z::ostreambuf(m_xraw);
408 m_ostr.rdbuf(m_xcmp);
409 }
410 else if (m_xraw == 0 && (m_status_bits & k_bz2_compression) != 0) {
411 //std::cerr << "output switched on bz2 compression" << std::endl;
412 m_xraw = m_ostr.rdbuf();
413 m_xcmp = new xstream::bz::ostreambuf(m_xraw);
414 m_ostr.rdbuf(m_xcmp);
415 }
416 else if (m_xraw == 0 && (m_status_bits & k_bits_compression) != 0) {
417 throw std::runtime_error("hddm_mc_s::ostream::configure_streambufs error - "
418 "unrecognized compression flag requested.");
419 }
420 else if (m_xraw != 0) {
421 m_ostr.rdbuf(m_xraw);
422 delete m_xcmp;
423 m_xcmp = 0;
424 m_xraw = 0;
425 configure_streambufs();
426 }
427}
428
429int istream::getTag(const std::string &src, int start,
430 std::string &tag, int &level)
431{
432 tag = "";
433 size_t p_btag = src.find("<",start);
434 size_t p_bline = src.find_last_of("\n",p_btag);
435 if (p_bline == std::string::npos)
436 {
437 p_bline = 0;
438 }
439 else
440 {
441 ++p_bline;
442 }
443 level = (p_btag-p_bline)/2;
444 size_t p_etag = p_btag;
445 for (size_t quotes=0; p_etag < src.size(); ++p_etag) {
446 if (src[p_etag] == '"') {
447 tag += "\"";
448 ++quotes;
449 }
450 else if (quotes/2*2 != quotes) {
451 tag += src[p_etag];
452 }
453 else if (src.find_first_of(" \t\n",p_etag) == 0) {
454 tag += " ";
455 p_etag = src.find_first_not_of(" \t\n",p_etag)-1;
456 }
457 else if (src[p_etag] == '>') {
458 tag += ">";
459 break;
460 }
461 else {
462 tag += src[p_etag];
463 }
464 }
465 if (p_etag == src.size()) {
466 std::stringstream sstr;
467 sstr << "hddm_mc_s::istream::getTag"
468 << " error - bad header format" << std::endl
469 << " tag " << tag << " at position " << start
470 << std::endl;
471 throw std::runtime_error(sstr.str());
472 }
473 return p_etag+2;
474}
475
476int istream::getEndTag(const std::string &src, int start,
477 const std::string &tag)
478{
479 if (tag.rfind("/>") == tag.size()-2) {
480 return src.find(tag,start) + tag.size()+1;
481 }
482 else {
483 std::string etag = "</";
484 etag += tag.substr(1,tag.find_first_of(' ')-1) + ">";
485 size_t p_etag = src.find(etag,start);
486 size_t p_quote = src.find_first_of('"',start);
487 while (p_quote != std::string::npos && p_quote < p_etag) {
488 p_quote = src.find_first_of('"',p_quote+1);
489 if (p_quote > p_etag) {
490 p_etag = src.find(etag,p_quote+1);
491 }
492 p_quote = src.find_first_of('"',p_quote+1);
493 }
494 if (p_etag == std::string::npos) {
495 std::stringstream sstr;
496 sstr << "hddm_mc_s::istream::getEndTag"
497 << " error - bad header format" << std::endl
498 << " tag " << tag << " at position " << start
499 << std::endl
500 << " end tag " << etag << " not found."
501 << std::endl;
502 throw std::runtime_error(sstr.str());
503 }
504 return p_etag + etag.size()+1;
505 }
506}
507
508void istream::collide(const std::string &itag, const std::string &rtag) {
509 std::string itagname = itag.substr(1,itag.find(" ")-1);
510 std::string rtagname = rtag.substr(1,rtag.find(" ")-1);
511 std::string errmsg = "hddm_mc_s::istream::collide warning:\n"
512 "tag " + itagname + " in input file "
513 "does not match c++ header hddm_mc_s.hpp\n"
514 " input file: " + itag + "\n"
515 " c++ header: " + rtag + "\n"
516 " === Tag " + itagname + " will be ignored,"
517 " rebuild to cure the problem ===";
518 if (itagname != "HDDM") {
519 std::cerr << errmsg << std::endl;
520 }
521 else {
522 throw std::runtime_error(errmsg);
523 }
524}
525
526chromosome istream::synthesize(const std::string &src, int p_src,
527 const std::string &ref, int p_ref)
528{
529 chromosome chrom;
530 int slevel, rlevel;
531 std::string stag, rtag;
532 p_src = getTag(src,p_src,stag,slevel);
533 p_ref = getTag(ref,p_ref,rtag,rlevel);
534 std::string stagname = stag.substr(1,stag.find(" ")-1);
535 std::string rtagname = rtag.substr(1,rtag.find(" ")-1);
536 if (stagname != rtagname) {
537 throw std::runtime_error("hddm_mc_s::istream::synthesize error - matching algorithm error #2");
538 }
539 else if (!tags_match(stag,rtag)) {
540 collide(stag,rtag);
541 return chrom;
542 }
543
544 int p2_src, p2_ref;
545 int s2level, r2level;
546 std::string s2tag, r2tag;
547 getTag(src,p2_src=p_src,s2tag,s2level);
548 while (s2level > slevel) {
549 codon *gene = new codon();
550 std::string s2tagname = s2tag.substr(1,s2tag.find(" ")-1);
551 getTag(ref,p2_ref=p_ref,r2tag,r2level);
552 int order_of_this_tag_in_ref = 1;
553 while (r2level == s2level) {
554 std::string r2tagname = r2tag.substr(1,r2tag.find(" ")-1);
555 if (s2tagname == r2tagname) {
556 if (!tags_match(s2tag,r2tag)) {
557 collide(s2tag,r2tag);
558 break;
559 }
560 else {
561 gene->m_order = order_of_this_tag_in_ref;
562 }
563 gene->m_sequence = synthesize(src,p2_src,ref,p2_ref);
564 break;
565 }
566 p2_ref = getEndTag(ref,p2_ref,r2tag);
567 getTag(ref,p2_ref,r2tag,r2level);
568 ++order_of_this_tag_in_ref;
569 }
570 gene->m_tagname = s2tagname;
571 chrom.push_back(*gene);
572 delete gene;
573 p2_src = getEndTag(src,p2_src,s2tag);
574 getTag(src,p2_src,s2tag,s2level);
575 }
576 return chrom;
577}