void nullpointer1()
{
checkNullPointer("int foo(const Token *tok)\n"
"{\n"
" while (tok);\n"
" tok = tok->next();\n"
"}\n");
ASSERT_EQUALS("[test.cpp:4]: (error) Possible null pointer dereference\n", errout.str());
checkNullPointer("void foo()\n"
"{\n"
" for (const Token *tok = tokens; tok; tok = tok->next())\n"
" {\n"
" while (tok && tok->str() != \";\")\n"
" tok = tok->next();\n"
" }\n"
"}\n");
ASSERT_EQUALS("[test.cpp:3]: (error) Possible null pointer dereference\n", errout.str());
checkNullPointer("void foo()\n"
"{\n"
" for (const Token *tok = tokens; tok; tok = tok ? tok->next() : NULL)\n"
" {\n"
" while (tok && tok->str() != \";\")\n"
" tok = tok->next();\n"
" }\n"
"}\n");
ASSERT_EQUALS("", errout.str());
}
// Dereferencing a pointer and then checking if it is null
void nullpointer4()
{
// errors..
checkNullPointer("void foo(int *p)\n"
"{\n"
" *p = 0;\n"
" if (!p)\n"
" ;\n"
"}\n");
ASSERT_EQUALS("[test.cpp:3]: (error) Possible null pointer dereference\n", errout.str());
// no error
checkNullPointer("void foo()\n"
"{\n"
" int *p;\n"
" f(&p);\n"
" if (!p)\n"
" ;\n"
"}\n");
ASSERT_EQUALS("", errout.str());
checkNullPointer("void foo()\n"
"{\n"
" int **p = f();\n"
" if (!p)\n"
" ;\n"
"}\n");
ASSERT_EQUALS("", errout.str());
checkNullPointer("void foo(int *p)\n"
"{\n"
" if (x)\n"
" p = 0;\n"
" else\n"
" *p = 0;\n"
" if (!p)\n"
" ;\n"
"}\n");
ASSERT_EQUALS("", errout.str());
checkNullPointer("void foo(int x)\n"
"{\n"
" int a = 2 * x;"
" if (x == 0)\n"
" ;\n"
"}\n");
ASSERT_EQUALS("", errout.str());
}
void Card::setStatic()
{
if(state->isActive())
{
delete state;
CardState *nState = new CardStateStatic(this);
checkNullPointer(nState);
state = nState;
}
}
void nullpointer2()
{
// Null pointer dereference can only happen with pointers
checkNullPointer("void foo()\n"
"{\n"
" Fred fred;\n"
" while (fred);\n"
" fred.hello();\n"
"}\n");
ASSERT_EQUALS("", errout.str());
}
Card::Card(unsigned short num, GameWindow *window, QWidget *parent)
: QWidget(parent),
number(num), gameWindow(window)
{
state = new CardStateStatic(this);
checkNullPointer(state);
std::string path = std::string(Card::IMG_PATH) + std::to_string(number) + std::string(Card::IMG_EXT);
QPixmap logo(path.c_str());
logo = logo.scaledToHeight(Card::DEFAULT_HEIGHT);
int height = logo.height(),
width = logo.width();
resize(width, height);
label = new QLabel(this);
checkNullPointer(label, [=]() {
delete state;
});
label->setGeometry(0, 0, width, height);
label->setPixmap(logo);
label->show();
}
/* read one or more query files specified with an option -i */
void getFileNames(int argc, char *argv[], char list[], char c, char ***fileNames, int *cntFiles, int *arg) {
char **r;
int numberOfFiles = 1;
// get all file names (supposition: file name cannot start with -)
while ((*arg + numberOfFiles) < argc && argv[*arg + numberOfFiles][0] != '-') {
*fileNames = (char **)erealloc(*fileNames, numberOfFiles * sizeof (char *));
r = *fileNames;
r[numberOfFiles - 1] = argv[*arg + numberOfFiles];
checkNullPointer(c, r[numberOfFiles - 1]);
++ numberOfFiles;
}
*cntFiles = numberOfFiles - 1; // set the argument
checkMultipleArgDef(list, c);
// position of the new argument (-1 because arg is increased by 1 as the last step of while loop)
*arg = *arg + numberOfFiles - 1;
}
Args *getArgs(int argc, char *argv[]){
Args *args;
// char **r;
char c;
int arg;
// int numberOfFiles;
char list[256] = {0}; // options are not yet set
args = (Args *)emalloc(sizeof(Args));
args->i = NULL;
args->j = NULL;
args->o = NULL;
args->h = 0;
args->p = 0;
args->e = 0;
args->d = NULL;
args->n = NAMELENGTH;
args->D = DEFAULT_D;
args->w = DEFAULT_W;
args->c = 0;
args->q = 10000;
args->W = NULL;
args->P = 1-DEFAULT_P;
args->v = 0;
arg = 1;
args->m = DEFAULT_M;
args->t = 0;
args->r = 0;
args->s = 0;
args->f = -1;
// if none of the options is set as an argument, then take o1
args->o1 = 0;
args->o2 = 0;
args->I = NULL;
args->M = 0; // default min window sum to be considered relevant
while(arg < argc){
c = argv[arg][1];
switch (c){
case 'i': /* query file; if the option -d is included */
checkNullPointer(c, argv[arg]);
//args->i = argv[arg]; /* then search for the query file: (1) in the program's dir (2) in the directory specified with -d*/
// read one or more query files specified with an option -i
getFileNames(argc, argv, list, c, &args->i, &args->queryFileNumber, &arg);
break;
case 'j': /* subject files */
/* check that -d and -j option are used mutually exclusive! */
if (args->d) {
eprintf("Options -d and -j are mutually exclusive");
}
else {
getFileNames(argc, argv, list, c, &args->j, &args->subjectFileNumber, &arg);
break;
}
case 'd': /* directory where the subject files are saved and possibly the query file */
if (args->j) {
eprintf("Options -d and -j are mutually exclusive");
}
else {
args->d = argv[++arg];
checkNullPointer(c, args->d);
checkMultipleArgDef(list, c);
break;
}
case 'o': /* output file */
checkNullPointer(c, argv[++arg]);
args->o = argv[arg];
checkMultipleArgDef(list, c);
break;
case 'n': /* number of characters from header line printed */
checkNullPointer(c, argv[++arg]);
args->n = atoi(argv[arg]);
if(args->n < 0) {
args->n = INT_MAX;
}
checkMultipleArgDef(list, c);
break;
case 'D': /* maximum depth of suffix tree */
args->D = atoi(argv[++arg]);
checkNullPointer(c, argv[arg]);
checkMultipleArgDef(list, c);
break;
case 'w': /* window width and window increment */
checkNullPointer(c, argv[++arg]);
args->w = atoi(argv[arg]);
checkMultipleArgDef(list, c);
break;
case 'c': /* sliding window increment */
checkNullPointer(c, argv[++arg]);
args->c = atoi(argv[arg]);
checkMultipleArgDef(list, c);
break;
case 'v': /* print program version test */
args->v = 1;
break;
case 'h': /* print help */
args->h = 1;
break;
case 'W': /* output file where window analysis for all subjects are printed */
args->W = argv[++arg];
checkNullPointer(c, args->W);
checkMultipleArgDef(list, c);
break;
case 'P': /* fraction of random shustrings excluded from analysis */
args->P = atof(argv[++arg]);
if (args->P < 0) {
args->P = 0;
}
else if(args->P > 1) {
args->P = 1;
}
args->P = 1 - args->P;
break;
case 'q': /* fast search - size of mini list*/
args->q = atol(argv[++arg]);
if (args->q < 0) {
args->q = 1000;
}
break;
case 'm': /* multiplier for maxshulen by chance alone -- used for defining significant intervals */
args->m = atol(argv[++arg]);
if (args->m < 0) {
args->m = DEFAULT_M;
}
break;
case 't': /* print run-time information */
args->t = 1;
break;
case 'r': /* print runner(s)-up information */
args->r = 1;
break;
case 'f': /* minimal length of recombination fragment */
args->f = atoi(argv[++arg]);
//if (args->f < 0) {
// args->f = (int)args->w;
//}
break;
case 'o1': /* each annotation has the same subject set over all windows within annotation */
args->o1 = 1;
break;
case 'o2': /* subject set of an annotation is a subset of all windows within annotation */
args->o2 = 1;
break;
case 'M': /* minimal sum: max shulen by chance alone x window size */
args->M = 1;
break;
case 'I': /* name of input file that contains list of intervals; used for windows analysis based on precomputed intervals */
args->I = argv[++arg];
checkNullPointer(c, args->I);
checkMultipleArgDef(list, c);
break;
default:
printf("# unknown argument: %c\n", c);
args->e = 1;
return args;
} // end switch
arg++;
} // end while
// allowed stdin?
// if (!args->i) {
// printf("ERROR[gt]: Query file must be specified using -i option!\n");
// args->e = 1;
//}
if (args->c == 0) {
args->c = (int)((float)args->w/10. + 0.5);
}
if (args->f < 0) {
//args->f = (int)args->c;
args->f = (int)((float)args->w / 4. + 0.5);
}
if (args->w < args->c) {
printf("ERROR: Sliding window increment is greater than window size\n");
args->e = 1;
}
if (!args->o1 && !args->o2) {
args->o1 = 1; // when none of the options is set, set o1 as default
}
else if (args->o1 && args->o2) {
printf("ERROR: Options 1 and 2 are mutually exclusive\n");
args->e = 1;
}
if (args->o && args->I) {
printf("Interval analysis exists, so it won't be computed again (-o will be ignored)\n");
}
return args;
}
extern "C" JNIEXPORT int
JVM_handle_linux_signal(int sig,
siginfo_t* info,
void* ucVoid,
int abort_if_unrecognized) {
// in fact this isn't ucontext_t* at all, but struct sigcontext*
// but Linux porting layer uses ucontext_t, so to minimize code change
// we cast as needed
ucontext_t* ucFake = (ucontext_t*) ucVoid;
sigcontext* uc = (sigcontext*)ucVoid;
Thread* t = ThreadLocalStorage::get_thread_slow();
SignalHandlerMark shm(t);
// Note: it's not uncommon that JNI code uses signal/sigset to install
// then restore certain signal handler (e.g. to temporarily block SIGPIPE,
// or have a SIGILL handler when detecting CPU type). When that happens,
// JVM_handle_linux_signal() might be invoked with junk info/ucVoid. To
// avoid unnecessary crash when libjsig is not preloaded, try handle signals
// that do not require siginfo/ucontext first.
if (sig == SIGPIPE || sig == SIGXFSZ) {
// allow chained handler to go first
if (os::Linux::chained_handler(sig, info, ucVoid)) {
return true;
} else {
if (PrintMiscellaneous && (WizardMode || Verbose)) {
char buf[64];
warning("Ignoring %s - see bugs 4229104 or 646499219",
os::exception_name(sig, buf, sizeof(buf)));
}
return true;
}
}
JavaThread* thread = NULL;
VMThread* vmthread = NULL;
if (os::Linux::signal_handlers_are_installed) {
if (t != NULL ){
if(t->is_Java_thread()) {
thread = (JavaThread*)t;
}
else if(t->is_VM_thread()){
vmthread = (VMThread *)t;
}
}
}
// decide if this trap can be handled by a stub
address stub = NULL;
address pc = NULL;
address npc = NULL;
//%note os_trap_1
if (info != NULL && uc != NULL && thread != NULL) {
pc = address(SIG_PC(uc));
npc = address(SIG_NPC(uc));
// Check to see if we caught the safepoint code in the
// process of write protecting the memory serialization page.
// It write enables the page immediately after protecting it
// so we can just return to retry the write.
if ((sig == SIGSEGV) && checkSerializePage(thread, (address)info->si_addr)) {
// Block current thread until the memory serialize page permission restored.
os::block_on_serialize_page_trap();
return 1;
}
if (checkPrefetch(uc, pc)) {
return 1;
}
// Handle ALL stack overflow variations here
if (sig == SIGSEGV) {
if (checkOverflow(uc, pc, (address)info->si_addr, thread, &stub)) {
return 1;
}
}
if (sig == SIGBUS &&
thread->thread_state() == _thread_in_vm &&
thread->doing_unsafe_access()) {
stub = StubRoutines::handler_for_unsafe_access();
}
if (thread->thread_state() == _thread_in_Java) {
do {
// Java thread running in Java code => find exception handler if any
// a fault inside compiled code, the interpreter, or a stub
if ((sig == SIGSEGV) && checkPollingPage(pc, (address)info->si_addr, &stub)) {
break;
}
if ((sig == SIGBUS) && checkByteBuffer(pc, &stub)) {
break;
}
if ((sig == SIGSEGV || sig == SIGBUS) &&
checkVerifyOops(pc, (address)info->si_addr, &stub)) {
break;
}
if ((sig == SIGSEGV) && checkZombie(uc, &pc, &stub)) {
break;
}
if ((sig == SIGILL) && checkICMiss(uc, &pc, &stub)) {
break;
}
if ((sig == SIGFPE) && checkFPFault(pc, info->si_code, thread, &stub)) {
break;
}
if ((sig == SIGSEGV) &&
checkNullPointer(pc, (intptr_t)info->si_addr, thread, &stub)) {
break;
}
} while (0);
// jni_fast_Get<Primitive>Field can trap at certain pc's if a GC kicks in
// and the heap gets shrunk before the field access.
if ((sig == SIGSEGV) || (sig == SIGBUS)) {
checkFastJNIAccess(pc, &stub);
}
}
if (stub != NULL) {
// save all thread context in case we need to restore it
thread->set_saved_exception_pc(pc);
thread->set_saved_exception_npc(npc);
set_cont_address(uc, stub);
return true;
}
}
// signal-chaining
if (os::Linux::chained_handler(sig, info, ucVoid)) {
return true;
}
if (!abort_if_unrecognized) {
// caller wants another chance, so give it to him
return false;
}
if (pc == NULL && uc != NULL) {
pc = os::Linux::ucontext_get_pc((ucontext_t*)uc);
}
// unmask current signal
sigset_t newset;
sigemptyset(&newset);
sigaddset(&newset, sig);
sigprocmask(SIG_UNBLOCK, &newset, NULL);
VMError err(t, sig, pc, info, ucVoid);
err.report_and_die();
ShouldNotReachHere();
}
// Dereferencing a struct and then checking if it is null
void nullpointer3()
{
// errors..
checkNullPointer("void foo(struct ABC *abc)\n"
"{\n"
" int *a = abc->a;\n"
" if (!abc)\n"
" ;\n"
"}\n");
ASSERT_EQUALS("[test.cpp:3]: (error) Possible null pointer dereference\n", errout.str());
// ok dereferencing in a condition
checkNullPointer("void foo(struct ABC *abc)\n"
"{\n"
" if (abc && abc->a);\n"
" if (!abc)\n"
" ;\n"
"}\n");
ASSERT_EQUALS("", errout.str());
// ok to use a linked list..
checkNullPointer("void foo(struct ABC *abc)\n"
"{\n"
" abc = abc->next;\n"
" if (!abc)\n"
" ;\n"
"}\n");
ASSERT_EQUALS("", errout.str());
// reassign struct..
checkNullPointer("void foo(struct ABC *abc)\n"
"{\n"
" a = abc->a;\n"
" abc = abc->next;\n"
" if (!abc)\n"
" ;\n"
"}\n");
ASSERT_EQUALS("", errout.str());
checkNullPointer("void foo(struct ABC *abc)\n"
"{\n"
" a = abc->a;\n"
" f(&abc);\n"
" if (!abc)\n"
" ;\n"
"}\n");
ASSERT_EQUALS("", errout.str());
// goto..
checkNullPointer("void foo(struct ABC *abc)\n"
"{\n"
" if (!abc)\n"
" goto out;"
" a = abc->a;\n"
" return;\n"
"out:\n"
" if (!abc)\n"
" ;\n"
"}\n");
ASSERT_EQUALS("", errout.str());
// loops..
checkNullPointer("void freeAbc(struct ABC *abc)\n"
"{\n"
" while (abc)\n"
" {\n"
" struct ABC *next = abc->next;\n"
" if (abc) delete abc;\n"
" abc = next;\n"
" }\n"
"}\n");
ASSERT_EQUALS("", errout.str());
checkNullPointer("void foo(struct ABC *abc)\n"
"{\n"
" int a = abc->a;"
" do\n"
" {\n"
" if (abc)\n"
" abc = abc->next;\n"
" --a;\n"
" }\n"
" while (a > 0)\n"
"}\n");
ASSERT_EQUALS("", errout.str());
}
void checkMultipleArgDef(char list[], char c) {
#elif WIN
static void checkMultipleArgDef(char list[], char c) {
#endif
if(!list[(int)c]){
list[(int)c] = 1;
}
else {
printf("Warning: -%c multiply defined\n", c); // or error ???????
}
}
/* check whether an argument is a null pointer */
#if UNIX
void checkNullPointer(char c, char *arg) {
#elif WIN
static void checkNullPointer(char c, char *arg) {
#endif
if (!arg) {
eprintf("[ERROR] Option -%c: argument is NULL!\n", c);
}
}
Args *getArgs(int argc, char *argv[]){
Args *args;
char **r;
char c;
int arg = 1;
int numberOfFiles = 0;
char list[256] = {0}; // options are not yet set
args = (Args *)emalloc(sizeof(Args));
args->j = NULL;
args->o = NULL;
args->h = 0;
args->p = 0;
args->e = 0;
args->t = 0;
args->g = 0;
args->d = NULL;
args->n = NULL;
args->D = DEFAULT_D;
args->subjectFileNumber = 0;
/* Parameters for the divergence calculation */
/* When this values are all set to 0, then the Kr results are the same as for the original divergence calculation from the old kr program */
/* These default values are set to increase the speed of the divergence calculation, with keeping the Kr results with relative error < 1%*/
args->E = DEFAULT_E;
args->T = DEFAULT_T;
args->M = DEFAULT_M;
//args->P = 0.5;
/* best tree results ? with args->P == 0 */
args->P = 0;
if (arg == argc) {
return args;
}
while (arg < argc) {
if (argv[arg][0] == '-') {
c = argv[arg][1];
switch (c) {
case 'j': /* subject files */
/* check that -d and -j option are used mutually exclusive! */
if (args->d) {
eprintf("Options -d and -j are mutually exclusive!");
}
else if (numberOfFiles > 0) {
eprintf("Input files were already defined!");
}
else {
// get all query subject names
// (supposition: file name cannot start with -)
numberOfFiles = 1;
while ((arg + numberOfFiles) < argc && argv[arg + numberOfFiles][0] != '-') {
args->j = (char **)erealloc(args->j, numberOfFiles * sizeof (char *));
r = args->j;
r[numberOfFiles - 1] = argv[arg + numberOfFiles];
checkNullPointer(c, r[numberOfFiles - 1]);
++ numberOfFiles;
}
args->subjectFileNumber = numberOfFiles - 1; // set the argument
if (args->subjectFileNumber == 0) {
checkNullPointer(c, NULL);
}
checkMultipleArgDef(list, c);
// position of the new argument (-1 because arg is increased by 1 as the last step of while loop)
arg = arg + numberOfFiles - 1;
break;
}
case 'd': /* directory where the subject files are saved and possibly the query file */
if (args->j) {
eprintf("Options -d and -j are mutually exclusive!");
}
else {
args->d = argv[++arg];
if (args->d[0] == '-') {
args->d = NULL;
}
checkNullPointer(c, args->d);
checkMultipleArgDef(list, c);
break;
}
case 'o': /* output file */
checkNullPointer(c, argv[++arg]);
args->o = argv[arg];
checkMultipleArgDef(list, c);
break;
case 'n': /* output file - phylip/neighbor format */
checkNullPointer(c, argv[++arg]);
args->n = argv[arg];
checkMultipleArgDef(list, c);
break;
//case 'n': /* number of characters from header line printed */
// checkNullPointer(c, argv[++arg]);
// args->n = atoi(argv[arg]);
// if(args->n < 0) {
// args->n = INT_MAX;
// }
// checkMultipleArgDef(list, c);
// break;
case 'D': /* maximum depth of suffix tree */
args->D = atoi(argv[++arg]);
checkNullPointer(c, argv[arg]);
checkMultipleArgDef(list, c);
break;
case 'p': /* print program information test */
args->p = 1;
break;
case 'g': /* use global GC content */
args->g = 1;
break;
case 'h': /* print help */
args->h = 1;
break;
case 't': /* print run-time */
args->t = 1;
break;
case 'P': /* fraction of random shustrings excluded from analysis */
args->P = atof(argv[++arg]);
if (args->P < 0) {
args->P = 0;
}
else if(args->P > 1) {
args->P = 1;
}
break;
/* parameters for the divergence calculation */
case 'E': /* function divergence: errd */
args->E = atof(argv[++arg]);
if (args->E < 0) {
args->E = 0;
}
else if (args->E > 1) {
args->E = DEFAULT_E;
}
break;
case 'T': /* function expShulen: t1 */
args->T = atof(argv[++arg]);
if (args->T < 0) {
args->T = 0;
}
else if (args->T > 1) {
args->T = DEFAULT_T;
}
break;
case 'M': /* function pmax: m_t */
args->M = atof(argv[++arg]);
if (args->M < 0) {
args->M = 0;
}
else if (args->M > 1) {
args->M = DEFAULT_M;
}
break;
default:
printf("# unknown argument: %c\n", c);
args->e = 1;
return args;
} // end switch
}
else {
// get all query subject names - "fake" option '*'
// (supposition: file name cannot start with -)
numberOfFiles = 0;
while (arg < argc && argv[arg][0] != '-') {
args->j = (char **)erealloc(args->j, (numberOfFiles + 1)* sizeof (char *));
r = args->j;
r[numberOfFiles] = argv[arg];
checkNullPointer('*', r[numberOfFiles]);
++ numberOfFiles;
++ arg;
}
args->subjectFileNumber = numberOfFiles; // set the argument
if (args->subjectFileNumber == 0) {
checkNullPointer('*', NULL);
}
checkMultipleArgDef(list, '*');
// position of the new argument (-1 because arg is increased by 1 as the last step of while loop, and -1 because it again increases in the while-loop)
arg = arg - 1;
}
arg++;
}
return args;
}
void printUsage(char *version){
printf("kr version %s ", version);
printf("distributed under the GNU General Public License.\n");
printf("purpose: estimate pairwise distances, K_r, from DNA sequences\n");
printf("usage: %s [options] [filenames]\n", progname());
printf(" or: %s [options] -j <FILE(s)> \n", progname());
printf(" or: %s [options] -d <DIRECTORY> \n", progname());
printf("options:\n");
printf("\t[-o <FILE> write output to FILE; default: FILE=stdout]\n");
printf("\t[-n <FILE> write detailed output to FILE]\n");
printf("\t[-t print run-time in the detailed output file; printed only when option -n is used]\n");
printf("\t[-D <NUM> maximum depth of suffix tree; default: %d]\n", DEFAULT_D);
printf("\t[-P <NUM> fraction of random shustrings excluded from analysis; P e [0, 1]; default: 0]\n");
printf("\t[-E <NUM> relative divergence error; default: %lf]\n", DEFAULT_E);
printf("\t[-T <NUM> relative error of the average shustring length; default: %lf]\n", DEFAULT_T);
printf("\t[-M <NUM> threshold for small values of logarithm; default: %lf]\n", DEFAULT_M);
printf("\t[-g use global GC content (fast); default: use pairwise GC content (slow, accurate)]\n");
printf("\t[-p print information about program]\n");
printf("\t[-h print this help message]\n");
}
