char *token_to_string(Token *tok)
{
switch (tok->type) {
case TTYPE_IDENT:
return tok->sval;
case TTYPE_PUNCT:
case TTYPE_CHAR: {
String *s = make_string();
string_append(s, tok->c);
return get_cstring(s);
}
case TTYPE_INT: {
String *s = make_string();
string_appendf(s, "%d", tok->ival);
return get_cstring(s);
}
case TTYPE_STRING: {
String *s = make_string();
string_appendf(s, "\"%s\"", tok->sval);
return get_cstring(s);
}
default:
error("internal error: unknown token type: %d", tok->type);
}
}
static void test_string(void) {
String *s = make_string();
string_append(s, 'a');
assert_string("a", get_cstring(s));
string_append(s, 'b');
assert_string("ab", get_cstring(s));
string_appendf(s, ".");
assert_string("ab.", get_cstring(s));
string_appendf(s, "%s", "0123456789");
assert_string("ab.0123456789", get_cstring(s));
}
/* special handling: two string arguments */
JNIEXPORT void JNICALL Java_org_infradead_libopenconnect_LibOpenConnect_setClientCert(
JNIEnv *jenv, jobject jobj, jstring jcert, jstring jsslkey)
{
struct libctx *ctx = getctx(jenv, jobj);
const char *cert = NULL, *sslkey = NULL;
if (ctx && !get_cstring(ctx->jenv, jcert, &cert) &&
!get_cstring(ctx->jenv, jsslkey, &sslkey))
openconnect_set_client_cert(ctx->vpninfo, cert, sslkey);
release_cstring(ctx->jenv, jcert, cert);
release_cstring(ctx->jenv, jsslkey, sslkey);
return;
}
/* special handling: multiple string arguments */
JNIEXPORT jint JNICALL Java_org_infradead_libopenconnect_LibOpenConnect_setupTunDevice(
JNIEnv *jenv, jobject jobj, jstring jarg0, jstring jarg1)
{
struct libctx *ctx = getctx(jenv, jobj);
const char *arg0 = NULL, *arg1 = NULL;
int ret = -ENOMEM;
if (ctx && !get_cstring(ctx->jenv, jarg0, &arg0) &&
!get_cstring(ctx->jenv, jarg1, &arg1))
ret = openconnect_setup_tun_device(ctx->vpninfo, arg0, arg1);
release_cstring(ctx->jenv, jarg0, arg0);
release_cstring(ctx->jenv, jarg1, arg1);
return ret;
}
JNIEXPORT void JNICALL Java_org_infradead_libopenconnect_LibOpenConnect_setMobileInfo(
JNIEnv *jenv, jobject jobj, jstring jarg0, jstring jarg1, jstring jarg2)
{
struct libctx *ctx = getctx(jenv, jobj);
const char *arg0 = NULL, *arg1 = NULL, *arg2 = NULL;
if (ctx &&
!get_cstring(ctx->jenv, jarg0, &arg0) &&
!get_cstring(ctx->jenv, jarg1, &arg1) &&
!get_cstring(ctx->jenv, jarg2, &arg2))
openconnect_set_mobile_info(ctx->vpninfo, arg0, arg1, arg2);
release_cstring(ctx->jenv, jarg0, arg0);
release_cstring(ctx->jenv, jarg1, arg1);
release_cstring(ctx->jenv, jarg2, arg2);
}
static Token *make_ident(String *s)
{
Token *r = malloc(sizeof(Token));
r->type = TTYPE_IDENT;
r->sval = get_cstring(s);
return r;
}
static Token *make_strtok(String *s)
{
Token *r = malloc(sizeof(Token));
r->type = TTYPE_STRING;
r->sval = get_cstring(s);
return r;
}
bool forecast_from_bridge_dict(DictionaryIterator* dict, Forecast* forecast) {
// TBD: Test results - J. Speicher (8/9/13)
get_int16(dict, DUMMY_INTEGER_KEY, &forecast->dummy_integer);
get_int16(dict, ANOTHER_DUMMY_INTEGER_KEY, &forecast->another_dummy_integer);
get_cstring(dict, DUMMY_STRING_KEY, &forecast->dummy_string);
return true;
};
static char *get_caller_list(void) {
String *s = make_string();
for (Iter *i = list_iter(functions); !iter_end(i);) {
string_appendf(s, "%s", iter_next(i));
if (!iter_end(i))
string_appendf(s, " -> ");
}
return get_cstring(s);
}
JNIEXPORT void JNICALL Java_org_infradead_libopenconnect_LibOpenConnect_setCSDWrapper(
JNIEnv *jenv, jobject jobj, jstring jarg0, jstring jarg1, jstring jarg2)
{
struct libctx *ctx = getctx(jenv, jobj);
const char *arg0 = NULL, *arg1 = NULL, *arg2 = NULL;
if (ctx &&
!get_cstring(ctx->jenv, jarg0, &arg0) &&
!get_cstring(ctx->jenv, jarg1, &arg1) &&
!get_cstring(ctx->jenv, jarg2, &arg2)) {
openconnect_setup_csd(ctx->vpninfo, getuid(), 1, arg0);
openconnect_set_csd_environ(ctx->vpninfo, "TMPDIR", arg1);
openconnect_set_csd_environ(ctx->vpninfo, "PATH", arg2);
}
release_cstring(ctx->jenv, jarg0, arg0);
release_cstring(ctx->jenv, jarg1, arg1);
release_cstring(ctx->jenv, jarg2, arg2);
}
static Token *read_number(char c) {
String *s = make_string();
string_append(s, c);
for (;;) {
int c = getc(stdin);
if (!isdigit(c) && c != '.') {
ungetc(c, stdin);
return make_number(get_cstring(s));
}
string_append(s, c);
}
}
// Adds one MyString to another
MyString MyString::operator+(MyString& lhs_string){
return MyString(get_cstring(), lhs_string.get_cstring());
}
static void *read_det_cov(void *vd)
{
int i,err;
FILE *fptr;
string *s;
tokens *tok;
void *tbuf;
char *p,*p1,cc,*fname;
struct contig *c,*ctg;
struct tdc_par *tp;
count *ct,ct1,ct2;
struct lk_compress *lkc;
u_int32_t x;
tp=vd;
ctg=tp->ctg;
lkc=tp->lkc;
while((fname=get_input_file())) {
s=0;
tok=0;
tbuf=0;
err=0;
fptr=open_readfile(fname,&i,lkc);
if(!fptr) return 0;
printf("Reading detailed coverage file '%s'\n",fname);
c=0;
ct=0;
x=0;
while(!err) {
s=fget_string(fptr,s,&tbuf);
if(!s->len) break;
tok=tokenize(get_cstring(s),'\t',tok);
if(tok->n_tok==2) {
p=tok->toks[0];
if(*p=='>') {
if(!c || strcmp(c->name,p+1)) {
HASH_FIND_STR(ctg,p+1,c);
}
if(c) {
p=tok->toks[1];
x=strtoul(p,&p1,10)-1;
if(p==p1 || *p1) {
err=10;
fprintf(stderr,"(a) Bad file format\n");
}
ct=c->counts;
}
}
} else if(c) {
if(tok->n_tok!=1) {
fprintf(stderr,"(b) Bad file format\n");
err=-1;
}
p=tok->toks[0];
while(x<c->size && (cc=*p++)) {
if(cc>=33 && cc<=125) {
cc-=33;
ct1=(count)cc;
} else if(cc==126) {
ct1=(count)strtoul(p,&p1,16);
p=p1+1;
} else {
fprintf(stderr,"(c) Bad file format (%d) '%s'\n",cc,tok->toks[0]);
err=-1;
}
if(!err) {
pthread_mutex_lock(&c->mut);
ct2=ct[x];
if(ct2<MAX_COUNT) {
if(MAX_COUNT-ct2<ct1) ct[x]=MAX_COUNT;
else ct[x]=ct2+ct1;
}
pthread_mutex_unlock(&c->mut);
x++;
}
}
}
}
fclose(fptr);
if(s) free_string(s);
if(tok) free_tokens(tok);
if(tbuf) free_fget_buffer(&tbuf);
signal(SIGCHLD,SIG_DFL);
while(waitpid(-1,&i,WNOHANG)>0);
}
return 0;
}
static int read_ranges_file(char *fname,struct contig **contig_ptr,struct lk_compress *lkc)
{
int i,err;
u_int32_t x1,x1a,x2,x3,x;
struct contig *ctg,*c;
struct range_blk *r,*r1;
char *estr;
FILE *fptr;
string *s;
tokens *tok;
void *tbuf;
s=0;
tok=0;
tbuf=0;
err=0;
fptr=open_readfile_and_check(fname,&i,lkc);
printf("Reading ranges file '%s'\n",fname);
ctg=0;
while(!err) {
s=fget_string(fptr,s,&tbuf);
if(!s->len) break;
tok=tokenize(get_cstring(s),'\t',tok);
if(tok->n_tok>=3) {
HASH_FIND_STR(ctg,tok->toks[0],c);
if(!c) {
c=lk_malloc(sizeof(struct contig));
c->name=strdup(tok->toks[0]);
c->size=0;
c->ranges=lk_malloc(sizeof(struct range_blk));
c->ranges->idx=0;
c->ranges->next=0;
c->tranges=0;
c->counts=0;
c->tcounts=0;
c->tot_count=0;
c->tot_tcount=0;
c->tot_bases=0;
c->tot_tbases=0;
HASH_ADD_KEYPTR(hh,ctg,c->name,strlen(c->name),c);
}
r=c->ranges;
if(r->idx==RANGE_BLK_SIZE) {
r=lk_malloc(sizeof(struct range_blk));
r->idx=0;
r->next=c->ranges;
c->ranges=r;
}
x1=(u_int32_t)getlnumcolumn(tok,1,0,&estr);
if(!estr) x2=(u_int32_t)getlnumcolumn(tok,2,0,&estr);
if(estr || x1<1 || x2<x1) {
err=1;
fprintf(stderr,"Error in coordinate format: %s\n",estr);
} else {
r->name[r->idx]=getstrcolumn(tok,3,0,0);
r->x1[r->idx]=x1;
r->x2[r->idx++]=x2;
}
}
}
fclose(fptr);
if(s) free_string(s);
if(tok) free_tokens(tok);
if(tbuf) free_fget_buffer(&tbuf);
signal(SIGCHLD,SIG_DFL);
x2=x3=0;
for(c=ctg; c && !err; c=c->hh.next) {
x1=0;
r=c->ranges;
c->ranges=0;
while(r) {
for(i=0; i<r->idx; i++) {
if(r->x2[i]>x1) x1=r->x2[i];
}
r1=r->next;
r->next=c->ranges;
c->ranges=r;
r=r1;
}
c->size=x1;
x1a=0;
if(!x1) err=2;
else {
x2+=x1;
c->counts=lk_malloc(sizeof(count)*c->size);
for(i=0; i<(int)c->size; i++) c->counts[i]=NO_COUNT;
for(r=c->ranges; r; r=r->next) {
for(i=0; i<r->idx; i++) {
for(x=r->x1[i]-1; x<r->x2[i]; x++) c->counts[x]=0;
}
}
for(i=0; i<(int)c->size; i++) if(!c->counts[i]) x1a++;
}
c->tot_bases=x1a;
x3+=x1a;
}
printf("total=%u, in ranges=%u\n",x2,x3);
while(waitpid(-1,&i,WNOHANG)>0);
*contig_ptr=err?0:ctg;
return err;
}
static int process_file(char *fname,struct contig *ctg,int block_size,int fmt,u_int64_t *number,struct lk_compress *lkc)
{
int i,k,err,sz,nn;
FILE *fptr;
string *s;
tokens *tok;
void *tbuf;
char *p,*p1;
struct match m;
struct contig *c;
count *ct;
u_int32_t x,x1;
s=0;
tok=0;
tbuf=0;
err=0;
nn=(fmt==GEM_FMT?1:0);
fptr=open_readfile(fname,&i,lkc);
if(!fptr) return -1;
printf("Reading matches file '%s'\n",fname);
while(!err) {
s=fget_string(fptr,s,&tbuf);
if(!s->len) break;
tok=tokenize(get_cstring(s),'\t',tok);
if(tok->n_tok>=4+nn) {
p=tok->toks[2+nn];
i=0;
if(!isdigit(*p)) continue;
while(*p && !err) {
k=(int)strtol(p,&p1,10);
i+=k;
if(i>1) break;
if(*p1) {
if(*p1!=':' && *p1!='+') err=5;
else p1++;
}
p=p1;
if(!k && i) break;
}
if(err) {
fprintf(stderr,"Bad format for match number column '%s'\n",tok->toks[3]);
err=0;
continue;
} else if(i==1) {
p=parse_match(tok->toks[3+nn],fmt,&m);
if(!p) {
/* err=10;*/
fprintf(stderr,"Bad format for match\n");
continue;
} else {
if(*number) {
(*number)--;
if(!(*number)) {
err=1;
break;
}
}
HASH_FIND_STR(ctg,m.ctg,c);
if(c) {
sz=strlen(tok->toks[1]);
ct=c->counts;
x=m.pos-1;
if(block_size>1) {
if(m.orientation) {
for(i=0; i<sz; i++) {
if(x<c->size) {
x1=x/block_size;
x1*=block_size;
if(ct[x1]<MAX_COUNT) ct[x1]++;
}
if(!x) break;
x--;
}
} else {
for(i=0; i<sz && x<c->size; i++) {
x1=x/block_size;
x1*=block_size;
if(ct[x1]<MAX_COUNT) ct[x1]++;
x++;
}
}
} else {
if(m.orientation) {
for(i=0; i<sz; i++) {
if(x<c->size) {
if(ct[x]<MAX_COUNT) ct[x]++;
}
if(!x) break;
x--;
}
} else {
for(i=0; i<sz && x<c->size; i++) {
if(ct[x]<MAX_COUNT) ct[x]++;
x++;
}
}
}
if((ct=c->tcounts)) {
x=m.pos-1;
if(block_size>1) {
if(m.orientation) {
for(i=0; i<sz; i++) {
if(x<c->tsize) {
x1=x/block_size;
x1*=block_size;
if(ct[x1]<MAX_COUNT) ct[x1]++;
}
if(!x) break;
x--;
}
} else {
for(i=0; i<sz && x<c->tsize; i++) {
x1=x/block_size;
x1*=block_size;
if(ct[x1]<MAX_COUNT) ct[x1]++;
x++;
}
}
} else {
if(m.orientation) {
for(i=0; i<sz; i++) {
if(x<c->tsize) {
if(ct[x]<MAX_COUNT) ct[x]++;
}
if(!x) break;
x--;
}
} else {
for(i=0; i<sz && x<c->tsize; i++) {
if(ct[x]<MAX_COUNT) ct[x]++;
x++;
}
}
}
}
}
}
}
}
}
fclose(fptr);
if(s) free_string(s);
if(tok) free_tokens(tok);
if(tbuf) free_fget_buffer(&tbuf);
signal(SIGCHLD,SIG_DFL);
while(waitpid(-1,&i,WNOHANG)>0);
return err;
}
static int read_target_file(char *fname,struct contig *ctg,int extend,struct lk_compress *lkc)
{
int i,err;
u_int32_t x1,x2,x3,x,cs,x1a;
struct contig *c;
struct range_blk *r;
char *estr;
FILE *fptr;
string *s;
tokens *tok;
void *tbuf;
s=0;
tok=0;
tbuf=0;
err=0;
fptr=open_readfile_and_check(fname,&i,lkc);
printf("Reading target file '%s'\n",fname);
while(!err) {
s=fget_string(fptr,s,&tbuf);
if(!s->len) break;
tok=tokenize(get_cstring(s),'\t',tok);
if(tok->n_tok>=3) {
HASH_FIND_STR(ctg,tok->toks[0],c);
if(c) {
r=c->tranges;
if(!r) {
r=c->tranges=lk_malloc(sizeof(struct range_blk));
r->idx=0;
} else {
if(r->idx==RANGE_BLK_SIZE) {
r=lk_malloc(sizeof(struct range_blk));
r->idx=0;
r->next=c->tranges;
c->tranges=r;
}
}
x1=(u_int32_t)getlnumcolumn(tok,1,0,&estr);
if(!estr) x2=(u_int32_t)getlnumcolumn(tok,2,0,&estr);
if(estr || x1<1 || x2<x1) {
err=1;
fprintf(stderr,"Error in coordinate format: %s\n",estr);
} else {
if(x1<=(unsigned int)extend) x1=1;
else x1-=extend;
x2+=extend;
if(x1<1) x1=1;
r->name[r->idx]=getstrcolumn(tok,3,0,0);
r->x1[r->idx]=x1;
r->x2[r->idx++]=x2;
}
} else {
printf("Not found %s\n",tok->toks[0]);
}
}
}
fclose(fptr);
if(s) free_string(s);
if(tok) free_tokens(tok);
if(tbuf) free_fget_buffer(&tbuf);
signal(SIGCHLD,SIG_DFL);
x2=x3=0;
for(c=ctg; c && !err; c=c->hh.next) {
if(!c->tranges) continue;
x1=0;
for(r=c->tranges; r; r=r->next) {
for(i=0; i<r->idx; i++) {
if(r->x2[i]>x1) x1=r->x2[i];
}
}
if(x1>c->size) x1=c->size;
c->tsize=x1;
x1a=0;
if(!x1) {
fprintf(stderr,"Illegal target range for %s\n",c->name);
err=2;
continue;
} else {
x2+=x1;
/* printf("%s\t%d\n",c->name,c->tsize);*/
c->tcounts=lk_malloc(sizeof(count)*c->tsize);
cs=c->tsize;
for(i=0; i<(int)cs; i++) c->tcounts[i]=NO_COUNT;
for(r=c->tranges; r; r=r->next) {
for(i=0; i<r->idx; i++) {
for(x=r->x1[i]-1; x<r->x2[i]; x++) {
if(x>=cs) break;
if(!c->counts[x]) c->tcounts[x]=0;
}
}
}
for(i=0; i<(int)cs; i++) if(!c->tcounts[i]) x1a++;
}
c->tot_tbases=x1a;
x3+=x1a;
}
printf("total=%u, on target=%u\n",x2,x3);
while(waitpid(-1,&i,WNOHANG)>0);
return err;
}