char *only_global(char *line,char **current_section,int *global)
{
char *c,*s=line,*globals,*found,*end_section;
globals=(char *)calloc(strlen(line)+1,sizeof(char *));
end_section=(char *)xmalloc(1);
while(1) {
if (*global) {
if((found=strstr(s,"<"))==NULL) {
strncat(globals,s,found-s);
break;
}
if((c=strstr(found,">"))==NULL) break;
*global=0;
strncat(globals,s,(found-s));
*current_section=(char *)xrealloc(*current_section,(c-found)+1);
memset(*current_section,'\0',(c-found)+1);
strncat(*current_section,found+1,c-found-1);
s=c;
}
if(*current_section!=NULL) {
end_section=(char *) xrealloc(end_section,strlen(*current_section)+strlen("</")+strlen(">")+1);
strcpy(end_section,"</");
strcat(end_section,*current_section);
strcat(end_section,">");
if((found=istrstr(s,end_section))==NULL) {
break;
}
s=found+strlen(end_section);
*global=1;
}
}
return(globals);
}
int fetchsms (char *pdu, int sim)
{
char answer[ANSWERSIZE];
int position;
int beginning;
int end;
int foo,err;
/* Added for STAC: the input data must be considered tainted! */
answer[0] = taint();
/* Input magically appears */
answer[ANSWERSIZE-1] = EOS;
/* Search for NEEDLE and skip it */
position=istrstr(answer,NEEDLE);
if (position==-1)
return 0;
beginning = position + NEEDLE_SZ + 1;
/* BAD */
r_strcpy(pdu,answer+beginning);
return sim;
}
int fetchsms (char *pdu, int sim)
{
char answer[ANSWERSIZE];
int position;
int beginning;
int end;
int foo,err;
/* Added for STAC: the input data must be considered tainted! */
answer[0] = taint();
/* Input magically appears */
answer[ANSWERSIZE-1] = EOS;
/* Search for NEEDLE and skip it */
position=istrstr(answer,NEEDLE);
if (position==-1)
return 0;
beginning = position + NEEDLE_SZ + 1;
/* Answer must contain NEEDLE2; we don't need to skip it. */
if (istrstr(answer, NEEDLE2) == -1)
return 0;
/* Find (something)\r(something)\r, where each (something) is at
* least MIN_DIFF characters
*
* If we don't find anything satisfying that, abort
*/
for( end=beginning ; answer[end] != EOS && answer[end] != '\r' ; end++ );
if ( answer[end] == EOS || end-beginning < MIN_DIFF)
return 0;
for( end=end+1 ; answer[end] != EOS && answer[end] !='\r' ; end++ );
if ( answer[end] == EOS || end-beginning < MIN_DIFF )
return 0;
/* Change the last '\r' to an EOS */
answer[end] = EOS;
/* BAD */
r_strcpy(pdu,answer+beginning);
return sim;
}
int fetchsms(char *pdu , int sim )
{ char answer[(2 + 2 * 256) + 2] ;
int position ;
int beginning ;
int end ;
int __retres ;
{answer[0] = (char )taint();
answer[((2 + 2 * 256) + 2) - 1] = (char)0;
position = istrstr(answer, "+C");
if (position == -1) {__retres = 0;
goto return_label;}
beginning = (position + 2) + 1;
end = beginning;
while (1) {if ((int )answer[end] != 0)
{if (! ((int )answer[end] != '\r')) {break;}
}
else {break;}
end ++;}
if ((int )answer[end] == 0) {__retres = 0;
goto return_label;}
else {if (end - beginning < 256) {__retres = 0;
goto return_label;}
}
end ++;
while (1) {if ((int )answer[end] != 0)
{if (! ((int )answer[end] != '\r')) {break;}
}
else {break;}
end ++;}
if ((int )answer[end] == 0) {__retres = 0;
goto return_label;}
else {if (end - beginning < 256) {__retres = 0;
goto return_label;}
}
/* STAC: BAD */
answer[end] = (char)0;
/* STAC: BAD */
r_strcpy(pdu, answer + beginning);
__retres = sim;
return_label: /* CIL Label */
return (__retres);}
}
int fetchsms(char *pdu , int sim )
{ char answer[(2 + 2 * 256) + 2] ;
int position ;
int beginning ;
int __retres ;
{answer[0] = (char )taint();
answer[((2 + 2 * 256) + 2) - 1] = (char)0;
position = istrstr(answer, "+C");
if (position == -1) {__retres = 0;
goto return_label;}
beginning = (position + 2) + 1;
/* STAC: BAD */
r_strcpy(pdu, answer + beginning);
__retres = sim;
return_label: /* CIL Label */
return (__retres);}
}
// ----------------------------------------------------------------------------
void CMultiReaderApp::xProcessNewick(
const CArgs& args,
CNcbiIstream& istr,
CNcbiOstream& ostr)
// ----------------------------------------------------------------------------
{
string strTree;
char c = istr.get();
while (!istr.eof()) {
strTree += c;
if (c == ';') {
CNcbiIstrstream istrstr(strTree.c_str());
auto_ptr<TPhyTreeNode> pTree(ReadNewickTree(istrstr) );
CRef<CBioTreeContainer> btc = MakeBioTreeContainer(pTree.get());
xWriteObject(*btc, ostr);
strTree.clear();
}
c = istr.get();
}
}
/*
*
* reads a variable out the configfile
* fp = stream
* var_name = variable name
* section_name = section name
* if NULL sections are ignored
* mode = 0 -> normal mode
* 1 -> get only global variables
* return = value
* = NULL bij een fout
*
*/
char * real_get_config(FILE *fp,char *section_name,char *var_name,int mode)
{
int l;
int sect=0,global=1;
char *r=NULL,*c=NULL,*ss=NULL,s[BUFFER_LEN],*start_section=NULL;
char *end_section=NULL,*current_section=NULL;
if(var_name==NULL)
return(NULL);
if(fp==NULL)
return NULL;
fseek(fp,0,SEEK_SET);
if (s==NULL)
return(NULL);
if (section_name!=NULL) {
start_section=(char *)xmalloc(strlen(section_name)+1+strlen("<")+strlen(">"));
end_section=(char *)xmalloc(strlen(section_name)+1+strlen("</")+strlen(">"));
strcpy(start_section,"<");
strcat(start_section,section_name);
strcat(start_section,">");
strcpy(end_section,"</");
strcat(end_section,section_name);
strcat(end_section,">");
}
else
sect=1;
while (fgets(s,BUFFER_LEN,fp)) {
if(!(strrchr(s,'\n')))
{errno=E2BIG;return(NULL);} /* line too long */
s[strlen(s)-1]='\0';
cut_rem(s);
if(mode==1) {
ss=only_global(s,¤t_section,&global);
}
else ss=s;
if(ss==NULL) return (NULL);
if (section_name!=NULL) {
if (!sect) {
if((c=istrstr(ss,start_section))!=NULL) {
ss=c;sect=1;
}
}
if (sect) {
if ((c=istrstr(ss,end_section))!=NULL) {
ss=c;sect=0;
}
}
}
if ((sect)&&(ss!=NULL)) {
c=mv_2_next(ss);
l=strlen(var_name);
if (get_item_size(c)==l) {
if (!strncasecmp(c,var_name,l)) {
c+=l;
c=mv_2_next(c);
if (r==NULL) r=(char *)xmalloc(strlen(c)+1);
else r=(char *) xrealloc(r,strlen(c)+1);
if(r==NULL) break;
strcpy(r,c);
}
}
}
}
if((mode==1)&&(ss!=NULL))
xfree(ss);
if(start_section!=NULL)
xfree(start_section);
if(end_section!=NULL)
xfree(end_section);
if(current_section!=NULL)
xfree(current_section);
return(r);
}
