soulB::checks_returns soulCH::prob_match(char *acl) {
/* Check probablity of bad URL */
// REDO ERRORS
const char *file_path; pack *package; float score=12.0;
float total_value=0; float score_add=0; int field_len=0;
fstream *probab_file = new fstream; char line_buffer[_1K];
if((db_io->get_config(file_path,prob_file,0,acl,NULL)) != TRUE) return CHECKS_ERROR;
if(open_file(file_path,probab_file)) return CHECKS_ERROR;
while(read_line(probab_file,line_buffer)) {
char *temp_string = line_buffer; char *temp_token = line_buffer; int second_token=0;
if(!(field_len=search_string(temp_string,'='))) { db_io->log(ERR,"The field %s was invalid.",package->data); return CONTINUE; }
int third_token = (field_len-1); temp_token+=field_len;
if(!isdigit(*temp_token)) { db_io->log(ERR,"The field %s had no contents or invalid contents",package->data); return CONTINUE; }
score_add = atof(temp_token);
if(!strncmp(temp_string,"SCORE",5)) {
if (!score_add || score_add <0) { db_io->log(ERR,"The score check in file %s was invalid, continuing but keeping default score of %d",file_path,(double)score);
} else { score = score_add; }
}
second_token=search_string(temp_string,'_');
if(!strncmp(temp_string,"WORD",4)) {
char word_store[_1K]={0};
if(!second_token) { db_io->log(ERR,"The field %s was invalid.",package->data); return CONTINUE; }
if((third_token-second_token)>=_1K) return CHECKS_ERROR;
temp_string+=second_token; strncpy(word_store,temp_string,third_token-second_token);
int how_many = find_in_line(word_store,input->url);
total_value+=(score_add*how_many);
}
if(!strncmp(temp_string,"LETTER",6)) {
char letter_store='\0';
if(!second_token) { db_io->log(ERR,"The field %s was invalid.",package->data); return CONTINUE; }
if(((third_token-second_token))!=1) { db_io->log(ERR,"Need a letter between LETTER_ and = in line %s. Skipping.",package->data); break; }
letter_store = temp_string[second_token];
int how_many = find_char_in_line(letter_store,input->url);
total_value+=(score_add*how_many);
}
}
if(DEBUG_STATE) db_io->log(DEBUG,"Prob check returned value of %d",total_value);
close_file(probab_file);
if(total_value >= score) return RETURN_DENIED;
return CONTINUE;
}
GList* get_kanji_by_key(const gchar *srchkey, GList *list, GjitenDicfile *dicfile) {
gint srch_resp = 0, roff = 0, rlen = 0;
gchar repstr[1024];
guint32 respos, oldrespos;
gint loopnum = 0;
gint srchpos = 0;
srch_resp = search_string(SRCH_START, dicfile, srchkey, &respos, &roff, &rlen, repstr);
if (srch_resp != SRCH_OK) return NULL;
oldrespos = srchpos = respos;
char *repstr2 = strdup(repstr);
kanjifile_entry* entry = do_kdicline(repstr2);
list = g_list_prepend(list, entry->kanji);
while (roff != 0) {
oldrespos = respos;
srchpos++;
loopnum++;
srch_resp = search_string(SRCH_CONT, dicfile, srchkey, &respos, &roff, &rlen, repstr);
if (srch_resp != SRCH_OK) break;
if (oldrespos == respos) continue;
char *repstr2 = strdup(repstr);
kanjifile_entry* entry = do_kdicline(repstr2);
list = g_list_prepend(list, entry->kanji);
}
return list;
}
static const char *
help_follow_link (const char *start, const char *lc_selected_item)
{
const char *p;
if (lc_selected_item == NULL)
return start;
for (p = lc_selected_item; *p && *p != CHAR_NODE_END && *p != CHAR_LINK_POINTER; p++)
;
if (*p == CHAR_LINK_POINTER)
{
int i;
char link_name[MAXLINKNAME];
link_name[0] = '[';
for (i = 1; *p != CHAR_LINK_END && *p && *p != CHAR_NODE_END && i < MAXLINKNAME - 3;)
link_name[i++] = *++p;
link_name[i - 1] = ']';
link_name[i] = '\0';
p = search_string (fdata, link_name);
if (p != NULL)
{
p += 1; /* Skip the newline following the start of the node */
return p;
}
}
/* Create a replacement page with the error message */
return _("Help file format error\n");
}
extern void make_rotation_groups(t_rot *rot, char **rotgnames, t_blocka *grps, char **gnames)
{
int g, ig = -1, i;
t_rotgrp *rotg;
for (g = 0; g < rot->ngrp; g++)
{
rotg = &rot->grp[g];
ig = search_string(rotgnames[g], grps->nr, gnames);
rotg->nat = grps->index[ig+1] - grps->index[ig];
if (rotg->nat > 0)
{
fprintf(stderr, "Rotation group %d '%s' has %d atoms\n", g, rotgnames[g], rotg->nat);
snew(rotg->ind, rotg->nat);
for (i = 0; i < rotg->nat; i++)
{
rotg->ind[i] = grps->a[grps->index[ig]+i];
}
}
else
{
gmx_fatal(FARGS, "Rotation group %d '%s' is empty", g, rotgnames[g]);
}
}
}
int main(int argc, char **argv)
{
char str[1000];
int i;
int j;
int k;
i = 1;
while (i < argc)
{
j = 0;
k = 0;
while (argv[i][j])
{
if (argv[i][j] != ' ')
{
str[k] = argv[i][j];
k++;
}
j++;
}
str[j] = '\0';
ft_strlowcase(str);
search_string(str);
i++;
}
return (0);
}
void check_input(char buf[],int n, int *id,char *retbuf){
int i,di,st,en;
i=search_string(buf,"\"id\"",n,4);
if(i>=0){
di=search_char(&(buf[i]),':',n-i);
if(di>=0){
i+=di+1;
sscanf(&(buf[i]),"%d",id);
}
}
i=search_string(buf,"\"params\"",n,8);
if(i>=0){
di=search_char(&(buf[i]),':',n-i);
if(di==-1) {
retbuf[0]=0;
return;
}
i+=di+1;
di=search_char(&(buf[i]),'[',n-i);
if(di==-1) {
retbuf[0]=0;
return;
}
i+=di+1;
di=search_char(&(buf[i]),'"',n-i);
if(di==-1) {
retbuf[0]=0;
return;
}
i+=di+1;
st=i;
di=search_char(&(buf[i]),'"',n-i);
if(di==-1) {
retbuf[0]=0;
return;
}
i+=di;
en=i;
for(i=0;i<en-st;i++){
retbuf[i]=buf[st+i];
}
retbuf[i]=0;
}
}
void load_config(struct config_t *config)
{
FILE *fp;
unsigned int port;
char buf[1024];
fp = open_file(CONFIG_FILE, "r");
fgets(buf, 1024, fp);
if (search_string(buf, "port") >= 0)
sscanf(buf + strlen("port: "), "%u", &port);
config->port = port;
fclose(fp);
}
static void
help_help (WDialog * h)
{
const char *p;
history_ptr = (history_ptr + 1) % HISTORY_SIZE;
history[history_ptr].page = currentpoint;
history[history_ptr].link = selected_item;
p = search_string (fdata, "[How to use help]");
if (p != NULL)
{
currentpoint = p + 1; /* Skip the newline following the start of the node */
selected_item = NULL;
send_message (h, NULL, MSG_DRAW, 0, NULL);
}
}
int main(void) {
char word[11];
int i, n, m;
root = create_empty_trie();
scanf("%d", &n);
for(i = 0; i < n; i++) {
scanf("%s", word);
add_string(root, word);
}
scanf("%d", &m);
for(i = 0; i < m; i++) {
scanf("%s", word);
printf("%d\n", search_string(root, word));
}
free_trie(root);
return 0;
}
BOOL WorkClass::ProcessVcprojFile( CString& strFileContent )
{
std::wstring search_string(strFileContent);
std::tr1::wregex reg(TEXT("Version=(\"\\d\\.\\d{2}\")"));
std::tr1::wsmatch results;
if (std::tr1::regex_search(search_string,results,reg))
{
std::wstring replace = TEXT("Version=\"9.00\"");
search_string = std::tr1::regex_replace(search_string,reg,replace);
}else
{
return SetLastError(ERR_INVALIDFORMAT),FALSE;
}
strFileContent.Format(TEXT("%s"),search_string.c_str());
return SetLastError(ERR_NONE),TRUE;
}
/*******************************************************************************
函数名称: WorkClass::ProcessSlnFile 处理sln文件
================================================================================
参数说明: CString & strFileContent sln文件内容
--------------------------------------------------------------------------------
返回值: BOOL
--------------------------------------------------------------------------------
文件作者: King.Sollyu QQ:191067617
*******************************************************************************/
BOOL WorkClass::ProcessSlnFile( CString& strFileContent )
{
std::wstring search_string(strFileContent);
std::tr1::wregex reg(TEXT("Version \\d+\\.\\d{2}"));
std::tr1::wsmatch results;
try
{
// 寻找当前版本信息 一般为：Version X.00
// 没有找到则说明格式错误
if (std::tr1::regex_search(search_string,results,reg))
{
// 将找到的格式替换为 10.00
std::wstring replace = TEXT("Version 10.00");
search_string = std::tr1::regex_replace(search_string,reg,replace);
// 查找版本格式后是否跟随 # Visual Studio 2008
// 不跟随就添加
std::tr1::wregex reg2 (TEXT("Version 10.00\r\n# Visual Studio \\d{4}"));
if (!std::tr1::regex_search(search_string,results,reg2))
{
replace = TEXT("Version 10.00\r\n# Visual Studio 2008");
search_string = std::tr1::regex_replace(search_string,reg,replace);
}else
{
std::tr1::wregex reg3 (TEXT("# Visual Studio \\d{4}"));
if (std::tr1::regex_search(search_string,results,reg3) != NULL)
{
replace = TEXT("# Visual Studio 2008");
search_string = std::tr1::regex_replace(search_string,reg3,replace);
}
}
}else
{
return SetLastError(ERR_INVALIDFORMAT),FALSE;
}
}
catch (...){ return SetLastError(ERR_UNKNOW),FALSE; }
strFileContent.Format(TEXT("%s"),search_string.c_str());
return SetLastError(ERR_NONE),TRUE;
}
int replace_string(char* data)
{
int pos, i=0, j=0, start[100], end[100],n_o_occur=0, maxchars=size;
char string[500], *replace_with, ch='a';
replace_with=malloc(500*sizeof(char));
move(32, 0);deleteln();
printw("Enter String to replace: "); // take the string to replace
while(ch!='\n')
{
ch=getch();
addch(ch);
if(ch!='\n'){string[i]=ch;i++;}
if(ch==27 )//escape key)
{
move(33,0); deleteln();
return 0;
}
}
string[i]='\0';
ch='a';
move(33, 0);
i=0;printw("Enter replacement string: "); // take the string to replace with
while(ch!='\n')
{
ch=getch();
addch(ch);
if(ch!='\n')
{replace_with[i]=ch;i++;}
if(ch==27 )//escape key)
{
move(33,0); deleteln();
return 0;
}
}
deleteln();
replace_with[i]='\0';
while((pos=search_string(string, data))!=-1) // now search the string to be replaced and get its position
{
delete_string(pos, strlen(string), data); // delete the searched string dfrom its position
insert_string(pos, replace_with, data); // insert the replacement string at that position
}
free(replace_with);
return 0;
}
static void
help_index (WDialog * h)
{
const char *new_item;
new_item = search_string (fdata, "[Contents]");
if (new_item == NULL)
message (D_ERROR, MSG_ERROR, _("Cannot find node %s in help file"), "[Contents]");
else
{
history_ptr = (history_ptr + 1) % HISTORY_SIZE;
history[history_ptr].page = currentpoint;
history[history_ptr].link = selected_item;
currentpoint = new_item + 1; /* Skip the newline following the start of the node */
selected_item = NULL;
send_message (h, NULL, MSG_DRAW, 0, NULL);
}
}
/*************************************************************************
* <Function-name="main" *
* *
* Description:Searches for a Particualr String and prints the function *
* in which the string is found and the Function path *
* *
* Parameters:argc and argv *
* *
* Returns:nothing *
* *
* Added By:SANDEEP *
* *
* *
************************************************************************/
int main(int argc,char **argv)
{
int i;
for(i=0;i<argc-4;i++)
{
fun_names(argc,argv,i);
search_string(argc,argv,i);
path(argc,argv,i);
if(occur>0)
{
printf("\n\n*************Total number of occurences are %d***************",occur);
}
else
printf("\n No Match Found");
s=0;
occur=0;
}
print_path(argc,argv);
return 0;
}
void pal::readdir(const string_t& path, const string_t& pattern, std::vector<pal::string_t>* list)
{
assert(list != nullptr);
std::vector<string_t>& files = *list;
string_t search_string(path);
append_path(&search_string, pattern.c_str());
WIN32_FIND_DATAW data = { 0 };
auto handle = ::FindFirstFileExW(search_string.c_str(), FindExInfoStandard, &data, FindExSearchNameMatch, NULL, 0);
if (handle == INVALID_HANDLE_VALUE)
{
return;
}
do
{
string_t filepath(data.cFileName);
files.push_back(filepath);
} while (::FindNextFileW(handle, &data));
::FindClose(handle);
}
int
main(int argc, char **argv) {
u_int8_t *buffer;
u_int16_t bufflen;
u_int8_t *new_buf;
search_str *pattern;
buffer = strdup("ANANANANANAPANAMNANAMPANAMANPANAMANPANANPANMANPANMANAPMANPAMNPAMNAPAMAN");
pattern = make_search_str("ANPANMAN", sizeof("ANPANMAN")-1 );
bufflen = strlen(buffer);
if((new_buf = search_string(buffer, &bufflen, pattern))) {
fprintf(stdout, "Substring Found!\n");
#ifdef PRINTDEBUG
printf("[");
new_buf -= pattern->ptrn_len;
u_int16_t len_ctr = 0;
while(len_ctr < pattern->ptrn_len) {
printf("%c", *new_buf);
new_buf++;
len_ctr++;
}
printf("]\n");
#endif
} else {
fprintf(stdout, "Substring not found!\n");
}
free(buffer);
destroy_search_str(pattern);
return(0);
}
//static
BOOL LLPanelMainInventory::incrementalFind(LLFolderViewItem* first_item, const char *find_text, BOOL backward)
{
LLPanelMainInventory* active_view = NULL;
LLFloaterReg::const_instance_list_t& inst_list = LLFloaterReg::getFloaterList("inventory");
for (LLFloaterReg::const_instance_list_t::const_iterator iter = inst_list.begin(); iter != inst_list.end(); ++iter)
{
LLPanelMainInventory* iv = dynamic_cast<LLPanelMainInventory*>(*iter);
if (iv)
{
if (gFocusMgr.childHasKeyboardFocus(iv))
{
active_view = iv;
break;
}
}
}
if (!active_view)
{
return FALSE;
}
std::string search_string(find_text);
if (search_string.empty())
{
return FALSE;
}
if (active_view->getPanel() &&
active_view->getPanel()->getRootFolder()->search(first_item, search_string, backward))
{
return TRUE;
}
return FALSE;
}
static void readdir(const pal::string_t& path, const pal::string_t& pattern, bool onlydirectories, std::vector<pal::string_t>* list)
{
assert(list != nullptr);
std::vector<pal::string_t>& files = *list;
pal::string_t normalized_path(path);
if (LongFile::ShouldNormalize(normalized_path))
{
if (!pal::realpath(&normalized_path))
{
return;
}
}
pal::string_t search_string(normalized_path);
append_path(&search_string, pattern.c_str());
WIN32_FIND_DATAW data = { 0 };
auto handle = ::FindFirstFileExW(search_string.c_str(), FindExInfoStandard, &data, FindExSearchNameMatch, NULL, 0);
if (handle == INVALID_HANDLE_VALUE)
{
return;
}
do
{
if (!onlydirectories || (data.dwFileAttributes & FILE_ATTRIBUTE_DIRECTORY))
{
pal::string_t filepath(data.cFileName);
if (filepath != _X(".") && filepath != _X(".."))
{
files.push_back(filepath);
}
}
} while (::FindNextFileW(handle, &data));
::FindClose(handle);
}
static int
alias_rtsp_out(struct libalias *la, struct ip *pip,
struct alias_link *lnk,
char *data,
const char *port_str)
{
int hlen, tlen, dlen;
struct tcphdr *tc;
int i, j, pos, state, port_dlen, new_dlen, delta;
u_short p[2], new_len;
u_short sport, eport, base_port;
u_short salias = 0, ealias = 0, base_alias = 0;
const char *transport_str = "transport:";
char newdata[2048], *port_data, *port_newdata, stemp[80];
int links_created = 0, pkt_updated = 0;
struct alias_link *rtsp_lnk = NULL;
struct in_addr null_addr;
/* Calculate data length of TCP packet */
tc = (struct tcphdr *)ip_next(pip);
hlen = (pip->ip_hl + tc->th_off) << 2;
tlen = ntohs(pip->ip_len);
dlen = tlen - hlen;
/* Find keyword, "Transport: " */
pos = search_string(data, dlen, transport_str);
if (pos < 0) {
return (-1);
}
port_data = data + pos;
port_dlen = dlen - pos;
memcpy(newdata, data, pos);
port_newdata = newdata + pos;
while (port_dlen > (int)strlen(port_str)) {
/* Find keyword, appropriate port string */
pos = search_string(port_data, port_dlen, port_str);
if (pos < 0) {
break;
}
memcpy(port_newdata, port_data, pos + 1);
port_newdata += (pos + 1);
p[0] = p[1] = 0;
sport = eport = 0;
state = 0;
for (i = pos; i < port_dlen; i++) {
switch (state) {
case 0:
if (port_data[i] == '=') {
state++;
}
break;
case 1:
if (ISDIGIT(port_data[i])) {
p[0] = p[0] * 10 + port_data[i] - '0';
} else {
if (port_data[i] == ';') {
state = 3;
}
if (port_data[i] == '-') {
state++;
}
}
break;
case 2:
if (ISDIGIT(port_data[i])) {
p[1] = p[1] * 10 + port_data[i] - '0';
} else {
state++;
}
break;
case 3:
base_port = p[0];
sport = htons(p[0]);
eport = htons(p[1]);
if (!links_created) {
links_created = 1;
/*
* Find an even numbered port
* number base that satisfies the
* contiguous number of ports we
* need
*/
null_addr.s_addr = 0;
if (0 == (salias = FindNewPortGroup(la, null_addr,
FindAliasAddress(la, pip->ip_src),
sport, 0,
RTSP_PORT_GROUP,
IPPROTO_UDP, 1))) {
#ifdef LIBALIAS_DEBUG
fprintf(stderr,
"PacketAlias/RTSP: Cannot find contiguous RTSP data ports\n");
#endif
} else {
base_alias = ntohs(salias);
for (j = 0; j < RTSP_PORT_GROUP; j++) {
/*
* Establish link
* to port found in
* RTSP packet
*/
rtsp_lnk = FindRtspOut(la, GetOriginalAddress(lnk), null_addr,
htons(base_port + j), htons(base_alias + j),
IPPROTO_UDP);
if (rtsp_lnk != NULL) {
#ifndef NO_FW_PUNCH
/*
* Punch
* hole in
* firewall
*/
PunchFWHole(rtsp_lnk);
#endif
} else {
#ifdef LIBALIAS_DEBUG
fprintf(stderr,
"PacketAlias/RTSP: Cannot allocate RTSP data ports\n");
#endif
break;
}
}
}
ealias = htons(base_alias + (RTSP_PORT_GROUP - 1));
}
if (salias && rtsp_lnk) {
pkt_updated = 1;
/* Copy into IP packet */
sprintf(stemp, "%d", ntohs(salias));
memcpy(port_newdata, stemp, strlen(stemp));
port_newdata += strlen(stemp);
if (eport != 0) {
*port_newdata = '-';
port_newdata++;
/* Copy into IP packet */
sprintf(stemp, "%d", ntohs(ealias));
memcpy(port_newdata, stemp, strlen(stemp));
port_newdata += strlen(stemp);
}
*port_newdata = ';';
port_newdata++;
}
state++;
break;
}
if (state > 3) {
break;
}
}
port_data += i;
port_dlen -= i;
}
if (!pkt_updated)
return (-1);
memcpy(port_newdata, port_data, port_dlen);
port_newdata += port_dlen;
*port_newdata = '\0';
/* Create new packet */
new_dlen = port_newdata - newdata;
memcpy(data, newdata, new_dlen);
SetAckModified(lnk);
tc = (struct tcphdr *)ip_next(pip);
delta = GetDeltaSeqOut(tc->th_seq, lnk);
AddSeq(lnk, delta + new_dlen - dlen, pip->ip_hl, pip->ip_len,
tc->th_seq, tc->th_off);
new_len = htons(hlen + new_dlen);
DifferentialChecksum(&pip->ip_sum,
&new_len,
&pip->ip_len,
1);
pip->ip_len = new_len;
tc->th_sum = 0;
#ifdef _KERNEL
tc->th_x2 = 1;
#else
tc->th_sum = TcpChecksum(pip);
#endif
return (0);
}
char *MPlex::get(char *word)
{
char buff[BUF_SIZE], *s, *e;
int i;
// See if the word is closed
strcpy(buff, "^");
strcat(buff, word);
strcat(buff, sTAGSEP);
compact_numbers(buff);
if (EXISTS(tree, buff))
{
e = REC(char *, tree);
#if 0
printf("word %s, lex entry %s is %s\n", word, buff, e);
#endif
return e;
}
// Try the lower case version
for (i = 0; buff[i]; ++i) buff[i] = tolower(buff[i]);
if (EXISTS(tree, buff))
{
e = REC(char *, tree);
#if 0
printf("word %s, lex entry %s is %s\n", word, buff, e);
#endif
return e;
}
// Get the search string corresponding to the word
if (use_codes)
search_string(buff, word);
else
strcpy(buff, word);
strcat(buff, sTAGSEP);
for (s = &buff[0]; strlen(s) > 0; s++)
{
if (strlen(s) > ntail + 1) continue;
#if 0
printf("looking for word '%s', search string is '%s'\n", word, s);
#endif
if (EXISTS(tree, s))
{
e = REC(char *, tree);
#if 0
printf("word '%s', lex entry %s is %s\n", word, s, e);
#endif
return e;
}
}
#if 0
printf("word %s, lex entry not found\n", word);
#endif
return NULL;
}
int texteditor(char *text, int maxchars, const int startrow, const int startcol,int maxrows,const int maxcols,const int displayrows,const int returnhandler,const char *permitted, bool ins, const bool allowcr)
{
int ky,position=0,row,col,scrollstart=0, x=0, y=0; //ky is most of the time the input user gives, position(it stays in sync with cursor) points to text row and col keep track of row or column being managed, scroll start keeps track of position from where scroll starts, x and y are xy coordinates on screen
char *where, *original, *savetext,**display, *last_undo; // where keeps the line of text for a while, original is the text as copied from text file
bool exitflag=false; // save text is used to keep a backup of our text so we may get previous text bac if something unusuall happens
// last undo is useless // display is 2 dimensional array to keep enough text in it to fill the diplay window
if (!maxchars) // if user has not specified maxchars
maxchars=maxrows*maxcols+1;
if (!maxrows || maxrows > maxchars-1) // if maxrows are not specified or maxchars are less then number of rows possible then make sure max rows are less then maxchars
maxrows=maxchars-1;
if (ins) // if ins variable is set
curs_set(2); //then set cursor to high visibility mode
else //else keep it normal
curs_set(1);
/* below we will allocate memory to our above declared arrays and assign data to them*/
if ((display = malloc(maxrows * sizeof(char *))) ==NULL) /*assign memory equal to number of maxrows to display*/
malloc_error(); //call the function to check if memory was successfully allocated
for(ky = 0; ky < maxrows; ky++) //now traverse all rows in display and allocated and assign memory equal to maxcols to each row of display
if ((display[ky] = malloc((maxcols+1) * sizeof(char)))==NULL)
malloc_error();
if ((original=malloc(maxchars*sizeof(char)))==NULL) //allocated memory to original
malloc_error();
strcpy(original,text);//copy text taken from file to original variable
if ((savetext=malloc(maxchars*sizeof(char)))==NULL)// allocate memory to savetext
malloc_error();
strcpy(savetext,text);//copy text to savetext
/*finished assigning**/
while (!exitflag) // our loop to stay in unless user presses a button to turn exit flag true initially it is set false
{
int counter; //counter to count
do //start of do while loop
{
counter=0;
where=text; //temporarily copy all text taken from file to where
for (row=0; row < maxrows; row++) // initialize display vriable making sure every row has a null in the start
{
display[row][0]=127; //assign a backspace character to first column of every row
display[row][1]='\0'; //assign a null character to second column of every row indicating that the row ends here
}
row=0; // set row to zero
while ((strlen(where) > maxcols || strchr(where,'\n') != NULL) && (display[maxrows-1][0]==127 || display[maxrows-1][0]=='\n')) //while loop
//keep traversing if both of following conditions are met successfully
//1. length of text(where) is more than number of columns which means there are more than one rows
// "OR" if a new row exist
//2. if first column of last row has a backspace OR an end of line character(means we haev not reached last row yet)
{
strncpy(display[row],where,maxcols); //copy text from where to current row of display from where specifyint he maximum columns it can have
display[row][maxcols]='\0'; // insert a null at the end of a row indicating that the row ends here
if (strchr(display[row],'\n') != NULL) // if there s a new line character in this row
left(display[row],strchr(display[row],'\n')-display[row]);//end the row where a new line character is found
else //in case there is no newline character in this row
left(display[row],strrchr(display[row],' ')-display[row]);//mark end of row at next white space charcter
if (display[maxrows-1][0]==127 || display[maxrows-1][0]=='\n')//if first column of last row has a backspace OR an end of line character
{
where+=strlen(display[row]); // move where pointer to the address before which text is already dealt with
if (where[0]=='\n' || where[0]==' ' || where[0]=='\0') //in case where points to and of newline characters
where++; //move one step forward
row++; //current is dealt with now we move to next row
}
}// while loop ends here text is assigned to display datas tructure properly
if (row == maxrows-1 && strlen(where) > maxcols) // if we have reached last row and remaining text is more than number of characters last row can have
{
strcpy(text,savetext); //copy the savetext to text
if (ky==127/*KEY_BACKSPACE*/) //if ky is KEY_BACKSPACE
position++; //increase position variable
counter=1; //set counter to be one since there is text remaining to be copied
}
}while (counter);//do while loop ends here
strcpy(display[row],where);//now copy remaining text from where to display row
ky=0; //set ky to be 0
if (strchr(display[maxrows-1],'\n') != NULL) //if first character of last row is a newline character
if (strchr(display[maxrows-1],'\n')[1] != '\0') //and second charcter is a newline character
ky=127/*KEY_BACKSPACE*/; //then set ky to be equal to backspace
col=position; //set current column to be equal to position of cursor we are at
row=0; // set row to pont to fisrt row
counter=0; //set counter to be 0
while (col > strlen(display[row])) //keep traversing if column is greator than number of columsn in current row
{
col-=strlen(display[row]); //set column= column - number of columns of current row
counter+=strlen(display[row]); //set counter to point at the end of current row
if (text[counter] ==' ' || text[counter]=='\n' || text[counter]=='\0') //in case text at current cursor position is a newline character
{
col--; //decrease col by one
counter++; //point to text charcter in text
}
row++; //increase row by one since current row has been properly taken care of
}
if (col > maxcols-1) //in case col is greator than total number of columns a row can hev
{
row++; //move to next row means increment row variable
col=0; //set col = 0 means point to first colunmn in next row
}
if (!ky) // otherwise ky==KEY_BACKSPACE and we're getting rid of the last character we entered to avoid pushing text into the last line +1
{
if (row < scrollstart) // in case current row is lower than scroll start
scrollstart--; // then decrease scroll start
if (row > scrollstart+displayrows-1) //in case current row is greator than scroll start plus number of displayrows
scrollstart++; //then increase scroll start
for (counter=0;counter < displayrows; counter++) //traverse all the display rows
{
mvhline(counter+startrow,startcol,' ',maxcols); //move to position counter+startrow on y coordinate and startcol on x coordinate and print spaces on all columns onwards from counter of this row
if (display[counter+scrollstart][0] != 127) //if current position has a backspace in it then
mvprintw(counter+startrow,startcol,"%s",display[counter+scrollstart]);//move to position counter+startrow on y and startcol on x and display text in display area
}
move(row+startrow-scrollstart,col+startcol); // move to end of text
ky=getch(); // text has been displayed now wait for user to press a key
}
switch(ky) // take actions based on pressed key
{
case 27: //escape
exitflag=true; //set exitflag to be true
break;
case KEY_F(2): //f2 key to delete all file contents
memset(text,'\0',maxchars); //make all the contens of file to be null
position=0; //set postion to be zero
scrollstart=0; //set scroll start to be zero
break;
case KEY_F(3): //f3 key to search for strings
getyx(stdscr,y,x);//get current coordinates of cursor
remove_search_marks(text);//remove searchmarks from text
search_string(NULL,text); //goto search function
clr_bottom(); //clear the interactive area below menu
move(y,x); //move back to textbox
break;
case KEY_F(4): //f4 to replace strings
getyx(stdscr,y,x); //get current coordinates of cursor
replace_string(text);//call the function to replace string
clr_bottom();
move(y,x);
break;
case KEY_F(5): //f5 key to save file
getyx(stdscr,y,x);
save_file(text); //call the function save file
clr_bottom();
move(y,x);
break;
case KEY_F(6): //f6 key to count number of words
clr_bottom();
count_words_chars(text); //call the function to count words and chars in text
case KEY_F(7): //f7 key to remove search marks
remove_search_marks(text); //remove search marks
case KEY_HOME: //move to start of current row
if (col) //if current column is not the first column
{
position=0;//set position to be zero
for (col=0; col < row; col++)//traverse until col is less then row
{
position += strlen(display[col]);//move cursor to end of current row in display array
if ((strchr(display[row],'\n') != NULL) || (strchr(display[row],' ') != NULL))//if there is a escape character ' ' or '\n' in current row
position++; // increment position and move to start of the row
}
}
break;
case KEY_END: //move to end of current row
if (col < strlen(display[row])) //if col is less than number of columns in current row
{
position=-1; //set potiion to -1
for (col=0; col <=row; col++) //traverse until col is less than or equal to row (row is position of current row)
{
position+=strlen(display[col]);//set position to be the end of curent row
if ((strchr(display[row],'\n') != NULL) || (strchr(display[row],' ') != NULL)) //if we haev reached enf of row
position++; //increment position so it may move to end of current row
}
}
break;
case KEY_PPAGE: //move to start of text
position=0; //set position to be zero
scrollstart=0; //set scroll start to be zero
break;
case KEY_NPAGE: //move to end of text
position=strlen(text); //set postion to be end of text
for (counter=0; counter < maxrows; counter++) //traverse until counter is less than total number of rows
if(display[counter][0]==127) //if the row at position counter's first character is backspace
break; //then break from loop
scrollstart=counter-displayrows; //else set scroll start to equal counter-displayrows
if (scrollstart < 0) //in case scroll start has decreased to become negative
scrollstart=0; //set it to be zero again
break;
case KEY_LEFT: //move cursor left
if (position) //if position is not zero
position--; //decrease by one
break;
case KEY_RIGHT: //move cursor right
if (position < strlen(text) && (row != maxrows-1 || col < maxcols-1))//if cursor is not already at end or far from end
position++; //increase position by one
break;
case KEY_UP: //move cursor up
if (row) //in case we are not on first row
{
if (col > strlen(display[row-1]))//if current column is greater then length of previous row
position=strlen(display[row-1]); //then set cursor at the end of above row
else
position=col; //else set position to col
ky=0; //set ky=0
for (col=0; col < row-1; col++) //traverse for col less than row above current row
{
position+=strlen(display[col]); //move cursor to end of column
ky+=strlen(display[col]); //move ky to next row
if ((strlen(display[col]) < maxcols) || (text[ky]==' ' && strlen(display[col])==maxcols))//if we are not already at end of row
{
position++; //increment position
ky++; //move to next row
}
}
}
break;
case KEY_DOWN:// move cursor to below row
if (row < maxrows-1) //if it's not last row
if (display[row+1][0] !=127) //if next row is not empty
{
if (col < strlen(display[row+1])) //if col is less than length of next row
position=col; //set position to be col
else
position=strlen(display[row+1]);//set position to be end of above row
ky=0;//set ky=0;
for (col=0; col <= row; col++)//traverse until we reach the current row
{
position+=strlen(display[col]);//move to next row
ky+=strlen(display[col]);//move to next row
if ((strlen(display[col]) < maxcols) || (text[ky]==' ' && strlen(display[col])==maxcols))//if we are not already at end of row
{
position++;
ky++;
}
}
}
break;
case KEY_IC: // insert key
ins=!ins;//invert the insert mode, turn it on if it's on or vice versa
if (ins)
curs_set(2);
else
curs_set(1);
break;
case 330://KEY_DC: // delete key
if (strlen(text))//if text exist
{
strcpy(savetext,text);//save text
memmove(&text[position],&text[position+1],maxchars-position);//move text to left by one character meanwhile eating the one character, search google for function memove and read about it...
}
break;
case KEY_BACKSPACE:// remove text
if (strlen(text) && position)//if text exist and cursor is already not at begiing of text
{
strcpy(savetext,text);//save text
position--;//decrease poition by one basically making cursor go back
memmove(&text[position],&text[position+1],maxchars-position);//move text to left by one character meanwhile eating the one character
}
break;
case 25: // ctrl-y delete entire line
if (display[1][0] != 127)//if there's text on first row
{
position-=col;//move cursor to start of first row
ky=0;//set ky=0
do
{
memmove(&text[position],&text[position+1],maxchars-position);//move text right by one
ky++;//increase ky
}
while (ky < strlen(display[row]));//keep doing it until ky is less than number of columns in current row
}
else
memset(text,'\0',maxchars);//other wise it's already empty
break;
case 10: // return // insert a line by pressing return button
switch (returnhandler)//see what do we want enter to do
{
case 1:// in case return handler==1
if (display[maxrows-1][0] == 127 || display[maxrows-1][0] == '\n')// if display area is not empty
{
memmove(&text[position+1],&text[position],maxchars-position);//move text to right by one, emptying the space for one charectre at potiions
text[position]='\n'; //insert a new row character at position in text
position++;//increase poition
}
break;
case 2:
ky=' ';//insert a space
ungetch(ky);//
break;
case 3:
exitflag=true;//exit
}
break;
default: //in case of any other characters than specified above
if (((permitted==NULL && ky > 31 && ky < 127) || (permitted != NULL && strchr(permitted,ky))) && strlen(text) < maxchars-1 && (row !=maxrows-1 || (strlen(display[maxrows-1]) < maxcols || (ins && (row!=maxrows-1 && col < maxcols )))))
{
if (ins || text[position+1]=='\n' || text[position]== '\n') //in ase insert mode is on or there is no text after this in current row
memmove(&text[position+1],&text[position],maxchars-position);//move text to right by one and add characters
text[position]=ky;//insert current key in text
if (row != maxrows-1 || col < maxcols-1)//in case insert mode is off and we're not at the end of row
position++;//increment position(move cursor to right)
}
}
if(!allowcr)//if isnert mode is allowed
if (text[0]=='\n') //if first char in text is a newline
{
memmove(&text[0],&text[1],maxchars-1);//movetext to left by one
if (position)//if position is not zero
position--;//decrease position
}
}//switch ends here
/*user decided to exit free all assigned memory */
free(original);//free memory of original
free(savetext);//free memory of savetext
free(last_undo);//free memory of last undo, it's not used at all so no need for it
for(scrollstart = 0; scrollstart < maxrows; scrollstart++)//traverse all rows of siplay and free their memory
free(display[scrollstart]);
free(display);//free dispay
/************************/
return 0;
}
void init_membed(FILE *fplog, gmx_membed_t *membed, int nfile, const t_filenm fnm[], gmx_mtop_t *mtop, t_inputrec *inputrec, t_state *state, t_commrec *cr,real *cpt)
{
char *ins;
int i,rm_bonded_at,fr_id,fr_i=0,tmp_id,warn=0;
int ng,j,max_lip_rm,ins_grp_id,ins_nat,mem_nat,ntype,lip_rm,tpr_version;
real prot_area;
rvec *r_ins=NULL;
t_block *ins_at,*rest_at;
pos_ins_t *pos_ins;
mem_t *mem_p;
rm_t *rm_p;
gmx_groups_t *groups;
gmx_bool bExcl=FALSE;
t_atoms atoms;
t_pbc *pbc;
char **piecename=NULL;
/* input variables */
const char *membed_input;
real xy_fac = 0.5;
real xy_max = 1.0;
real z_fac = 1.0;
real z_max = 1.0;
int it_xy = 1000;
int it_z = 0;
real probe_rad = 0.22;
int low_up_rm = 0;
int maxwarn=0;
int pieces=1;
gmx_bool bALLOW_ASYMMETRY=FALSE;
snew(ins_at,1);
snew(pos_ins,1);
if(MASTER(cr))
{
/* get input data out membed file */
membed_input = opt2fn("-membed",nfile,fnm);
get_input(membed_input,&xy_fac,&xy_max,&z_fac,&z_max,&it_xy,&it_z,&probe_rad,&low_up_rm,&maxwarn,&pieces,&bALLOW_ASYMMETRY);
tpr_version = get_tpr_version(ftp2fn(efTPX,nfile,fnm));
if (tpr_version<58)
gmx_fatal(FARGS,"Version of *.tpr file to old (%d). Rerun grompp with gromacs VERSION 4.0.3 or newer.\n",tpr_version);
if( !EI_DYNAMICS(inputrec->eI) )
gmx_input("Change integrator to a dynamics integrator in mdp file (e.g. md or sd).");
if(PAR(cr))
gmx_input("Sorry, parallel g_membed is not yet fully functional.");
#ifdef GMX_OPENMM
gmx_input("Sorry, g_membed does not work with openmm.");
#endif
if(*cpt>=0)
{
fprintf(stderr,"\nSetting -cpt to -1, because embedding cannot be restarted from cpt-files.\n");
*cpt=-1;
}
groups=&(mtop->groups);
atoms=gmx_mtop_global_atoms(mtop);
snew(mem_p,1);
fprintf(stderr,"\nSelect a group to embed in the membrane:\n");
get_index(&atoms,opt2fn_null("-mn",nfile,fnm),1,&(ins_at->nr),&(ins_at->index),&ins);
ins_grp_id = search_string(ins,groups->ngrpname,(groups->grpname));
fprintf(stderr,"\nSelect a group to embed %s into (e.g. the membrane):\n",ins);
get_index(&atoms,opt2fn_null("-mn",nfile,fnm),1,&(mem_p->mem_at.nr),&(mem_p->mem_at.index),&(mem_p->name));
pos_ins->pieces=pieces;
snew(pos_ins->nidx,pieces);
snew(pos_ins->subindex,pieces);
snew(piecename,pieces);
if (pieces>1)
{
fprintf(stderr,"\nSelect pieces to embed:\n");
get_index(&atoms,opt2fn_null("-mn",nfile,fnm),pieces,pos_ins->nidx,pos_ins->subindex,piecename);
}
else
{
/*use whole embedded group*/
snew(pos_ins->nidx,1);
snew(pos_ins->subindex,1);
pos_ins->nidx[0]=ins_at->nr;
pos_ins->subindex[0]=ins_at->index;
}
if(probe_rad<0.2199999)
{
warn++;
fprintf(stderr,"\nWarning %d:\nA probe radius (-rad) smaller than 0.2 can result in overlap between waters "
"and the group to embed, which will result in Lincs errors etc.\nIf you are sure, you can increase maxwarn.\n\n",warn);
}
if(xy_fac<0.09999999)
{
warn++;
fprintf(stderr,"\nWarning %d:\nThe initial size of %s is probably too smal.\n"
"If you are sure, you can increase maxwarn.\n\n",warn,ins);
}
if(it_xy<1000)
{
warn++;
fprintf(stderr,"\nWarning %d;\nThe number of steps used to grow the xy-coordinates of %s (%d) is probably too small.\n"
"Increase -nxy or, if you are sure, you can increase maxwarn.\n\n",warn,ins,it_xy);
}
if( (it_z<100) && ( z_fac<0.99999999 || z_fac>1.0000001) )
{
warn++;
fprintf(stderr,"\nWarning %d;\nThe number of steps used to grow the z-coordinate of %s (%d) is probably too small.\n"
"Increase -nz or, if you are sure, you can increase maxwarn.\n\n",warn,ins,it_z);
}
if(it_xy+it_z>inputrec->nsteps)
{
warn++;
fprintf(stderr,"\nWarning %d:\nThe number of growth steps (-nxy + -nz) is larger than the number of steps in the tpr.\n"
"If you are sure, you can increase maxwarn.\n\n",warn);
}
fr_id=-1;
if( inputrec->opts.ngfrz==1)
gmx_fatal(FARGS,"You did not specify \"%s\" as a freezegroup.",ins);
for(i=0;i<inputrec->opts.ngfrz;i++)
{
tmp_id = mtop->groups.grps[egcFREEZE].nm_ind[i];
if(ins_grp_id==tmp_id)
{
fr_id=tmp_id;
fr_i=i;
}
}
if (fr_id == -1 )
gmx_fatal(FARGS,"\"%s\" not as freezegroup defined in the mdp-file.",ins);
for(i=0;i<DIM;i++)
if( inputrec->opts.nFreeze[fr_i][i] != 1)
gmx_fatal(FARGS,"freeze dimensions for %s are not Y Y Y\n",ins);
ng = groups->grps[egcENER].nr;
if (ng == 1)
gmx_input("No energy groups defined. This is necessary for energy exclusion in the freeze group");
for(i=0;i<ng;i++)
{
for(j=0;j<ng;j++)
{
if (inputrec->opts.egp_flags[ng*i+j] == EGP_EXCL)
{
bExcl = TRUE;
if ( (groups->grps[egcENER].nm_ind[i] != ins_grp_id) || (groups->grps[egcENER].nm_ind[j] != ins_grp_id) )
gmx_fatal(FARGS,"Energy exclusions \"%s\" and \"%s\" do not match the group to embed \"%s\"",
*groups->grpname[groups->grps[egcENER].nm_ind[i]],
*groups->grpname[groups->grps[egcENER].nm_ind[j]],ins);
}
}
}
if (!bExcl)
gmx_input("No energy exclusion groups defined. This is necessary for energy exclusion in the freeze group");
/* Guess the area the protein will occupy in the membrane plane Calculate area per lipid*/
snew(rest_at,1);
ins_nat = init_ins_at(ins_at,rest_at,state,pos_ins,groups,ins_grp_id,xy_max);
/* Check moleculetypes in insertion group */
check_types(ins_at,rest_at,mtop);
mem_nat = init_mem_at(mem_p,mtop,state->x,state->box,pos_ins);
prot_area = est_prot_area(pos_ins,state->x,ins_at,mem_p);
if ( (prot_area>7.5) && ( (state->box[XX][XX]*state->box[YY][YY]-state->box[XX][YY]*state->box[YY][XX])<50) )
{
warn++;
fprintf(stderr,"\nWarning %d:\nThe xy-area is very small compared to the area of the protein.\n"
"This might cause pressure problems during the growth phase. Just try with\n"
"current setup (-maxwarn + 1), but if pressure problems occur, lower the\n"
"compressibility in the mdp-file or use no pressure coupling at all.\n\n",warn);
}
if(warn>maxwarn)
gmx_fatal(FARGS,"Too many warnings.\n");
printf("The estimated area of the protein in the membrane is %.3f nm^2\n",prot_area);
printf("\nThere are %d lipids in the membrane part that overlaps the protein.\nThe area per lipid is %.4f nm^2.\n",mem_p->nmol,mem_p->lip_area);
/* Maximum number of lipids to be removed*/
max_lip_rm=(int)(2*prot_area/mem_p->lip_area);
printf("Maximum number of lipids that will be removed is %d.\n",max_lip_rm);
printf("\nWill resize the protein by a factor of %.3f in the xy plane and %.3f in the z direction.\n"
"This resizing will be done with respect to the geometrical center of all protein atoms\n"
"that span the membrane region, i.e. z between %.3f and %.3f\n\n",xy_fac,z_fac,mem_p->zmin,mem_p->zmax);
/* resize the protein by xy and by z if necessary*/
snew(r_ins,ins_at->nr);
init_resize(ins_at,r_ins,pos_ins,mem_p,state->x,bALLOW_ASYMMETRY);
membed->fac[0]=membed->fac[1]=xy_fac;
membed->fac[2]=z_fac;
membed->xy_step =(xy_max-xy_fac)/(double)(it_xy);
membed->z_step =(z_max-z_fac)/(double)(it_z-1);
resize(r_ins,state->x,pos_ins,membed->fac);
/* remove overlapping lipids and water from the membrane box*/
/*mark molecules to be removed*/
snew(pbc,1);
set_pbc(pbc,inputrec->ePBC,state->box);
snew(rm_p,1);
lip_rm = gen_rm_list(rm_p,ins_at,rest_at,pbc,mtop,state->x, r_ins, mem_p,pos_ins,probe_rad,low_up_rm,bALLOW_ASYMMETRY);
lip_rm -= low_up_rm;
if(fplog)
for(i=0;i<rm_p->nr;i++)
fprintf(fplog,"rm mol %d\n",rm_p->mol[i]);
for(i=0;i<mtop->nmolblock;i++)
{
ntype=0;
for(j=0;j<rm_p->nr;j++)
if(rm_p->block[j]==i)
ntype++;
printf("Will remove %d %s molecules\n",ntype,*(mtop->moltype[mtop->molblock[i].type].name));
}
if(lip_rm>max_lip_rm)
{
warn++;
fprintf(stderr,"\nWarning %d:\nTrying to remove a larger lipid area than the estimated protein area\n"
"Try making the -xyinit resize factor smaller.\n\n",warn);
}
/*remove all lipids and waters overlapping and update all important structures*/
rm_group(inputrec,groups,mtop,rm_p,state,ins_at,pos_ins);
rm_bonded_at = rm_bonded(ins_at,mtop);
if (rm_bonded_at != ins_at->nr)
{
fprintf(stderr,"Warning: The number of atoms for which the bonded interactions are removed is %d, "
"while %d atoms are embedded. Make sure that the atoms to be embedded are not in the same"
"molecule type as atoms that are not to be embedded.\n",rm_bonded_at,ins_at->nr);
}
if(warn>maxwarn)
gmx_fatal(FARGS,"Too many warnings.\nIf you are sure these warnings are harmless, you can increase -maxwarn");
if (ftp2bSet(efTOP,nfile,fnm))
top_update(opt2fn("-mp",nfile,fnm),ins,rm_p,mtop);
sfree(pbc);
sfree(rest_at);
if (pieces>1) { sfree(piecename); }
membed->it_xy=it_xy;
membed->it_z=it_z;
membed->pos_ins=pos_ins;
membed->r_ins=r_ins;
}
}
void make_pull_groups(t_pull *pull, char **pgnames, t_blocka *grps, char **gnames)
{
int d, nchar, g, ig = -1, i;
char *ptr, pulldim1[STRLEN];
t_pullgrp *pgrp;
ptr = pulldim;
i = 0;
for (d = 0; d < DIM; d++)
{
if (sscanf(ptr, "%s%n", pulldim1, &nchar) != 1)
{
gmx_fatal(FARGS, "Less than 3 pull dimensions given in pull_dim: '%s'",
pulldim);
}
if (gmx_strncasecmp(pulldim1, "N", 1) == 0)
{
pull->dim[d] = 0;
}
else if (gmx_strncasecmp(pulldim1, "Y", 1) == 0)
{
pull->dim[d] = 1;
i++;
}
else
{
gmx_fatal(FARGS, "Please use Y(ES) or N(O) for pull_dim only (not %s)",
pulldim1);
}
ptr += nchar;
}
if (i == 0)
{
gmx_fatal(FARGS, "All entries in pull_dim are N");
}
for (g = 0; g < pull->ngrp+1; g++)
{
pgrp = &pull->grp[g];
if (g == 0 && strcmp(pgnames[g], "") == 0)
{
pgrp->nat = 0;
}
else
{
ig = search_string(pgnames[g], grps->nr, gnames);
pgrp->nat = grps->index[ig+1] - grps->index[ig];
}
if (pgrp->nat > 0)
{
fprintf(stderr, "Pull group %d '%s' has %d atoms\n",
g, pgnames[g], pgrp->nat);
snew(pgrp->ind, pgrp->nat);
for (i = 0; i < pgrp->nat; i++)
{
pgrp->ind[i] = grps->a[grps->index[ig]+i];
}
if (pull->eGeom == epullgCYL && g == 0 && pgrp->nweight > 0)
{
gmx_fatal(FARGS, "Weights are not supported for the reference group with cylinder pulling");
}
if (pgrp->nweight > 0 && pgrp->nweight != pgrp->nat)
{
gmx_fatal(FARGS, "Number of weights (%d) for pull group %d '%s' does not match the number of atoms (%d)",
pgrp->nweight, g, pgnames[g], pgrp->nat);
}
if (pgrp->nat == 1)
{
/* No pbc is required for this group */
pgrp->pbcatom = -1;
}
else
{
if (pgrp->pbcatom > 0)
{
pgrp->pbcatom -= 1;
}
else if (pgrp->pbcatom == 0)
{
pgrp->pbcatom = pgrp->ind[(pgrp->nat-1)/2];
}
else
{
/* Use cosine weighting */
pgrp->pbcatom = -1;
}
}
if (g > 0 && pull->eGeom != epullgDIST)
{
for (d = 0; d < DIM; d++)
{
if (pgrp->vec[d] != 0 && pull->dim[d] == 0)
{
gmx_fatal(FARGS, "ERROR: pull_vec%d has non-zero %c-component while pull_dim in N\n", g, 'x'+d);
}
}
}
if ((pull->eGeom == epullgDIR || pull->eGeom == epullgCYL) &&
g > 0 && norm2(pgrp->vec) == 0)
{
gmx_fatal(FARGS, "pull_vec%d can not be zero with geometry %s",
g, EPULLGEOM(pull->eGeom));
}
if ((pull->eGeom == epullgPOS) && pgrp->rate != 0 &&
g > 0 && norm2(pgrp->vec) == 0)
{
gmx_fatal(FARGS, "pull_vec%d can not be zero with geometry %s and non-zero rate",
g, EPULLGEOM(pull->eGeom));
}
}
else
{
if (g == 0)
{
if (pull->eGeom == epullgCYL)
{
gmx_fatal(FARGS, "Absolute reference groups are not supported with geometry %s", EPULLGEOM(pull->eGeom));
}
}
else
{
gmx_fatal(FARGS, "Pull group %d '%s' is empty", g, pgnames[g]);
}
pgrp->pbcatom = -1;
}
}
}
int main(void)
{
int choice;
char buf[15] = { 0 };
struct sigaction sa;
struct addr_info info = { 0 };
memset(&sa, 0, sizeof(sa));
sa.sa_handler = timer_handler;
sigemptyset(&sa.sa_mask);
sa.sa_flags = SA_RESTART;
if (sigaction(SIGALRM, &sa, NULL) == -1) {
perror("sigaction()");
exit(EXIT_FAILURE);
}
alarm(60);
setbuf(stdin, NULL);
setbuf(stdout, NULL);
setbuf(stderr, NULL);
dl_iterate_phdr(callback, &info);
for (;;) {
printf("ROP helper 13.37\n");
printf("1. print libc address\n");
printf("2. print function address\n");
printf("3. insert ROP chain\n");
printf("4. search for string\n");
printf("5. quit\n");
printf("Choice: ");
if (!fgets(buf, sizeof(buf), stdin))
break;
choice = atoi(buf);
switch (choice) {
case 1:
printf("[+] libc start address: %p\n", info.base);
break;
case 2:
print_func_addr();
break;
case 3:
insert_rop();
break;
case 4:
search_string(info.base, info.size);
break;
case 5:
printf("Bye!\n");
goto out;
default:
printf("Invalid option!\n");
}
printf("\n");
}
out:
return 0;
}
uintptr_t basic_searcher::search_string(const char* str) const
{
return search_string(str, strlen(str)+1);
}
/* event callback */
gboolean
help_interactive_display (const gchar * event_group_name, const gchar * event_name,
gpointer init_data, gpointer data)
{
const dlg_colors_t help_colors = {
HELP_NORMAL_COLOR, /* common text color */
0, /* unused in help */
HELP_BOLD_COLOR, /* bold text color */
0, /* unused in help */
HELP_TITLE_COLOR /* title color */
};
WButtonBar *help_bar;
Widget *md;
char *hlpfile = NULL;
char *filedata;
ev_help_t *event_data = (ev_help_t *) data;
(void) event_group_name;
(void) event_name;
(void) init_data;
if (event_data->filename != NULL)
g_file_get_contents (event_data->filename, &filedata, NULL, NULL);
else
filedata = load_mc_home_file (mc_global.share_data_dir, MC_HELP, &hlpfile);
if (filedata == NULL)
message (D_ERROR, MSG_ERROR, _("Cannot open file %s\n%s"),
event_data->filename ? event_data->filename : hlpfile, unix_error_string (errno));
g_free (hlpfile);
if (filedata == NULL)
return TRUE;
translate_file (filedata);
g_free (filedata);
if (fdata == NULL)
return TRUE;
if ((event_data->node == NULL) || (*event_data->node == '\0'))
event_data->node = "[main]";
main_node = search_string (fdata, event_data->node);
if (main_node == NULL)
{
message (D_ERROR, MSG_ERROR, _("Cannot find node %s in help file"), event_data->node);
/* Fallback to [main], return if it also cannot be found */
main_node = search_string (fdata, "[main]");
if (main_node == NULL)
{
interactive_display_finish ();
return TRUE;
}
}
help_lines = min (LINES - 4, max (2 * LINES / 3, 18));
whelp =
dlg_create (TRUE, 0, 0, help_lines + 4, HELP_WINDOW_WIDTH + 4,
help_colors, help_callback, NULL, "[Help]", _("Help"),
DLG_TRYUP | DLG_CENTER | DLG_WANT_TAB);
selected_item = search_string_node (main_node, STRING_LINK_START) - 1;
currentpoint = main_node + 1; /* Skip the newline following the start of the node */
for (history_ptr = HISTORY_SIZE; history_ptr;)
{
history_ptr--;
history[history_ptr].page = currentpoint;
history[history_ptr].link = selected_item;
}
help_bar = buttonbar_new (TRUE);
WIDGET (help_bar)->y -= WIDGET (whelp)->y;
WIDGET (help_bar)->x -= WIDGET (whelp)->x;
md = mousedispatch_new (1, 1, help_lines, HELP_WINDOW_WIDTH - 2);
add_widget (whelp, md);
add_widget (whelp, help_bar);
buttonbar_set_label (help_bar, 1, Q_ ("ButtonBar|Help"), help_map, NULL);
buttonbar_set_label (help_bar, 2, Q_ ("ButtonBar|Index"), help_map, NULL);
buttonbar_set_label (help_bar, 3, Q_ ("ButtonBar|Prev"), help_map, NULL);
buttonbar_set_label (help_bar, 4, "", help_map, NULL);
buttonbar_set_label (help_bar, 5, "", help_map, NULL);
buttonbar_set_label (help_bar, 6, "", help_map, NULL);
buttonbar_set_label (help_bar, 7, "", help_map, NULL);
buttonbar_set_label (help_bar, 8, "", help_map, NULL);
buttonbar_set_label (help_bar, 9, "", help_map, NULL);
buttonbar_set_label (help_bar, 10, Q_ ("ButtonBar|Quit"), help_map, NULL);
dlg_run (whelp);
interactive_display_finish ();
dlg_destroy (whelp);
return TRUE;
}
void make_pull_groups(pull_params_t *pull,
char **pgnames,
const t_blocka *grps, char **gnames)
{
int g, ig = -1, i;
t_pull_group *pgrp;
/* Absolute reference group (might not be used) is special */
pgrp = &pull->group[0];
pgrp->nat = 0;
pgrp->pbcatom = -1;
pgrp->pbcatom_input = -1;
for (g = 1; g < pull->ngroup; g++)
{
pgrp = &pull->group[g];
pgrp->pbcatom_input = pgrp->pbcatom;
if (strcmp(pgnames[g], "") == 0)
{
gmx_fatal(FARGS, "Pull option pull_group%d required by grompp has not been set.", g);
}
ig = search_string(pgnames[g], grps->nr, gnames);
pgrp->nat = grps->index[ig+1] - grps->index[ig];
fprintf(stderr, "Pull group %d '%s' has %d atoms\n",
g, pgnames[g], pgrp->nat);
if (pgrp->nat == 0)
{
gmx_fatal(FARGS, "Pull group %d '%s' is empty", g, pgnames[g]);
}
snew(pgrp->ind, pgrp->nat);
for (i = 0; i < pgrp->nat; i++)
{
pgrp->ind[i] = grps->a[grps->index[ig]+i];
}
if (pgrp->nweight > 0 && pgrp->nweight != pgrp->nat)
{
gmx_fatal(FARGS, "Number of weights (%d) for pull group %d '%s' does not match the number of atoms (%d)",
pgrp->nweight, g, pgnames[g], pgrp->nat);
}
if (pgrp->nat == 1)
{
/* No pbc is required for this group */
pgrp->pbcatom = -1;
}
else
{
if (pgrp->pbcatom > 0)
{
pgrp->pbcatom -= 1;
}
else if (pgrp->pbcatom == 0)
{
pgrp->pbcatom = pgrp->ind[(pgrp->nat-1)/2];
}
else
{
/* Use cosine weighting */
pgrp->pbcatom = -1;
}
}
}
}
//Read the string and execute instructions
void GcodeProcessor::process_string(char instruction[])
{
//the character / means delete block... used for comments and stuff.
if (instruction[0] == '/'
|| instruction[0] == ';'
|| instruction[0] == '#'){
return;
}
// float currentPosition[] ={getUnitsX(), getUnitsY(), getUnitsZ() };
Point currentPosition = getMachine().getCurrentPosition();
Point target ;
int code = 0;
//Get Target
target.x = currentPosition.x ;
target.y = currentPosition.y ;
target.z = currentPosition.z ;
if (has_command('X', instruction)) target.x = search_string('X', instruction);
if (has_command('Y', instruction)) target.y = search_string('Y', instruction);
if (has_command('Z', instruction)) target.z = search_string('Z', instruction);
if(!abs_mode){
target.x = currentPosition.x + search_string('X', instruction);
target.y = currentPosition.y + search_string('Y', instruction);;
target.z = currentPosition.z + search_string('X', instruction);;
}
//set our target.
// getMachine().set_target(target);
double feedrate = search_string('F', instruction);
if (feedrate > 0) nominalFeedRate = feedrate;
// handle no G code but has Coordinates remember the last feed rate
if( ( has_command('X', instruction) ||
has_command('Y', instruction) ||
has_command('Z', instruction))&&
! has_command('G', instruction)){
// setFeedRate(nominalFeedRate);
getMachine().goTo(target);
}
if ( has_command('G', instruction) )
{
//which one?
code = (int)search_string('G', instruction);
switch (code)
{
//Rapid Positioning
case 0:
getMachine().setMaxFeedRate();
getMachine().goTo(target);
break;
//Linear Interpolation
case 1:
getMachine().setFeedRate(nominalFeedRate);
getMachine().goTo(target);
break;
//Clockwise arc
case 2:
//Counterclockwise arc
case 3:
// Centre coordinates are always relative
centr.x = search_string('I', instruction) + currentPosition.x;
centr.y = search_string('J', instruction) + currentPosition.y;
centr.z = target.z;
bool clockwise;
clockwise = (code==2);
getMachine().moveAlongCurve( centr, target, clockwise);
break;
case 4:
// delay(1000*(int)search_string('P', instruction, size));
break;
//Inches for Units
case 20:
getMachine().setInches();
break;
//mm for Units
case 21:
getMachine().setMillimeters();
break;
//go home.
case 28:
getMachine().goToOrigin();
break;
//go home via an intermediate point.
case 30:
getMachine().setMaxFeedRate();
getMachine().goTo(target);
//go home.
getMachine().goToOrigin();
break;
//Absolute Positioning
case 90:
abs_mode = true;
break;
//Incremental Positioning
case 91:
abs_mode = false;
break;
//Set as home
case 92:
getMachine().setPosition(Point());
break;
/*
//Inverse Time Feed Mode
case 93:
break; //TODO: add this
//Feed per Minute Mode
case 94:
break; //TODO: add this
*/
default:
break;
// Serial.print("huh? G");
// Serial.println(code,DEC);
}
}
if (has_command('F', instruction))
{
double rate = search_string('F', instruction);
getMachine().setFeedRate(rate);
nominalFeedRate = rate;
}
//find us an m code.
if (has_command('M', instruction))
{
code = search_string('M', instruction);
switch (code)
{
//TODO: this is a bug because search_string returns 0. gotta fix that.
case 0:
true;
break;
/*
case 0:
//todo: stop program
break;
case 1:
//todo: optional stop
break;
case 2:
//todo: program end
break;
*/
//set max extruder speed, 0-255 PWM
// case 100:
// extruder_speed = (int)(search_string('P', instruction, size));
// break;
//
// //turn extruder on, forward
// case 101:
// extruder_set_direction(1);
// extruder_set_speed(extruder_speed);
// break;
//
// //turn extruder on, reverse
// case 102:
// extruder_set_direction(0);
// extruder_set_speed(extruder_speed);
// break;
//
// //turn extruder off
// case 103:
// extruder_set_speed(0);
// break;
//
// //custom code for temperature control
// case 104:
// extruder_set_temperature((int)search_string('P', instruction, size));
//
// //warmup if we're too cold.
// while (extruder_get_temperature() < extruder_target_celsius)
// {
// extruder_manage_temperature();
// Serial.print("T:");
// Serial.println(extruder_get_temperature());
// delay(1000);
// }
//
// break;
//
// //custom code for temperature reading
// case 105:
// Serial.print("T:");
// Serial.println(extruder_get_temperature());
// break;
//
// //turn fan on
// case 106:
// extruder_set_cooler(255);
// break;
//
// //turn fan off
// case 107:
// extruder_set_cooler(0);
// break;
default:
break;
// Serial.print("Huh? M");
// Serial.println(code);
}
}
//tell our host we're done.
// Serial.println("ok");
// Serial.println(line, DEC);
}
