void Ui::deposit(Account* const& account) {
double amount = 0;
std::string description = "";
Date* date = new Date();
std::string polar;
std::cout << "\n***\n";
std::cout << "* MAKE A NEW DEPOSIT\n";
std::cout << "**********\n\n";
std::cout << "Please enter amount to deposit.\n";
amount = getUserInput();
std::cout << "Do you want to describe your deposit (Y/N)?\n";
polar = getUserInput("polar");
if (polar == "no") {
account->deposit(amount, description, date);
return;
}
std::cout << "Please describe your deposit.\n";
description = getUserInput("description");
std::cout << "Please enter the date.\n";
date->setDate();
account->deposit(amount, description, date);
}
void Ui::withdraw(Account* const& account) {
double amount = 0;
std::string description = "";
Date* date = new Date();
std::string polar;
std::cout << "\n***\n";
std::cout << "* MAKE A NEW WITHDRAWAL\n";
std::cout << "**********\n\n";
std::cout << "Please enter amount to withdraw.\n";
amount = getUserInput();
std::cout << "Do you want to describe your withdrawal (Y/N)?\n";
polar = getUserInput("polar");
if (polar == "no") {
account->withdraw(amount, description, date);
return;
}
std::cout << "Please describe your withdrawal.\n";
description = getUserInput("description");
std::cout << "Please enter the date.\n";
date->setDate();
account->withdraw(amount, description, date);
}
int main()
{
char input;
cout << "========= R E S T A U R A N T S I N C U P E R T I N O =========";
listHead *restaurants = new listHead(hashSize);
readFile(restaurants);
restaurants->getHashPtr()->printHashTableSequence();
// Display menu
displayMenu();
// Get user's input
input = getUserInput();
// While the user does not want to quit...
while (input != 'q')
{
// Call appropriate operation
operationManager(restaurants, input);
// Get user's input
input = getUserInput();
}
saveToFile(restaurants);
cout << "\n======================== T H A N K Y O U =========================";
}
std::string Ui::createAccount() {
std::string username;
std::string password = "******";
std::string repassword = "******";
std::cout << "\n***\n";
std::cout << "* ACCOUNT CREATION\n";
std::cout << "**********\n\n";
std::cout << "Please enter new username.\n";
username = getUserInput("username");
while (password != repassword) {
std::cout << "Please enter a password.\n";
password = getUserInput("password");
std::cout << "Please reenter password.\n";
repassword = getUserInput("password");
if (password != repassword) {
std::cout << "The password does not match.\n\n";
}
}
if (Account::create(username, password)) {
return username;
}
return "";
}
bool ThreePointTouchScreenCalibrator::calibrate(TouchScreenCalibration*& calibrationResults) {
Point p1Panel,p2Panel,p3Panel,p1Touch,p2Touch,p3Touch;
// register as an event subscriber with the touch screen
_clicked=true;
_ts.TouchScreenReadyEventSender.insertSubscriber(TouchScreenReadyEventSourceSlot::bind(this,&ThreePointTouchScreenCalibrator::onTouchScreenReady));
// point 1 is at 25%,50%, 2 is at 75%,25% and 3 is at 75%,75%
getUserInput(25,50,p1Panel,p1Touch);
getUserInput(75,25,p2Panel,p2Touch);
getUserInput(75,75,p3Panel,p3Touch);
// deregister our interest in clicks
_ts.TouchScreenReadyEventSender.removeSubscriber(TouchScreenReadyEventSourceSlot::bind(this,&ThreePointTouchScreenCalibrator::onTouchScreenReady));
// given the three points, expected and raw, we can do the mapping
calibrationResults=new ThreePointTouchScreenCalibration(p1Panel,p2Panel,p3Panel,p1Touch,p2Touch,p3Touch);
return true;
}
Account* Ui::loadAccount(const std::string& username) {
Account* account;
if (username.length() == 0) {
std::string username;
std::string actualPassword;
std::string password;
std::cout << "\n***\n";
std::cout << "* LOAD ACCOUNT\n";
std::cout << "**********\n\n";
std::cout << "Please enter the username of the account.\n";
username = getUserInput("username");
if (!Account::validate(username)) {
return nullptr;
}
std::cout << "Please enter password.\n";
password = getUserInput("password");
if (!Account::authenticate(username, password)) {
return nullptr;
}
account = Account::load(username);
}
else {
account = Account::load(username);
}
return account;
}
static char* InputUserPassword(KonohaContext *kctx, const char *message)
{
char buff[BUFSIZ] = {0};
const char *file = PLATAPI shortFilePath((getThisFileName(kctx)));
char cid[64] = {0};
file2CId(file, cid);
// char hostname[BUFSIZ] = {0};
// gethostname(hostname, BUFSIZ);
// struct addrinfo *res;
// struct in_Addr addr;
// int err;
// if((err = getaddrinfo(hostname, NULL, NULL, &res)) != 0) {
// PLATAPI syslog_i(5/*LOG_NOTICE*/, "{\"Method\": \"DScriptError\", \"CId\": \"%s\", \"Body\": \"error %d\"}", cid, err);
// exit(1);
// }
// addr.s_Addr = ((struct sockaddr_in *)(res->ai_Addr))->sin_Addr.s_Addr;
// char host[16] = {0};
// memcpy(host, inet_ntoa(addr), 16);
// freeaddrinfo(res);
const char host[] = "127.0.0.1"; // TODO get localhost IP
int port = 8090; // TODO random port scan
PLATAPI LoggerModule.syslog_i(5/*LOG_NOTICE*/, "{\"Method\": \"DScriptPassword\", \"CId\": \"%s\", \"Body\": \"%s\", \"Ip\": \"%s:%d\"}" , cid, message, host, port);
getUserInput(kctx, buff, cid, host, port);
size_t len = strlen(buff) + 1;
char *p = malloc(len);
if(p != NULL) {
memcpy(p, buff, len);
}
return p;
}
int main (int argc, char* argv[])
{
//create an array of processes called queue.
ticks = 0;
loop = 0;
queue q;
createQueue(q);
while (loop == 0)
{
ticks++;
printf("%d",ticks);
int i;
for (i = 1; i < getQueueSize(q); i++)
{
if (ticks - q.items[i].timeStamp > ticks)
{
if (getQueueSize(q) > 0)
{
scheduleProcess(q);
}
}
}
getUserInput(q);
if (ticks % 10 == 0)
{
for (i = 1; i < getQueueSize(q); i++)
{
q.items[i].priority = q.items[i].priority + 1;
}
}
}
}
int main()
{
srand((unsigned int) time(NULL));
int grid[ROWS][COLS];
initGrid(ROWS, COLS, grid);
printGrid(ROWS, COLS, grid);
int i, g;
g = getUserInput();
for(i = 0; i < g; i++)
{
generation++;
proccessGeneration(ROWS, COLS, grid);
printGrid(ROWS, COLS, grid);
sleep(99999);
putchar('\n');
}
return 0;
}
std::string Ui::accountMenu() {
std::cout << "This is the account options menu. ";
std::cout << "Please choose from the following options:\n\n";
std::cout << "1) Update account information.\n";
std::cout << "2) Show withdrawals.\n";
std::cout << "3) Show deposits.\n";
std::cout << "4) Make a new withdrawal\n";
std::cout << "5) Make a new deposit\n";
std::cout << "6) Go back to main menu\n";
int nChoices = 6;
int userChose = getUserInput(nChoices);
switch (userChose) {
case 1:
return "updateAccount";
case 2:
return "getWithdrawals";
case 3:
return "getDeposits";
case 4:
return "withdraw";
case 5:
return "deposit";
case 6:
return "quitAccountMenu";
}
}
int main(void) {
printf("Hello, please input a base 10 number that you would like converted to base 2: ");
unsigned long long int baseTen = getUserInput();
printf("Number %llu converted to base 2 = ", baseTen);
convert(baseTen);
printf("\n");
return 0;
}
int playerMove()
{
int random;
printf("1. Attack\n");
printf("2. Heal\n");
printf("Selection: ");
random = getUserInput(2);
return random;
}
int main()
{
getUserInput();
findMST();
int i = 0;
printf("最小生成树上节点相邻的情况为：\n");
for (; i < totalNum; ++i){//打印最小生成树情况
if(MST[i].parent != MST[i].node)
printf("边%d (%c, %c) 权值：%.2f\n", i, i + 65, MST[i].parent + 65, MST[i].cost);
}
system("pause");
return 0;
}
void Ui::deleteAccount() {
std::string username;
std::string actualPassword;
std::string password;
std::cout << "\n***\n";
std::cout << "* ACCOUNT DELETION\n";
std::cout << "**********\n\n";
std::cout << "Please enter the username of the account to be deleted.\n";
username = getUserInput("username");
if (!Account::validate(username)) {
return;
}
std::cout << "Please enter password.\n";
password = getUserInput("password");
if (!Account::authenticate(username, password)) {
return;
}
Account::remove(username);
}
void Ui::updateAccount(Account* const& account) {
std::string firstName;
std::string lastName;
std::string polar = "no";
std::string username = account->getUsername();
std::string oldPassword;
std::string newPassword = "******";
std::string renewPassword = "******";
std::cout << "\n***\n";
std::cout << "* UPDATE ACCOUNT INFORMATION\n";
std::cout << "**********\n\n";
while (polar == "no") {
std::cout << "Please enter your first name.\n";
firstName = getUserInput("all");
std::cout << "Please enter your last name.\n";
lastName = getUserInput("all");
std::cout << "Your full name is " << firstName << ' ' << lastName;
std::cout << ". Is this correct (Y/N)?\n";
polar = getUserInput("polar");
}
std::cout << "Do you want to change your password (Y/N)?\n";
polar = getUserInput("polar");
if (polar == "no") {
account->update(firstName, lastName);
return;
}
std::cout << "Please enter password.\n";
oldPassword = getUserInput("password");
if (!Account::authenticate(username, oldPassword)) {
return;
}
while (newPassword != renewPassword) {
std::cout << "Please enter a new password.\n";
newPassword = getUserInput("password");
std::cout << "Please reenter password.\n";
renewPassword = getUserInput("password");
if (newPassword != renewPassword) {
std::cout << "The password does not match.\n\n";
}
}
account->update(firstName, lastName, newPassword);
}
// The function is to process a player's move from displaying the board, getting
// user input to dealing with user input.
// It takes player, board array and gameNum as parameter.
// gameNum is used to record how many turns the user and computer have played.
void playerToMove(int player,Hole board[],int* gameNum){
char userInput;
int playerDone = 0;
int i = 0;
do{
if ((player == 1 && i > 0) || player == 0)
displayBoard(board);
userInput = getUserInput(player, gameNum, playerDone, board);
playerDone = pieceToMove(player, userInput, board);
if(checkEndGame(board) == 0)
break;
i++;
}while (playerDone);
} //end of playerToMove
int main(){
std::vector<std::string> words;
std::cout << "Quit by entering \"q\"" << std::endl;
while(1){
words = getUserInput();
words = sort(words);
for(unsigned int i = 0; i < words.size(); i++){
std::cout << words[i] + " ";
}
std::cout << std::endl;
}
return 0;
}
int main(int argc,char* argv[])
{
signal(SIGINT, sig_handler);
signal(SIGTERM, sig_handler);
signal(SIGQUIT, sig_handler);
signal(SIGTSTP, sig_handler);
int isExit = 0;
do {
char rawInput[255];
isExit = getUserInput(rawInput);
if(isExit == 1) break;
if (isExit == 0)
tokenizeInput(rawInput);
} while(isExit = 1);
return 0;
}
int main(int argc, char const *argv[])
{
srand((unsigned int) time(NULL)); //Takes the current time and uses it as a seed for the random number generator
int grid[ROWS][COLS]; //Make grid
initGrid(ROWS, COLS, grid); //Initialize grid
printGrid(ROWS, COLS, grid); //Print grid to screen
int i, g;
g = getUserInput();
for (i = 0; i < g; i++)
{
generation++;
processGeneration(ROWS, COLS, grid);
printGrid(ROWS, COLS, grid);
sleep(100);
}
return 0;
}
// The function is to process a player's move from displaying the board, getting
// user input to dealing with user input.
// It takes player, board array and gameNum as parameter.
// gameNum is used to record how many turns the user and computer have played.
void playerToMove(int player,Hole board[],int gameNum){
char userInput;
int playerDone = 0;
do{
displayBoard(board);
userInput = getUserInput(player, gameNum, playerDone, board);
playerDone = pieceToMove(player, userInput, board);
if(checkEndGame(board) == 0)
break;
}while (playerDone);
//displayBoard(board);
//printf("---------------------------------------------------\n sepertat");
/* if(oneGameDone){ */
/* printf("-----------------------------------------------------\n"); */
/* displayBoard(board); */
/* } */
} //end of playerToMove
int main(void)
{
int iChoice = 0;
// size console window to 100x40
if(!initConsole())
{
// show error box
showError("Error", "Console Window could not be initialized.\nExiting program.");
return EXIT_FAILURE;
}
// LogIn / Register Menu
showStartScreen();
do
{
// choose between LogIn and Register
getUserInput("%i", &iChoice, "\tChoose: ", "\n\tYour input is invalid. Please choose again.\n");
}
while(iChoice != 1 && iChoice != 2);
// LogIn / Register
if(iChoice == 1)
{
// loop until valid login
while(!showLogin());
}
else
{
// loop until valid registration
while(!showRegister());
}
// loop until user quits manually
while(startApplication());
return EXIT_SUCCESS;
}
bool AudioApp::Start()
{
// While a windows quit message has not been posted.
while(mMessage.message != WM_QUIT)
{
// Get waiting windows messages.
if(PeekMessage( &mMessage, 0, 0, 0, PM_REMOVE ))
{
// Dispatch messages.
TranslateMessage( &mMessage );
DispatchMessage( &mMessage );
}
else
{
// Tick the game timer, and update the player.
mGameTimer->tick();
mPlayer->update();
// React to any user input.
getUserInput();
// Update the monster object, and check player-monster proximity.
mMonster->update(mPlayer, mGameTimer->getDeltaTime());
checkMonsterDistance();
// Play and update ambience sounds.
mAmbience->play();
mBatAmbience->play();
mRockSlide->update(mPlayer, mGameTimer->getDeltaTime());
mBatFlock->update(mPlayer, mGameTimer->getDeltaTime());
}
}
// If application has exited the loop, shutdown the application.
ShutDown();
return true;
}
int main(int argc, char* argv[])
{
//SUGGESTION = 18; //Does not work
int theNumber; //Local variable of main
theNumber = 20;
printf("Todays number is 30, not %d\n", theNumber);
printf("Tomorrow's number is 31, not %d\n", theNumber);
int todaysNumber;
todaysNumber = 30;
printf("Todays number is %d, not %d\n", todaysNumber, theNumber);
printf("Tomorrow's number is %d, not %d\n", todaysNumber+1, theNumber);
todaysNumber = getUserInput();
printf("Todays number is %d, not %d\n", todaysNumber, theNumber);
printf("Tomorrow's number is %d, not %d\n", todaysNumber+1, theNumber);
return 0;
}
/*
* Takes in the following parameters
* File - The file to en-/decode
* Key - file containing the key used for en-/decoding the file
*/
int main (int argc, char **argv) {
// Check if the program was started with two parameters (file and key)
if (argc == 3){
FileContainer files;
int securityDistance;
if (checkFiles(argv) != 0) {
files = openAndReadKey(argv[2]);
char action = getUserInput();
int choice = encodeOrDecode(action);
switch (encodeOrDecode(action)) {
case 0:
printMessage(TYPE_INFO, CHOICE_EXIT);
free(files.key);
exit(0);
case 1:
securityDistance = getWantedSecLvl();
printMessage(TYPE_INFO, INFO_ENCODING_START);
encodeFile(files, argv[1], securityDistance);
printMessage(TYPE_INFO, INFO_ENCODING_END);
break;
case 2:
printMessage(TYPE_INFO, INFO_DECODING_START);
decodeFile(files, argv[1]);
printMessage(TYPE_INFO, INFO_DECODING_END);
break;
default:
break;
}
}
} else {
printMessage(TYPE_ERROR, ERROR_PARAMETERS);
}
return 0;
}
std::string Ui::mainMenu() {
std::cout << "This is the Checking Account App. ";
std::cout << "Please choose from the following options:\n\n";
std::cout << "1) Create new account.\n";
std::cout << "2) Delete an existing account.\n";
std::cout << "3) Load an existing account.\n";
std::cout << "4) Quit\n\n";
int nChoices = 4;
int userChose = getUserInput(nChoices);
switch (userChose) {
case 1:
return "createAccount";
case 2:
return "deleteAccount";
case 3:
return "loadAccount";
case 4:
return "quit";
}
}
static int InputUserApproval(KonohaContext *kctx, const char *message, const char *yes, const char *no, int defval)
{
char buff[BUFSIZ] = {0};
const char *ykey = defval ? "Y" : "y";
const char *nkey = defval ? "n" : "N";
if(message == NULL || message[0] == '\0') message = "Do you approve?";
if(yes == NULL || yes[0] == '\0') yes = "yes";
if(no == NULL || no[0] == '\0') no = "no";
const char *file = PLATAPI shortFilePath((getThisFileName(kctx)));
char cid[64] = {0};
file2CId(file, cid);
// char hostname[BUFSIZ] = {0};
// gethostname(hostname, BUFSIZ);
// struct addrinfo *res;
// struct in_Addr addr;
// int err;
// if((err = getaddrinfo(hostname, NULL, NULL, &res)) != 0) {
// PLATAPI syslog_i(5/*LOG_NOTICE*/, "{\"Method\": \"DScriptError\", \"CId\": \"%s\", \"Body\": \"error %d\"}", cid, err);
// exit(1);
// }
// addr.s_Addr = ((struct sockaddr_in *)(res->ai_Addr))->sin_Addr.s_Addr;
// char host[16] = {0};
// memcpy(host, inet_ntoa(addr), 16);
// freeaddrinfo(res);
const char host[] = "127.0.0.1"; // TODO get localhost IP
int port = 8090; // TODO random port scan
PLATAPI LoggerModule.syslog_i(5/*LOG_NOTICE*/, "{\"Method\": \"DScriptApproval\", \"CId\": \"%s\", \"Body\": \"%s (%s %s, %s %s): \", \"Ip\": \"%s:%d\"}" , cid, message, yes, ykey, no, nkey, host, port);
getUserInput(kctx, buff, cid, host, port);
if(defval) {
return ((buff[0] == 'N' || buff[0] == 'n') && buff[1] == 0) ? false : true;
}
else {
return ((buff[0] == 'Y' || buff[0] == 'y') && buff[1] == 0) ? false : true;
}
}
int main(){
/*Declare variables*/
char *comp = "4";
char *promptString = "Please enter a value: ";
char *userInputReturn = (char *)malloc(BUFFERSIZE);
int i = 0;
/*initialize the unit testing framework*/
cunit_init();
/*Get user input*/
userInputReturn = getUserInput(promptString);
/*Replace first \n with null terminator for later comparison*/
userInputReturn[strcspn(userInputReturn,"\n")] = '\0';
/*Make comparison and place \n back to userInputReturn variable*/
i = strcmp(comp, userInputReturn);
userInputReturn[strcspn(userInputReturn,"\n")] = '\n';
assert_eq("Input not in correct format", i, 0);
return 0;
}
void run() {
displayTitle();
displayIntroMessage();
outputFlagContainer *outputFlags = malloc(sizeof(outputFlagContainer));
while(true) {
displayPreGameMenu();
outputFlags = getUserInput(outputFlags);
if (outputFlags->HELP) {
displayHelpMessage();
} else if (outputFlags->YES || outputFlags->PLAY) {
gameloop(outputFlags);
} else if (outputFlags->QUIT || outputFlags->NO) {
displayQuitMessage();
break;
} else {
displayBadInputMessage();
}
}
free(outputFlags);
}
int main( int argc, char *argv[] ) {
char seqChar[MAXSEQLENGTH];
int seqNum[MAXSEQLENGTH+1];
DBL_TYPE pf;
int complexity = 3;
int length, tmpLength;
char inputFile[ MAXLINE];
int vs;
char sampleFile[MAXLINE];
//permAvgPairs stores the expected value of each
//class of base pairs, grouped by permutation or complex, respectively
int inputFileSpecified;
FILE *F_sample = NULL; // ppairs file
int index;
strcpy( inputFile, "");
nupack_sample = 1;
nupack_num_samples = 10;
struct timeval rand_time;
gettimeofday(&rand_time,0);
nupack_random_seed = (rand_time.tv_sec)*1000000 + rand_time.tv_usec;
inputFileSpecified = ReadCommandLineNPK( argc, argv, inputFile);
if(NupackShowHelp) {
printf("Usage: sample [OPTIONS] PREFIX\n");
printf("Randomly sample unpseudoknotted structures from the equilibrium distribution\n");
printf("Example: sample -multi -T 25 -material dna -samples 100 example\n");
PrintNupackThermoHelp();
PrintNupackUtilitiesHelp();
exit(1);
}
if( !inputFileSpecified ) {
printf("Enter output file prefix: ");
scanf("%s", inputFile);
strcat(inputFile,".in"); // Here, .in is just a placeholder
}
if(!inputFileSpecified ||
!ReadInputFile( inputFile, seqChar, &vs, NULL, NULL, NULL) ) {
if (inputFileSpecified==0) getUserInput( seqChar, &vs, NULL, NULL);
else abort();
}
strncpy(sampleFile,inputFile,strlen(inputFile)-3);
sampleFile[strlen(inputFile)-3] = '\0';
strcat(sampleFile,".sample");
header( argc, argv, "sample", sampleFile);
printInputs( argc, argv, seqChar, vs, NULL, NULL,sampleFile);
tmpLength = length = strlen( seqChar);
convertSeq(seqChar, seqNum, tmpLength);
int ns1,ns2;
getSequenceLength(seqChar, &ns1);
getSequenceLengthInt(seqNum, &ns2);
init_genrand(nupack_random_seed);
pairPr = NULL;
if (complexity != 3) {
printf("Sampling supported only for complexity = 3. Exiting\n");
exit(1);
}
nupack_sample_list = (char **)calloc(nupack_num_samples, sizeof(char *));
printf("Number of Samples = %i\n",nupack_num_samples);
for(index = 0 ; index < nupack_num_samples ; index++) {
nupack_sample_list[index] = (char *) calloc(tmpLength+1,sizeof(char));
}
printf("Started Calculation\n");
pf = pfuncFull(seqNum, complexity, DNARNACOUNT, DANGLETYPE, TEMP_K - ZERO_C_IN_KELVIN, 0,
SODIUM_CONC, MAGNESIUM_CONC, USE_LONG_HELIX_FOR_SALT_CORRECTION);
printf("Finished Calculation\n");
if ((F_sample = fopen(sampleFile,"a")) == NULL) {
printf("Error opening file %s!\n",sampleFile);
exit(1);
}
// Print the free energy to the output file
fprintf(F_sample,"%s Free energy: %.8Le kcal/mol\n",
COMMENT_STRING,-kB*TEMP_K*logl(pf));
fprintf(F_sample,"%s Number of Samples: %i\n",COMMENT_STRING,nupack_num_samples);
// Put newline for stylistic reasons
fprintf(F_sample,"\n");
for(index = 0 ; index < nupack_num_samples ; index++) {
fprintf(F_sample, "%s\n",nupack_sample_list[index]);
free(nupack_sample_list[index]);
nupack_sample_list[index] = NULL;
}
free(nupack_sample_list);
#ifdef GC_DEBUG
CHECK_LEAKS();
#endif
return 0;
}
int main( int argc, char *argv[] ) {
//This function will calculate the all structures within a fixed
//range of the "algorithmic" mfe. The algorithmic mfe is the
//minimum free energy of a structure, ignoring symmetry corrections.
//The output is a list of the structures, including the difference
//from the algorithmic mfe, followed by the symmetry factor and the
//corrected energies, after adjusting for symmetries. The list is
//sorted by the corrected energies.
char seq[ MAXSEQLENGTH];
int seqNum[ MAXSEQLENGTH+1];
int isNicked[ MAXSEQLENGTH];
int nNicks = 0;
int nicks[MAXSTRANDS];
int nickIndex;
int **etaN;
int complexity = 3;
int length, tmpLength;
float gap = -1;
int i;
int vs;
char outFile[MAXLINE];
int inputFileSpecified;
FILE *fp;
dnaStructures mfeStructs = {NULL, 0, 0, 0, NAD_INFINITY};
//this struct will store
//all the structures within the given range
char inputFile[ MAXLINE];
strcpy( inputFile, "");
inputFileSpecified = ReadCommandLineNPK( argc, argv, inputFile);
if(NupackShowHelp) {
printf("Usage: subopt [OPTIONS] PREFIX\n");
printf("Calculate and store all structures within the specified energy gap\n");
printf("of the MFE structure.\n");
printf("Example: subopt -multi -T 25 -material dna example\n");
PrintNupackThermoHelp();
PrintNupackUtilitiesHelp();
exit(1);
}
if( !inputFileSpecified ) {
printf("Enter output file prefix: ");
scanf("%s", inputFile);
strcat(inputFile,".in"); // Here, .in is just a placeholder
}
if( !inputFileSpecified ||
!ReadInputFile( inputFile, seq, &vs, &gap, NULL, NULL) ) {
if (inputFileSpecified==0) getUserInput( seq, &vs, &gap, NULL);
else abort();
}
strncpy(outFile,inputFile,strlen(inputFile)-3);
outFile[strlen(inputFile)-3] = '\0';
strcat(outFile,".subopt");
header( argc, argv, "subopt", outFile);
printInputs( argc, argv, seq, vs, &gap, NULL, outFile);
// Add newline for stylistic reasons
fp = fopen(outFile,"a");
fprintf(fp,"\n");
fclose(fp);
if( !DO_PSEUDOKNOTS ) {
complexity = 3;
}
else {
complexity = 5;
}
tmpLength = length = strlen( seq);
convertSeq(seq, seqNum, tmpLength);
mfeFullWithSym_SubOpt( seqNum, tmpLength, &mfeStructs, complexity,
DNARNACOUNT, DANGLETYPE,
TEMP_K - ZERO_C_IN_KELVIN,
vs, (DBL_TYPE) gap, 0, SODIUM_CONC, MAGNESIUM_CONC,
USE_LONG_HELIX_FOR_SALT_CORRECTION);
//the rest is for printing purposes
for( i = 0; i < tmpLength; i++) {
isNicked[i] = 0;
if( seq[i] == '+') {
length--;
isNicked[ i - nNicks++ -1] = 1;
}
}
//initialize nicks
for( i = 0; i < MAXSTRANDS; i++) {
nicks[i] = -1;
}
nickIndex = 0;
for( i = 0; i < length; i++) {
if( isNicked[i])
nicks[ nickIndex++] = i;
}
//overkill, but convenient
etaN = (int**) malloc( (length*(length+1)/2 + (length+1))*sizeof( int*));
InitEtaN( etaN, nicks, length);
PrintDnaStructures( &mfeStructs, etaN, nicks, vs, outFile);
clearDnaStructures( &mfeStructs);
return 0;
}
