void Evaluation::evaluation()
{
std::ifstream file(this->inputFile);
if (file.is_open())
{
std::string line;
float resp;
int realClass, predictedClass;
while (getline(file, line))
{
std::vector<std::string> split = splitString(line, ' ');
predictedClass = atoi(split[1].c_str()) - 1; // Victor started them from 1
realClass = atoi(split[2].c_str()) - 1; // Victor started them from 1
resp = static_cast<float>(atof(split[3].c_str()));
this->confusionMat[realClass][predictedClass]++;
this->confusionMatScores[realClass][predictedClass].push_back(resp);
}
file.close();
generateOutput();
}
else
std::cerr << "Wrong input file." << std::endl;
}
void MainWindow::generate_f(){
QString polyString = polyField->text();
QString startString = startValueField->text();
polyString.remove(0,1);
if(polyString.length() != startString.length()){
resultDoc->setPlainText("Invalid Input");
return;
}
if(!checkInput(polyString)){
return;
}
if(!checkInput(startString)){
return;
}
if((polyData = convertData(polyString)) == NULL){
resultDoc->setPlainText("Invalid Input");
return;
}
if((data = convertData(startString)) == NULL){
resultDoc->setPlainText("Invalid Input");
return;
}
std::reverse(polyData->begin(), polyData->end());
generateOutput();
}
void JSCLanguageBase::add(const AdditionalClass& additionalClass) {
std::vector<JSCPropertyPointer> properties;
for (const auto& propertyPair : additionalClass.properties) {
JSCPropertyType type = JSCProperty::propertyStringToType(std::get<0>(propertyPair));
if (JSCProperty_Unknown == type) {
SIAWarning("unsupported property type: %s", std::get<0>(propertyPair).c_str());
continue;
}
JSCPropertyPointer property(new JSCProperty(type));
property->setPath({std::get<1>(propertyPair)});
property->setRequired(!std::get<2>(propertyPair));
properties.push_back(property);
}
JSCObjectPointer newClass(new JSCObject(properties));
newClass->setRootName(additionalClass.className);
newClass->setPath({additionalClass.name});
newClass->setCodeGenerate(true);
newClass->setRequired(!additionalClass.optional);
m_additionalClasses.push_back(newClass);
for (const auto& out : generateOutput(newClass)) {
m_outputs.push_back(out);
}
}
/*! Default main. The idea of separating this from the rest of doxygen,
* is to make it possible to write your own main, with a different
* generateOutput() function for instance.
*/
int main(int argc,char **argv)
{
initDoxygen();
readConfiguration(argc,argv);
checkConfiguration();
adjustConfiguration();
parseInput();
generateOutput();
return 0;
}
void JSCLanguageBase::add(const JSCObjectPointer& object) {
if (isIgnore(object)) {
SIADebug("Ignore class with name: %s", object->rootName().c_str());
return;
}
for (const auto& out : generateOutput(object)) {
m_outputs.push_back(out);
}
}
void JSCLanguageBase::add(const JSCEnumPointer& enumObj) {
if (isIgnore(enumObj)) {
SIADebug("Ignore enum with name: %s", enumObj->enumName().c_str());
return;
}
for (const auto& out : generateOutput(enumObj)) {
m_outputs.push_back(out);
}
}
/**
* @brief Main code generator dispatch.
*
* According to the type of the input signal, generateCode calls
* the appropriate generator with appropriate arguments.
*
* @param sig The signal expression to compile.
* @param priority The environment priority of the expression.
* @return <string> The LaTeX code translation of the signal.
*/
string DocCompiler::generateCode (Tree sig, int priority)
{
int i;
double r;
Tree c, sel, x, y, z, u, label, ff, largs, type, name, file;
if ( getUserData(sig) ) { printGCCall(sig,"generateXtended"); return generateXtended (sig, priority); }
else if ( isSigInt(sig, &i) ) { printGCCall(sig,"generateNumber"); return generateNumber (sig, docT(i)); }
else if ( isSigReal(sig, &r) ) { printGCCall(sig,"generateNumber"); return generateNumber (sig, docT(r)); }
else if ( isSigInput(sig, &i) ) { printGCCall(sig,"generateInput"); return generateInput (sig, docT(i+1)); }
else if ( isSigOutput(sig, &i, x) ) { printGCCall(sig,"generateOutput"); return generateOutput (sig, docT(i+1), CS(x, priority)); }
else if ( isSigFixDelay(sig, x, y) ) { printGCCall(sig,"generateFixDelay"); return generateFixDelay (sig, x, y, priority); }
else if ( isSigPrefix(sig, x, y) ) { printGCCall(sig,"generatePrefix"); return generatePrefix (sig, x, y, priority); }
else if ( isSigIota(sig, x) ) { printGCCall(sig,"generateIota"); return generateIota (sig, x); }
else if ( isSigBinOp(sig, &i, x, y) ) { printGCCall(sig,"generateBinOp"); return generateBinOp (sig, i, x, y, priority); }
else if ( isSigFFun(sig, ff, largs) ) { printGCCall(sig,"generateFFun"); return generateFFun (sig, ff, largs, priority); }
else if ( isSigFConst(sig, type, name, file) ) { printGCCall(sig,"generateFConst"); return generateFConst (sig, tree2str(file), tree2str(name)); }
else if ( isSigFVar(sig, type, name, file) ) { printGCCall(sig,"generateFVar"); return generateFVar (sig, tree2str(file), tree2str(name)); }
// new special tables for documentation purposes
else if ( isSigDocConstantTbl(sig, x, y) ) { printGCCall(sig,"generateDocConstantTbl"); return generateDocConstantTbl (sig, x, y); }
else if ( isSigDocWriteTbl(sig,x,y,z,u) ) { printGCCall(sig,"generateDocWriteTbl"); return generateDocWriteTbl (sig, x, y, z, u); }
else if ( isSigDocAccessTbl(sig, x, y) ) { printGCCall(sig, "generateDocAccessTbl"); return generateDocAccessTbl(sig, x, y); }
else if ( isSigSelect2(sig, sel, x, y) ) { printGCCall(sig,"generateSelect2"); return generateSelect2 (sig, sel, x, y, priority); }
else if ( isSigSelect3(sig, sel, x, y, z) ) { printGCCall(sig,"generateSelect3"); return generateSelect3 (sig, sel, x, y, z, priority); }
else if ( isProj(sig, &i, x) ) { printGCCall(sig,"generateRecProj"); return generateRecProj (sig, x, i, priority); }
else if ( isSigIntCast(sig, x) ) { printGCCall(sig,"generateIntCast"); return generateIntCast (sig, x, priority); }
else if ( isSigFloatCast(sig, x) ) { printGCCall(sig,"generateFloatCast"); return generateFloatCast(sig, x, priority); }
else if ( isSigButton(sig, label) ) { printGCCall(sig,"generateButton"); return generateButton (sig, label); }
else if ( isSigCheckbox(sig, label) ) { printGCCall(sig,"generateCheckbox"); return generateCheckbox (sig, label); }
else if ( isSigVSlider(sig, label,c,x,y,z) ) { printGCCall(sig,"generateVSlider"); return generateVSlider (sig, label, c,x,y,z); }
else if ( isSigHSlider(sig, label,c,x,y,z) ) { printGCCall(sig,"generateHSlider"); return generateHSlider (sig, label, c,x,y,z); }
else if ( isSigNumEntry(sig, label,c,x,y,z) ) { printGCCall(sig,"generateNumEntry"); return generateNumEntry (sig, label, c,x,y,z); }
else if ( isSigVBargraph(sig, label,x,y,z) ) { printGCCall(sig,"generateVBargraph"); return CS(z, priority);}//generateVBargraph (sig, label, x, y, CS(z, priority)); }
else if ( isSigHBargraph(sig, label,x,y,z) ) { printGCCall(sig,"generateHBargraph"); return CS(z, priority);}//generateHBargraph (sig, label, x, y, CS(z, priority)); }
else if ( isSigAttach(sig, x, y) ) { printGCCall(sig,"generateAttach"); return generateAttach (sig, x, y, priority); }
else if ( isSigEnable(sig, x, y) ) { printGCCall(sig,"generateEnable"); return generateEnable (sig, x, y, priority); }
else {
stringstream error;
error << "ERROR in d signal, unrecognized signal : " << *sig << endl;
throw faustexception(error.str());
}
faustassert(0);
return "error in generate code";
}
int SoundGen2GS::readBuffer(int16 *buffer, const int numSamples) {
static uint data_available = 0;
static uint data_offset = 0;
uint n = numSamples << 1;
uint8 *p = (uint8*)buffer;
while (n > data_available) {
memcpy(p, (uint8*)_out + data_offset, data_available);
p += data_available;
n -= data_available;
advancePlayer();
data_available = generateOutput() << 1;
data_offset = 0;
}
memcpy(p, (uint8*)_out + data_offset, n);
data_offset += n;
data_available -= n;
return numSamples;
}
int
main (int argc, const char* const argv[])
{
char garbage[2];
int command;
double sigma;
if (4 > argc || 5 < argc) {
fprintf (stderr,
"syntax: %s <input file> <output file> <command #> ...\n",
argv[0]);
return 2;
}
if (1 != sscanf (argv[3], "%d%1s", &command, garbage) ||
1 > command || 3 < command) {
fprintf (stderr, "Command must be from 1 to 3.\n");
fprintf (stderr, " 1 -- gaussian filter <sigma>\n");
fprintf (stderr, " 2 -- greyscale\n");
fprintf (stderr, " 3 -- invert colors\n");
return 2;
}
if (1 == command &&
(5 != argc ||
1 != sscanf (argv[4], "%lf%1s", &sigma, garbage) ||
0 >= sigma || 100 <= sigma)) {
fprintf (stderr, "Sigma must be greater than 0 and less than 100.\n");
return 2;
}
Image* inputImage = decode (argv[1]);
printf ("Width: %d, height: %d\n", inputImage->width, inputImage->height);
Image* outputImage = generateOutput (inputImage);
int height = inputImage->height;
int width = inputImage->width;
uint8_t* inRed = inputImage->redChannel;
uint8_t* inBlue = inputImage->blueChannel;
uint8_t* inGreen = inputImage->greenChannel;
uint8_t* inAlpha = inputImage->alphaChannel;
uint8_t* outRed = outputImage->redChannel;
uint8_t* outBlue = outputImage->blueChannel;
uint8_t* outGreen = outputImage->greenChannel;
uint8_t* outAlpha = outputImage->alphaChannel;
switch (command) {
case 1: {
int radius = ceil (3 * sigma);
int fSize = 1 + 2 * radius;
double* gauss = malloc (sizeof (gauss[0]) * fSize * fSize);
gaussianFilter (gauss, sigma);
convolveImage (width, height, inRed, inGreen, inBlue, inAlpha,
radius, gauss, outRed, outGreen, outBlue, outAlpha);
encode (argv[2], outputImage);
break;
}
case 2:
greyscale (width, height, inRed, inGreen, inBlue, inAlpha,
gMonoMult, outRed, outGreen, outBlue, outAlpha);
encode (argv[2], outputImage);
break;
case 3:
invertColors (width, height, inRed, inGreen, inBlue, inAlpha,
outRed, outGreen, outBlue, outAlpha);
encode (argv[2], outputImage);
break;
}
freeImage (inputImage);
freeImage (outputImage);
return 0;
}
Result VideoHandle::getDirection()
{
vector<Point> List;
Mat frame;
Mat prev;
for(int i=10;i--;)
getUndistortFrame();
prev = getUndistortFrame();
while(true)
{
int prev_clock = clock();
frame = getUndistortFrame();
if(frame.empty()) exit(1);
Mat temp;
subtract(prev, frame, temp);
const Size size = Size(160, 120);
resize(temp, temp, size, 0, 0, CV_INTER_LINEAR);// FIXME
cvtColor(temp, temp, CV_BGR2GRAY);
threshold(temp, temp, 20, 255, CV_THRESH_BINARY);
Moments m = ::moments(temp);
Point p = Point(m.m10/m.m00, m.m01/m.m00);
cout << "Point : " << p.x << " " << p.y << endl;
List.push_back(p);
if (p.x < 5 || p.y < 5 || p.x > size.width-5 || p.y > size.height-5) { // FIXME
cout << "233333333333333" << endl;
List.clear();
}
const int TIMES = 1;// FIXME
Point sum = Point(0, 0);
for(int i=1;i<=TIMES;i++)
{
if(List.size() < TIMES + 1) continue;
Point a = List[List.size() - i];
Point b = List[List.size() - i - 1];
Point sub = Point(a.x-b.x, a.y-b.y);
sum.x += sub.x;
sum.y += sub.y;
}
sum.x /= TIMES;
sum.y /= TIMES;
cout << "vector : " << sum.x << " " << sum.y << endl;
if(sum.x*sum.x + sum.y*sum.y >= 30) { //FIXME 建议修改为||关系
Result ret = generateOutput(p, Point(p.x+sum.x, p.y+sum.y));
ret.angle *= -1;
return ret;
}
int now_clock = clock();
double speed = double(now_clock - prev_clock) / CLOCKS_PER_SEC;
cout << "speed : " << speed << " " << (1.0/speed) << endl;
}
}
Result VideoHandle::getDirectionPoints()
{
Mat frame;
Mat prev;
vector<Point> List;
for (int i=30;i--;) getFrame();
prev = getFrame();
while(true)
{
int prev_clock = clock();
frame = getFrame();
if(frame.empty()) break;
Mat temp;
subtract(prev, frame, temp);
const Size size = Size(160, 120);
resize(temp, temp, size, 0, 0, CV_INTER_LINEAR);
cvtColor(temp, temp, CV_BGR2GRAY);
threshold(temp, temp, 20, 255, CV_THRESH_BINARY);
morphologyEx(temp.clone(), temp, MORPH_OPEN, Mat::ones(3, 3, CV_8U));
Moments m = ::moments(temp);
Point p = Point(m.m10/m.m00, m.m01/m.m00);
// Mat_<Point2f> points(1,1), dst(1,1);
// points(0) = Point2f(p.x,p.y);
// undistortPoints(points, dst, distortmtx, distortdist);
// p.x = - dst(0).y * size.width;
// p.y = - dst(0).x * size.height;
cout << "Point : " << p.x << " " << p.y << endl;
List.push_back(p);
if (p.x < 5 || p.y < 5 || p.x > size.width - 6 || p.y > size.height - 6) {
cout << "455555555555555" << endl;
List.clear();
}
const int TIMES = 1;
Point sum = Point(0, 0);
for(int i=1;i<=TIMES;i++)
{
if(List.size() < TIMES + 1) continue;
Point a = List[List.size() - i];
Point b = List[List.size() - i - 1];
Point sub = Point(a.x-b.x, a.y-b.y);
sum.x += sub.x;
sum.y += sub.y;
}
sum.x /= TIMES;
sum.y /= TIMES;
cout << "vector : " << sum.x << " " << sum.y << endl;
if(abs(sum.x) >= 2 || abs(sum.y) >= 2) {
Result ret = generateOutput(p, Point(p.x+sum.x, p.y+sum.y));
ret.angle *= -1;
return ret;
}
int now_clock = clock();
double speed = double(now_clock - prev_clock) / CLOCKS_PER_SEC;
cout << "speed : " << speed << " " << (1.0/speed) << endl;
}
}
int main(int argc,char *argv[])
{
//Handles user input
if(argc<4 || argc>5)
{
printf("Incorrect number of arguments\n");
printf("Number of arguments: %d\n",argc);
exit(1);
}
//const char *inputFilename=argv[1];
const char *inputFilename=argv[1];
printf("Inputfile: %s\n",inputFilename);
const char *outputFilename=argv[2];
char garbage[2];
int command;
double sigma=3;
if(1!=sscanf(argv[3],"%d%1s",&command,garbage) || command<0 || command>11)
{
printf("Incorrect command\n");
exit(1);
}
if(command>0 && command<11 && argc==5)
{
printf("Incorrect number of arguments, exclude the sigma value");
exit(1);
}
if(((command==0 || command==11) && argc==5 && 1!=sscanf(argv[4],"%lf%1s",&sigma,garbage)) || sigma<0)
{
printf("Incorrect sigma value\n");
exit(1);
}
Filter *filters=initializeFilters(sigma);
Image *inputImage=decode(inputFilename);
printf("Width: %d, height: %d\n",inputImage->width,inputImage->height);
Image *outputImage=generateOutput(inputImage);
uint8_t *inRed=inputImage->redChannel;
uint8_t *inBlue=inputImage->blueChannel;
uint8_t *inGreen=inputImage->greenChannel;
uint8_t *inAlpha=inputImage->alphaChannel;
uint8_t *outRed=outputImage->redChannel;
uint8_t *outBlue=outputImage->blueChannel;
uint8_t *outGreen=outputImage->greenChannel;
uint8_t *outAlpha=outputImage->alphaChannel;
int height=inputImage->height;
int width=inputImage->width;
switch(command)
{
case(0):
{
convolveImage(inRed,inBlue,inGreen,inAlpha,outRed,outBlue,outGreen,
outAlpha,filters[0].filter,filters[0].radius,width,height);
break;
}
case(1):
{
convolveImage(inRed,inBlue,inGreen,inAlpha,outRed,outBlue,outGreen,
outAlpha,filters[1].filter,filters[1].radius,width,height);
break;
}
case(2):
{
convolveImage(inRed,inBlue,inGreen,inAlpha,outRed,outBlue,outGreen,
outAlpha,filters[2].filter,filters[2].radius,width,height);
break;
}
case(3):
{
convolveImage(inRed,inBlue,inGreen,inAlpha,outRed,outBlue,outGreen,
outAlpha,filters[3].filter,filters[3].radius,width,height);
break;
}
case(4):
{
convolveImage(inRed,inBlue,inGreen,inAlpha,outRed,outBlue,outGreen,
outAlpha,filters[4].filter,filters[4].radius,width,height);
break;
}
case(5):
{
convolveImage(inRed,inBlue,inGreen,inAlpha,outRed,outBlue,outGreen,
outAlpha,filters[5].filter,filters[5].radius,width,height);
break;
}
case(6):
{
convolveImage(inRed,inBlue,inGreen,inAlpha,outRed,outBlue,outGreen,
outAlpha,filters[6].filter,filters[6].radius,width,height);
break;
}
case(7):
{
convertToGray(inRed,inBlue,inGreen,inAlpha,outRed,outBlue,outGreen,
outAlpha,gMonoMult,width,height);
break;
}
case(8):
{
invertImage(inRed,inBlue,inGreen,inAlpha,outRed,outBlue,outGreen,
outAlpha,width,height);
break;
}
case(9):
{
flipImage(inRed,inBlue,inGreen,inAlpha,outRed,outBlue,outGreen,
outAlpha,width,height);
break;
}
case(10):
{
pixelate(inRed,inBlue,inGreen,inAlpha,outRed,outBlue,outGreen,
outAlpha,8,8,width,height);
break;
}
case(11):
{
Image *invImage=generateOutput(inputImage);
Image *blurImage=generateOutput(inputImage);
pencilSketch(inRed,inBlue,inGreen,inAlpha,invImage->redChannel,
invImage->blueChannel,invImage->greenChannel,
invImage->alphaChannel,blurImage->redChannel,
blurImage->blueChannel,blurImage->greenChannel,
blurImage->alphaChannel,outRed,outBlue,outGreen,
outAlpha,filters[0].filter,filters[0].radius,width,height,
gMonoMult);
//NOTE THAT I NEED TO FREE EACH OF THE CHANNEL INDIVIDUALLY
//MAKE A FREE IMAGE FUNCTION
freeImage(invImage);
freeImage(blurImage);
break;
}
default:
exit(1);
}
if(command!=12)
encode(outputFilename,outputImage);
free((double*)filters[0].filter);
free(filters);
freeImage(inputImage);
freeImage(outputImage);
return 0;
}
int main(int argc, char **argv)
{
/*
* Parse options.
*/
for (int i = 1; i < argc; i++)
{
const char *psz = argv[i];
if (*psz == '-')
{
if (!strcmp(psz, "--output") || !strcmp(psz, "-o"))
{
if (++i >= argc)
{
fprintf(stderr, "syntax error: File name expected after '%s'.\n", psz);
return RTEXITCODE_SYNTAX;
}
g_pszOutput = argv[i];
}
else if (!strcmp(psz, "--library") || !strcmp(psz, "-l"))
{
if (++i >= argc)
{
fprintf(stderr, "syntax error: Library name expected after '%s'.\n", psz);
return RTEXITCODE_SYNTAX;
}
g_pszLibrary = argv[i];
}
else if (!strcmp(psz, "--explicit-load-function"))
g_fWithExplictLoadFunction = true;
else if (!strcmp(psz, "--no-explicit-load-function"))
g_fWithExplictLoadFunction = false;
/** @todo Support different load methods so this can be used on system libs and
* such if we like. */
else if ( !strcmp(psz, "--help")
|| !strcmp(psz, "-help")
|| !strcmp(psz, "-h")
|| !strcmp(psz, "-?") )
return usage(argv[0]);
else if ( !strcmp(psz, "--version")
|| !strcmp(psz, "-V"))
{
printf("$Revision: 98271 $\n");
return RTEXITCODE_SUCCESS;
}
else
{
fprintf(stderr, "syntax error: Unknown option '%s'.\n", psz);
return RTEXITCODE_SYNTAX;
}
}
else
{
if (g_cInputs >= RT_ELEMENTS(g_apszInputs))
{
fprintf(stderr, "syntax error: Too many input files, max is %d.\n", (int)RT_ELEMENTS(g_apszInputs));
return RTEXITCODE_SYNTAX;
}
g_apszInputs[g_cInputs++] = argv[i];
}
}
if (g_cInputs == 0)
{
fprintf(stderr, "syntax error: No input file specified.\n");
return RTEXITCODE_SYNTAX;
}
if (!g_pszOutput)
{
fprintf(stderr, "syntax error: No output file specified.\n");
return RTEXITCODE_SYNTAX;
}
if (!g_pszLibrary)
{
fprintf(stderr, "syntax error: No library name specified.\n");
return RTEXITCODE_SYNTAX;
}
/*
* Do the job.
*/
RTEXITCODE rcExit = parseInputs();
if (rcExit == RTEXITCODE_SUCCESS)
rcExit = generateOutput();
return rcExit;
}
int main (int argc, char *argv[])
{
char *queryString;
if ((Conf = confp_open(getenv("FUSIONSEQ_CONFPATH"))) == NULL)
return EXIT_FAILURE;
cgiInit();
cgiHeader("text/html");
queryString = cgiGet2Post();
if (queryString[0] == '\0') {
puts ("<html>");
puts ("<head>");
html_printGenericStyleSheet (12);
puts ("<title>geneFusions</title>\n");
puts ("</head>");
puts ("<body>");
puts ("<h1>Identification of potential gene fusions using paired-end reads</h1><br><br>");
printf ("<form action=%s/geneFusions_cgi method=get>", confp_get(Conf, "WEB_URL_CGI"));
puts ("<b>Data prefix</b>: ");
puts ("<input type=text name=prefix>");
puts ("<br><br><br>");
puts ("<b>Minimum number of paired-end reads connecting two genes</b>: ");
puts ("<select name=minNum>");
puts ("<option value=2>2");
puts ("<option value=3>3");
puts ("<option value=5 selected>5");
puts ("<option value=10>10");
puts ("</select>");
puts ("<br><br><br>");
puts ("<b>Type of gene fusion</b>: ");
puts ("<select name=type>");
puts ("<option value=read-through>Read-through events");
puts ("<option value=cis>Cis events");
puts ("<option value=intra>Intra-chromosomal events");
puts ("<option value=same>Genes on the same chromosome");
puts ("<option value=inter>Genes on different chromosomes");
puts ("<option value=all selected>All potential gene fusions");
puts ("</select>");
puts ("<br><br><br>");
puts ("<input type=submit value=Submit>");
puts ("<input type=reset value=Reset>");
puts ("</form>");
puts ("</body>");
puts ("</html>");
fflush (stdout);
}
else {
int first;
Stringa item = stringCreate (20);
Stringa value = stringCreate (20);
char *iPtr,*vPtr,*prefix,*type;
int minNum;
first = 1;
cgiGetInit ();
while (cgiGetNextPair (&first,item,value)) {
iPtr = string (item);
vPtr = string (value);
if (strEqual (iPtr,"prefix")) {
prefix = hlr_strdup (vPtr);
}
if (strEqual (iPtr,"type")) {
type = hlr_strdup (vPtr);
}
if (strEqual (iPtr,"minNum")) {
minNum = atoi (vPtr);
}
}
generateOutput (prefix,type,minNum);
}
confp_close(Conf);
return EXIT_SUCCESS;
}
int main(int argc, char *argv[])
{
parseCommandLineOptions(argc, argv);
initializeRandomNumberGeneratorTo(rng_seed);
initializeOutput();
setInitialConditions();
if (graphicsModeEnabled()) initializeDisplay();
perturbation_length=fixed_perturbation_length;
for(monte_carlo_steps=start_mcs; monte_carlo_steps<=end_mcs; monte_carlo_steps++)
{
updatePairList();
generateOutput();
attempted_moves = 0;
accepted_moves = 0;
for (monte_carlo_step_counter=0; monte_carlo_step_counter<number_of_molecules; monte_carlo_step_counter++)
{
double boltzmann_factor;
double the_exponential;
delta_energy = 0;
attemptMove();
attempted_moves++;
if (delta_energy < 0)
{
change_flag = 1;
accepted_moves++;
continue; /* move accepted */
}
// the following uses reduced temperature
the_exponential = 0.0 - delta_energy/temperature;
/* evaluate exponential, unless it's arbitrarily small */
if (the_exponential > -25)
{
boltzmann_factor = exp(the_exponential);
if (boltzmann_factor > rnd())
{
change_flag = 1;
accepted_moves++;
continue; /* move accepted */
}
}
// revert move
x[particle_number] -= dx;
y[particle_number] -= dy;
z[particle_number] -= dz;
}
if (monte_carlo_steps < relaxation_allowance)
{
acceptance_ratio = (0.0 + accepted_moves)/(0.0 + attempted_moves);
if (acceptance_ratio < target_acceptance_ratio) perturbation_length *= .9;
else if (perturbation_length*perturbation_length*perturbation_length*16 < box_x*box_y*box_z) perturbation_length *=1.1;
}
else perturbation_length = fixed_perturbation_length;
if (graphicsModeEnabled() && changeFlagIsSet()) drawGraphicalRepresentation();
}
finalizeOutput();
return 0;
} /* end main */
int main(int argc, char *argv[]) {
char line[MAXLINE];
//create an array that keeps track of where switches are
//initialize it with values of -1
int isSwitch[argc];
for (int i = 0; i < argc; i++) {
isSwitch[i] = -1;
}
isSwitch[0] = 1;
//if one of the arguments is --help, print the help page and exit
for (int i = 1; i < argc; i++) {
if (strcmp("--help", argv[i]) ==0 ) {
FILE *help;
if ((help = fopen("help.txt", "r")) != NULL ) {
for (;;) {
fgets(line, sizeof(line), help);
if(feof(help)) {
break;
}
printf("%s", line);
}
fclose(help);
}
return 0;
}
}
//if there is only one input, then just take standard input
if (argc == 1) {
fgets(line, sizeof(line), stdin);
while (!feof(stdin)) {
takeInput(line);
fgets(line, sizeof(line), stdin);
}
return 0;
}
//call the function that finds switches
checkSwitches(argv, isSwitch, argc);
//check for any errors
if (error == 1)
return 1;
//check for a bad mapfile
if (badMap == 1) {
printf("Error: invalid map file. The map file a list of characters.");
printf(" Each character must be separated by a space.\n");
return 1;
}
//if there are only switches, take standard input
if (allSwitches(isSwitch, argc) == 1) {
fgets(line, sizeof(line), stdin);
while (!feof(stdin)) {
generateOutput(line);
fgets(line, sizeof(line), stdin);
}
return 0;
}
/* Now we know there is more than one argument, so we'll go through
the arguments */
int z = 1;
while (z < argc ) {
//make sure that the argument we're on is not a switch
if ( isSwitch[z] != 1) {
//check if the argument is a hypen or if there are no arguments
// except switches, meaning we stop and collect terminal output
if (argv[z][0] == '-' ) {
fgets(line, sizeof(line), stdin);
while (!feof(stdin)) {
generateOutput(line);
fgets(line, sizeof(line), stdin);
}
}
//if the argument is not a hyphen, it's a file
else if ((fp = fopen( argv[z], "r")) != NULL ) {
for (;;) {
fgets(line, sizeof(line), fp);
if(feof(fp)) {
break;
}
generateOutput(line);
}
fclose(fp);
}
//otherwise, the argument is an invalid file
else {
printf("Error: No such file %s\n", argv[z]);
break;
}
}
z++;
}
return 0;
}
