11 * Created by Sarah Westcott on 2/19/09.
12 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
16 /* This file contains all the standard incudes we use in the project as well as some common utilities. */
44 typedef unsigned long long ull;
55 /***********************************************************************/
57 // snagged from http://www.parashift.com/c++-faq-lite/misc-technical-issues.html#faq-39.2
58 // works for now, but there should be a way to do it without killing the whole program
60 class BadConversion : public runtime_error {
62 BadConversion(const string& s) : runtime_error(s){ }
65 //**********************************************************************************************************************
68 inline void convert(const string& s, T& x, bool failIfLeftoverChars = true){
71 if (!(i >> x) || (failIfLeftoverChars && i.get(c)))
72 throw BadConversion(s);
74 //**********************************************************************************************************************
77 inline bool convertTestFloat(const string& s, T& x, bool failIfLeftoverChars = true){
80 if (!(i >> x) || (failIfLeftoverChars && i.get(c)))
87 //**********************************************************************************************************************
90 inline bool convertTest(const string& s, T& x, bool failIfLeftoverChars = true){
93 if (!(i >> x) || (failIfLeftoverChars && i.get(c)))
95 cout << "'" << s << "' is unable to be converted into an integer.\n";
101 //**********************************************************************************************************************
104 string toString(const T&x){
110 //**********************************************************************************************************************
113 string toHex(const T&x){
120 //**********************************************************************************************************************
123 string toString(const T&x, int i){
127 output << fixed << x;
133 /***********************************************************************/
135 inline void gobble(istream& f){
138 while(isspace(d=f.get())) {;}
143 /***********************************************************************/
145 inline float roundDist(float dist, int precision){
147 return int(dist * precision + 0.5)/float(precision);
151 /***********************************************************************/
153 inline int getNumNames(string names){
159 for(int i=0;i<names.size();i++){
170 /**************************************************************************************************/
172 inline vector<vector<double> > binomial(int maxOrder){
174 vector<vector<double> > binomial(maxOrder+1);
176 for(int i=0;i<=maxOrder;i++){
177 binomial[i].resize(maxOrder+1);
186 for(int i=2;i<=maxOrder;i++){
190 for(int i=2;i<=maxOrder;i++){
191 for(int j=1;j<=maxOrder;j++){
192 if(i==j){ binomial[i][j]=1; }
193 if(j>i) { binomial[i][j]=0; }
194 else { binomial[i][j]=binomial[i-1][j-1]+binomial[i-1][j]; }
201 /***********************************************************************/
203 inline string getRootName(string longName){
205 string rootName = longName;
207 if(longName.find_last_of(".") != longName.npos){
208 int pos = longName.find_last_of('.')+1;
209 rootName = longName.substr(0, pos);
214 /***********************************************************************/
216 inline string getSimpleName(string longName){
218 string simpleName = longName;
220 if(longName.find_last_of("/") != longName.npos){
221 int pos = longName.find_last_of('/')+1;
222 simpleName = longName.substr(pos, longName.length());
227 /***********************************************************************/
229 inline int factorial(int num){
232 for (int i = 1; i <= num; i++) {
238 /**************************************************************************************************
240 double min(double x, double y)
246 /***********************************************************************/
248 inline string getPathName(string longName){
250 string rootPathName = longName;
252 if(longName.find_last_of('/') != longName.npos){
253 int pos = longName.find_last_of('/')+1;
254 rootPathName = longName.substr(0, pos);
260 /***********************************************************************/
262 inline string getExtension(string longName){
264 string extension = longName;
266 if(longName.find_last_of('.') != longName.npos){
267 int pos = longName.find_last_of('.');
268 extension = longName.substr(pos, longName.length());
274 /***********************************************************************/
276 inline int openInputFile(string fileName, ifstream& fileHandle){
278 fileHandle.open(fileName.c_str());
280 cerr << "Error: Could not open " << fileName << endl;
289 /***********************************************************************/
291 inline int openOutputFile(string fileName, ofstream& fileHandle){
293 fileHandle.open(fileName.c_str(), ios::trunc);
295 cerr << "Error: Could not open " << fileName << endl;
303 /***********************************************************************/
305 inline int openOutputFileAppend(string fileName, ofstream& fileHandle){
307 fileHandle.open(fileName.c_str(), ios::app);
309 cerr << "Error: Could not open " << fileName << endl;
319 /***********************************************************************/
321 //This function parses the estimator options and puts them in a vector
322 inline void splitAtDash(string& estim, vector<string>& container) {
326 while (estim.find_first_of('-') != -1) {
327 individual = estim.substr(0,estim.find_first_of('-'));
328 if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
329 estim = estim.substr(estim.find_first_of('-')+1, estim.length());
330 container.push_back(individual);
334 container.push_back(estim);
336 catch(exception& e) {
337 cout << "Standard Error: " << e.what() << " has occurred in the mothur class Function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
341 cout << "An unknown error has occurred in the mothur class function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
347 /***********************************************************************/
348 //This function parses the label options and puts them in a set
349 inline void splitAtDash(string& estim, set<string>& container) {
353 while (estim.find_first_of('-') != -1) {
354 individual = estim.substr(0,estim.find_first_of('-'));
355 if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
356 estim = estim.substr(estim.find_first_of('-')+1, estim.length());
357 container.insert(individual);
361 container.insert(estim);
363 catch(exception& e) {
364 cout << "Standard Error: " << e.what() << " has occurred in the mothur class Function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
368 cout << "An unknown error has occurred in the mothur class function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
373 /***********************************************************************/
374 //This function parses the line options and puts them in a set
375 inline void splitAtDash(string& estim, set<int>& container) {
380 while (estim.find_first_of('-') != -1) {
381 individual = estim.substr(0,estim.find_first_of('-'));
382 if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
383 estim = estim.substr(estim.find_first_of('-')+1, estim.length());
384 convert(individual, lineNum); //convert the string to int
385 container.insert(lineNum);
389 convert(estim, lineNum); //convert the string to int
390 container.insert(lineNum);
392 catch(exception& e) {
393 cout << "Standard Error: " << e.what() << " has occurred in the mothur class Function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
397 cout << "An unknown error has occurred in the mothur class function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
402 /***********************************************************************/
403 //This function parses the a string and puts peices in a vector
404 inline void splitAtComma(string& estim, vector<string>& container) {
408 while (estim.find_first_of(',') != -1) {
409 individual = estim.substr(0,estim.find_first_of(','));
410 if ((estim.find_first_of(',')+1) <= estim.length()) { //checks to make sure you don't have comma at end of string
411 estim = estim.substr(estim.find_first_of(',')+1, estim.length());
412 container.push_back(individual);
416 container.push_back(estim);
418 catch(exception& e) {
419 cout << "Standard Error: " << e.what() << " has occurred in the mothur class Function splitAtComma. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
423 cout << "An unknown error has occurred in the mothur class function splitAtComma. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
427 /***********************************************************************/
429 //This function splits up the various option parameters
430 inline void splitAtComma(string& prefix, string& suffix){
432 prefix = suffix.substr(0,suffix.find_first_of(','));
433 if ((suffix.find_first_of(',')+2) <= suffix.length()) { //checks to make sure you don't have comma at end of string
434 suffix = suffix.substr(suffix.find_first_of(',')+1, suffix.length());
436 while(suffix.at(0) == ' ')
437 suffix = suffix.substr(1, suffix.length());
441 catch(exception& e) {
442 cout << "Standard Error: " << e.what() << " has occurred in the mothur class Function splitAtComma. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
446 cout << "An unknown error has occurred in the mothur class function splitAtComma. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
451 /***********************************************************************/
453 //This function separates the key value from the option value i.e. dist=96_...
454 inline void splitAtEquals(string& key, string& value){
456 if(value.find_first_of('=') != -1){
457 key = value.substr(0,value.find_first_of('='));
458 if ((value.find_first_of('=')+1) <= value.length()) {
459 value = value.substr(value.find_first_of('=')+1, value.length());
466 catch(exception& e) {
467 cout << "Standard Error: " << e.what() << " has occurred in the mothur class Function splitAtEquals. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
471 cout << "An unknown error has occurred in the mothur class function splitAtEquals. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
476 /**************************************************************************************************/
478 inline bool inUsersGroups(string groupname, vector<string> Groups) {
480 for (int i = 0; i < Groups.size(); i++) {
481 if (groupname == Groups[i]) { return true; }
485 catch(exception& e) {
486 cout << "Standard Error: " << e.what() << " has occurred in the mothur class Function inUsersGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
490 cout << "An unknown error has occurred in the mothur class function inUsersGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
495 /***********************************************************************/
496 //this function determines if the user has given us labels that are smaller than the given label.
497 //if so then it returns true so that the calling function can run the previous valid distance.
498 //it's a "smart" distance function. It also checks for invalid labels.
499 inline bool anyLabelsToProcess(string label, set<string>& userLabels, string errorOff) {
501 set<string>::iterator it;
502 vector<float> orderFloat;
503 map<string, float> userMap; //the conversion process removes trailing 0's which we need to put back
504 map<string, float>::iterator it2;
506 bool smaller = false;
508 //unique is the smallest line
509 if (label == "unique") { return false; }
510 else { convert(label, labelFloat); }
512 //go through users set and make them floats
513 for(it = userLabels.begin(); it != userLabels.end(); ++it) {
516 if ((*it != "unique") && (convertTestFloat(*it, temp) == true)){
518 orderFloat.push_back(temp);
520 }else if (*it == "unique") {
521 orderFloat.push_back(-1.0);
522 userMap["unique"] = -1.0;
524 if (errorOff == "") { cout << *it << " is not a valid label." << endl; }
525 userLabels.erase(*it);
531 sort(orderFloat.begin(), orderFloat.end());
533 /*************************************************/
534 //is this label bigger than any of the users labels
535 /*************************************************/
537 //loop through order until you find a label greater than label
538 for (int i = 0; i < orderFloat.size(); i++) {
539 if (orderFloat[i] < labelFloat) {
541 if (orderFloat[i] == -1) {
542 if (errorOff == "") { cout << "Your file does not include the label unique." << endl; }
543 userLabels.erase("unique");
546 if (errorOff == "") { cout << "Your file does not include the label "; }
548 for (it2 = userMap.begin(); it2!= userMap.end(); it2++) {
549 if (it2->second == orderFloat[i]) {
551 //remove small labels
556 if (errorOff == "") { cout << s << ". I will use the next smallest distance. " << endl; }
558 //since they are sorted once you find a bigger one stop looking
565 catch(exception& e) {
566 cout << "Standard Error: " << e.what() << " has occurred in the mothur class Function anyLabelsToProcess. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
570 cout << "An unknown error has occurred in the mothur class function anyLabelsToProcess. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
576 /**************************************************************************************************/