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 int openInputFile(string fileName, ifstream& fileHandle){
264 fileHandle.open(fileName.c_str());
266 cerr << "Error: Could not open " << fileName << endl;
275 /***********************************************************************/
277 inline int openOutputFile(string fileName, ofstream& fileHandle){
279 fileHandle.open(fileName.c_str(), ios::trunc);
281 cerr << "Error: Could not open " << fileName << endl;
289 /***********************************************************************/
291 inline int openOutputFileAppend(string fileName, ofstream& fileHandle){
293 fileHandle.open(fileName.c_str(), ios::app);
295 cerr << "Error: Could not open " << fileName << endl;
305 /***********************************************************************/
307 //This function parses the estimator options and puts them in a vector
308 inline void splitAtDash(string& estim, vector<string>& container) {
312 while (estim.find_first_of('-') != -1) {
313 individual = estim.substr(0,estim.find_first_of('-'));
314 if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
315 estim = estim.substr(estim.find_first_of('-')+1, estim.length());
316 container.push_back(individual);
320 container.push_back(estim);
322 catch(exception& e) {
323 cout << "Standard Error: " << e.what() << " has occurred in the mothur class Function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
327 cout << "An unknown error has occurred in the mothur class function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
333 /***********************************************************************/
334 //This function parses the label options and puts them in a set
335 inline void splitAtDash(string& estim, set<string>& container) {
339 while (estim.find_first_of('-') != -1) {
340 individual = estim.substr(0,estim.find_first_of('-'));
341 if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
342 estim = estim.substr(estim.find_first_of('-')+1, estim.length());
343 container.insert(individual);
347 container.insert(estim);
349 catch(exception& e) {
350 cout << "Standard Error: " << e.what() << " has occurred in the mothur class Function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
354 cout << "An unknown error has occurred in the mothur class function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
359 /***********************************************************************/
360 //This function parses the line options and puts them in a set
361 inline void splitAtDash(string& estim, set<int>& container) {
366 while (estim.find_first_of('-') != -1) {
367 individual = estim.substr(0,estim.find_first_of('-'));
368 if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
369 estim = estim.substr(estim.find_first_of('-')+1, estim.length());
370 convert(individual, lineNum); //convert the string to int
371 container.insert(lineNum);
375 convert(estim, lineNum); //convert the string to int
376 container.insert(lineNum);
378 catch(exception& e) {
379 cout << "Standard Error: " << e.what() << " has occurred in the mothur class Function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
383 cout << "An unknown error has occurred in the mothur class function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
388 /***********************************************************************/
389 //This function parses the a string and puts peices in a vector
390 inline void splitAtComma(string& estim, vector<string>& container) {
394 while (estim.find_first_of(',') != -1) {
395 individual = estim.substr(0,estim.find_first_of(','));
396 if ((estim.find_first_of(',')+1) <= estim.length()) { //checks to make sure you don't have comma at end of string
397 estim = estim.substr(estim.find_first_of(',')+1, estim.length());
398 container.push_back(individual);
402 container.push_back(estim);
404 catch(exception& e) {
405 cout << "Standard Error: " << e.what() << " has occurred in the mothur class Function splitAtComma. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
409 cout << "An unknown error has occurred in the mothur class function splitAtComma. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
413 /***********************************************************************/
415 //This function splits up the various option parameters
416 inline void splitAtComma(string& prefix, string& suffix){
418 prefix = suffix.substr(0,suffix.find_first_of(','));
419 if ((suffix.find_first_of(',')+2) <= suffix.length()) { //checks to make sure you don't have comma at end of string
420 suffix = suffix.substr(suffix.find_first_of(',')+1, suffix.length());
422 while(suffix.at(0) == ' ')
423 suffix = suffix.substr(1, suffix.length());
427 catch(exception& e) {
428 cout << "Standard Error: " << e.what() << " has occurred in the mothur class Function splitAtComma. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
432 cout << "An unknown error has occurred in the mothur class function splitAtComma. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
437 /***********************************************************************/
439 //This function separates the key value from the option value i.e. dist=96_...
440 inline void splitAtEquals(string& key, string& value){
442 if(value.find_first_of('=') != -1){
443 key = value.substr(0,value.find_first_of('='));
444 if ((value.find_first_of('=')+1) <= value.length()) {
445 value = value.substr(value.find_first_of('=')+1, value.length());
452 catch(exception& e) {
453 cout << "Standard Error: " << e.what() << " has occurred in the mothur class Function splitAtEquals. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
457 cout << "An unknown error has occurred in the mothur class function splitAtEquals. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
462 /**************************************************************************************************/
464 inline bool inUsersGroups(string groupname, vector<string> Groups) {
466 for (int i = 0; i < Groups.size(); i++) {
467 if (groupname == Groups[i]) { return true; }
471 catch(exception& e) {
472 cout << "Standard Error: " << e.what() << " has occurred in the mothur class Function inUsersGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
476 cout << "An unknown error has occurred in the mothur class function inUsersGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
481 /***********************************************************************/
482 //this function determines if the user has given us labels that are smaller than the given label.
483 //if so then it returns true so that the calling function can run the previous valid distance.
484 //it's a "smart" distance function. It also checks for invalid labels.
485 inline bool anyLabelsToProcess(string label, set<string>& userLabels, string errorOff) {
487 set<string>::iterator it;
488 vector<float> orderFloat;
489 map<string, float> userMap; //the conversion process removes trailing 0's which we need to put back
490 map<string, float>::iterator it2;
492 bool smaller = false;
494 //unique is the smallest line
495 if (label == "unique") { return false; }
496 else { convert(label, labelFloat); }
498 //go through users set and make them floats
499 for(it = userLabels.begin(); it != userLabels.end(); ++it) {
502 if ((*it != "unique") && (convertTestFloat(*it, temp) == true)){
504 orderFloat.push_back(temp);
506 }else if (*it == "unique") {
507 orderFloat.push_back(-1.0);
508 userMap["unique"] = -1.0;
510 if (errorOff == "") { cout << *it << " is not a valid label." << endl; }
511 userLabels.erase(*it);
517 sort(orderFloat.begin(), orderFloat.end());
519 /*************************************************/
520 //is this label bigger than any of the users labels
521 /*************************************************/
523 //loop through order until you find a label greater than label
524 for (int i = 0; i < orderFloat.size(); i++) {
525 if (orderFloat[i] < labelFloat) {
527 if (orderFloat[i] == -1) {
528 if (errorOff == "") { cout << "Your file does not include the label unique." << endl; }
529 userLabels.erase("unique");
532 if (errorOff == "") { cout << "Your file does not include the label "; }
534 for (it2 = userMap.begin(); it2!= userMap.end(); it2++) {
535 if (it2->second == orderFloat[i]) {
537 //remove small labels
542 if (errorOff == "") { cout << s << ". I will use the next smallest distance. " << endl; }
544 //since they are sorted once you find a bigger one stop looking
551 catch(exception& e) {
552 cout << "Standard Error: " << e.what() << " has occurred in the mothur class Function anyLabelsToProcess. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
556 cout << "An unknown error has occurred in the mothur class function anyLabelsToProcess. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
562 /**************************************************************************************************/