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working on windows paralellization, added trimOligos class to be used by trim.flows...
[mothur.git] / mothurout.cpp
1 /*
2  *  mothurOut.cpp
3  *  Mothur
4  *
5  *  Created by westcott on 2/25/10.
6  *  Copyright 2010 Schloss Lab. All rights reserved.
7  *
8  */
9
10 #include "mothurout.h"
11
12
13 /******************************************************/
14 MothurOut* MothurOut::getInstance() {
15         if( _uniqueInstance == 0) {
16                 _uniqueInstance = new MothurOut();
17         }
18         return _uniqueInstance;
19 }
20 /*********************************************************************************************/
21 void MothurOut::printCurrentFiles()  {
22         try {
23                 if (accnosfile != "")           {  mothurOut("accnos=" + accnosfile); mothurOutEndLine();                       }
24                 if (columnfile != "")           {  mothurOut("column=" + columnfile); mothurOutEndLine();                       }
25                 if (designfile != "")           {  mothurOut("design=" + designfile); mothurOutEndLine();                       }
26                 if (fastafile != "")            {  mothurOut("fasta=" + fastafile); mothurOutEndLine();                         }
27                 if (groupfile != "")            {  mothurOut("group=" + groupfile); mothurOutEndLine();                         }
28                 if (listfile != "")                     {  mothurOut("list=" + listfile); mothurOutEndLine();                           }
29                 if (namefile != "")                     {  mothurOut("name=" + namefile); mothurOutEndLine();                           }
30                 if (oligosfile != "")           {  mothurOut("oligos=" + oligosfile); mothurOutEndLine();                       }
31                 if (orderfile != "")            {  mothurOut("order=" + orderfile); mothurOutEndLine();                         }
32                 if (ordergroupfile != "")       {  mothurOut("ordergroup=" + ordergroupfile); mothurOutEndLine();       }
33                 if (phylipfile != "")           {  mothurOut("phylip=" + phylipfile); mothurOutEndLine();                       }
34                 if (qualfile != "")                     {  mothurOut("qfile=" + qualfile); mothurOutEndLine();                          }
35                 if (rabundfile != "")           {  mothurOut("rabund=" + rabundfile); mothurOutEndLine();                       }
36                 if (relabundfile != "")         {  mothurOut("relabund=" + relabundfile); mothurOutEndLine();           }
37                 if (sabundfile != "")           {  mothurOut("sabund=" + sabundfile); mothurOutEndLine();                       }
38                 if (sfffile != "")                      {  mothurOut("sff=" + sfffile); mothurOutEndLine();                                     }
39                 if (sharedfile != "")           {  mothurOut("shared=" + sharedfile); mothurOutEndLine();                       }
40                 if (taxonomyfile != "")         {  mothurOut("taxonomy=" + taxonomyfile); mothurOutEndLine();           }
41                 if (treefile != "")                     {  mothurOut("tree=" + treefile); mothurOutEndLine();                           }
42                 if (flowfile != "")                     {  mothurOut("flow=" + flowfile); mothurOutEndLine();                           }
43                 if (processors != "1")          {  mothurOut("processors=" + processors); mothurOutEndLine();           }
44                 
45         }
46         catch(exception& e) {
47                 errorOut(e, "MothurOut", "printCurrentFiles");
48                 exit(1);
49         }
50 }
51 /*********************************************************************************************/
52 bool MothurOut::hasCurrentFiles()  {
53         try {
54                 bool hasCurrent = false;
55                 
56                 if (accnosfile != "")           {  return true;                 }
57                 if (columnfile != "")           {  return true;                 }
58                 if (designfile != "")           {  return true;                 }
59                 if (fastafile != "")            {  return true;                 }
60                 if (groupfile != "")            {  return true;                 }
61                 if (listfile != "")                     {  return true;                 }
62                 if (namefile != "")                     {  return true;                 }
63                 if (oligosfile != "")           {  return true;                 }
64                 if (orderfile != "")            {  return true;                 }
65                 if (ordergroupfile != "")       {  return true;                 }
66                 if (phylipfile != "")           {  return true;                 }
67                 if (qualfile != "")                     {  return true;                 }
68                 if (rabundfile != "")           {  return true;                 }
69                 if (relabundfile != "")         {  return true;                 }
70                 if (sabundfile != "")           {  return true;                 }
71                 if (sfffile != "")                      {  return true;                 }
72                 if (sharedfile != "")           {  return true;                 }
73                 if (taxonomyfile != "")         {  return true;                 }
74                 if (treefile != "")                     {  return true;                 }
75                 if (flowfile != "")                     {  return true;                 }
76                 if (processors != "1")          {  return true;                 }
77                 
78                 return hasCurrent;
79                 
80         }
81         catch(exception& e) {
82                 errorOut(e, "MothurOut", "hasCurrentFiles");
83                 exit(1);
84         }
85 }
86
87 /*********************************************************************************************/
88 void MothurOut::clearCurrentFiles()  {
89         try {
90                 phylipfile = "";
91                 columnfile = "";
92                 listfile = "";
93                 rabundfile = "";
94                 sabundfile = "";
95                 namefile = "";
96                 groupfile = "";
97                 designfile = "";
98                 orderfile = "";
99                 treefile = "";
100                 sharedfile = "";
101                 ordergroupfile = "";
102                 relabundfile = "";
103                 fastafile = "";
104                 qualfile = "";
105                 sfffile = "";
106                 oligosfile = "";
107                 accnosfile = "";
108                 taxonomyfile = "";      
109                 flowfile = "";
110                 processors = "1";
111         }
112         catch(exception& e) {
113                 errorOut(e, "MothurOut", "clearCurrentFiles");
114                 exit(1);
115         }
116 }
117 /*********************************************************************************************/
118 void MothurOut::setFileName(string filename)  {
119         try {
120                 logFileName = filename;
121                 
122                 #ifdef USE_MPI
123                         int pid;
124                         MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
125                                         
126                         if (pid == 0) { //only one process should output to screen
127                 #endif
128                 
129                 openOutputFile(filename, out);
130                 
131                 #ifdef USE_MPI
132                         }
133                 #endif
134         }
135         catch(exception& e) {
136                 errorOut(e, "MothurOut", "setFileName");
137                 exit(1);
138         }
139 }
140 /*********************************************************************************************/
141 void MothurOut::setDefaultPath(string pathname)  {
142         try {
143         
144                 //add / to name if needed
145                 string lastChar = pathname.substr(pathname.length()-1);
146                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
147                         if (lastChar != "/") { pathname += "/"; }
148                 #else
149                         if (lastChar != "\\") { pathname += "\\"; }     
150                 #endif
151                 
152                 defaultPath = pathname;
153                 
154         }
155         catch(exception& e) {
156                 errorOut(e, "MothurOut", "setDefaultPath");
157                 exit(1);
158         }
159 }
160 /*********************************************************************************************/
161 void MothurOut::setOutputDir(string pathname)  {
162         try {
163                 outputDir = pathname;
164         }
165         catch(exception& e) {
166                 errorOut(e, "MothurOut", "setOutputDir");
167                 exit(1);
168         }
169 }
170 /*********************************************************************************************/
171 void MothurOut::closeLog()  {
172         try {
173                 
174                 #ifdef USE_MPI
175                         int pid;
176                         MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
177                                         
178                         if (pid == 0) { //only one process should output to screen
179                 #endif
180                 
181                 out.close();
182                 
183                 #ifdef USE_MPI
184                         }
185                 #endif
186         }
187         catch(exception& e) {
188                 errorOut(e, "MothurOut", "closeLog");
189                 exit(1);
190         }
191 }
192
193 /*********************************************************************************************/
194 MothurOut::~MothurOut() {
195         try {
196                 _uniqueInstance = 0;
197                 
198         }
199         catch(exception& e) {
200                 errorOut(e, "MothurOut", "MothurOut");
201                 exit(1);
202         }
203 }
204 /*********************************************************************************************/
205 void MothurOut::mothurOut(string output) {
206         try {
207                 
208                 #ifdef USE_MPI
209                         int pid;
210                         MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
211                                         
212                         if (pid == 0) { //only one process should output to screen
213                 #endif
214                 
215                 cout << output;
216                 out << output;
217                 
218                 #ifdef USE_MPI
219                         }
220                 #endif
221         }
222         catch(exception& e) {
223                 errorOut(e, "MothurOut", "MothurOut");
224                 exit(1);
225         }
226 }
227 /*********************************************************************************************/
228 void MothurOut::mothurOutEndLine() {
229         try {
230                 #ifdef USE_MPI
231                         int pid;
232                         MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
233                                         
234                         if (pid == 0) { //only one process should output to screen
235                 #endif
236                 
237                 cout << endl;
238                 out << endl;
239                 
240                 #ifdef USE_MPI
241                         }
242                 #endif
243         }
244         catch(exception& e) {
245                 errorOut(e, "MothurOut", "MothurOutEndLine");
246                 exit(1);
247         }
248 }
249 /*********************************************************************************************/
250 void MothurOut::mothurOut(string output, ofstream& outputFile) {
251         try {
252                 
253 #ifdef USE_MPI
254                 int pid;
255                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
256                 
257                 if (pid == 0) { //only one process should output to screen
258 #endif
259                         
260                         cout << output;
261                         out << output;
262                         outputFile << output;
263                         
264 #ifdef USE_MPI
265                 }
266 #endif
267         }
268         catch(exception& e) {
269                 errorOut(e, "MothurOut", "MothurOut");
270                 exit(1);
271         }
272 }
273 /*********************************************************************************************/
274 void MothurOut::mothurOutEndLine(ofstream& outputFile) {
275         try {
276 #ifdef USE_MPI
277                 int pid;
278                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
279                 
280                 if (pid == 0) { //only one process should output to screen
281 #endif
282                         
283                         cout << endl;
284                         out << endl;
285                         outputFile << endl;
286                         
287 #ifdef USE_MPI
288                 }
289 #endif
290         }
291         catch(exception& e) {
292                 errorOut(e, "MothurOut", "MothurOutEndLine");
293                 exit(1);
294         }
295 }
296 /*********************************************************************************************/
297 void MothurOut::mothurOutJustToLog(string output) {
298         try {
299                 #ifdef USE_MPI
300                         int pid;
301                         MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
302                                         
303                         if (pid == 0) { //only one process should output to screen
304                 #endif
305                 
306                 out << output;
307                 
308                 #ifdef USE_MPI
309                         }
310                 #endif
311         }
312         catch(exception& e) {
313                 errorOut(e, "MothurOut", "MothurOutJustToLog");
314                 exit(1);
315         }
316 }
317 /*********************************************************************************************/
318 void MothurOut::errorOut(exception& e, string object, string function) {
319         //double vm, rss;
320         //mem_usage(vm, rss);
321         
322         mothurOut("[ERROR]: ");
323         mothurOut(toString(e.what()));
324         mothurOut(" has occurred in the " + object + " class function " + function + ". Please contact Pat Schloss at mothur.bugs@gmail.com, and be sure to include the mothur.logFile with your inquiry.");
325         mothurOutEndLine();
326 }
327 /*********************************************************************************************/
328 //The following was originally from http://stackoverflow.com/questions/669438/how-to-get-memory-usage-at-run-time-in-c 
329 // process_mem_usage(double &, double &) - takes two doubles by reference,
330 // attempts to read the system-dependent data for a process' virtual memory
331 // size and resident set size, and return the results in KB.
332 //
333 // On failure, returns 0.0, 0.0
334 int MothurOut::mem_usage(double& vm_usage, double& resident_set) {
335   #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
336   
337            vm_usage     = 0.0;
338            resident_set = 0.0;
339
340            // 'file' stat seems to give the most reliable results
341            //
342            ifstream stat_stream("/proc/self/stat",ios_base::in);
343
344            // dummy vars for leading entries in stat that we don't care about
345            //
346            string pid, comm, state, ppid, pgrp, session, tty_nr;
347            string tpgid, flags, minflt, cminflt, majflt, cmajflt;
348            string utime, stime, cutime, cstime, priority, nice;
349            string O, itrealvalue, starttime;
350
351            // the two fields we want
352            //
353            unsigned long vsize;
354            long rss;
355
356            stat_stream >> pid >> comm >> state >> ppid >> pgrp >> session >> tty_nr
357                                    >> tpgid >> flags >> minflt >> cminflt >> majflt >> cmajflt
358                                    >> utime >> stime >> cutime >> cstime >> priority >> nice
359                                    >> O >> itrealvalue >> starttime >> vsize >> rss; // don't care about the rest
360
361            long page_size_kb = sysconf(_SC_PAGE_SIZE) / 1024; // in case x86-64 is configured to use 2MB pages
362            vm_usage     = vsize / 1024.0;
363            resident_set = rss * page_size_kb;
364            
365            mothurOut("Memory Usage: vm = " + toString(vm_usage) + " rss = " + toString(resident_set) + "\n");
366                 return 0;
367
368         #else
369 /*              //windows memory usage
370                 // Get the list of process identifiers.
371                 DWORD aProcesses[1024], cbNeeded, cProcesses;
372                 
373                 if ( !EnumProcesses( aProcesses, sizeof(aProcesses), &cbNeeded ) ){ return 1; }
374
375                 // Calculate how many process identifiers were returned.
376                 cProcesses = cbNeeded / sizeof(DWORD);
377
378                 // Print the memory usage for each process
379                 for (int i = 0; i < cProcesses; i++ ) {
380                         DWORD processID = aProcesses[i];
381                         
382                         PROCESS_MEMORY_COUNTERS pmc;
383
384                         HANDLE hProcess = OpenProcess((PROCESS_QUERY_INFORMATION | PROCESS_VM_READ), FALSE, processID);
385
386                         // Print the process identifier.
387                         printf( "\nProcess ID: %u\n", processID);
388                         
389                         if (NULL != hProcess) {
390
391                                 if ( GetProcessMemoryInfo( hProcess, &pmc, sizeof(pmc)) ) {
392                                         printf( "\tPageFaultCount: 0x%08X\n", pmc.PageFaultCount );
393                                         printf( "\tPeakWorkingSetSize: 0x%08X\n", pmc.PeakWorkingSetSize );
394                                         printf( "\tWorkingSetSize: 0x%08X\n", pmc.WorkingSetSize );
395                                         printf( "\tQuotaPeakPagedPoolUsage: 0x%08X\n", pmc.QuotaPeakPagedPoolUsage );
396                                         printf( "\tQuotaPagedPoolUsage: 0x%08X\n", pmc.QuotaPagedPoolUsage );
397                                         printf( "\tQuotaPeakNonPagedPoolUsage: 0x%08X\n", pmc.QuotaPeakNonPagedPoolUsage );
398                                         printf( "\tQuotaNonPagedPoolUsage: 0x%08X\n", pmc.QuotaNonPagedPoolUsage );
399                                         printf( "\tPagefileUsage: 0x%08X\n", pmc.PagefileUsage ); 
400                                         printf( "\tPeakPagefileUsage: 0x%08X\n", pmc.PeakPagefileUsage );
401                                 }
402                                 CloseHandle(hProcess);
403                         }
404                 }
405 */
406                         return 0;
407
408         #endif
409 }
410
411
412 /***********************************************************************/
413 int MothurOut::openOutputFileAppend(string fileName, ofstream& fileHandle){
414         try {
415                 fileName = getFullPathName(fileName);
416                 
417                 fileHandle.open(fileName.c_str(), ios::app);
418                 if(!fileHandle) {
419                         mothurOut("[ERROR]: Could not open " + fileName); mothurOutEndLine();
420                         return 1;
421                 }
422                 else {
423                         return 0;
424                 }
425         }
426         catch(exception& e) {
427                 errorOut(e, "MothurOut", "openOutputFileAppend");
428                 exit(1);
429         }
430 }
431 /***********************************************************************/
432 void MothurOut::gobble(istream& f){
433         try {
434                 
435                 char d;
436                 while(isspace(d=f.get()))               { ;}
437                 f.putback(d);
438         }
439         catch(exception& e) {
440                 errorOut(e, "MothurOut", "gobble");
441                 exit(1);
442         }
443 }
444 /***********************************************************************/
445 void MothurOut::gobble(istringstream& f){
446         try {
447                 char d;
448                 while(isspace(d=f.get()))               {;}
449                 f.putback(d);
450         }
451         catch(exception& e) {
452                 errorOut(e, "MothurOut", "gobble");
453                 exit(1);
454         }
455 }
456
457 /***********************************************************************/
458
459 string MothurOut::getline(istringstream& fileHandle) {
460         try {
461         
462                 string line = "";
463                 
464                 while (!fileHandle.eof())       {
465                         //get next character
466                         char c = fileHandle.get(); 
467                         
468                         //are you at the end of the line
469                         if ((c == '\n') || (c == '\r') || (c == '\f')){  break; }       
470                         else {          line += c;              }
471                 }
472                 
473                 return line;
474                 
475         }
476         catch(exception& e) {
477                 errorOut(e, "MothurOut", "getline");
478                 exit(1);
479         }
480 }
481 /***********************************************************************/
482
483 string MothurOut::getline(ifstream& fileHandle) {
484         try {
485         
486                 string line = "";
487                 
488                 while (fileHandle)      {
489                         //get next character
490                         char c = fileHandle.get(); 
491                         
492                         //are you at the end of the line
493                         if ((c == '\n') || (c == '\r') || (c == '\f') || (c == EOF)){  break;   }       
494                         else {          line += c;              }
495                 }
496                 
497                 return line;
498                 
499         }
500         catch(exception& e) {
501                 errorOut(e, "MothurOut", "getline");
502                 exit(1);
503         }
504 }
505 /***********************************************************************/
506
507 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
508 #ifdef USE_COMPRESSION
509 inline bool endsWith(string s, const char * suffix){
510   size_t suffixLength = strlen(suffix);
511   return s.size() >= suffixLength && s.substr(s.size() - suffixLength, suffixLength).compare(suffix) == 0;
512 }
513 #endif
514 #endif
515
516 string MothurOut::getRootName(string longName){
517         try {
518         
519                 string rootName = longName;
520
521 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
522 #ifdef USE_COMPRESSION
523     if (endsWith(rootName, ".gz") || endsWith(rootName, ".bz2")) {
524       int pos = rootName.find_last_of('.');
525       rootName = rootName.substr(0, pos);
526       cerr << "shortening " << longName << " to " << rootName << "\n";
527     }
528 #endif
529 #endif
530                 if(rootName.find_last_of(".") != rootName.npos){
531                         int pos = rootName.find_last_of('.')+1;
532                         rootName = rootName.substr(0, pos);
533                 }
534
535                 return rootName;
536         }
537         catch(exception& e) {
538                 errorOut(e, "MothurOut", "getRootName");
539                 exit(1);
540         }
541 }
542 /***********************************************************************/
543
544 string MothurOut::getSimpleName(string longName){
545         try {
546                 string simpleName = longName;
547                 
548                 size_t found;
549                 found=longName.find_last_of("/\\");
550
551                 if(found != longName.npos){
552                         simpleName = longName.substr(found+1);
553                 }
554                 
555                 return simpleName;
556         }
557         catch(exception& e) {
558                 errorOut(e, "MothurOut", "getSimpleName");
559                 exit(1);
560         }
561 }
562
563 /***********************************************************************/
564
565 int MothurOut::getRandomIndex(int highest){
566         try {
567                 
568                 int random = (int) ((float)(highest+1) * (float)(rand()) / ((float)RAND_MAX+1.0));
569                 
570                 return random;
571         }
572         catch(exception& e) {
573                 errorOut(e, "MothurOut", "getRandomIndex");
574                 exit(1);
575         }       
576         
577 }
578 /**********************************************************************/
579
580 string MothurOut::getPathName(string longName){
581         try {
582                 string rootPathName = longName;
583                 
584                 if(longName.find_last_of("/\\") != longName.npos){
585                         int pos = longName.find_last_of("/\\")+1;
586                         rootPathName = longName.substr(0, pos);
587                 }
588                 
589                 return rootPathName;
590         }
591         catch(exception& e) {
592                 errorOut(e, "MothurOut", "getPathName");
593                 exit(1);
594         }       
595
596 }
597 /***********************************************************************/
598
599 string MothurOut::hasPath(string longName){
600         try {
601                 string path = "";
602                 
603                 size_t found;
604                 found=longName.find_last_of("~/\\");
605
606                 if(found != longName.npos){
607                         path = longName.substr(0, found+1);
608                 }
609                 
610                 return path;
611         }
612         catch(exception& e) {
613                 errorOut(e, "MothurOut", "hasPath");
614                 exit(1);
615         }       
616 }
617
618 /***********************************************************************/
619
620 string MothurOut::getExtension(string longName){
621         try {
622                 string extension = longName;
623                 
624                 if(longName.find_last_of('.') != longName.npos){
625                         int pos = longName.find_last_of('.');
626                         extension = longName.substr(pos, longName.length());
627                 }
628                 
629                 return extension;
630         }
631         catch(exception& e) {
632                 errorOut(e, "MothurOut", "getExtension");
633                 exit(1);
634         }       
635 }
636 /***********************************************************************/
637 bool MothurOut::isBlank(string fileName){
638         try {
639                 
640                 fileName = getFullPathName(fileName);
641                 
642                 ifstream fileHandle;
643                 fileHandle.open(fileName.c_str());
644                 if(!fileHandle) {
645                         mothurOut("[ERROR]: Could not open " + fileName); mothurOutEndLine();
646                         return false;
647                 }else {
648                         //check for blank file
649                         gobble(fileHandle);
650                         if (fileHandle.eof()) { fileHandle.close(); return true;  }
651                         fileHandle.close();
652                 }
653                 return false;
654         }
655         catch(exception& e) {
656                 errorOut(e, "MothurOut", "isBlank");
657                 exit(1);
658         }       
659 }
660 /***********************************************************************/
661
662 string MothurOut::getFullPathName(string fileName){
663         try{
664         
665         string path = hasPath(fileName);
666         string newFileName;
667         int pos;
668         
669         if (path == "") { return fileName; } //its a simple name
670         else { //we need to complete the pathname
671                 // ex. ../../../filename 
672                 // cwd = /user/work/desktop
673                                 
674                 string cwd;
675                 //get current working directory 
676                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)   
677                         
678                         if (path.find("~") != -1) { //go to home directory
679                                 string homeDir;
680                         
681                                 char *homepath = NULL;
682                                 homepath = getenv ("HOME");
683                                 if ( homepath != NULL) { homeDir = homepath; }
684                                 else { homeDir = "";  }
685
686                                 newFileName = homeDir + fileName.substr(fileName.find("~")+1);
687                                 return newFileName;
688                         }else { //find path
689                                 if (path.rfind("./") == string::npos) { return fileName; } //already complete name
690                                 else { newFileName = fileName.substr(fileName.rfind("./")+2); } //save the complete part of the name
691                                 
692                                 //char* cwdpath = new char[1024];
693                                 //size_t size;
694                                 //cwdpath=getcwd(cwdpath,size);
695                                 //cwd = cwdpath;
696                                 
697                                 char *cwdpath = NULL;
698                                 cwdpath = getcwd(NULL, 0); // or _getcwd
699                                 if ( cwdpath != NULL) { cwd = cwdpath; }
700                                 else { cwd = "";  }
701
702                                 
703                                 //rip off first '/'
704                                 string simpleCWD;
705                                 if (cwd.length() > 0) { simpleCWD = cwd.substr(1); }
706                                 
707                                 //break apart the current working directory
708                                 vector<string> dirs;
709                                 while (simpleCWD.find_first_of('/') != string::npos) {
710                                         string dir = simpleCWD.substr(0,simpleCWD.find_first_of('/'));
711                                         simpleCWD = simpleCWD.substr(simpleCWD.find_first_of('/')+1, simpleCWD.length());
712                                         dirs.push_back(dir);
713                                 }
714                                 //get last one              // ex. ../../../filename = /user/work/desktop/filename
715                                 dirs.push_back(simpleCWD);  //ex. dirs[0] = user, dirs[1] = work, dirs[2] = desktop
716                                 
717                         
718                                 int index = dirs.size()-1;
719                 
720                                 while((pos = path.rfind("./")) != string::npos) { //while you don't have a complete path
721                                         if (pos == 0) { break;  //you are at the end
722                                         }else if (path[(pos-1)] == '.') { //you want your parent directory ../
723                                                 path = path.substr(0, pos-1);
724                                                 index--;
725                                                 if (index == 0) {  break; }
726                                         }else if (path[(pos-1)] == '/') { //you want the current working dir ./
727                                                 path = path.substr(0, pos);
728                                         }else if (pos == 1) { break;  //you are at the end
729                                         }else { cout << "cannot resolve path for " <<  fileName << endl; return fileName; }
730                                 }
731                         
732                                 for (int i = index; i >= 0; i--) {
733                                         newFileName = dirs[i] +  "/" + newFileName;             
734                                 }
735                                 
736                                 newFileName =  "/" +  newFileName;
737                                 return newFileName;
738                         }       
739                 #else
740                         if (path.find("~") != string::npos) { //go to home directory
741                                 string homeDir = getenv ("HOMEPATH");
742                                 newFileName = homeDir + fileName.substr(fileName.find("~")+1);
743                                 return newFileName;
744                         }else { //find path
745                                 if (path.rfind(".\\") == string::npos) { return fileName; } //already complete name
746                                 else { newFileName = fileName.substr(fileName.rfind(".\\")+2); } //save the complete part of the name
747                                                         
748                                 char *cwdpath = NULL;
749                                 cwdpath = getcwd(NULL, 0); // or _getcwd
750                                 if ( cwdpath != NULL) { cwd = cwdpath; }
751                                 else { cwd = "";  }
752                                 
753                                 //break apart the current working directory
754                                 vector<string> dirs;
755                                 while (cwd.find_first_of('\\') != -1) {
756                                         string dir = cwd.substr(0,cwd.find_first_of('\\'));
757                                         cwd = cwd.substr(cwd.find_first_of('\\')+1, cwd.length());
758                                         dirs.push_back(dir);
759                 
760                                 }
761                                 //get last one
762                                 dirs.push_back(cwd);  //ex. dirs[0] = user, dirs[1] = work, dirs[2] = desktop
763                                         
764                                 int index = dirs.size()-1;
765                                         
766                                 while((pos = path.rfind(".\\")) != string::npos) { //while you don't have a complete path
767                                         if (pos == 0) { break;  //you are at the end
768                                         }else if (path[(pos-1)] == '.') { //you want your parent directory ../
769                                                 path = path.substr(0, pos-1);
770                                                 index--;
771                                                 if (index == 0) {  break; }
772                                         }else if (path[(pos-1)] == '\\') { //you want the current working dir ./
773                                                 path = path.substr(0, pos);
774                                         }else if (pos == 1) { break;  //you are at the end
775                                         }else { cout << "cannot resolve path for " <<  fileName << endl; return fileName; }
776                                 }
777                         
778                                 for (int i = index; i >= 0; i--) {
779                                         newFileName = dirs[i] +  "\\" + newFileName;            
780                                 }
781                                 
782                                 return newFileName;
783                         }
784                         
785                 #endif
786         }
787         }
788         catch(exception& e) {
789                 errorOut(e, "MothurOut", "getFullPathName");
790                 exit(1);
791         }       
792 }
793 /***********************************************************************/
794
795 int MothurOut::openInputFile(string fileName, ifstream& fileHandle, string m){
796         try {
797                         //get full path name
798                         string completeFileName = getFullPathName(fileName);
799 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
800 #ifdef USE_COMPRESSION
801       // check for gzipped or bzipped file
802       if (endsWith(completeFileName, ".gz") || endsWith(completeFileName, ".bz2")) {
803         string tempName = string(tmpnam(0));
804         mkfifo(tempName.c_str(), 0666);
805         int fork_result = fork();
806         if (fork_result < 0) {
807           cerr << "Error forking.\n";
808           exit(1);
809         } else if (fork_result == 0) {
810           string command = (endsWith(completeFileName, ".gz") ? "zcat " : "bzcat ") + completeFileName + string(" > ") + tempName;
811           cerr << "Decompressing " << completeFileName << " via temporary named pipe " << tempName << "\n";
812           system(command.c_str());
813           cerr << "Done decompressing " << completeFileName << "\n";
814           mothurRemove(tempName);
815           exit(EXIT_SUCCESS);
816         } else {
817           cerr << "waiting on child process " << fork_result << "\n";
818           completeFileName = tempName;
819         }
820       }
821 #endif
822 #endif
823                         fileHandle.open(completeFileName.c_str());
824                         if(!fileHandle) {
825                                 //mothurOut("[ERROR]: Could not open " + completeFileName); mothurOutEndLine();
826                                 return 1;
827                         }else {
828                                 //check for blank file
829                                 gobble(fileHandle);
830                                 return 0;
831                         }
832         }
833         catch(exception& e) {
834                 errorOut(e, "MothurOut", "openInputFile - no Error");
835                 exit(1);
836         }
837 }
838 /***********************************************************************/
839
840 int MothurOut::openInputFile(string fileName, ifstream& fileHandle){
841         try {
842
843                 //get full path name
844                 string completeFileName = getFullPathName(fileName);
845 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
846 #ifdef USE_COMPRESSION
847   // check for gzipped or bzipped file
848   if (endsWith(completeFileName, ".gz") || endsWith(completeFileName, ".bz2")) {
849     string tempName = string(tmpnam(0));
850     mkfifo(tempName.c_str(), 0666);
851     int fork_result = fork();
852     if (fork_result < 0) {
853       cerr << "Error forking.\n";
854       exit(1);
855     } else if (fork_result == 0) {
856       string command = (endsWith(completeFileName, ".gz") ? "zcat " : "bzcat ") + completeFileName + string(" > ") + tempName;
857       cerr << "Decompressing " << completeFileName << " via temporary named pipe " << tempName << "\n";
858       system(command.c_str());
859       cerr << "Done decompressing " << completeFileName << "\n";
860       mothurRemove(tempName);
861       exit(EXIT_SUCCESS);
862     } else {
863       cerr << "waiting on child process " << fork_result << "\n";
864       completeFileName = tempName;
865     }
866   }
867 #endif
868 #endif
869
870                 fileHandle.open(completeFileName.c_str());
871                 if(!fileHandle) {
872                         mothurOut("[ERROR]: Could not open " + completeFileName); mothurOutEndLine();
873                         return 1;
874                 }
875                 else {
876                         //check for blank file
877                         gobble(fileHandle);
878                         if (fileHandle.eof()) { mothurOut("[ERROR]: " + completeFileName + " is blank. Please correct."); mothurOutEndLine();  }
879                         
880                         return 0;
881                 }
882         }
883         catch(exception& e) {
884                 errorOut(e, "MothurOut", "openInputFile");
885                 exit(1);
886         }       
887 }
888 /***********************************************************************/
889
890 int MothurOut::renameFile(string oldName, string newName){
891         try {
892                 ifstream inTest;
893                 int exist = openInputFile(newName, inTest, "");
894                 
895         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)           
896                 if (exist == 0) { //you could open it so you want to delete it
897                         inTest.close();
898                         string command = "rm " + newName;
899                         system(command.c_str());
900                 }
901                                 
902                 string command = "mv " + oldName + " " + newName;
903                 system(command.c_str());
904         #else
905                 mothurRemove(newName);
906                 int renameOk = rename(oldName.c_str(), newName.c_str());
907         #endif
908                 return 0;
909                 
910         }
911         catch(exception& e) {
912                 errorOut(e, "MothurOut", "renameFile");
913                 exit(1);
914         }       
915 }
916
917 /***********************************************************************/
918
919 int MothurOut::openOutputFile(string fileName, ofstream& fileHandle){
920         try { 
921         
922                 string completeFileName = getFullPathName(fileName);
923 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
924 #ifdef USE_COMPRESSION
925     // check for gzipped file
926     if (endsWith(completeFileName, ".gz") || endsWith(completeFileName, ".bz2")) {
927       string tempName = string(tmpnam(0));
928       mkfifo(tempName.c_str(), 0666);
929       cerr << "Compressing " << completeFileName << " via temporary named pipe " << tempName << "\n";
930       int fork_result = fork();
931       if (fork_result < 0) {
932         cerr << "Error forking.\n";
933         exit(1);
934       } else if (fork_result == 0) {
935         string command = string(endsWith(completeFileName, ".gz") ?  "gzip" : "bzip2") + " -v > " + completeFileName + string(" < ") + tempName;
936         system(command.c_str());
937         exit(0);
938       } else {
939         completeFileName = tempName;
940       }
941     }
942 #endif
943 #endif
944                 fileHandle.open(completeFileName.c_str(), ios::trunc);
945                 if(!fileHandle) {
946                         mothurOut("[ERROR]: Could not open " + completeFileName); mothurOutEndLine();
947                         return 1;
948                 }
949                 else {
950                         return 0;
951                 }
952         }
953         catch(exception& e) {
954                 errorOut(e, "MothurOut", "openOutputFile");
955                 exit(1);
956         }       
957
958 }
959
960 /**************************************************************************************************/
961 void MothurOut::appendFiles(string temp, string filename) {
962         try{
963                 ofstream output;
964                 ifstream input;
965         
966                 //open output file in append mode
967                 openOutputFileAppend(filename, output);
968                 int ableToOpen = openInputFile(temp, input, "no error");
969                 //int ableToOpen = openInputFile(temp, input);
970                 
971                 if (ableToOpen == 0) { //you opened it
972                         while(char c = input.get()){
973                                 if(input.eof())         {       break;                  }
974                                 else                            {       output << c;    }
975                         }
976                         input.close();
977                 }
978                 
979                 output.close();
980         }
981         catch(exception& e) {
982                 errorOut(e, "MothurOut", "appendFiles");
983                 exit(1);
984         }       
985 }
986
987 /**************************************************************************************************/
988 string MothurOut::sortFile(string distFile, string outputDir){
989         try {   
990         
991                 //if (outputDir == "") {  outputDir += hasPath(distFile);  }
992                 string outfile = getRootName(distFile) + "sorted.dist";
993
994                 
995                 //if you can, use the unix sort since its been optimized for years
996                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
997                         string command = "sort -n -k +3 " + distFile + " -o " + outfile;
998                         system(command.c_str());
999                 #else //you are stuck with my best attempt...
1000                         //windows sort does not have a way to specify a column, only a character in the line
1001                         //since we cannot assume that the distance will always be at the the same character location on each line
1002                         //due to variable sequence name lengths, I chose to force the distance into first position, then sort and then put it back.
1003                 
1004                         //read in file line by file and put distance first
1005                         string tempDistFile = distFile + ".temp";
1006                         ifstream input;
1007                         ofstream output;
1008                         openInputFile(distFile, input);
1009                         openOutputFile(tempDistFile, output);
1010
1011                         string firstName, secondName;
1012                         float dist;
1013                         while (input) {
1014                                 input >> firstName >> secondName >> dist;
1015                                 output << dist << '\t' << firstName << '\t' << secondName << endl;
1016                                 gobble(input);
1017                         }
1018                         input.close();
1019                         output.close();
1020                 
1021         
1022                         //sort using windows sort
1023                         string tempOutfile = outfile + ".temp";
1024                         string command = "sort " + tempDistFile + " /O " + tempOutfile;
1025                         system(command.c_str());
1026                 
1027                         //read in sorted file and put distance at end again
1028                         ifstream input2;
1029                         openInputFile(tempOutfile, input2);
1030                         openOutputFile(outfile, output);
1031                 
1032                         while (input2) {
1033                                 input2 >> dist >> firstName >> secondName;
1034                                 output << firstName << '\t' << secondName << '\t' << dist << endl;
1035                                 gobble(input2);
1036                         }
1037                         input2.close();
1038                         output.close();
1039                 
1040                         //remove temp files
1041                         mothurRemove(tempDistFile);
1042                         mothurRemove(tempOutfile);
1043                 #endif
1044                 
1045                 return outfile;
1046         }
1047         catch(exception& e) {
1048                 errorOut(e, "MothurOut", "sortFile");
1049                 exit(1);
1050         }       
1051 }
1052 /**************************************************************************************************/
1053 vector<unsigned long long> MothurOut::setFilePosFasta(string filename, int& num) {
1054         try {
1055                         vector<unsigned long long> positions;
1056                         ifstream inFASTA;
1057                         //openInputFile(filename, inFASTA);
1058                         inFASTA.open(filename.c_str(), ios::binary);
1059                                                 
1060                         string input;
1061                         unsigned long long count = 0;
1062                         while(!inFASTA.eof()){
1063                                 //input = getline(inFASTA); 
1064                                 //cout << input << '\t' << inFASTA.tellg() << endl;
1065                                 //if (input.length() != 0) {
1066                                 //      if(input[0] == '>'){    unsigned long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1);  cout << (pos - input.length() - 1) << endl; }
1067                                 //}
1068                                 //gobble(inFASTA); //has to be here since windows line endings are 2 characters and mess up the positions
1069                                 char c = inFASTA.get(); count++;
1070                                 if (c == '>') {
1071                                         positions.push_back(count-1);
1072                                         //cout << count << endl;
1073                                 }
1074                         }
1075                         inFASTA.close();
1076                 
1077                         num = positions.size();
1078                 
1079                         /*FILE * pFile;
1080                         long size;
1081                 
1082                         //get num bytes in file
1083                         pFile = fopen (filename.c_str(),"rb");
1084                         if (pFile==NULL) perror ("Error opening file");
1085                         else{
1086                                 fseek (pFile, 0, SEEK_END);
1087                                 size=ftell (pFile);
1088                                 fclose (pFile);
1089                         }*/
1090                         
1091                         unsigned long long size = positions[(positions.size()-1)];
1092                         ifstream in;
1093                         openInputFile(filename, in);
1094                         
1095                         in.seekg(size);
1096                 
1097                         while(in.get()){
1098                                 if(in.eof())            {       break;  }
1099                                 else                            {       size++; }
1100                         }
1101                         in.close();
1102                 
1103                         positions.push_back(size);
1104                         positions[0] = 0;
1105                 
1106                         return positions;
1107         }
1108         catch(exception& e) {
1109                 errorOut(e, "MothurOut", "setFilePosFasta");
1110                 exit(1);
1111         }
1112 }
1113 /**************************************************************************************************/
1114 vector<unsigned long long> MothurOut::setFilePosEachLine(string filename, int& num) {
1115         try {
1116                         filename = getFullPathName(filename);
1117                         
1118                         vector<unsigned long long> positions;
1119                         ifstream in;
1120                         //openInputFile(filename, in);
1121                         in.open(filename.c_str(), ios::binary);
1122                 
1123                         string input;
1124                         unsigned long long count = 0;
1125                         positions.push_back(0);
1126                 
1127                         while(!in.eof()){
1128                                 //unsigned long long lastpos = in.tellg();
1129                                 //input = getline(in); 
1130                                 //if (input.length() != 0) {
1131                                         //unsigned long long pos = in.tellg(); 
1132                                         //if (pos != -1) { positions.push_back(pos - input.length() - 1);       }
1133                                         //else {  positions.push_back(lastpos);  }
1134                                 //}
1135                                 //gobble(in); //has to be here since windows line endings are 2 characters and mess up the positions
1136                                 
1137                                 
1138                                 //getline counting reads
1139                                 char d = in.get(); count++;
1140                                 while ((d != '\n') && (d != '\r') && (d != '\f') && (d != in.eof()))    {
1141                                         //get next character
1142                                         d = in.get(); 
1143                                         count++;
1144                                 }
1145                                 
1146                                 if (!in.eof()) {
1147                                         d=in.get(); count++;
1148                                         while(isspace(d) && (d != in.eof()))            { d=in.get(); count++;}
1149                                 }
1150                                 positions.push_back(count-1);
1151                                 cout << count-1 << endl;
1152                         }
1153                         in.close();
1154                 
1155                         num = positions.size()-1;
1156                 
1157                         FILE * pFile;
1158                         unsigned long long size;
1159                         
1160                         //get num bytes in file
1161                         pFile = fopen (filename.c_str(),"rb");
1162                         if (pFile==NULL) perror ("Error opening file");
1163                         else{
1164                                 fseek (pFile, 0, SEEK_END);
1165                                 size=ftell (pFile);
1166                                 fclose (pFile);
1167                         }
1168                 
1169                         positions[(positions.size()-1)] = size;
1170                 
1171                         return positions;
1172         }
1173         catch(exception& e) {
1174                 errorOut(e, "MothurOut", "setFilePosEachLine");
1175                 exit(1);
1176         }
1177 }
1178 /**************************************************************************************************/
1179
1180 vector<unsigned long long> MothurOut::divideFile(string filename, int& proc) {
1181         try{
1182         
1183                 vector<unsigned long long> filePos;
1184                 filePos.push_back(0);
1185                 
1186                 FILE * pFile;
1187                 unsigned long long size;
1188                 
1189                 filename = getFullPathName(filename);
1190                 
1191                 //get num bytes in file
1192                 pFile = fopen (filename.c_str(),"rb");
1193                 if (pFile==NULL) perror ("Error opening file");
1194                 else{
1195                         fseek (pFile, 0, SEEK_END);
1196                         size=ftell (pFile);
1197                         fclose (pFile);
1198                 }
1199         
1200                 //estimate file breaks
1201                 unsigned long long chunkSize = 0;
1202                 chunkSize = size / proc;
1203
1204                 //file to small to divide by processors
1205                 if (chunkSize == 0)  {  proc = 1;       filePos.push_back(size); return filePos;        }
1206         
1207                 //for each process seekg to closest file break and search for next '>' char. make that the filebreak
1208                 for (int i = 0; i < proc; i++) {
1209                         unsigned long long spot = (i+1) * chunkSize;
1210                         
1211                         ifstream in;
1212                         openInputFile(filename, in);
1213                         in.seekg(spot);
1214                         
1215                         //look for next '>'
1216                         unsigned long long newSpot = spot;
1217                         while (!in.eof()) {
1218                            char c = in.get();
1219                            if (c == '>') {   in.putback(c); newSpot = in.tellg(); break;  }
1220                         }
1221                 
1222                         //there was not another sequence before the end of the file
1223                         unsigned long long sanityPos = in.tellg();
1224
1225                         if (sanityPos == -1) {  break;  }
1226                         else {  filePos.push_back(newSpot);  }
1227                         
1228                         in.close();
1229                 }
1230                 
1231                 //save end pos
1232                 filePos.push_back(size);
1233
1234                 //sanity check filePos
1235                 for (int i = 0; i < (filePos.size()-1); i++) {
1236                         if (filePos[(i+1)] <= filePos[i]) {  filePos.erase(filePos.begin()+(i+1)); i--; }
1237                 }
1238
1239                 proc = (filePos.size() - 1);
1240                 
1241                 return filePos;
1242         }
1243         catch(exception& e) {
1244                 errorOut(e, "MothurOut", "divideFile");
1245                 exit(1);
1246         }
1247 }
1248 /**************************************************************************************************/
1249 int MothurOut::divideFile(string filename, int& proc, vector<string>& files) {
1250         try{
1251                 
1252                 vector<unsigned long long> filePos = divideFile(filename, proc);
1253                 
1254                 for (int i = 0; i < (filePos.size()-1); i++) {
1255                         
1256                         //read file chunk
1257                         ifstream in;
1258                         openInputFile(filename, in);
1259                         in.seekg(filePos[i]);
1260                         unsigned long long size = filePos[(i+1)] - filePos[i];
1261                         char* chunk = new char[size];
1262                         in.read(chunk, size);
1263                         in.close();
1264                         
1265                         //open new file
1266                         string fileChunkName = filename + "." + toString(i) + ".tmp";
1267                         ofstream out; 
1268                         openOutputFile(fileChunkName, out);
1269                         
1270                         out << chunk << endl;
1271                         out.close();
1272                         delete[] chunk;
1273                         
1274                         //save name
1275                         files.push_back(fileChunkName);
1276                 }
1277                                 
1278                 return 0;
1279         }
1280         catch(exception& e) {
1281                 errorOut(e, "MothurOut", "divideFile");
1282                 exit(1);
1283         }
1284 }
1285 /***********************************************************************/
1286
1287 bool MothurOut::isTrue(string f){
1288         try {
1289                 
1290                 for (int i = 0; i < f.length(); i++) { f[i] = toupper(f[i]); }
1291                 
1292                 if ((f == "TRUE") || (f == "T")) {      return true;    }
1293                 else {  return false;  }
1294         }
1295         catch(exception& e) {
1296                 errorOut(e, "MothurOut", "isTrue");
1297                 exit(1);
1298         }
1299 }
1300
1301 /***********************************************************************/
1302
1303 float MothurOut::roundDist(float dist, int precision){
1304         try {
1305                 return int(dist * precision + 0.5)/float(precision);
1306         }
1307         catch(exception& e) {
1308                 errorOut(e, "MothurOut", "roundDist");
1309                 exit(1);
1310         }
1311 }
1312 /***********************************************************************/
1313
1314 float MothurOut::ceilDist(float dist, int precision){
1315         try {
1316                 return int(ceil(dist * precision))/float(precision);
1317         }
1318         catch(exception& e) {
1319                 errorOut(e, "MothurOut", "ceilDist");
1320                 exit(1);
1321         }
1322 }
1323 /**********************************************************************************************************************/
1324 int MothurOut::readNames(string namefile, map<string, string>& nameMap) { 
1325         try {
1326                 
1327                 //open input file
1328                 ifstream in;
1329                 openInputFile(namefile, in);
1330                 
1331                 while (!in.eof()) {
1332                         if (control_pressed) { break; }
1333                         
1334                         string firstCol, secondCol;
1335                         in >> firstCol >> secondCol; gobble(in);
1336                         
1337                         nameMap[firstCol] = secondCol;
1338                 }
1339                 in.close();
1340                 
1341                 return 0;
1342                 
1343         }
1344         catch(exception& e) {
1345                 errorOut(e, "MothurOut", "readNames");
1346                 exit(1);
1347         }
1348 }
1349
1350 /**********************************************************************************************************************/
1351 map<string, int> MothurOut::readNames(string namefile) { 
1352         try {
1353                 
1354                 map<string, int> nameMap;
1355                 
1356                 //open input file
1357                 ifstream in;
1358                 openInputFile(namefile, in);
1359                 
1360                 while (!in.eof()) {
1361                         if (control_pressed) { break; }
1362                         
1363                         string firstCol, secondCol;
1364                         in >> firstCol >> secondCol; gobble(in);
1365                         
1366                         int num = getNumNames(secondCol);
1367                         
1368                         nameMap[firstCol] = num;
1369                 }
1370                 in.close();
1371                 
1372                 return nameMap;
1373                 
1374         }
1375         catch(exception& e) {
1376                 errorOut(e, "MothurOut", "readNames");
1377                 exit(1);
1378         }
1379 }
1380 /**********************************************************************************************************************/
1381 int MothurOut::readNames(string namefile, vector<seqPriorityNode>& nameVector, map<string, string>& fastamap) { 
1382         try {
1383                 int error = 0;
1384                 
1385                 //open input file
1386                 ifstream in;
1387                 openInputFile(namefile, in);
1388                 
1389                 while (!in.eof()) {
1390                         if (control_pressed) { break; }
1391                         
1392                         string firstCol, secondCol;
1393                         in >> firstCol >> secondCol; gobble(in);
1394                         
1395                         int num = getNumNames(secondCol);
1396                         
1397                         map<string, string>::iterator it = fastamap.find(firstCol);
1398                         if (it == fastamap.end()) {
1399                                 error = 1;
1400                                 mothurOut("[ERROR]: " + firstCol + " is not in your fastafile, but is in your namesfile, please correct."); mothurOutEndLine();
1401                         }else {
1402                                 seqPriorityNode temp(num, it->second, firstCol);
1403                                 nameVector.push_back(temp);
1404                         }
1405                 }
1406                 in.close();
1407                 
1408                 return error;
1409                 
1410         }
1411         catch(exception& e) {
1412                 errorOut(e, "MothurOut", "readNames");
1413                 exit(1);
1414         }
1415 }
1416
1417 /***********************************************************************/
1418
1419 int MothurOut::getNumNames(string names){
1420         try {
1421                 int count = 0;
1422                 
1423                 if(names != ""){
1424                         count = 1;
1425                         for(int i=0;i<names.size();i++){
1426                                 if(names[i] == ','){
1427                                         count++;
1428                                 }
1429                         }
1430                 }
1431                 
1432                 return count;
1433         }
1434         catch(exception& e) {
1435                 errorOut(e, "MothurOut", "getNumNames");
1436                 exit(1);
1437         }
1438 }
1439 /***********************************************************************/
1440
1441 void MothurOut::mothurRemove(string filename){
1442         try {
1443                 filename = getFullPathName(filename);
1444                 remove(filename.c_str());
1445         }
1446         catch(exception& e) {
1447                 errorOut(e, "MothurOut", "mothurRemove");
1448                 exit(1);
1449         }
1450 }
1451 /**************************************************************************************************/
1452
1453 vector<vector<double> > MothurOut::binomial(int maxOrder){
1454         try {
1455         vector<vector<double> > binomial(maxOrder+1);
1456         
1457     for(int i=0;i<=maxOrder;i++){
1458                 binomial[i].resize(maxOrder+1);
1459                 binomial[i][0]=1;
1460                 binomial[0][i]=0;
1461     }
1462     binomial[0][0]=1;
1463         
1464     binomial[1][0]=1;
1465     binomial[1][1]=1;
1466         
1467     for(int i=2;i<=maxOrder;i++){
1468                 binomial[1][i]=0;
1469     }
1470         
1471     for(int i=2;i<=maxOrder;i++){
1472                 for(int j=1;j<=maxOrder;j++){
1473                         if(i==j){       binomial[i][j]=1;                                                                       }
1474                         if(j>i) {       binomial[i][j]=0;                                                                       }
1475                         else    {       binomial[i][j]=binomial[i-1][j-1]+binomial[i-1][j];     }
1476                 }
1477     }
1478         
1479         return binomial;
1480         
1481         }
1482         catch(exception& e) {
1483                 errorOut(e, "MothurOut", "binomial");
1484                 exit(1);
1485         }
1486 }
1487 /**************************************************************************************************/
1488 unsigned int MothurOut::fromBase36(string base36){
1489         try {
1490                 unsigned int num = 0;
1491                 
1492                 map<char, int> converts;
1493                 converts['A'] = 0;
1494                 converts['a'] = 0;
1495                 converts['B'] = 1;
1496                 converts['b'] = 1;
1497                 converts['C'] = 2;
1498                 converts['c'] = 2;
1499                 converts['D'] = 3;
1500                 converts['d'] = 3;
1501                 converts['E'] = 4;
1502                 converts['e'] = 4;
1503                 converts['F'] = 5;
1504                 converts['f'] = 5;
1505                 converts['G'] = 6;
1506                 converts['g'] = 6;
1507                 converts['H'] = 7;
1508                 converts['h'] = 7;
1509                 converts['I'] = 8;
1510                 converts['i'] = 8;
1511                 converts['J'] = 9;
1512                 converts['j'] = 9;
1513                 converts['K'] = 10;
1514                 converts['k'] = 10;
1515                 converts['L'] = 11;
1516                 converts['l'] = 11;
1517                 converts['M'] = 12;
1518                 converts['m'] = 12;
1519                 converts['N'] = 13;
1520                 converts['n'] = 13;
1521                 converts['O'] = 14;
1522                 converts['o'] = 14;
1523                 converts['P'] = 15;
1524                 converts['p'] = 15;
1525                 converts['Q'] = 16;
1526                 converts['q'] = 16;
1527                 converts['R'] = 17;
1528                 converts['r'] = 17;
1529                 converts['S'] = 18;
1530                 converts['s'] = 18;
1531                 converts['T'] = 19;
1532                 converts['t'] = 19;
1533                 converts['U'] = 20;
1534                 converts['u'] = 20;
1535                 converts['V'] = 21;
1536                 converts['v'] = 21;
1537                 converts['W'] = 22;
1538                 converts['w'] = 22;
1539                 converts['X'] = 23;
1540                 converts['x'] = 23;
1541                 converts['Y'] = 24;
1542                 converts['y'] = 24;
1543                 converts['Z'] = 25;
1544                 converts['z'] = 25;
1545                 converts['0'] = 26;
1546                 converts['1'] = 27;
1547                 converts['2'] = 28;
1548                 converts['3'] = 29;
1549                 converts['4'] = 30;
1550                 converts['5'] = 31;
1551                 converts['6'] = 32;
1552                 converts['7'] = 33;
1553                 converts['8'] = 34;
1554                 converts['9'] = 35;             
1555                 
1556                 int i = 0;
1557                 while (i < base36.length()) {
1558                         char c = base36[i];
1559                         num = 36 * num + converts[c];
1560                         i++;
1561                 }
1562                 
1563                 return num;
1564                 
1565         }
1566         catch(exception& e) {
1567                 errorOut(e, "MothurOut", "fromBase36");
1568                 exit(1);
1569         }
1570 }
1571 /***********************************************************************/
1572
1573 int MothurOut::factorial(int num){
1574         try {
1575                 int total = 1;
1576                 
1577                 for (int i = 1; i <= num; i++) {
1578                         total *= i;
1579                 }
1580                 
1581                 return total;
1582         }
1583         catch(exception& e) {
1584                 errorOut(e, "MothurOut", "factorial");
1585                 exit(1);
1586         }
1587 }
1588 /***********************************************************************/
1589
1590 int MothurOut::getNumSeqs(ifstream& file){
1591         try {
1592                 int numSeqs = count(istreambuf_iterator<char>(file),istreambuf_iterator<char>(), '>');
1593                 file.seekg(0);
1594                 return numSeqs;
1595         }
1596         catch(exception& e) {
1597                 errorOut(e, "MothurOut", "getNumSeqs");
1598                 exit(1);
1599         }       
1600 }
1601 /***********************************************************************/
1602 void MothurOut::getNumSeqs(ifstream& file, int& numSeqs){
1603         try {
1604                 string input;
1605                 numSeqs = 0;
1606                 while(!file.eof()){
1607                         input = getline(file);
1608                         if (input.length() != 0) {
1609                                 if(input[0] == '>'){ numSeqs++; }
1610                         }
1611                 }
1612         }
1613         catch(exception& e) {
1614                 errorOut(e, "MothurOut", "getNumSeqs");
1615                 exit(1);
1616         }       
1617 }
1618 /***********************************************************************/
1619
1620 //This function parses the estimator options and puts them in a vector
1621 void MothurOut::splitAtChar(string& estim, vector<string>& container, char symbol) {
1622         try {
1623                 string individual = "";
1624                 int estimLength = estim.size();
1625                 for(int i=0;i<estimLength;i++){
1626                         if(estim[i] == symbol){
1627                                 container.push_back(individual);
1628                                 individual = "";                                
1629                         }
1630                         else{
1631                                 individual += estim[i];
1632                         }
1633                 }
1634                 container.push_back(individual);
1635
1636         }
1637         catch(exception& e) {
1638                 errorOut(e, "MothurOut", "splitAtChar");
1639                 exit(1);
1640         }       
1641 }
1642
1643 /***********************************************************************/
1644
1645 //This function parses the estimator options and puts them in a vector
1646 void MothurOut::splitAtDash(string& estim, vector<string>& container) {
1647         try {
1648                 string individual = "";
1649                 int estimLength = estim.size();
1650                 for(int i=0;i<estimLength;i++){
1651                         if(estim[i] == '-'){
1652                                 container.push_back(individual);
1653                                 individual = "";                                
1654                         }
1655                         else{
1656                                 individual += estim[i];
1657                         }
1658                 }
1659                 container.push_back(individual);
1660
1661         
1662         /*      string individual;
1663                 
1664                 while (estim.find_first_of('-') != -1) {
1665                         individual = estim.substr(0,estim.find_first_of('-'));
1666                         if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
1667                                 estim = estim.substr(estim.find_first_of('-')+1, estim.length());
1668                                 container.push_back(individual);
1669                         }
1670                 }
1671                 //get last one
1672                 container.push_back(estim); */
1673         }
1674         catch(exception& e) {
1675                 errorOut(e, "MothurOut", "splitAtDash");
1676                 exit(1);
1677         }       
1678 }
1679
1680 /***********************************************************************/
1681 //This function parses the label options and puts them in a set
1682 void MothurOut::splitAtDash(string& estim, set<string>& container) {
1683         try {
1684                 string individual = "";
1685                 int estimLength = estim.size();
1686                 for(int i=0;i<estimLength;i++){
1687                         if(estim[i] == '-'){
1688                                 container.insert(individual);
1689                                 individual = "";                                
1690                         }
1691                         else{
1692                                 individual += estim[i];
1693                         }
1694                 }
1695                 container.insert(individual);
1696
1697         //      string individual;
1698                 
1699         //      while (estim.find_first_of('-') != -1) {
1700         //              individual = estim.substr(0,estim.find_first_of('-'));
1701         //              if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
1702         //                      estim = estim.substr(estim.find_first_of('-')+1, estim.length());
1703         //                      container.insert(individual);
1704         //              }
1705         //      }
1706                 //get last one
1707         //      container.insert(estim);
1708         
1709         }
1710         catch(exception& e) {
1711                 errorOut(e, "MothurOut", "splitAtDash");
1712                 exit(1);
1713         }       
1714 }
1715 /***********************************************************************/
1716 //This function parses the line options and puts them in a set
1717 void MothurOut::splitAtDash(string& estim, set<int>& container) {
1718         try {
1719                 string individual;
1720                 int lineNum;
1721                 
1722                 while (estim.find_first_of('-') != -1) {
1723                         individual = estim.substr(0,estim.find_first_of('-'));
1724                         if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
1725                                 estim = estim.substr(estim.find_first_of('-')+1, estim.length());
1726                                 convert(individual, lineNum); //convert the string to int
1727                                 container.insert(lineNum);
1728                         }
1729                 }
1730                 //get last one
1731                 convert(estim, lineNum); //convert the string to int
1732                 container.insert(lineNum);
1733         }
1734         catch(exception& e) {
1735                 errorOut(e, "MothurOut", "splitAtDash");
1736                 exit(1);
1737         }       
1738 }
1739 /***********************************************************************/
1740 //This function parses the a string and puts peices in a vector
1741 void MothurOut::splitAtComma(string& estim, vector<string>& container) {
1742         try {
1743                 string individual = "";
1744                 int estimLength = estim.size();
1745                 for(int i=0;i<estimLength;i++){
1746                         if(estim[i] == ','){
1747                                 container.push_back(individual);
1748                                 individual = "";                                
1749                         }
1750                         else{
1751                                 individual += estim[i];
1752                         }
1753                 }
1754                 container.push_back(individual);
1755                 
1756                 
1757                 
1758                 
1759 //              string individual;
1760 //              
1761 //              while (estim.find_first_of(',') != -1) {
1762 //                      individual = estim.substr(0,estim.find_first_of(','));
1763 //                      if ((estim.find_first_of(',')+1) <= estim.length()) { //checks to make sure you don't have comma at end of string
1764 //                              estim = estim.substr(estim.find_first_of(',')+1, estim.length());
1765 //                              container.push_back(individual);
1766 //                      }
1767 //              }
1768 //              //get last one
1769 //              container.push_back(estim);
1770         }
1771         catch(exception& e) {
1772                 errorOut(e, "MothurOut", "splitAtComma");
1773                 exit(1);
1774         }       
1775 }
1776 /***********************************************************************/
1777
1778 //This function splits up the various option parameters
1779 void MothurOut::splitAtComma(string& prefix, string& suffix){
1780         try {
1781                 prefix = suffix.substr(0,suffix.find_first_of(','));
1782                 if ((suffix.find_first_of(',')+2) <= suffix.length()) {  //checks to make sure you don't have comma at end of string
1783                         suffix = suffix.substr(suffix.find_first_of(',')+1, suffix.length());
1784                         string space = " ";
1785                         while(suffix.at(0) == ' ')
1786                                 suffix = suffix.substr(1, suffix.length());
1787                 }
1788
1789         }
1790         catch(exception& e) {
1791                 errorOut(e, "MothurOut", "splitAtComma");
1792                 exit(1);
1793         }       
1794 }
1795 /***********************************************************************/
1796
1797 //This function separates the key value from the option value i.e. dist=96_...
1798 void MothurOut::splitAtEquals(string& key, string& value){              
1799         try {
1800                 if(value.find_first_of('=') != -1){
1801                         key = value.substr(0,value.find_first_of('='));
1802                         if ((value.find_first_of('=')+1) <= value.length()) {
1803                                 value = value.substr(value.find_first_of('=')+1, value.length());
1804                         }
1805                 }else{
1806                         key = value;
1807                         value = 1;
1808                 }
1809         }
1810         catch(exception& e) {
1811                 errorOut(e, "MothurOut", "splitAtEquals");
1812                 exit(1);
1813         }       
1814 }
1815
1816 /**************************************************************************************************/
1817
1818 bool MothurOut::inUsersGroups(string groupname, vector<string> Groups) {
1819         try {
1820                 for (int i = 0; i < Groups.size(); i++) {
1821                         if (groupname == Groups[i]) { return true; }
1822                 }
1823                 return false;
1824         }
1825         catch(exception& e) {
1826                 errorOut(e, "MothurOut", "inUsersGroups");
1827                 exit(1);
1828         }       
1829 }
1830 /**************************************************************************************************/
1831 //returns true if any of the strings in first vector are in second vector
1832 bool MothurOut::inUsersGroups(vector<string> groupnames, vector<string> Groups) {
1833         try {
1834                 
1835                 for (int i = 0; i < groupnames.size(); i++) {
1836                         if (inUsersGroups(groupnames[i], Groups)) { return true; }
1837                 }
1838                 return false;
1839         }
1840         catch(exception& e) {
1841                 errorOut(e, "MothurOut", "inUsersGroups");
1842                 exit(1);
1843         }       
1844 }
1845 /***********************************************************************/
1846 //this function determines if the user has given us labels that are smaller than the given label.
1847 //if so then it returns true so that the calling function can run the previous valid distance.
1848 //it's a "smart" distance function.  It also checks for invalid labels.
1849 bool MothurOut::anyLabelsToProcess(string label, set<string>& userLabels, string errorOff) {
1850         try {
1851                 
1852                 set<string>::iterator it;
1853                 vector<float> orderFloat;
1854                 map<string, float> userMap;  //the conversion process removes trailing 0's which we need to put back
1855                 map<string, float>::iterator it2;
1856                 float labelFloat;
1857                 bool smaller = false;
1858                 
1859                 //unique is the smallest line
1860                 if (label == "unique") {  return false;  }
1861                 else { 
1862                         if (convertTestFloat(label, labelFloat)) {
1863                                 convert(label, labelFloat); 
1864                         }else { //cant convert 
1865                                 return false;
1866                         }
1867                 }
1868                 
1869                 //go through users set and make them floats
1870                 for(it = userLabels.begin(); it != userLabels.end();) {
1871                         
1872                         float temp;
1873                         if ((*it != "unique") && (convertTestFloat(*it, temp) == true)){
1874                                 convert(*it, temp);
1875                                 orderFloat.push_back(temp);
1876                                 userMap[*it] = temp;
1877                                 it++;
1878                         }else if (*it == "unique") { 
1879                                 orderFloat.push_back(-1.0);
1880                                 userMap["unique"] = -1.0;
1881                                 it++;
1882                         }else {
1883                                 if (errorOff == "") {  mothurOut(*it + " is not a valid label."); mothurOutEndLine();  }
1884                                 userLabels.erase(it++); 
1885                         }
1886                 }
1887                 
1888                 //sort order
1889                 sort(orderFloat.begin(), orderFloat.end());
1890                 
1891                 /*************************************************/
1892                 //is this label bigger than any of the users labels
1893                 /*************************************************/
1894                                 
1895                 //loop through order until you find a label greater than label
1896                 for (int i = 0; i < orderFloat.size(); i++) {
1897                         if (orderFloat[i] < labelFloat) {
1898                                 smaller = true;
1899                                 if (orderFloat[i] == -1) { 
1900                                         if (errorOff == "") { mothurOut("Your file does not include the label unique."); mothurOutEndLine(); }
1901                                         userLabels.erase("unique");
1902                                 }
1903                                 else {  
1904                                         if (errorOff == "") { mothurOut("Your file does not include the label "); mothurOutEndLine(); }
1905                                         string s = "";
1906                                         for (it2 = userMap.begin(); it2!= userMap.end(); it2++) {  
1907                                                 if (it2->second == orderFloat[i]) {  
1908                                                         s = it2->first;  
1909                                                         //remove small labels
1910                                                         userLabels.erase(s);
1911                                                         break;
1912                                                 }
1913                                         }
1914                                         if (errorOff == "") {mothurOut( s +  ". I will use the next smallest distance. "); mothurOutEndLine(); }
1915                                 }
1916                         //since they are sorted once you find a bigger one stop looking
1917                         }else { break; }
1918                 }
1919                 
1920                 return smaller;
1921                                                 
1922         }
1923         catch(exception& e) {
1924                 errorOut(e, "MothurOut", "anyLabelsToProcess");
1925                 exit(1);
1926         }       
1927 }
1928
1929 /**************************************************************************************************/
1930 bool MothurOut::checkReleaseVersion(ifstream& file, string version) {
1931         try {
1932                 
1933                 bool good = true;
1934                 
1935                 string line = getline(file);  
1936
1937                 //before we added this check
1938                 if (line[0] != '#') {  good = false;  }
1939                 else {
1940                         //rip off #
1941                         line = line.substr(1);
1942                         
1943                         vector<string> versionVector;
1944                         splitAtChar(version, versionVector, '.');
1945                         
1946                         //check file version
1947                         vector<string> linesVector;
1948                         splitAtChar(line, linesVector, '.');
1949                         
1950                         if (versionVector.size() != linesVector.size()) { good = false; }
1951                         else {
1952                                 for (int j = 0; j < versionVector.size(); j++) {
1953                                         int num1, num2;
1954                                         convert(versionVector[j], num1);
1955                                         convert(linesVector[j], num2);
1956                                         
1957                                         //if mothurs version is newer than this files version, then we want to remake it
1958                                         if (num1 > num2) {  good = false; break;  }
1959                                 }
1960                         }
1961                         
1962                 }
1963                 
1964                 if (!good) {  file.close();  }
1965                 else { file.seekg(0);  }
1966                 
1967                 return good;
1968         }
1969         catch(exception& e) {
1970                 errorOut(e, "MothurOut", "checkReleaseVersion");                
1971                 exit(1);
1972         }
1973 }
1974 /**************************************************************************************************/
1975 bool MothurOut::isContainingOnlyDigits(string input) {
1976         try{
1977                 
1978                 //are you a digit in ascii code
1979                 for (int i = 0;i < input.length(); i++){
1980                         if( input[i]>47 && input[i]<58){}
1981                         else { return false; }
1982                 }
1983                 
1984                 return true;
1985         }
1986         catch(exception& e) {
1987                 errorOut(e, "MothurOut", "isContainingOnlyDigits");             
1988                 exit(1);
1989         }
1990 }
1991 /**************************************************************************************************/
1992
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1996