X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothur.h;h=fdaa06362db6ecda7054fe4ff9b21442487c19d4;hb=6777912b79eb6d011163da47f3ada09d1a9293c1;hp=84dbdb3dee2879829909b38654c80057d9d5fdb5;hpb=c4fb347858dd8cfea4d2933f429fff4130dca65b;p=mothur.git diff --git a/mothur.h b/mothur.h index 84dbdb3..fdaa063 100644 --- a/mothur.h +++ b/mothur.h @@ -21,6 +21,8 @@ #include #include #include +#include + //exception #include @@ -45,10 +47,22 @@ #include #include +/***********************************************************************/ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) #include #include + + #ifdef USE_READLINE + #include + #include + #endif + + //#include + //#include +#else + #include //allows unbuffered screen capture from stdin + #include //get cwd #endif using namespace std; @@ -60,7 +74,6 @@ using namespace std; #define isnan(x) ((x) != (x)) #define isinf(x) (fabs(x) == std::numeric_limits::infinity()) - typedef unsigned long ull; struct IntNode { @@ -70,6 +83,9 @@ struct IntNode { int rcoef; IntNode* left; IntNode* right; + + IntNode(int lv, int rv, IntNode* l, IntNode* r) : lvalue(lv), rvalue(rv), left(l), right(r) {}; + IntNode() {}; }; struct ThreadNode { @@ -78,6 +94,27 @@ struct ThreadNode { IntNode* right; }; +/************************************************************/ +struct clusterNode { + int numSeq; + int parent; + int smallChild; //used to make linkTable work with list and rabund. represents bin number of this cluster node + clusterNode(int num, int par, int kid) : numSeq(num), parent(par), smallChild(kid) {}; +}; +/************************************************************/ +struct seqDist { + int seq1; + int seq2; + float dist; + seqDist() {} + seqDist(int s1, int s2, float d) : seq1(s1), seq2(s2), dist(d) {} + ~seqDist() {} +}; +//******************************************************************************************************************** +//sorts lowest to highest +inline bool compareSequenceDistance(seqDist left, seqDist right){ + return (left.dist < right.dist); +} /***********************************************************************/ // snagged from http://www.parashift.com/c++-faq-lite/misc-technical-issues.html#faq-39.2 @@ -178,7 +215,6 @@ inline void gobble(istream& f){ f.putback(d); } - /***********************************************************************/ inline string getline(ifstream& fileHandle) { @@ -272,9 +308,6 @@ inline void errorOut(exception& e, string object, string function) { } - - - /***********************************************************************/ inline bool isTrue(string f){ @@ -360,11 +393,18 @@ inline string getSimpleName(string longName){ string simpleName = longName; - if(longName.find_last_of("/") != longName.npos){ - int pos = longName.find_last_of('/')+1; - simpleName = longName.substr(pos, longName.length()); - } + size_t found; + found=longName.find_last_of("/\\"); + if(found != longName.npos){ + simpleName = longName.substr(found+1); + } + + //if(longName.find_last_of("/") != longName.npos){ + // int pos = longName.find_last_of('/')+1; + // simpleName = longName.substr(pos, longName.length()); + //} + return simpleName; } @@ -393,13 +433,28 @@ inline string getPathName(string longName){ string rootPathName = longName; - if(longName.find_last_of('/') != longName.npos){ - int pos = longName.find_last_of('/')+1; + if(longName.find_last_of("/\\") != longName.npos){ + int pos = longName.find_last_of("/\\")+1; rootPathName = longName.substr(0, pos); } - + return rootPathName; } +/***********************************************************************/ + +inline string hasPath(string longName){ + + string path = ""; + + size_t found; + found=longName.find_last_of("/\\"); + + if(found != longName.npos){ + path = longName.substr(0, found+1); + } + + return path; +} /***********************************************************************/ @@ -414,33 +469,190 @@ inline string getExtension(string longName){ return extension; } +/***********************************************************************/ +inline bool isBlank(string fileName){ + + ifstream fileHandle; + fileHandle.open(fileName.c_str()); + if(!fileHandle) { + mothurOut("Error: Could not open " + fileName); mothurOutEndLine(); + return false; + }else { + //check for blank file + gobble(fileHandle); + if (fileHandle.eof()) { fileHandle.close(); return true; } + } + return false; +} +/***********************************************************************/ +inline string getFullPathName(string fileName){ + + string path = hasPath(fileName); + string newFileName; + int pos; + + if (path == "") { return fileName; } //its a simple name + else { //we need to complete the pathname + // ex. ../../../filename + // cwd = /user/work/desktop + + string cwd; + //get current working directory + #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) + if (path.rfind("./") == -1) { return fileName; } //already complete name + else { newFileName = fileName.substr(fileName.rfind("./")+2); } //save the complete part of the name + + char* cwdpath; + size_t size; + cwdpath=getcwd(cwdpath,size); + cwd = cwdpath; + + //rip off first '/' + string simpleCWD; + if (cwd.length() > 0) { simpleCWD = cwd.substr(1); } + + //break apart the current working directory + vector dirs; + while (simpleCWD.find_first_of('/') != -1) { + string dir = simpleCWD.substr(0,simpleCWD.find_first_of('/')); + simpleCWD = simpleCWD.substr(simpleCWD.find_first_of('/')+1, simpleCWD.length()); + dirs.push_back(dir); + } + //get last one // ex. ../../../filename = /user/work/desktop/filename + dirs.push_back(simpleCWD); //ex. dirs[0] = user, dirs[1] = work, dirs[2] = desktop + + int index = dirs.size()-1; + + while((pos = path.rfind("./")) != -1) { //while you don't have a complete path + if (path[(pos-1)] == '.') { //you want your parent directory ../ + path = path.substr(0, pos-1); + index--; + if (index == 0) { break; } + }else if (path[(pos-1)] == '/') { //you want the current working dir ./ + path = path.substr(0, pos); + }else if (pos == 1) { break; + }else { mothurOut("cannot resolve path for " + fileName); mothurOutEndLine(); return fileName; } + } + + for (int i = index; i >= 0; i--) { + newFileName = dirs[i] + "/" + newFileName; + } + + newFileName = "/" + newFileName; + return newFileName; + + #else + if (path.rfind(".\\") == -1) { return fileName; } //already complete name + else { newFileName = fileName.substr(fileName.rfind(".\\")+2); } //save the complete part of the name + + char *cwdpath = NULL; + cwdpath = getcwd(NULL, 0); // or _getcwd + if ( cwdpath != NULL) { cwd = cwdpath; } + else { cwd = ""; } + + //break apart the current working directory + vector dirs; + while (cwd.find_first_of('\\') != -1) { + string dir = cwd.substr(0,cwd.find_first_of('\\')); + cwd = cwd.substr(cwd.find_first_of('\\')+1, cwd.length()); + dirs.push_back(dir); + + } + //get last one + dirs.push_back(cwd); //ex. dirs[0] = user, dirs[1] = work, dirs[2] = desktop + + int index = dirs.size()-1; + + while((pos = path.rfind(".\\")) != -1) { //while you don't have a complete path + if (path[(pos-1)] == '.') { //you want your parent directory ../ + path = path.substr(0, pos-1); + index--; + if (index == 0) { break; } + }else if (path[(pos-1)] == '\\') { //you want the current working dir ./ + path = path.substr(0, pos); + }else if (pos == 1) { break; + }else { mothurOut("cannot resolve path for " + fileName); mothurOutEndLine(); return fileName; } + } + + for (int i = index; i >= 0; i--) { + newFileName = dirs[i] + "\\" + newFileName; + } + + return newFileName; + + #endif + } + +} /***********************************************************************/ -inline int openInputFile(string fileName, ifstream& fileHandle){ +inline int openInputFile(string fileName, ifstream& fileHandle, string m){ + + //get full path name + string completeFileName = getFullPathName(fileName); - fileHandle.open(fileName.c_str()); + fileHandle.open(completeFileName.c_str()); if(!fileHandle) { - mothurOut("Error: Could not open " + fileName); mothurOutEndLine(); + return 1; + }else { + //check for blank file + gobble(fileHandle); + return 0; + } +} +/***********************************************************************/ + +inline int openInputFile(string fileName, ifstream& fileHandle){ + //get full path name + string completeFileName = getFullPathName(fileName); + + fileHandle.open(completeFileName.c_str()); + if(!fileHandle) { + mothurOut("Error: Could not open " + completeFileName); mothurOutEndLine(); return 1; } else { //check for blank file gobble(fileHandle); - if (fileHandle.eof()) { mothurOut(fileName + " is blank. Please correct."); mothurOutEndLine(); return 1; } + if (fileHandle.eof()) { mothurOut(completeFileName + " is blank. Please correct."); mothurOutEndLine(); return 1; } return 0; } } +/***********************************************************************/ + +inline int renameFile(string oldName, string newName){ + + ifstream inTest; + int exist = openInputFile(newName, inTest, ""); + +#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) + if (exist == 0) { //you could open it so you want to delete it + inTest.close(); + string command = "rm " + newName; + system(command.c_str()); + } + + string command = "mv " + oldName + " " + newName; + system(command.c_str()); +#else + remove(newName.c_str()); + renameOk = rename(oldName.c_str(), newName.c_str()); +#endif + return 0; +} /***********************************************************************/ inline int openOutputFile(string fileName, ofstream& fileHandle){ + + string completeFileName = getFullPathName(fileName); - fileHandle.open(fileName.c_str(), ios::trunc); + fileHandle.open(completeFileName.c_str(), ios::trunc); if(!fileHandle) { - mothurOut("Error: Could not open " + fileName); mothurOutEndLine(); + mothurOut("Error: Could not open " + completeFileName); mothurOutEndLine(); return 1; } else { @@ -458,7 +670,16 @@ inline int getNumSeqs(ifstream& file){ return numSeqs; } +/***********************************************************************/ +inline bool inVector(string member, vector group){ + + for (int i = 0; i < group.size(); i++) { + if (group[i] == member) { return true; } + } + + return false; +} /***********************************************************************/ //This function parses the estimator options and puts them in a vector @@ -733,6 +954,92 @@ inline bool anyLabelsToProcess(string label, set& userLabels, string err } } +/**************************************************************************************************/ +inline void appendFiles(string temp, string filename) { + try{ + ofstream output; + ifstream input; + + //open output file in append mode + openOutputFileAppend(filename, output); + openInputFile(temp, input); + + while(char c = input.get()){ + if(input.eof()) { break; } + else { output << c; } + } + + input.close(); + output.close(); + } + catch(exception& e) { + errorOut(e, "mothur", "appendFiles"); + exit(1); + } +} + +/**************************************************************************************************/ +inline string sortFile(string distFile){ + try { + string outfile = getRootName(distFile) + "sorted.dist"; + + //if you can, use the unix sort since its been optimized for years + #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) + string command = "sort -n -k +3 " + distFile + " -o " + outfile; + system(command.c_str()); + #else //you are stuck with my best attempt... + //windows sort does not have a way to specify a column, only a character in the line + //since we cannot assume that the distance will always be at the the same character location on each line + //due to variable sequence name lengths, I chose to force the distance into first position, then sort and then put it back. + + //read in file line by file and put distance first + string tempDistFile = distFile + ".temp"; + ifstream input; + ofstream output; + openInputFile(distFile, input); + openOutputFile(tempDistFile, output); + + string firstName, secondName; + float dist; + while (input) { + input >> firstName >> secondName >> dist; + output << dist << '\t' << firstName << '\t' << secondName << endl; + gobble(input); + } + input.close(); + output.close(); + + + //sort using windows sort + string tempOutfile = outfile + ".temp"; + string command = "sort " + tempDistFile + " /O " + tempOutfile; + system(command.c_str()); + + //read in sorted file and put distance at end again + ifstream input2; + openInputFile(tempOutfile, input2); + openOutputFile(outfile, output); + + while (input2) { + input2 >> dist >> firstName >> secondName; + output << firstName << '\t' << secondName << '\t' << dist << endl; + gobble(input2); + } + input2.close(); + output.close(); + + //remove temp files + remove(tempDistFile.c_str()); + remove(tempOutfile.c_str()); + #endif + + return outfile; + } + catch(exception& e) { + errorOut(e, "mothur", "sortFile"); + exit(1); + } +} /**************************************************************************************************/ #endif