X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothur.h;h=2404a84f08672c2178bd3e0a33946124348a72a7;hb=a8367302932de9be5434e77f6e5829d7609e2aec;hp=062c4814dfa4addeeb923f586c601717daca7c66;hpb=e189982e0a9b7352ad57cc38ccee675f128be22e;p=mothur.git diff --git a/mothur.h b/mothur.h index 062c481..2404a84 100644 --- a/mothur.h +++ b/mothur.h @@ -254,6 +254,13 @@ inline float roundDist(float dist, int precision){ return int(dist * precision + 0.5)/float(precision); +} +/***********************************************************************/ + +inline float ceilDist(float dist, int precision){ + + return int(ceil(dist * precision))/float(precision); + } /***********************************************************************/ @@ -379,7 +386,7 @@ inline string hasPath(string longName){ string path = ""; size_t found; - found=longName.find_last_of("/\\"); + found=longName.find_last_of("~/\\"); if(found != longName.npos){ path = longName.substr(0, found+1); @@ -433,91 +440,103 @@ inline string getFullPathName(string fileName){ 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 = new char[1024]; + if (path.find("~") != -1) { //go to home directory + string homeDir = getenv ("HOME"); + newFileName = homeDir + fileName.substr(fileName.find("~")+1); + return newFileName; + }else { //find path + 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 = new char[1024]; - size_t size; - cwdpath=getcwd(cwdpath,size); - - cwd = cwdpath; - - //rip off first '/' - string simpleCWD; - if (cwd.length() > 0) { simpleCWD = cwd.substr(1); } + size_t size; + cwdpath=getcwd(cwdpath,size); - //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 + 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; - int index = dirs.size()-1; - - while((pos = path.rfind("./")) != -1) { //while you don't have a complete path - if (pos == 0) { break; //you are at the end - }else 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; //you are at the end - }else { cout << "cannot resolve path for " << fileName << endl; return fileName; } - } - - for (int i = index; i >= 0; i--) { - newFileName = dirs[i] + "/" + newFileName; - } + while((pos = path.rfind("./")) != -1) { //while you don't have a complete path + if (pos == 0) { break; //you are at the end + }else 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; //you are at the end + }else { cout << "cannot resolve path for " << fileName << endl; return fileName; } + } - newFileName = "/" + newFileName; - return newFileName; + 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; + if (path.find("~") != -1) { //go to home directory + string homeDir = getenv ("HOMEPATH"); + newFileName = homeDir + fileName.substr(fileName.find("~")+1); + return newFileName; + }else { //find path + 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 = ""; } - while((pos = path.rfind(".\\")) != -1) { //while you don't have a complete path - if (pos == 0) { break; //you are at the end - }else 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; //you are at the end - }else { cout << "cannot resolve path for " << fileName << endl; return fileName; } - } + //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); - for (int i = index; i >= 0; i--) { - newFileName = dirs[i] + "\\" + newFileName; - } + } + //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 (pos == 0) { break; //you are at the end + }else 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; //you are at the end + }else { cout << "cannot resolve path for " << fileName << endl; return fileName; } + } - return newFileName; + for (int i = index; i >= 0; i--) { + newFileName = dirs[i] + "\\" + newFileName; + } + + return newFileName; + } #endif } @@ -558,7 +577,7 @@ inline int openInputFile(string fileName, ifstream& fileHandle){ else { //check for blank file gobble(fileHandle); - if (fileHandle.eof()) { cout << completeFileName << " is blank. Please correct." << endl; return 1; } + if (fileHandle.eof()) { cout << completeFileName << " is blank. Please correct." << endl; } return 0; } @@ -613,6 +632,19 @@ inline int getNumSeqs(ifstream& file){ return numSeqs; } +/***********************************************************************/ +inline void getNumSeqs(ifstream& file, int& numSeqs){ + + string input; + numSeqs = 0; + while(!file.eof()){ + input = getline(file); + if (input.length() != 0) { + if(input[0] == '>'){ numSeqs++; } + } + } +} + /***********************************************************************/ inline bool inVector(string member, vector group){ @@ -796,7 +828,13 @@ inline bool anyLabelsToProcess(string label, set& userLabels, string err //unique is the smallest line if (label == "unique") { return false; } - else { convert(label, labelFloat); } + else { + if (convertTestFloat(label, labelFloat)) { + convert(label, labelFloat); + }else { //cant convert + return false; + } + } //go through users set and make them floats for(it = userLabels.begin(); it != userLabels.end(); ++it) { @@ -865,14 +903,16 @@ inline void appendFiles(string temp, string filename) { //open output file in append mode openOutputFileAppend(filename, output); - openInputFile(temp, input); + int ableToOpen = openInputFile(temp, input, "no error"); - while(char c = input.get()){ - if(input.eof()) { break; } - else { output << c; } + if (ableToOpen == 0) { //you opened it + while(char c = input.get()){ + if(input.eof()) { break; } + else { output << c; } + } + input.close(); } - input.close(); output.close(); } catch(exception& e) { @@ -964,7 +1004,7 @@ inline vector setFilePosFasta(string filename, int& num) { num = positions.size(); - FILE * pFile; + /*FILE * pFile; long size; //get num bytes in file @@ -974,7 +1014,19 @@ inline vector setFilePosFasta(string filename, int& num) { fseek (pFile, 0, SEEK_END); size=ftell (pFile); fclose (pFile); + }*/ + + long size = positions[(positions.size()-1)]; + ifstream in; + openInputFile(filename, in); + + in.seekg(size); + + while(char c = in.get()){ + if(in.eof()) { break; } + else { size++; } } + in.close(); positions.push_back(size);