X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothur.h;h=cf6ae69dc85fc866c34588118575222772897dcf;hb=b5a791c81d432082bf38755a08b33863f255341d;hp=5b519bb2111d27259d1969f81e41b805e4a33935;hpb=5a9f3cce3e2e053c249e3e97507ce180f0854d76;p=mothur.git diff --git a/mothur.h b/mothur.h index 5b519bb..cf6ae69 100644 --- a/mothur.h +++ b/mothur.h @@ -21,6 +21,7 @@ #include #include #include +#include //exception #include @@ -44,10 +45,22 @@ #include #include #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 #endif using namespace std; @@ -69,6 +82,9 @@ 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 { @@ -77,6 +93,22 @@ 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() {} +}; /***********************************************************************/ // snagged from http://www.parashift.com/c++-faq-lite/misc-technical-issues.html#faq-39.2 @@ -170,6 +202,15 @@ inline int openOutputFileAppend(string fileName, ofstream& fileHandle){ } /***********************************************************************/ +inline void gobble(istream& f){ + + char d; + while(isspace(d=f.get())) {;} + f.putback(d); + +} +/***********************************************************************/ + inline string getline(ifstream& fileHandle) { try { @@ -180,7 +221,7 @@ inline string getline(ifstream& fileHandle) { char c = fileHandle.get(); //are you at the end of the line - if ((c == '\n') || (c == '\r') || (c == '\f')){ break; } + if ((c == '\n') || (c == '\r') || (c == '\f')){ break; } else { line += c; } } @@ -256,23 +297,11 @@ inline void errorOut(exception& e, string object, string function) { mothurOut("Error: "); mothurOut(toString(e.what())); - mothurOut(" has occurred in the " + object + " class function " + function + ". Please contact Pat Schloss at pschloss@microbio.umass.edu, and be sure to include the mothur.logFile with your inquiry."); + 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."); mothurOutEndLine(); } - - - -/***********************************************************************/ - -inline void gobble(istream& f){ - - char d; - while(isspace(d=f.get())) {;} - f.putback(d); - -} /***********************************************************************/ inline bool isTrue(string f){ @@ -412,7 +441,21 @@ 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 int openInputFile(string fileName, ifstream& fileHandle){ @@ -423,6 +466,10 @@ inline int openInputFile(string fileName, ifstream& fileHandle){ return 1; } else { + //check for blank file + gobble(fileHandle); + if (fileHandle.eof()) { mothurOut(fileName + " is blank. Please correct."); mothurOutEndLine(); return 1; } + return 0; } @@ -452,7 +499,16 @@ 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 @@ -727,6 +783,92 @@ 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