#include <iomanip>
#include <fstream>
#include <sstream>
+#include <signal.h>
//exception
#include <stdexcept>
#include <ctime>
#include <limits>
-using namespace std;
+/***********************************************************************/
-#ifdef _WIN32
- #define exp(x) (exp((double) x))
- #define sqrt(x) (sqrt((double) x))
- #define log10(x) (log10((double) x))
- #define log2(x) (log10(x)/log10(2))
- #define isnan(x) ((x) != (x))
- #define isinf(x) (fabs(x) == std::numeric_limits<double>::infinity())
-#else
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
#include <sys/wait.h>
#include <unistd.h>
+
+ #ifdef USE_READLINE
+ #include <readline/readline.h>
+ #include <readline/history.h>
+ #endif
+
+ //#include <readline/readline.h>
+ //#include <readline/history.h>
+#else
+ #include <conio.h> //allows unbuffered screen capture from stdin
#endif
+using namespace std;
+
+#define exp(x) (exp((double) x))
+#define sqrt(x) (sqrt((double) x))
+#define log10(x) (log10((double) x))
+#define log2(x) (log10(x)/log10(2))
+#define isnan(x) ((x) != (x))
+#define isinf(x) (fabs(x) == std::numeric_limits<double>::infinity())
+
-typedef unsigned long long ull;
+typedef unsigned long ull;
struct IntNode {
int lvalue;
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 {
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
if (!(i >> x) || (failIfLeftoverChars && i.get(c)))
throw BadConversion(s);
}
+
//**********************************************************************************************************************
template<typename T>
return output.str();
}
-
/***********************************************************************/
inline int openOutputFileAppend(string fileName, ofstream& fileHandle){
fileHandle.open(fileName.c_str(), ios::app);
if(!fileHandle) {
- cerr << "Error: Could not open " << fileName << endl;
+ cout << "Error: Could not open " << fileName << endl;
return 1;
}
else {
}
}
+/***********************************************************************/
+
+inline void gobble(istream& f){
+
+ char d;
+ while(isspace(d=f.get())) {;}
+ f.putback(d);
+
+}
+/***********************************************************************/
+inline string getline(ifstream& fileHandle) {
+ try {
+
+ string line = "";
+
+ while (!fileHandle.eof()) {
+ //get next character
+ char c = fileHandle.get();
+
+ //are you at the end of the line
+ if ((c == '\n') || (c == '\r') || (c == '\f')){ break; }
+ else { line += c; }
+ }
+
+ return line;
+
+ }
+ catch(exception& e) {
+ cout << "Error in mothur function getline" << endl;
+ exit(1);
+ }
+}
/**************************************************************************************************/
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){
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){
fileHandle.open(fileName.c_str());
if(!fileHandle) {
- cerr << "Error: Could not open " << fileName << endl;
+ mothurOut("Error: Could not open " + fileName); mothurOutEndLine();
return 1;
}
else {
+ //check for blank file
+ gobble(fileHandle);
+ if (fileHandle.eof()) { mothurOut(fileName + " is blank. Please correct."); mothurOutEndLine(); return 1; }
+
return 0;
}
fileHandle.open(fileName.c_str(), ios::trunc);
if(!fileHandle) {
- cerr << "Error: Could not open " << fileName << endl;
+ mothurOut("Error: Could not open " + fileName); mothurOutEndLine();
return 1;
}
else {
return numSeqs;
}
+/***********************************************************************/
+inline bool inVector(string member, vector<string> 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
}
}
+/**************************************************************************************************/
+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
projects / mothur.git / blobdiff