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
}
}
+/**************************************************************************************************/
+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