X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=formatcolumn.cpp;h=109c09ccb7c99af1f82e976078509a9239ce326b;hp=d43f85d16907d92583ba95069002661253569a6c;hb=a8e2df1b96a57f5f29576b08361b86a96a8eff4f;hpb=19fcbbdba99658f5eca244803280f9ee7f9f6607

diff --git a/formatcolumn.cpp b/formatcolumn.cpp
index d43f85d..109c09c 100644
--- a/formatcolumn.cpp
+++ b/formatcolumn.cpp
@@ -82,7 +82,7 @@ int FormatColumnMatrix::read(NameAssignment* nameMap){
 		string outfile = m->getRootName(squareFile) + "sorted.dist.temp";
 		
 		//use the unix sort 
-		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 			string command = "sort -n " + squareFile + " -o " + outfile;
 			system(command.c_str());
 		#else //sort using windows sort
@@ -179,6 +179,169 @@ int FormatColumnMatrix::read(NameAssignment* nameMap){
 		exit(1);
 	}
 }
+/***********************************************************************/
+
+int FormatColumnMatrix::read(CountTable* nameMap){
+	try {		
+        
+		string firstName, secondName;
+		float distance;
+		int nseqs = nameMap->size();
+        
+		list = new ListVector(nameMap->getListVector());
+        
+		Progress* reading = new Progress("Formatting matrix:     ", nseqs * nseqs);
+        
+		int lt = 1;
+		int refRow = 0;	//we'll keep track of one cell - Cell(refRow,refCol) - and see if it's transpose
+		int refCol = 0; //shows up later - Cell(refCol,refRow).  If it does, then its a square matrix
+        
+		//need to see if this is a square or a triangular matrix...
+		
+		ofstream out;
+		string tempOutFile = filename + ".temp";
+		m->openOutputFile(tempOutFile, out);
+        
+		while(fileHandle && lt == 1){  //let's assume it's a triangular matrix...
+            
+			if (m->control_pressed) { out.close();  m->mothurRemove(tempOutFile); fileHandle.close();  delete reading; return 0; }
+            
+			fileHandle >> firstName >> secondName >> distance;	// get the row and column names and distance
+            
+			int itA = nameMap->get(firstName);
+			int itB = nameMap->get(secondName);
+            
+			if (distance == -1) { distance = 1000000; }
+            
+			if((distance < cutoff) && (itA != itB)){
+				if(refRow == refCol){		// in other words, if we haven't loaded refRow and refCol...
+					refRow = itA;
+					refCol = itB;
+					
+					//making it square
+					out << itA << '\t' << itB << '\t' << distance << endl;
+					out << itB << '\t' << itA << '\t' << distance << endl;
+				}
+				else if(refRow == itA && refCol == itB){	lt = 0;		} //you are square
+				else if(refRow == itB && refCol == itA){	lt = 0;		}  //you are square
+				else{	//making it square
+					out << itA << '\t' << itB << '\t' << distance << endl;
+					out << itB << '\t' << itA << '\t' << distance << endl;
+				}
+				
+				reading->update(itA * nseqs / 2);
+			}
+			m->gobble(fileHandle);
+		}
+		out.close();
+		fileHandle.close();
+        
+		string squareFile;
+		if(lt == 0){  // oops, it was square
+			squareFile = filename;
+		}else{ squareFile = tempOutFile; }
+		
+		//sort file by first column so the distances for each row are together
+		string outfile = m->getRootName(squareFile) + "sorted.dist.temp";
+		
+		//use the unix sort 
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+        string command = "sort -n " + squareFile + " -o " + outfile;
+        system(command.c_str());
+#else //sort using windows sort
+        string command = "sort " + squareFile + " /O " + outfile;
+        system(command.c_str());
+#endif
+		
+		if (m->control_pressed) { m->mothurRemove(tempOutFile); m->mothurRemove(outfile); delete reading; return 0; }
+        
+		//output to new file distance for each row and save positions in file where new row begins
+		ifstream in;
+		m->openInputFile(outfile, in);
+		
+		distFile = outfile + ".rowFormatted";
+		m->openOutputFile(distFile, out);
+		
+		rowPos.resize(nseqs, -1);
+		int currentRow;
+		int first, second;
+		float dist;
+		map<int, float> rowMap;
+		map<int, float>::iterator itRow;
+		
+		//get first currentRow
+		in >> first;
+		currentRow = first;
+		
+		string firstString = toString(first);
+		for(int k = 0; k < firstString.length(); k++)  {   in.putback(firstString[k]);  }
+		
+		while(!in.eof()) {
+			
+			if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(distFile); m->mothurRemove(tempOutFile); m->mothurRemove(outfile); delete reading; return 0; }
+			
+			in >> first >> second >> dist; m->gobble(in);
+			
+			if (first != currentRow) {
+				//save position in file of each new row
+				rowPos[currentRow] = out.tellp();
+				
+				out << currentRow << '\t' << rowMap.size() << '\t';
+				
+				for (itRow = rowMap.begin(); itRow != rowMap.end(); itRow++) {
+					out << itRow->first << '\t' << itRow->second << '\t';
+				}
+				out << endl;
+				
+				currentRow = first;
+				rowMap.clear();
+				
+				//save row you just read
+				if (dist < cutoff) {
+					rowMap[second] = dist;
+				}
+			}else{
+				if (dist < cutoff) {
+					rowMap[second] = dist;
+				}
+			}
+		}
+		
+		//print last Row
+		//save position in file of each new row
+		rowPos[currentRow] = out.tellp();
+		
+		out << currentRow << '\t' << rowMap.size() << '\t';
+		
+		for (itRow = rowMap.begin(); itRow != rowMap.end(); itRow++) {
+			out << itRow->first << '\t' << itRow->second << '\t';
+		}
+		out << endl;
+		
+		
+		in.close();
+		out.close();
+		
+		if (m->control_pressed) {  m->mothurRemove(distFile); m->mothurRemove(tempOutFile); m->mothurRemove(outfile);  delete reading; return 0; }
+		
+		m->mothurRemove(tempOutFile);
+		m->mothurRemove(outfile);
+		
+		reading->finish();
+		
+		delete reading;
+		list->setLabel("0");
+		
+		if (m->control_pressed) {  m->mothurRemove(distFile);  return 0; }
+        
+		return 1;
+        
+	}
+	catch(exception& e) {
+		m->errorOut(e, "FormatColumnMatrix", "read");
+		exit(1);
+	}
+}
 
 /***********************************************************************/
 FormatColumnMatrix::~FormatColumnMatrix(){}