X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=fullmatrix.cpp;h=6151a65202901fa24ec6ff91166017a682483c62;hb=9ca2caadbeac83bb84b3330d9204b1b659d62941;hp=64d7b6af2dbe39279164fbe299c86a617af278e7;hpb=3659285c05daa94306a7b61dd97ec945b23d472b;p=mothur.git

diff --git a/fullmatrix.cpp b/fullmatrix.cpp
index 64d7b6a..6151a65 100644
--- a/fullmatrix.cpp
+++ b/fullmatrix.cpp
@@ -39,6 +39,7 @@ FullMatrix::FullMatrix(ifstream& filehandle) {
 			if(isalnum(d)){ 
 				square = true;
 				filehandle.putback(d);
+				
 				for(int i=0;i<numSeqs;i++){
 					filehandle >> matrix[0][i];
 				}
@@ -56,14 +57,9 @@ FullMatrix::FullMatrix(ifstream& filehandle) {
 		if (square == true) { readSquareMatrix(filehandle); }
 		else { readLTMatrix(filehandle); }
 		
-		
-		
-	printMatrix(cout);
 		//sort sequences so they are gathered in groups for processing
 		sortGroups(0, numSeqs-1);
-		cout << "after sort" << endl;
-	printMatrix(cout);
-		
+			
 	}
 	catch(exception& e) {
 		cout << "Standard Error: " << e.what() << " has occurred in the FullMatrix class Function FullMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
@@ -83,6 +79,7 @@ void FullMatrix::readSquareMatrix(ifstream& filehandle) {
 		
 		int count = 0;
 		float distance;
+		
 		string group, name;
 		
 		for(int i=1;i<numSeqs;i++){
@@ -123,6 +120,7 @@ void FullMatrix::readLTMatrix(ifstream& filehandle) {
 		
 		int count = 0;
 		float distance;
+
 		string group, name;
 		
 		for(int i=1;i<numSeqs;i++){
@@ -141,6 +139,7 @@ void FullMatrix::readLTMatrix(ifstream& filehandle) {
 				count++;
 				reading->update(count);
 			}
+			
 		}
 		reading->finish();
 		delete reading;
@@ -204,8 +203,6 @@ void FullMatrix::sortGroups(int low, int high){
 				
 				i++; 
 				j--;
-cout << "swapping rows " << i << " " << j << endl;
-printMatrix(cout); cout << endl;
 			}
 		} while(i <= j);
 
@@ -253,5 +250,80 @@ void FullMatrix::printMatrix(ostream& out) {
 	}
 
 }
+
+/**************************************************************************/
+void FullMatrix::getMinsForRowsVectors(){
+	try{
+		numGroups = globaldata->gGroupmap->namesOfGroups.size();
+		
+		//sort globaldata->gGroupmap.namesOfGroups so that it will match the matrix
+		sort(globaldata->gGroupmap->namesOfGroups.begin(), globaldata->gGroupmap->namesOfGroups.end());
+		
+		/*************************************************/
+		//find where in matrix each group starts and stops
+		/*************************************************/
+		vector<int> bounds;  //bounds[1] = starting row in matrix from group B, bounds[2] = starting row in matrix from group C, bounds[3] = no need to find upper bound of C because its numSeqs.
+		bounds.resize(numGroups);
+		
+		bounds[0] = 0;
+		bounds[numGroups] = numSeqs-1;
+		//for each group find bounds of subgroup/comparison
+		for (int i = 1; i < numGroups; i++) {
+			getBounds(bounds[i], globaldata->gGroupmap->namesOfGroups[i]);
+		}
+		
+		/************************************************************/
+		//fill the minsForRows vectors for each group the user wants
+		/************************************************************/
+		int countx = bounds[1]; //where second group starts
+		int county = bounds[1]; 
+		
+		//go through the entire matrix
+		for (int x = 0; x < numSeqs; x++) {
+			for (int y = 0; y < numSeqs; y++) {
+				//if have not changed groups
+				if ((x < countx) && (y < county)) {
+					
+				}
+			}
+		}
+					
+				
+			
+	
+	}
+	catch(exception& e) {
+		cout << "Standard Error: " << e.what() << " has occurred in the FullMatrix class Function getMinsForRowsVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the FullMatrix class function getMinsForRowsVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+
+}
+
 /**************************************************************************/
+void FullMatrix::getBounds(int& higher, string group) {
+	try{
+		bool gotLower = false;
+		
+		//for each group find bounds of subgroup/comparison
+		for (it = index.begin(); it != index.end(); it++) {
+			if (it->second.groupname == group) {
+				if (gotLower != true) { gotLower = true; }
+			}else if ((gotLower == true) && (it->second.groupname != group)) {  higher = it->first; break; }
+		}
+	
+	}
+	catch(exception& e) {
+		cout << "Standard Error: " << e.what() << " has occurred in the FullMatrix class Function getBounds. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the FullMatrix class function getBounds. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+
+}