X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=fullmatrix.cpp;fp=fullmatrix.cpp;h=090e2fee84b1ee6fcc85382eb6de047fdd43cc22;hb=42b802c0006d8b13bd5b27ea48d032a85d3f2102;hp=66c67b7da0999281af64e9836c9a0f94aff3a698;hpb=310c5a316ea91da78ad8ead12802f3c02ba5704d;p=mothur.git

diff --git a/fullmatrix.cpp b/fullmatrix.cpp
index 66c67b7..090e2fe 100644
--- a/fullmatrix.cpp
+++ b/fullmatrix.cpp
@@ -16,7 +16,6 @@ FullMatrix::FullMatrix(ifstream& filehandle) {
 		globaldata = GlobalData::getInstance();
 		groupmap = globaldata->gGroupmap;
 		
-		float minSoFar = 0.0;
 		string name, group;
 		filehandle >> numSeqs >> name;
 		
@@ -41,17 +40,9 @@ FullMatrix::FullMatrix(ifstream& filehandle) {
 				square = true;
 				filehandle.putback(d);
 				
-				if (numSeqs >= 2) {
-					//save first distance that is not distance to itself as minimum
-					filehandle >> matrix[0][0] >> minSoFar;
-					matrix[0][1] = minSoFar;
-				}
-				
-				for(int i=2;i<numSeqs;i++){
+				for(int i=0;i<numSeqs;i++){
 					filehandle >> matrix[0][i];
-					if (matrix[0][i] < minSoFar) { minSoFar = matrix[0][i]; }
 				}
-				index[0].minDist = minSoFar;
 				break;
 			}
 			
@@ -87,8 +78,8 @@ void FullMatrix::readSquareMatrix(ifstream& filehandle) {
 		reading = new Progress("Reading matrix:    ", numSeqs * numSeqs);
 		
 		int count = 0;
-		float distance, minSoFar;
-		minSoFar = 0.0;
+		float distance;
+		
 		string group, name;
 		
 		for(int i=1;i<numSeqs;i++){
@@ -98,23 +89,15 @@ void FullMatrix::readSquareMatrix(ifstream& filehandle) {
 			index[i].groupname = group;
 			index[i].seqName = name;
 			
-			filehandle >> minSoFar;
-			matrix[i][0] = minSoFar;
-			
 			if(group == "not found") {	cout << "Error: Sequence '" << name << "' was not found in the group file, please correct." << endl; exit(1); }
 				
-			for(int j=1;j<numSeqs;j++){
+			for(int j=0;j<numSeqs;j++){
 				filehandle >> distance;
-				
-				if ((distance < minSoFar) && (i != j)) { minSoFar = distance; }
 					
 				matrix[i][j] = distance;
 				count++;
 				reading->update(count);
 			}
-			
-			//save minimum value for each row
-			index[i].minDist = minSoFar;
 		}
 		reading->finish();
 		delete reading;
@@ -136,8 +119,7 @@ void FullMatrix::readLTMatrix(ifstream& filehandle) {
 		reading = new Progress("Reading matrix:    ", numSeqs * (numSeqs - 1) / 2);
 		
 		int count = 0;
-		float distance, minSoFar;
-		minSoFar = 0.0;
+		float distance;
 
 		string group, name;
 		
@@ -147,24 +129,17 @@ void FullMatrix::readLTMatrix(ifstream& filehandle) {
 			group = groupmap->getGroup(name);
 			index[i].groupname = group;
 			index[i].seqName = name;
-			
-			filehandle >> minSoFar;
-			matrix[i][0] = minSoFar;
 	
 			if(group == "not found") {	cout << "Error: Sequence '" << name << "' was not found in the group file, please correct." << endl;  exit(1); }
 				
-			for(int j=1;j<i;j++){
+			for(int j=0;j<i;j++){
 				filehandle >> distance;
-				
-				if (distance < minSoFar)  { minSoFar = distance; }
 					
 				matrix[i][j] = distance;  matrix[j][i] = distance;
 				count++;
 				reading->update(count);
 			}
 			
-			//save minimum value for each row
-			index[i].minDist = minSoFar;
 		}
 		reading->finish();
 		delete reading;
@@ -275,5 +250,81 @@ void FullMatrix::printMatrix(ostream& out) {
 	}
 
 }
+
 /**************************************************************************/
+void FullMatrix::getMinsForRowsVectors(){
+	try{
+		numGroups = globaldata->gGroupmap->namesOfGroups.size();
+		numUserGroups = globaldata->Groups.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[0] = 0, bounds[1] = starting row in matrix from group B, bounds[2] = starting row in matrix from group C, bounds[3] = no need to find C because its numSeqs.
+		bounds.resize(numGroups);
+		
+		bounds[numGroups] = numSeqs;
+		//for each group find bounds of subgroup/comparison
+		for (int i = 0; i < numGroups; i++) {
+			getBounds(bounds[i], globaldata->gGroupmap->namesOfGroups[i]);
+		}
+		
+		/************************************************************/
+		//fill the minsForRows vectors for each group the user wants
+		/************************************************************/
+		int countx = bounds[0]; //where second group starts
+		int county = bounds[0]; 
+		
+		//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)) {
+					if (inUsersGroups(index[x].groupname, globaldata->Groups)) {
+					}
+				}
+			}
+		}
+					
+				
+			
+	
+	}
+	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);
+	}
+
+}