working on libshuff

[mothur.git] / fullmatrix.cpp

diff --git a/fullmatrix.cpp b/fullmatrix.cpp
index 66c67b7da0999281af64e9836c9a0f94aff3a698..090e2fee84b1ee6fcc85382eb6de047fdd43cc22 100644 (file)
--- 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);
+       }
+
+}