added nseqs and sharednseqs calculators, removed excess tabs in output files.

[mothur.git] / fullmatrix.cpp

diff --git a/fullmatrix.cpp b/fullmatrix.cpp
index 6ea2318d740003f8cf46ec7e63815c175e1893ca..6151a65202901fa24ec6ff91166017a682483c62 100644 (file)
--- 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];
                                }
@@ -78,6 +79,7 @@ void FullMatrix::readSquareMatrix(ifstream& filehandle) {
                
                int count = 0;
                float distance;
+               
                string group, name;
                
                for(int i=1;i<numSeqs;i++){
@@ -118,6 +120,7 @@ void FullMatrix::readLTMatrix(ifstream& filehandle) {
                
                int count = 0;
                float distance;
+
                string group, name;
                
                for(int i=1;i<numSeqs;i++){
@@ -136,6 +139,7 @@ void FullMatrix::readLTMatrix(ifstream& filehandle) {
                                count++;
                                reading->update(count);
                        }
+                       
                }
                reading->finish();
                delete reading;
@@ -246,5 +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);
+       }
+
+}