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

[mothur.git] / fullmatrix.cpp

diff --git a/fullmatrix.cpp b/fullmatrix.cpp
index 090e2fee84b1ee6fcc85382eb6de047fdd43cc22..6151a65202901fa24ec6ff91166017a682483c62 100644 (file)
--- a/fullmatrix.cpp
+++ b/fullmatrix.cpp
@@ -255,7 +255,6 @@ 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());
@@ -263,28 +262,28 @@ void FullMatrix::getMinsForRowsVectors(){
                /*************************************************/
                //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.
+               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[numGroups] = numSeqs;
+               bounds[0] = 0;
+               bounds[numGroups] = numSeqs-1;
                //for each group find bounds of subgroup/comparison
-               for (int i = 0; i < numGroups; i++) {
+               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[0]; //where second group starts
-               int county = bounds[0]; 
+               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)) {
-                                       if (inUsersGroups(index[x].groupname, globaldata->Groups)) {
-                                       }
+                                       
                                }
                        }
                }