libshuff and updated help to include libshuff and modifications to read.dist.

[mothur.git] / fullmatrix.cpp

diff --git a/fullmatrix.cpp b/fullmatrix.cpp
index 6c09639fcbb4c48497ba2b17a61851ba2435c6af..8eb48139a85c910e74881c15a050b8064c39dfbd 100644 (file)
--- a/fullmatrix.cpp
+++ b/fullmatrix.cpp
@@ -233,7 +233,7 @@ void FullMatrix::printMatrix(ostream& out) {
                for (int i = 0; i < numSeqs; i++) {
                        out << "row " << i << " group = " << index[i].groupname << " name = " << index[i].seqName << endl;
                        for (int j = 0; j < numSeqs; j++) {
-                               //out << matrix[i][j] << " ";
+                               out << matrix[i][j] << " ";
                        }
                        out << endl;
                }
@@ -393,49 +393,27 @@ void FullMatrix::printMinsForRows(ostream& out) {
        }
 
 }
+
 /**************************************************************************/
 //shuffles the sequences in the 2 groups passed in.
-void FullMatrix::shuffle(int box){
+void FullMatrix::shuffle(string groupA, string groupB){
        try{
                vector<int> rows2Swap;
                vector<int> shuffled;
                float y = 0;
                string name = "";
                
-               /****************************/
-               //find the box the user wants
-               /****************************/
-               int count = 0;
-               int lowBoundy = bounds[0]; //where first group starts
-               int highBoundy = bounds[1]; //where second group starts
-               int county = 1; //index in bound
-               
-               //find the bounds for the box the user wants
-               for (int i = 0; i < (numGroups * numGroups); i++) {
-               
-                       //are you at the box?
-                       if (count == box) { break; }
-                       else { count++; }
                        
-                       //move to next box
-                       if (county < numGroups) {
-                               county++;
-                               highBoundy = bounds[county];
-                               lowBoundy = bounds[county-1];
-                       }else{ //you are moving to a new row of "boxes"
-                               county = 1;
-                               highBoundy = bounds[county];
-                               lowBoundy = bounds[county-1];
-                       }
-               }
-       
-               /************************/
-               //save its rows locations
-               /************************/
+               /********************************/
+               //save rows you want to randomize
+               /********************************/
                //go through the matrix map to find the rows from groups you want to randomize
-               for (int y = lowBoundy; y < highBoundy; y++) {
-                       rows2Swap.push_back(y);
-                       shuffled.push_back(y);
+               for (it = index.begin(); it != index.end(); it++) {
+                       //is this row from group A or B?
+                       if ((it->second.groupname == groupA) || (it->second.groupname == groupB)) {
+                               rows2Swap.push_back(it->first);
+                               shuffled.push_back(it->first);
+                       }
                }
                
                //randomize rows to shuffle in shuffled
@@ -445,6 +423,7 @@ void FullMatrix::shuffle(int box){
                //swap rows and columns to randomize box
                /***************************************/
                for (int i = 0; i < shuffled.size(); i++) {
+
                        //record the swaps you are making so you can undo them in restore function
                        restoreIndex[i].a = shuffled[i];
                        restoreIndex[i].b = rows2Swap[i];
@@ -467,6 +446,7 @@ void FullMatrix::shuffle(int box){
                        name = index[shuffled[i]].seqName;
                        index[shuffled[i]].seqName = index[rows2Swap[i]].seqName;
                        index[rows2Swap[i]].seqName = name;
+
                }
        }
        catch(exception& e) {
@@ -488,6 +468,7 @@ void FullMatrix::restore(){
                //reverse iterate through swaps and undo them to restore original matrix and index map.
                for(it2 = restoreIndex.rbegin(); it2 != restoreIndex.rend(); it2++) {
                        /* swap rows */
+
                        for (int h = 0; h < numSeqs; h++) {
                                y = matrix[it2->second.a][h];
                                matrix[it2->second.a][h] = matrix[it2->second.b][h]; 
@@ -506,6 +487,7 @@ void FullMatrix::restore(){
                        name = index[it2->second.a].seqName;
                        index[it2->second.a].seqName = index[it2->second.b].seqName;
                        index[it2->second.b].seqName = name;
+
                }
 
                //clear restore for next shuffle