added modify names parameter to set.dir

[mothur.git] / libshuff.cpp

diff --git a/libshuff.cpp b/libshuff.cpp
index e6c83f7a42b20cb674675fd6608f9da5dd9f7fa6..5f1bdefe6ea95e36c6b30800a690af2ceecb1fbb 100644 (file)
--- a/libshuff.cpp
+++ b/libshuff.cpp
@@ -17,13 +17,14 @@ void swap(int& i,int& j){   int t = i;  i = j;  j = t;      }
 
 Libshuff::Libshuff(FullMatrix* D, int it, float step, float co) : matrix(D), iters(it), stepSize(step), cutOff(co){
        try{
+               m = MothurOut::getInstance();
                groupNames = matrix->getGroups();
                groupSizes = matrix->getSizes();
                numGroups = matrix->getNumGroups();
                initializeGroups(matrix);
        }
        catch(exception& e) {
-               errorOut(e, "Libshuff", "Libshuff");
+               m->errorOut(e, "Libshuff", "Libshuff");
                exit(1);
        }
 }
@@ -49,7 +50,7 @@ void Libshuff::initializeGroups(FullMatrix* matrix){
                }
        }
        catch(exception& e) {
-               errorOut(e, "Libshuff", "initializeGroups");
+               m->errorOut(e, "Libshuff", "initializeGroups");
                exit(1);
        }
 }
@@ -64,7 +65,6 @@ vector<vector<vector<double> > > Libshuff::getSavedMins(){
 
 vector<double> Libshuff::getMinX(int x){
        try{
-
                vector<double> minX(groupSizes[x], 0);
                for(int i=0;i<groupSizes[x];i++){
                        minX[i] = (groupSizes[x] > 1 ? (i==0 ? matrix->get(groups[x][0], groups[x][1]) : matrix->get(groups[x][i], groups[x][0])) : 0.0); //get the first value in row i of this block
@@ -79,7 +79,7 @@ vector<double> Libshuff::getMinX(int x){
                return minX;
        }
        catch(exception& e) {
-               errorOut(e, "Libshuff", "getMinX");
+               m->errorOut(e, "Libshuff", "getMinX");
                exit(1);
        }
 }
@@ -100,7 +100,7 @@ vector<double> Libshuff::getMinXY(int x, int y){
                return minXY;
        }
        catch(exception& e) {
-               errorOut(e, "Libshuff", "getMinXY");
+               m->errorOut(e, "Libshuff", "getMinXY");
                exit(1);
        }
 }
@@ -126,7 +126,7 @@ void Libshuff::randomizeGroups(int x, int y){
                for(int k=0;k<groupSizes[y];k++)        {       groups[y][k]=v[index++];        }
        }
        catch(exception& e) {
-               errorOut(e, "Libshuff", "randomizeGroups");
+               m->errorOut(e, "Libshuff", "randomizeGroups");
                exit(1);
        }
 }