moved mothur's source into a folder to make grabbing just the source easier on github

[mothur.git] / libshuff.cpp

diff --git a/libshuff.cpp b/libshuff.cpp
deleted file mode 100644 (file)
index 5f1bdef..0000000
--- a/libshuff.cpp
+++ /dev/null
@@ -1,142 +0,0 @@
-/*
- *  libshuffform.cpp
- *  Mothur
- *
- *  Created by Pat Schloss on 4/8/09.
- *  Copyright 2009 Patrick D. Schloss. All rights reserved.
- *
- */
-
-#include "libshuff.h"
-
-/***********************************************************************/
-
-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) {
-               m->errorOut(e, "Libshuff", "Libshuff");
-               exit(1);
-       }
-}
-
-/***********************************************************************/
-
-void Libshuff::initializeGroups(FullMatrix* matrix){
-       try{
-               groups.resize(numGroups);
-               savedGroups.resize(numGroups);
-               
-               savedGroups.resize(numGroups);
-               for(int i=0;i<numGroups;i++) {
-                       groups[i].resize(groupSizes[i]);
-                       savedGroups[i].resize(groupSizes[i]);
-               }
-               int index=0;
-               for(int i=0;i<numGroups;i++){
-
-                       for(int j=0;j<groupSizes[i];j++){
-                               savedGroups[i][j] = groups[i][j] = index++;
-                       }
-               }
-       }
-       catch(exception& e) {
-               m->errorOut(e, "Libshuff", "initializeGroups");
-               exit(1);
-       }
-}
-
-/***********************************************************************/
-
-vector<vector<vector<double> > > Libshuff::getSavedMins(){
-       return savedMins;
-}
-
-/***********************************************************************/
-
-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
-                       //minX[i] = matrix->get(groups[x][i], groups[x][0]);
-                       for(int j=0;j<groupSizes[x];j++){
-                               if(i != j)      {
-                                       double dx = matrix->get(groups[x][i], groups[x][j]);
-                                       if(dx < minX[i]){       minX[i] = dx;   }
-                               }
-                       }
-               }
-               return minX;
-       }
-       catch(exception& e) {
-               m->errorOut(e, "Libshuff", "getMinX");
-               exit(1);
-       }
-}
-
-/***********************************************************************/
-
-vector<double> Libshuff::getMinXY(int x, int y){
-       try{
-               vector<double> minXY(groupSizes[x], 0);
-
-               for(int i=0;i<groupSizes[x];i++){
-                       minXY[i] = matrix->get(groups[x][i], groups[y][0]);
-                       for(int j=0;j<groupSizes[y];j++){
-                               double dxy = matrix->get(groups[x][i], groups[y][j]);
-                               if(dxy<minXY[i]){       minXY[i] = dxy; }
-                       }
-               }
-               return minXY;
-       }
-       catch(exception& e) {
-               m->errorOut(e, "Libshuff", "getMinXY");
-               exit(1);
-       }
-}
-
-/***********************************************************************/
-
-void Libshuff::randomizeGroups(int x, int y){
-       try{
-               int nv = groupSizes[x]+groupSizes[y];
-               vector<int> v(nv);
-               
-               int index=0;
-               for(int k=0;k<groupSizes[x];k++)        {       v[index++] = groups[x][k];      }
-               for(int k=0;k<groupSizes[y];k++)        {       v[index++] = groups[y][k];      }
-               
-               for(int k=nv-1;k>0;k--){
-                       int z = (int)(rand() % k);
-                       swap(v[z],v[k]);
-               }
-               
-               index=0;
-               for(int k=0;k<groupSizes[x];k++)        {       groups[x][k]=v[index++];        }
-               for(int k=0;k<groupSizes[y];k++)        {       groups[y][k]=v[index++];        }
-       }
-       catch(exception& e) {
-               m->errorOut(e, "Libshuff", "randomizeGroups");
-               exit(1);
-       }
-}
-
-/***********************************************************************/
-
-void Libshuff::resetGroup(int x){
-       
-       for(int k=0;k<groupSizes[x];k++)        {       groups[x][k] = savedGroups[x][k];       }
-       
-}
-
-/***********************************************************************/