added else if (matrix == "sim2") { }

[mothur.git] / cooccurrencecommand.cpp

diff --git a/cooccurrencecommand.cpp b/cooccurrencecommand.cpp
index 465ddced27b92345392d2752657bc1e3b7453f58..e1d60b7c18553b0d3de4df1e0dd6a87ea60b17af 100644 (file)
--- a/cooccurrencecommand.cpp
+++ b/cooccurrencecommand.cpp
@@ -317,15 +317,16 @@ int CooccurrenceCommand::getCooccurrence(vector<SharedRAbundVector*>& thisLookUp
                 }
             }
         }
-        else if (matrix == "sim2") {
-            for(int i=0;i<nrows;i++) {
-                start = 0.0;
-                for(int j=0;j<ncols;j++) {
-                    probabilityMatrix[ncols * i + j] = start + 1/double(ncols);
-                    start = start + 1/double(ncols);
-                }
-            }
-        }
+        //don't need a prob matrix because we just shuffle the rows, may use this in the future
+//        else if (matrix == "sim2") {
+//            for(int i=0;i<nrows;i++) {
+//                start = 0.0;
+//                for(int j=0;j<ncols;j++) {
+//                    probabilityMatrix[ncols * i + j] = start + 1/double(ncols);
+//                    start = start + 1/double(ncols);
+//                }
+//            }
+//        }
         
         else if (matrix == "sim3") {
             for(int j=0;j<ncols;j++) {
@@ -384,7 +385,7 @@ int CooccurrenceCommand::getCooccurrence(vector<SharedRAbundVector*>& thisLookUp
                 }
             }
         }
-        else if (matrix == "sim9") { }
+        else if (matrix == "sim9" || matrix == "sim2") { }
         else {
             m->mothurOut("[ERROR]: No model selected! \n");
             m->control_pressed = true;
@@ -404,77 +405,12 @@ int CooccurrenceCommand::getCooccurrence(vector<SharedRAbundVector*>& thisLookUp
         double current;
         double randnum;
         int count;
-        
-        //burn-in
-        for(int i=0;i<10000;i++){
-            nullmatrix.clear();
-            //zero-fill the null matrix
-            nullmatrix.assign(nrows, vector<int>(ncols, 0));
-            
-            if(matrix == "sim1" || matrix == "sim6" || matrix == "sim8" || matrix == "sim7") {
-                count = 0;
-                while(count < n) {
-                nextnum:
-                    previous = 0.0;
-                    randnum = rand() / double(RAND_MAX);
-                    for(int i=0;i<nrows;i++) {
-                        for(int j=0;j<ncols;j++) {
-                            current = probabilityMatrix[ncols * i + j];
-                            if(randnum <= current && randnum > previous) {
-                                nullmatrix[i][j] = 1;
-                                count++;
-                                if (count > n) break;
-                                else
-                                    goto nextnum;
-                            }
-                            previous = current;
-                        }
-                    }
-                }
-            }
-            
-            else if(matrix == "sim2" || matrix == "sim4") {
-                for(int i=0;i<nrows;i++) {
-                    previous = 0.0;
-                    count = 0;
-                    while(count < rowtotal[i]) {
-                        randnum = rand() / double(RAND_MAX);
-                        for(int j=0;j<ncols;j++) {
-                            current = probabilityMatrix[ncols * i + j];
-                            if(randnum <= current && randnum > previous && nullmatrix[i][j] != 1) {
-                                nullmatrix[i][j] = 1;
-                                count++;
-                                previous = 0.0;
-                                break;
-                            }
-                            previous = current;
-                        }
-                    }
-                }
-            }
-            
-            else if(matrix == "sim3" || matrix == "sim5") {
-                //columns
-                for(int j=0;j<ncols;j++) {
-                    count = 0;
-                    while(count < columntotal[j]) {
-                        randnum = rand() / double(RAND_MAX);
-                        for(int i=0;i<nrows;i++) {
-                            current = probabilityMatrix[ncols * i + j];
-                            if(randnum <= current && randnum > previous && nullmatrix[i][j] != 1) {
-                                nullmatrix[i][j] = 1;
-                                count++;
-                                previous = 0.0;
-                                break;
-                            }
-                            previous = current;
-                        }
-                    }
-                }
-            }
-            
+
+        //burn-in for sim9    
+        if(matrix == "sim9") {
+            for(int i=0;i<10000;i++) trial.swap_checkerboards (co_matrix, rowtotal, columntotal, ncols, nrows);
         }
-        
+
         //populate null matrix from probability matrix, do this a lot.
         for(int i=0;i<runs;i++){
             nullmatrix.clear();
@@ -503,7 +439,16 @@ int CooccurrenceCommand::getCooccurrence(vector<SharedRAbundVector*>& thisLookUp
                 }
             }
             
-            else if(matrix == "sim2" || matrix == "sim4") {
+            else if (matrix == "sim2") {
+                for(int i=0;i<nrows;i++) {
+                    random_shuffle( co_matrix[i].begin(), co_matrix[i].end() ); 
+                }
+                //do this for the scoring since those all have nullmatrix as a parameter
+                //nullmatrix gets cleared at the begining of each run
+                nullmatrix = co_matrix;
+            }
+            
+            else if(matrix == "sim4") {
                 for(int i=0;i<nrows;i++) {
                     previous = 0.0;
                     count = 0;