added concensus command and updated calcs

[mothur.git] / bootstrapsharedcommand.cpp

diff --git a/bootstrapsharedcommand.cpp b/bootstrapsharedcommand.cpp
index 56611a8f1e5af0eea6b64eef76e3ec1588b7298f..e88972cc19aae9c2e21efa665177925c3e86cf46 100644 (file)
--- a/bootstrapsharedcommand.cpp
+++ b/bootstrapsharedcommand.cpp
@@ -17,6 +17,7 @@
 #include "sharedthetayc.h"
 #include "sharedthetan.h"
 #include "sharedmorisitahorn.h"
+#include "sharedbraycurtis.h"
 
 
 //**********************************************************************************************************************
@@ -35,7 +36,7 @@ BootSharedCommand::BootSharedCommand(){
                        if (validCalculator->isValidCalculator("boot", globaldata->Estimators[i]) == true) { 
                                if (globaldata->Estimators[i] == "jabund") {    
                                        treeCalculators.push_back(new JAbund());
-                               }else if (globaldata->Estimators[i] == "sorensonabund") { 
+                               }else if (globaldata->Estimators[i] == "sorabund") { 
                                        treeCalculators.push_back(new SorAbund());
                                }else if (globaldata->Estimators[i] == "jclass") { 
                                        treeCalculators.push_back(new Jclass());
@@ -51,6 +52,8 @@ BootSharedCommand::BootSharedCommand(){
                                        treeCalculators.push_back(new ThetaN());
                                }else if (globaldata->Estimators[i] == "morisitahorn") { 
                                        treeCalculators.push_back(new MorHorn());
+                               }else if (globaldata->Estimators[i] == "braycurtis") { 
+                                       treeCalculators.push_back(new BrayCurtis());
                                }
                        }
                }
@@ -88,6 +91,7 @@ int BootSharedCommand::execute(){
        try {
                int count = 1;  
                EstOutput data;
+               vector<SharedRAbundVector*> subset;
        
                //if the users entered no valid calculators don't execute command
                if (treeCalculators.size() == 0) { return 0; }
@@ -160,15 +164,19 @@ int BootSharedCommand::execute(){
                                                for (int k = 0; k < lookup.size(); k++) { // pass cdd each set of groups to commpare
                                                        for (int l = k; l < lookup.size(); l++) {
                                                                if (k != l) { //we dont need to similiarity of a groups to itself
+                                                                       subset.clear(); //clear out old pair of sharedrabunds
+                                                                       //add new pair of sharedrabunds
+                                                                       subset.push_back(lookup[k]); subset.push_back(lookup[l]); 
+                                                                       
                                                                        //get estimated similarity between 2 groups
-                                                                       data = treeCalculators[i]->getValues(lookup[k], lookup[l]); //saves the calculator outputs
+                                                                       data = treeCalculators[i]->getValues(subset); //saves the calculator outputs
                                                                        //save values in similarity matrix
                                                                        simMatrix[k][l] = data[0];
                                                                        simMatrix[l][k] = data[0];
                                                                }
                                                        }
                                                }
-                                       
+                               
                                                //creates tree from similarity matrix and write out file
                                                createTree(out[i]);
                                        }
@@ -216,8 +224,8 @@ void BootSharedCommand::createTree(ostream* out){
                //do merges and create tree structure by setting parents and children
                //there are numGroups - 1 merges to do
                for (int i = 0; i < (numGroups - 1); i++) {
-                       
-                       float largest = 0.0;
+               
+                       float largest = -1.0;
                        int row, column;
                        //find largest value in sims matrix by searching lower triangle
                        for (int j = 1; j < simMatrix.size(); j++) {
@@ -229,7 +237,7 @@ void BootSharedCommand::createTree(ostream* out){
                        //set non-leaf node info and update leaves to know their parents
                        //non-leaf
                        t->tree[numGroups + i].setChildren(index[row], index[column]);
-                       
+               
                        //parents
                        t->tree[index[row]].setParent(numGroups + i);
                        t->tree[index[column]].setParent(numGroups + i);
@@ -240,36 +248,36 @@ void BootSharedCommand::createTree(ostream* out){
                        //branchlengths
                        t->tree[index[row]].setBranchLength(blength - t->tree[index[row]].getLengthToLeaves());
                        t->tree[index[column]].setBranchLength(blength - t->tree[index[column]].getLengthToLeaves());
-                       
+               
                        //set your length to leaves to your childs length plus branchlength
                        t->tree[numGroups + i].setLengthToLeaves(t->tree[index[row]].getLengthToLeaves() + t->tree[index[row]].getBranchLength());
                        
-                       
+               
                        //update index 
                        index[row] = numGroups+i;
                        index[column] = numGroups+i;
                        
                        //zero out highest value that caused the merge.
-                       simMatrix[row][column] = 0.0;
-                       simMatrix[column][row] = 0.0;
-                       
+                       simMatrix[row][column] = -1.0;
+                       simMatrix[column][row] = -1.0;
+               
                        //merge values in simsMatrix
                        for (int n = 0; n < simMatrix.size(); n++)      {
                                //row becomes merge of 2 groups
                                simMatrix[row][n] = (simMatrix[row][n] + simMatrix[column][n]) / 2;
                                simMatrix[n][row] = simMatrix[row][n];
                                //delete column
-                               simMatrix[column][n] = 0.0;
-                               simMatrix[n][column] = 0.0;
+                               simMatrix[column][n] = -1.0;
+                               simMatrix[n][column] = -1.0;
                        }
                }
-       
+
                //assemble tree
                t->assembleTree();
-               
+       
                //print newick file
                t->print(*out);
-               
+       
                //delete tree
                delete t;