added bootstrap.shared command and fixed some bugs with heatmap

[mothur.git] / sharedordervector.cpp

diff --git a/sharedordervector.cpp b/sharedordervector.cpp
index 4cc1d18fd80179af4ce8c5069a4e8144ca95dd81..41daa8024713190e997fcb845c144731252386ed 100644 (file)
--- a/sharedordervector.cpp
+++ b/sharedordervector.cpp
@@ -29,7 +29,7 @@ SharedOrderVector::SharedOrderVector(string id, vector<individual>  ov) :
 //This function is used to read a .shared file for the collect.shared, rarefaction.shared and summary.shared commands
 //if you don't use a list and groupfile.  
 
-SharedOrderVector::SharedOrderVector(ifstream& f) : DataVector() {
+SharedOrderVector::SharedOrderVector(ifstream& f) : DataVector() {  //reads in a shared file
        try {
                globaldata = GlobalData::getInstance();
                maxRank = 0; numBins = 0; numSeqs = 0;
@@ -55,7 +55,7 @@ SharedOrderVector::SharedOrderVector(ifstream& f) : DataVector() {
                        f >> inputData;
                        
                        for (int j = 0; j < inputData; j++) {
-                               push_back(i+1, i+1, groupN);
+                               push_back(i, i, groupN);
                                numSeqs++;
                        }
                }
@@ -80,7 +80,7 @@ SharedOrderVector::SharedOrderVector(ifstream& f) : DataVector() {
                                f >> inputData;
                                
                                for (int j = 0; j < inputData; j++) {
-                                       push_back(i+1, i+1, groupN);
+                                       push_back(i, i, groupN);
                                        numSeqs++;
                                }
                        }
@@ -96,8 +96,9 @@ SharedOrderVector::SharedOrderVector(ifstream& f) : DataVector() {
                f.seekg(pos, ios::beg);
        
                if (globaldata->gGroupmap == NULL) { globaldata->gGroupmap = groupmap; }
-       
+               
                updateStats();
+               
        }
        catch(exception& e) {
                cout << "Standard Error: " << e.what() << " has occurred in the SharedOrderVector class Function SharedOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
@@ -111,21 +112,18 @@ SharedOrderVector::SharedOrderVector(ifstream& f) : DataVector() {
 /***********************************************************************/
 
 int SharedOrderVector::getNumBins(){
-       if(needToUpdate == 1){  updateStats();  }
        return numBins;
 }
 
 /***********************************************************************/
 
 int SharedOrderVector::getNumSeqs(){
-       if(needToUpdate == 1){  updateStats();  }
        return numSeqs;
 }
 
 /***********************************************************************/
 
 int SharedOrderVector::getMaxRank(){
-       if(needToUpdate == 1){  updateStats();  }
        return maxRank;
 }
 
@@ -139,8 +137,8 @@ void SharedOrderVector::set(int index, int binNumber, int abund, string groupNam
        data[index].group = groupName;
        data[index].bin = binNumber;
        data[index].abundance = abund;
-       needToUpdate = 1;
-       
+       //if (abund > maxRank) { maxRank = abund; }
+       updateStats();
 }
 
 /***********************************************************************/
@@ -158,8 +156,10 @@ void SharedOrderVector::push_back(int binNumber, int abund, string groupName){
        newGuy.abundance = abund;
        newGuy.bin = binNumber;
        data.push_back(newGuy);
-       needToUpdate = 1;
-       
+       //numSeqs++;
+       //numBins++;
+       //if (abund > maxRank) { maxRank = abund; }
+       updateStats();
 }
 
 /***********************************************************************/