working on pam

[mothur.git] / sharedrabundfloatvector.cpp

diff --git a/sharedrabundfloatvector.cpp b/sharedrabundfloatvector.cpp
index b6d916a1900edc643291df4432728d3619a711a6..9eeb0f21bf3626620806c49372ab36efd0ff0831 100644 (file)
--- a/sharedrabundfloatvector.cpp
+++ b/sharedrabundfloatvector.cpp
@@ -62,13 +62,13 @@ SharedRAbundFloatVector::SharedRAbundFloatVector(ifstream& f) : DataVector(), ma
                                
                                //parse labels to save
                                istringstream iStringStream(label);
-                               m->binLabelsInFile.clear();
+                               m->sharedBinLabelsInFile.clear();
                                while(!iStringStream.eof()){
                                        if (m->control_pressed) { break; }
                                        string temp;
                                        iStringStream >> temp;  m->gobble(iStringStream);
                     
-                                       m->binLabelsInFile.push_back(temp);
+                                       m->sharedBinLabelsInFile.push_back(temp);
                                }
                                
                                f >> label >> groupN >> num;
@@ -78,7 +78,7 @@ SharedRAbundFloatVector::SharedRAbundFloatVector(ifstream& f) : DataVector(), ma
                 
                 //make binlabels because we don't have any
                 string snumBins = toString(num);
-                m->binLabelsInFile.clear();
+                m->sharedBinLabelsInFile.clear();
                 for (int i = 0; i < num; i++) {  
                     //if there is a bin label use it otherwise make one
                     string binLabel = "Otu";
@@ -88,7 +88,7 @@ SharedRAbundFloatVector::SharedRAbundFloatVector(ifstream& f) : DataVector(), ma
                         for (int h = 0; h < diff; h++) { binLabel += "0"; }
                     }
                     binLabel += sbinNumber;
-                    m->binLabelsInFile.push_back(binLabel);
+                    m->sharedBinLabelsInFile.push_back(binLabel);
                 }
             }
                }else { 
@@ -99,7 +99,7 @@ SharedRAbundFloatVector::SharedRAbundFloatVector(ifstream& f) : DataVector(), ma
         }
                
                //reset labels, currentLabels may have gotten changed as otus were eliminated because of group choices or sampling
-               m->currentBinLabels = m->binLabelsInFile;
+               m->currentSharedBinLabels = m->sharedBinLabelsInFile;
                
                holdLabel = label;
                
@@ -129,7 +129,6 @@ SharedRAbundFloatVector::SharedRAbundFloatVector(ifstream& f) : DataVector(), ma
                while ((nextLabel == holdLabel) && (f.eof() != true)) {
                        f >> groupN >> num;
             
-            if (num != 1000) { break; }
                        count++;
                        
                        allGroups.push_back(groupN);
@@ -153,7 +152,6 @@ SharedRAbundFloatVector::SharedRAbundFloatVector(ifstream& f) : DataVector(), ma
                
                m->saveNextLabel = nextLabel;
                m->setAllGroups(allGroups);
-       
        }
        catch(exception& e) {
                m->errorOut(e, "SharedRAbundFloatVector", "SharedRAbundFloatVector");
@@ -193,6 +191,16 @@ float SharedRAbundFloatVector::getAbundance(int index){
        return data[index].abundance;   
 }
 /***********************************************************************/
+//returns vector of abundances
+vector<float> SharedRAbundFloatVector::getAbundances(){
+    vector<float> abunds;
+    for (int i = 0; i < data.size(); i++) {
+        abunds.push_back(data[i].abundance);
+    }
+    
+       return abunds;
+}
+/***********************************************************************/
 individualFloat SharedRAbundFloatVector::get(int index){
        return data[index];     
 }
@@ -287,7 +295,7 @@ void SharedRAbundFloatVector::printHeaders(ostream& output){
                                        for (int h = 0; h < diff; h++) { binLabel += "0"; }
                                }
                                binLabel += sbinNumber;
-                               if (i < m->currentBinLabels.size()) {  binLabel = m->currentBinLabels[i]; }
+                               if (i < m->currentSharedBinLabels.size()) {  binLabel = m->currentSharedBinLabels[i]; }
                                
                                output << binLabel << '\t'; 
                        }
@@ -302,7 +310,7 @@ void SharedRAbundFloatVector::printHeaders(ostream& output){
                                        for (int h = 0; h < diff; h++) { binLabel += "0"; }
                                }
                                binLabel += sbinNumber;
-                               if (i < m->currentBinLabels.size()) {  binLabel = m->currentBinLabels[i]; }
+                               if (i < m->currentSharedBinLabels.size()) {  binLabel = m->currentSharedBinLabels[i]; }
                                
                                output << binLabel << '\t'; 
                        }
@@ -310,7 +318,7 @@ void SharedRAbundFloatVector::printHeaders(ostream& output){
                        output << endl;
                }
                
-               m->printedHeaders = true;
+               m->printedSharedHeaders = true;
        }
        catch(exception& e) {
                m->errorOut(e, "SharedRAbundVector", "printHeaders");
@@ -542,7 +550,7 @@ int SharedRAbundFloatVector::eliminateZeroOTUS(vector<SharedRAbundFloatVector*>&
                                        for (int h = 0; h < diff; h++) { binLabel += "0"; }
                                }
                                binLabel += sbinNumber; 
-                               if (i < m->currentBinLabels.size()) {  binLabel = m->currentBinLabels[i]; }
+                               if (i < m->currentSharedBinLabels.size()) {  binLabel = m->currentSharedBinLabels[i]; }
                                
                                newBinLabels.push_back(binLabel);
                        }
@@ -551,7 +559,7 @@ int SharedRAbundFloatVector::eliminateZeroOTUS(vector<SharedRAbundFloatVector*>&
                for (int j = 0; j < thislookup.size(); j++) {  delete thislookup[j];  }
                
                thislookup = newLookup;
-               m->currentBinLabels = newBinLabels;
+               m->currentSharedBinLabels = newBinLabels;
                
                return 0;