working on pam

[mothur.git] / sharedrabundfloatvector.cpp

diff --git a/sharedrabundfloatvector.cpp b/sharedrabundfloatvector.cpp
index bea2f8c83808b287428bc309f513b8b64d548366..9eeb0f21bf3626620806c49372ab36efd0ff0831 100644 (file)
--- a/sharedrabundfloatvector.cpp
+++ b/sharedrabundfloatvector.cpp
@@ -48,7 +48,7 @@ SharedRAbundFloatVector::SharedRAbundFloatVector(ifstream& f) : DataVector(), ma
                //are we at the beginning of the file??
                if (m->saveNextLabel == "") {  
                        f >> label; 
-                       
+            
                        //is this a shared file that has headers
                        if (label == "label") { 
                                //gets "group"
@@ -62,25 +62,45 @@ 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;
-                       }
-               }else { label = m->saveNextLabel; }
+                               f >> label >> groupN >> num;
+                       }else {
+                //read in first row since you know there is at least 1 group.
+                f >> groupN >> num;
+                
+                //make binlabels because we don't have any
+                string snumBins = toString(num);
+                m->sharedBinLabelsInFile.clear();
+                for (int i = 0; i < num; i++) {  
+                    //if there is a bin label use it otherwise make one
+                    string binLabel = "Otu";
+                    string sbinNumber = toString(i+1);
+                    if (sbinNumber.length() < snumBins.length()) { 
+                        int diff = snumBins.length() - sbinNumber.length();
+                        for (int h = 0; h < diff; h++) { binLabel += "0"; }
+                    }
+                    binLabel += sbinNumber;
+                    m->sharedBinLabelsInFile.push_back(binLabel);
+                }
+            }
+               }else { 
+            label = m->saveNextLabel; 
+            
+            //read in first row since you know there is at least 1 group.
+            f >> groupN >> num;
+        }
                
                //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;
                
-               //read in first row since you know there is at least 1 group.
-               f >> groupN >> num;
-
                holdLabel = label;
                
                //add new vector to lookup
@@ -108,6 +128,7 @@ SharedRAbundFloatVector::SharedRAbundFloatVector(ifstream& f) : DataVector(), ma
                //read the rest of the groups info in
                while ((nextLabel == holdLabel) && (f.eof() != true)) {
                        f >> groupN >> num;
+            
                        count++;
                        
                        allGroups.push_back(groupN);
@@ -131,7 +152,6 @@ SharedRAbundFloatVector::SharedRAbundFloatVector(ifstream& f) : DataVector(), ma
                
                m->saveNextLabel = nextLabel;
                m->setAllGroups(allGroups);
-       
        }
        catch(exception& e) {
                m->errorOut(e, "SharedRAbundFloatVector", "SharedRAbundFloatVector");
@@ -171,6 +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];     
 }
@@ -265,7 +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'; 
                        }
@@ -280,7 +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'; 
                        }
@@ -288,7 +318,7 @@ void SharedRAbundFloatVector::printHeaders(ostream& output){
                        output << endl;
                }
                
-               m->printedHeaders = true;
+               m->printedSharedHeaders = true;
        }
        catch(exception& e) {
                m->errorOut(e, "SharedRAbundVector", "printHeaders");
@@ -348,7 +378,7 @@ SharedRAbundVector SharedRAbundFloatVector::getSharedRAbundVector(){
                exit(1);
        }               
 }
-/***********************************************************************/
+***********************************************************************/
 vector<SharedRAbundFloatVector*> SharedRAbundFloatVector::getSharedRAbundFloatVectors(){
        try {
                SharedUtil* util;
@@ -419,7 +449,7 @@ SharedSAbundVector SharedRAbundVector::getSharedSAbundVector(){
                exit(1);
        }
 }
-/***********************************************************************/
+***********************************************************************/
 
 SAbundVector SharedRAbundFloatVector::getSAbundVector() {
        try {
@@ -461,7 +491,7 @@ SharedOrderVector SharedRAbundFloatVector::getSharedOrderVector() {
                exit(1);
        }
 }
-/***********************************************************************/
+***********************************************************************/
 //this is not functional, not sure how to handle it yet, but I need the stub because it is a pure function
 OrderVector SharedRAbundFloatVector::getOrderVector(map<string,int>* nameMap = NULL) {
        try {
@@ -520,7 +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);
                        }
@@ -529,7 +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;