changed get.sharedotu to get.sharedseqs

[mothur.git] / sharedrabundvector.cpp

diff --git a/sharedrabundvector.cpp b/sharedrabundvector.cpp
index 246712824907240690d86c07632ed1cc58966182..142f787e24ac3663c19783874721299a071336cf 100644 (file)
--- a/sharedrabundvector.cpp
+++ b/sharedrabundvector.cpp
@@ -51,11 +51,7 @@ SharedRAbundVector::SharedRAbundVector(string id, vector<individual> rav) : Data
                }
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SharedRAbundVector class Function SharedRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the SharedRAbundVector class function SharedRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "SharedRAbundVector", "SharedRAbundVector");
                exit(1);
        }
 }
@@ -105,6 +101,8 @@ SharedRAbundVector::SharedRAbundVector(ifstream& f) : DataVector(), maxRank(0),
                        
                }
                
+               gobble(f);
+               
                if (f.eof() != true) { f >> nextLabel; }
                
                //read the rest of the groups info in
@@ -130,6 +128,7 @@ SharedRAbundVector::SharedRAbundVector(ifstream& f) : DataVector(), maxRank(0),
                                lookup[count]->push_back(inputData, i, groupN); //abundance, bin, group
                        }
                        
+                       gobble(f);
                                
                        if (f.eof() != true) { f >> nextLabel; }
                }
@@ -141,11 +140,7 @@ SharedRAbundVector::SharedRAbundVector(ifstream& f) : DataVector(), maxRank(0),
                
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SharedRAbundVector class Function SharedRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the SharedRAbundVector class function SharedRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "SharedRAbundVector", "SharedRAbundVector");
                exit(1);
        }
 }
@@ -163,11 +158,7 @@ void SharedRAbundVector::set(int binNumber, int newBinSize, string groupname){
                numSeqs += (newBinSize - oldBinSize);
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SharedRAbundVector class Function set. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the SharedRAbundVector class function set. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "SharedRAbundVector", "set");
                exit(1);
        }
 }
@@ -228,11 +219,7 @@ void SharedRAbundVector::push_back(int binSize, int otu, string groupName){
                numSeqs += binSize;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SharedRAbundVector class Function push_back. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the SharedRAbundVector class function push_back. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "SharedRAbundVector", "push_back");
                exit(1);
        }
 }
@@ -256,11 +243,7 @@ void SharedRAbundVector::insert(int binSize, int otu, string groupName){
                numSeqs += binSize;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SharedRAbundVector class Function insert. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the SharedRAbundVector class function insert. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "SharedRAbundVector", "insert");
                exit(1);
        }
 }
@@ -284,11 +267,7 @@ void SharedRAbundVector::push_front(int binSize, int otu, string groupName){
                numSeqs += binSize;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SharedRAbundVector class Function push_front. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the SharedRAbundVector class function push_front. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "SharedRAbundVector", "push_front");
                exit(1);
        }
 }
@@ -334,11 +313,7 @@ void SharedRAbundVector::print(ostream& output){
                output << endl;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SharedRAbundVector class Function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the SharedRAbundVector class function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "SharedRAbundVector", "print");
                exit(1);
        }
 }
@@ -399,11 +374,7 @@ vector<SharedRAbundVector*> SharedRAbundVector::getSharedRAbundVectors(){
                return lookup;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SharedRAbundVector class Function getSharedRAbundVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the SharedRAbundVector class function getSharedRAbundVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "SharedRAbundVector", "getSharedRAbundVectors");
                exit(1);
        }
 }
@@ -411,20 +382,19 @@ vector<SharedRAbundVector*> SharedRAbundVector::getSharedRAbundVectors(){
 
 RAbundVector SharedRAbundVector::getRAbundVector() {
        try {
-               RAbundVector rav(data.size());
+               RAbundVector rav;
                
                for (int i = 0; i < data.size(); i++) {
-                       rav.set(i, data[i].abundance);
+                       if(data[i].abundance != 0) {
+                               rav.push_back(data[i].abundance);
+                       }
                }
-       
+               
+               rav.setLabel(label);
                return rav;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SharedRAbundVector class Function getRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the SharedRAbundVector class function getRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "SharedRAbundVector", "getRAbundVector");
                exit(1);
        }
 }
@@ -439,11 +409,7 @@ RAbundVector SharedRAbundVector::getRAbundVector2() {
                return rav;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SharedRAbundVector class Function getRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the SharedRAbundVector class function getRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "SharedRAbundVector", "getRAbundVector2");
                exit(1);
        }
 }
@@ -465,11 +431,7 @@ SharedSAbundVector SharedRAbundVector::getSharedSAbundVector(){
                return sav;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SharedRAbundVector class Function getSharedSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the SharedRAbundVector class function getSharedSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "SharedRAbundVector", "getSharedSAbundVector");
                exit(1);
        }
 }
@@ -488,11 +450,7 @@ SAbundVector SharedRAbundVector::getSAbundVector() {
                return sav;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SharedRAbundVector class Function getSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the SharedRAbundVector class function getSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "SharedRAbundVector", "getSAbundVector");           
                exit(1);
        }
 }
@@ -516,11 +474,7 @@ SharedOrderVector SharedRAbundVector::getSharedOrderVector() {
                return ov;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SharedRAbundVector class Function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the SharedRAbundVector class function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "SharedRAbundVector", "getSharedOrderVector");
                exit(1);
        }
 }
@@ -541,11 +495,7 @@ OrderVector SharedRAbundVector::getOrderVector(map<string,int>* nameMap = NULL)
                return ov;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SharedRAbundVector class Function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the SharedRAbundVector class function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "SharedRAbundVector", "getOrderVector");
                exit(1);
        }
 }