changed cluster.classic so that it does not adjust the cutoff

[mothur.git] / sharedordervector.cpp

diff --git a/sharedordervector.cpp b/sharedordervector.cpp
index d0c97f9ab5a16655a381ffb3390dbb4cf94d420a..3944212ea99e688cea1e04af5bd559044869505d 100644 (file)
--- a/sharedordervector.cpp
+++ b/sharedordervector.cpp
@@ -33,7 +33,7 @@ SharedOrderVector::SharedOrderVector(ifstream& f) : DataVector() {  //reads in a
                
                if (globaldata->gGroupmap == NULL) {  groupmap = new GroupMap(); }
                
-               int num, inputData, pos, count;
+               int num, inputData, count;
                count = 0;  numSeqs = 0;
                string holdLabel, nextLabel, groupN;
                individual newguy;
@@ -57,8 +57,7 @@ SharedOrderVector::SharedOrderVector(ifstream& f) : DataVector() {  //reads in a
                        }
                }
                
-               //save position in file in case next line is a new label.
-               pos = f.tellg();
+               m->gobble(f); 
                
                if (f.eof() != true) { f >> nextLabel; }
                
@@ -82,15 +81,14 @@ SharedOrderVector::SharedOrderVector(ifstream& f) : DataVector() {  //reads in a
                                }
                        }
                        
-                       //save position in file in case next line is a new label.
-                       pos = f.tellg();
-       
+                       m->gobble(f);
+                               
                        if (f.eof() != true) { f >> nextLabel; }
 
                }
                
                //put file pointer back since you are now at a new distance label
-               f.seekg(pos, ios::beg);
+               for (int i = 0; i < nextLabel.length(); i++) { f.unget();  }
        
                if (globaldata->gGroupmap == NULL) { globaldata->gGroupmap = groupmap; }
                
@@ -98,11 +96,7 @@ SharedOrderVector::SharedOrderVector(ifstream& f) : DataVector() {  //reads in a
                
        }
        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";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the SharedOrderVector class function SharedOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               m->errorOut(e, "SharedOrderVector", "SharedOrderVector");
                exit(1);
        }
 }
@@ -172,11 +166,7 @@ void SharedOrderVector::print(ostream& output){
                output << endl;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SharedOrderVector class Function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the SharedOrderVector class function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               m->errorOut(e, "SharedOrderVector", "print");
                exit(1);
        }
 }
@@ -185,7 +175,7 @@ void SharedOrderVector::print(ostream& output){
 /***********************************************************************/
 
 void SharedOrderVector::resize(int){
-       cout << "resize() did nothing in class SharedOrderVector";
+       m->mothurOut("resize() did nothing in class SharedOrderVector");
 }
 
 /***********************************************************************/
@@ -228,13 +218,9 @@ RAbundVector SharedOrderVector::getRAbundVector(){
                return rav;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SharedOrderVector class Function getRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               m->errorOut(e, "SharedOrderVector", "getRAbundVector");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the SharedOrderVector class function getRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }       
 }
 /***********************************************************************/
 
@@ -252,11 +238,7 @@ OrderVector SharedOrderVector::getOrderVector(map<string,int>* nameMap = NULL) {
                return ov;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SharedOrderVector class Function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the SharedOrderVector class function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               m->errorOut(e, "SharedOrderVector", "getOrderVector");
                exit(1);
        }
 }
@@ -286,14 +268,9 @@ SharedRAbundVector SharedOrderVector::getSharedRAbundVector(string group) {
                return sharedRav;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SharedOrderVector class Function getSharedRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               m->errorOut(e, "SharedOrderVector", "getSharedRAbundVector");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the SharedOrderVector class function getSharedRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       
 }
 /***********************************************************************/
 vector<SharedRAbundVector*> SharedOrderVector::getSharedRAbundVector() {
@@ -308,14 +285,9 @@ vector<SharedRAbundVector*> SharedOrderVector::getSharedRAbundVector() {
                return lookup;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SharedOrderVector class Function getSharedRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               m->errorOut(e, "SharedOrderVector", "getSharedRAbundVector");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the SharedOrderVector class function getSharedRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       
 }
 /***********************************************************************/
 SharedSAbundVector SharedOrderVector::getSharedSAbundVector(string group) {
@@ -326,14 +298,9 @@ SharedSAbundVector SharedOrderVector::getSharedSAbundVector(string group) {
                                
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SharedOrderVector class Function getSharedRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               m->errorOut(e, "SharedOrderVector", "getSharedSAbundVector");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the SharedOrderVector class function getSharedRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       
 }
 
 /***********************************************************************/
@@ -366,13 +333,9 @@ void SharedOrderVector::updateStats(){
                
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SharedOrderVector class Function updateStats. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               m->errorOut(e, "SharedOrderVector", "updateStats");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the SharedOrderVector class function updateStats. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }       
 }
 
 /***********************************************************************/