changes to filter.seqs

[mothur.git] / inputdata.cpp

diff --git a/inputdata.cpp b/inputdata.cpp
index cbf44ed11a96a03c251fcc3025b185c2020c2830..8e54ab787c683535dd132caf0881aab3399945b9 100644 (file)
--- a/inputdata.cpp
+++ b/inputdata.cpp
@@ -15,7 +15,7 @@
 /***********************************************************************/
 
 InputData::InputData(string fName, string f) : format(f){
-       
+       m = MothurOut::getInstance();
        openInputFile(fName, fileHandle);
        filename = fName;
        
@@ -34,7 +34,7 @@ InputData::~InputData(){
 
 InputData::InputData(string fName, string orderFileName, string f) : format(f){
        try {
-               
+               m = MothurOut::getInstance();
                ifstream ofHandle;
                openInputFile(orderFileName, ofHandle);
                string name;
@@ -52,7 +52,7 @@ InputData::InputData(string fName, string orderFileName, string f) : format(f){
                openInputFile(fName, fileHandle);
        }
        catch(exception& e) {
-               errorOut(e, "InputData", "InputData");
+               m->errorOut(e, "InputData", "InputData");
                exit(1);
        }
 }
@@ -63,7 +63,7 @@ ListVector* InputData::getListVector(){
                if(fileHandle){
                        if(format == "list") {
                                list = new ListVector(fileHandle);
-                       }
+                       }else{ list = NULL;  }
                                        
                        gobble(fileHandle);
                        return list;
@@ -73,7 +73,7 @@ ListVector* InputData::getListVector(){
                }
        }
        catch(exception& e) {
-               errorOut(e, "InputData", "getListVector");
+               m->errorOut(e, "InputData", "getListVector");
                exit(1);
        }
 }
@@ -101,7 +101,7 @@ ListVector* InputData::getListVector(string label){
                                        else {  delete list;    }
                                        gobble(in);
                                }
-                       }
+                       }else{ list = NULL;  }
                        
                        in.close();
                        return list;
@@ -111,7 +111,7 @@ ListVector* InputData::getListVector(string label){
                }
        }
        catch(exception& e) {
-               errorOut(e, "InputData", "getListVector");
+               m->errorOut(e, "InputData", "getListVector");
                exit(1);
        }
 }
@@ -124,7 +124,7 @@ SharedListVector* InputData::getSharedListVector(){
                if(fileHandle){
                        if (format == "shared")  {
                                SharedList = new SharedListVector(fileHandle);
-                       }
+                       }else{ SharedList = NULL;  }
                                        
                        gobble(fileHandle);
                        return SharedList;
@@ -134,7 +134,7 @@ SharedListVector* InputData::getSharedListVector(){
                }
        }
        catch(exception& e) {
-               errorOut(e, "InputData", "getSharedListVector");
+               m->errorOut(e, "InputData", "getSharedListVector");
                exit(1);
        }
 }
@@ -162,7 +162,7 @@ SharedListVector* InputData::getSharedListVector(string label){
                                        gobble(in);
                                }
 
-                       }
+                       }else{ SharedList = NULL;  }
                                
                        in.close();
                        return SharedList;
@@ -172,7 +172,7 @@ SharedListVector* InputData::getSharedListVector(string label){
                }
        }
        catch(exception& e) {
-               errorOut(e, "InputData", "getSharedListVector");
+               m->errorOut(e, "InputData", "getSharedListVector");
                exit(1);
        }
 }
@@ -186,7 +186,7 @@ SharedOrderVector* InputData::getSharedOrderVector(){
                if(fileHandle){
                        if (format == "sharedfile")  {
                                SharedOrder = new SharedOrderVector(fileHandle);
-                       }
+                       }else{ SharedOrder = NULL;  }
                                
                        gobble(fileHandle);
                        return SharedOrder;
@@ -196,7 +196,7 @@ SharedOrderVector* InputData::getSharedOrderVector(){
                }
        }
        catch(exception& e) {
-               errorOut(e, "InputData", "getSharedOrderVector");
+               m->errorOut(e, "InputData", "getSharedOrderVector");
                exit(1);
        }
 }
@@ -225,7 +225,7 @@ SharedOrderVector* InputData::getSharedOrderVector(string label){
                                        gobble(in);
                                }
 
-                       }
+                       }else{ SharedOrder = NULL;  }
                                
                        in.close();
                        return SharedOrder;
@@ -235,7 +235,7 @@ SharedOrderVector* InputData::getSharedOrderVector(string label){
                }
        }
        catch(exception& e) {
-               errorOut(e, "InputData", "getSharedOrderVector");
+               m->errorOut(e, "InputData", "getSharedOrderVector");
                exit(1);
        }
 }
@@ -262,11 +262,12 @@ OrderVector* InputData::getOrderVector(){
                        else if(format == "sabund"){
                                input = new SAbundVector(fileHandle);
                        }
-                                       
+                       
                        gobble(fileHandle);
-                       output = new OrderVector();
-                       *output = (input->getOrderVector());
                        
+                       output = new OrderVector();     
+                       *output = (input->getOrderVector());
+               
                        return output;
                }
                else{
@@ -274,7 +275,7 @@ OrderVector* InputData::getOrderVector(){
                }
        }
        catch(exception& e) {
-               errorOut(e, "InputData", "getOrderVector");
+               m->errorOut(e, "InputData", "getOrderVector");
                exit(1);
        }
 }
@@ -377,7 +378,7 @@ OrderVector* InputData::getOrderVector(string label){
                }
        }
        catch(exception& e) {
-               errorOut(e, "InputData", "getOrderVector");
+               m->errorOut(e, "InputData", "getOrderVector");
                exit(1);
        }
 }
@@ -407,7 +408,7 @@ vector<SharedRAbundVector*> InputData::getSharedRAbundVectors(){
                
        }
        catch(exception& e) {
-               errorOut(e, "InputData", "getSharedRAbundVectors");
+               m->errorOut(e, "InputData", "getSharedRAbundVectors");
                exit(1);
        }
 }
@@ -465,7 +466,7 @@ vector<SharedRAbundVector*> InputData::getSharedRAbundVectors(string label){
        
        }
        catch(exception& e) {
-               errorOut(e, "InputData", "getSharedRAbundVectors");
+               m->errorOut(e, "InputData", "getSharedRAbundVectors");
                exit(1);
        }
 }
@@ -504,7 +505,7 @@ SAbundVector* InputData::getSAbundVector(){
                }
        }
        catch(exception& e) {
-               errorOut(e, "InputData", "getSAbundVector");
+               m->errorOut(e, "InputData", "getSAbundVector");
                exit(1);
        }
 }
@@ -606,7 +607,7 @@ SAbundVector* InputData::getSAbundVector(string label){
                }
        }
        catch(exception& e) {
-               errorOut(e, "InputData", "getSAbundVector");
+               m->errorOut(e, "InputData", "getSAbundVector");
                exit(1);
        }
 }
@@ -643,7 +644,7 @@ RAbundVector* InputData::getRAbundVector(){
                }
        }
        catch(exception& e) {
-               errorOut(e, "InputData", "getRAbundVector");
+               m->errorOut(e, "InputData", "getRAbundVector");
                exit(1);
        }
 }
@@ -744,7 +745,7 @@ RAbundVector* InputData::getRAbundVector(string label){
                }
        }
        catch(exception& e) {
-               errorOut(e, "InputData", "getRAbundVector");
+               m->errorOut(e, "InputData", "getRAbundVector");
                exit(1);
        }
 }