added read.shared, broke up globaldata a bit

[mothur.git] / inputdata.cpp

diff --git a/inputdata.cpp b/inputdata.cpp
index 4ed9c2711d2f11b0182ec165884d3747eeb0be80..95e9d34974e005b50629d48502257fd7579f08c9 100644 (file)
--- a/inputdata.cpp
+++ b/inputdata.cpp
@@ -89,7 +89,7 @@ ListVector* InputData::getListVector(){
 SharedListVector* InputData::getSharedListVector(){
        try {
                if(fileHandle){
-                       if (format == "shared"){
+                       if (format == "shared")  {
                                SharedList = new SharedListVector(fileHandle);
                        }
                                        
@@ -110,6 +110,33 @@ SharedListVector* InputData::getSharedListVector(){
        }       
 }
 
+/***********************************************************************/
+
+SharedOrderVector* InputData::getSharedOrderVector(){
+       try {
+               if(fileHandle){
+                       if (format == "sharedfile")  {
+                               SharedOrder = new SharedOrderVector(fileHandle);
+                       }
+                               
+                       gobble(fileHandle);
+                       return SharedOrder;
+                       
+               }else{
+                       return 0;
+               }
+       }
+       catch(exception& e) {
+               cout << "Standard Error: " << e.what() << " has occurred in the InputData class Function getSharedOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the InputData class function getSharedOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }       
+}
+
+
 
 /***********************************************************************/
 
@@ -119,7 +146,7 @@ OrderVector* InputData::getOrderVector(){
                        if(format == "list") {
                                input = new ListVector(fileHandle);
                        }
-                       else if(format == "shared") {
+                       else if (format == "shared")  {
                                input = new SharedListVector(fileHandle);
                        }
                        else if(format == "rabund"){
@@ -138,7 +165,7 @@ OrderVector* InputData::getOrderVector(){
                        gobble(fileHandle);
                        output = new OrderVector();
                        *output = (input->getOrderVector());
-                       //delete input;
+                       
                        return output;
                }
                else{
@@ -163,7 +190,7 @@ SAbundVector* InputData::getSAbundVector(){
                        if (format == "list") {
                                input = new ListVector(fileHandle);
                        }
-                       else if(format == "shared") {
+                       else if (format == "shared")  {
                                input = new SharedListVector(fileHandle);
                        }
                        else if(format == "rabund"){