chimeracode

[mothur.git] / readphylip.cpp

diff --git a/readphylip.cpp b/readphylip.cpp
index bc39b52ca071d126bc9adc671e8d202c9a112dd6..5f92275eb9e6d4c8e3ee21241bbd6f626a295bc1 100644 (file)
--- a/readphylip.cpp
+++ b/readphylip.cpp
@@ -38,7 +38,7 @@ void ReadPhylipMatrix::read(NameAssignment* nameMap){
                         }
                         else{
                                 list = new ListVector(nameMap->getListVector());
-                                if(nameMap->count(name)==0){        cout << "Error: Sequence '" << name << "' was not found in the names file, please correct" << endl; }
+                                if(nameMap->count(name)==0){        mothurOut("Error: Sequence '" + name + "' was not found in the names file, please correct"); mothurOutEndLine(); }
                         }
         
                         char d;
@@ -59,13 +59,13 @@ void ReadPhylipMatrix::read(NameAssignment* nameMap){
                         }
         
                         Progress* reading;
-        
+      
                         if(square == 0){
 
                                 reading = new Progress("Reading matrix:     ", nseqs * (nseqs - 1) / 2);
                 
                                 int        index = 0;
-                
+               
                                 for(int i=1;i<nseqs;i++){
                                         fileHandle >> name;
                                         matrixNames.push_back(name);
@@ -89,7 +89,7 @@ void ReadPhylipMatrix::read(NameAssignment* nameMap){
                                 
                                         }
                                         else{
-                                                if(nameMap->count(name)==0){        cout << "Error: Sequence '" << name << "' was not found in the names file, please correct" << endl; }
+                                                if(nameMap->count(name)==0){        mothurOut("Error: Sequence '" + name + "' was not found in the names file, please correct"); mothurOutEndLine(); }
                                 
                                                 for(int j=0;j<i;j++){
                                                         fileHandle >> distance;
@@ -133,7 +133,7 @@ void ReadPhylipMatrix::read(NameAssignment* nameMap){
                                         
                                         }
                                         else{
-                                                if(nameMap->count(name)==0){        cout << "Error: Sequence '" << name << "' was not found in the names file, please correct" << endl; }
+                                                if(nameMap->count(name)==0){        mothurOut("Error: Sequence '" + name + "' was not found in the names file, please correct"); mothurOutEndLine(); }
                                 
                                                 for(int j=0;j<nseqs;j++){
                                                         fileHandle >> distance;
@@ -156,30 +156,26 @@ void ReadPhylipMatrix::read(NameAssignment* nameMap){
                         list->setLabel("0");
                         fileHandle.close();
 
-                        if(nameMap != NULL){
+                     /*   if(nameMap != NULL){
                                 for(int i=0;i<matrixNames.size();i++){
                                         nameMap->erase(matrixNames[i]);
                                 }
                                 if(nameMap->size() > 0){
                                         //should probably tell them what is missing if we missed something
-                                        cout << "missed something" << '\t' << nameMap->size() << endl;
+                                        mothurOut("missed something\t" + toString(nameMap->size())); mothurOutEndLine();
                                 }
-                        }
+                        } */
 
                 }
         catch(exception& e) {
-                cout << "Standard Error: " << e.what() << " has occurred in the ReadPhylipMatrix class Function read. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "ReadPhylipMatrix", "read");
                 exit(1);
         }
-        catch(...) {
-                cout << "An unknown error has occurred in the ReadPhylipMatrix class function read. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-                exit(1);
-        }
-}
+       }
 
 /***********************************************************************/
 
 ReadPhylipMatrix::~ReadPhylipMatrix(){
-        delete D;
-        delete list;
+       // delete D;
+       // delete list;
 }