created mothurOut class to handle logfiles

[mothur.git] / pcacommand.cpp

diff --git a/pcacommand.cpp b/pcacommand.cpp
index c17053e29cb31812f681333078199c9abaea02fa..644473a8baa2b86253118e7b766b0e965fcb80a8 100644 (file)
--- a/pcacommand.cpp
+++ b/pcacommand.cpp
@@ -12,7 +12,7 @@
 
 //**********************************************************************************************************************
 
-PCACommand::PCACommand(string option){
+PCACommand::PCACommand(string option)  {
        try {
                abort = false;
                
@@ -61,12 +61,12 @@ PCACommand::PCACommand(string option){
                        }
                        
                        //error checking on files       
-                       if (phylipfile == "")   { mothurOut("You must provide a distance file before running the pca command."); mothurOutEndLine(); abort = true; }            
+                       if (phylipfile == "")   { m->mothurOut("You must provide a distance file before running the pca command."); m->mothurOutEndLine(); abort = true; }              
                }
 
        }
        catch(exception& e) {
-               errorOut(e, "PCACommand", "PCACommand");
+               m->errorOut(e, "PCACommand", "PCACommand");
                exit(1);
        }
 }
@@ -74,10 +74,10 @@ PCACommand::PCACommand(string option){
 void PCACommand::help(){
        try {
        
-               mothurOut("The pca command..."); mothurOutEndLine();
+               m->mothurOut("The pca command..."); m->mothurOutEndLine();
        }
        catch(exception& e) {
-               errorOut(e, "PCACommand", "help");
+               m->errorOut(e, "PCACommand", "help");
                exit(1);
        }
 }
@@ -129,10 +129,15 @@ int PCACommand::execute(){
                
                output(fbase, names, G, d);
                
+               m->mothurOutEndLine();
+               m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+               for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
+               m->mothurOutEndLine();
+               
                return 0;
        }
        catch(exception& e) {
-               errorOut(e, "PCACommand", "execute");
+               m->errorOut(e, "PCACommand", "execute");
                exit(1);
        }
 }
@@ -152,7 +157,7 @@ void PCACommand::get_comment(istream& f, char begin, char end){
                d = f.peek();
        }
        catch(exception& e) {
-               errorOut(e, "PCACommand", "get_comment");
+               m->errorOut(e, "PCACommand", "get_comment");
                exit(1);
        }
 }      
@@ -201,7 +206,7 @@ void PCACommand::read_phylip(istream& f, int square_m, vector<string>& name_list
                }
        }
        catch(exception& e) {
-               errorOut(e, "PCACommand", "read_phylip");
+               m->errorOut(e, "PCACommand", "read_phylip");
                exit(1);
        }
 
@@ -243,7 +248,7 @@ void PCACommand::read(string fname, vector<string>& names, vector<vector<double>
                read_phylip(f, m, names, D);
        }
                catch(exception& e) {
-               errorOut(e, "PCACommand", "read");
+               m->errorOut(e, "PCACommand", "read");
                exit(1);
        }
 }
@@ -275,7 +280,7 @@ void PCACommand::matrix_mult(vector<vector<double> > first, vector<vector<double
                }
        }
        catch(exception& e) {
-               errorOut(e, "PCACommand", "matrix_mult");
+               m->errorOut(e, "PCACommand", "matrix_mult");
                exit(1);
        }
 
@@ -309,7 +314,7 @@ void PCACommand::recenter(double offset, vector<vector<double> > D, vector<vecto
                matrix_mult(A,C,G);
        }
        catch(exception& e) {
-               errorOut(e, "PCACommand", "recenter");
+               m->errorOut(e, "PCACommand", "recenter");
                exit(1);
        }
 
@@ -402,7 +407,7 @@ void PCACommand::tred2(vector<vector<double> >& a, vector<double>& d, vector<dou
                }
        }
        catch(exception& e) {
-               errorOut(e, "PCACommand", "tred2");
+               m->errorOut(e, "PCACommand", "tred2");
                exit(1);
        }
 
@@ -486,7 +491,7 @@ void PCACommand::qtli(vector<double>& d, vector<double>& e, vector<vector<double
                }
        }
        catch(exception& e) {
-               errorOut(e, "PCACommand", "qtli");
+               m->errorOut(e, "PCACommand", "qtli");
                exit(1);
        }
 }
@@ -508,10 +513,12 @@ void PCACommand::output(string fnameRoot, vector<string> name_list, vector<vecto
                ofstream pcaData((fnameRoot+"pca").c_str(), ios::trunc);
                pcaData.setf(ios::fixed, ios::floatfield);
                pcaData.setf(ios::showpoint);   
+               outputNames.push_back(fnameRoot+"pca");
                
                ofstream pcaLoadings((fnameRoot+"pca.loadings").c_str(), ios::trunc);
                pcaLoadings.setf(ios::fixed, ios::floatfield);
-               pcaLoadings.setf(ios::showpoint);       
+               pcaLoadings.setf(ios::showpoint);
+               outputNames.push_back(fnameRoot+"pca.loadings");        
                
                pcaLoadings << "axis\tloading\n";
                for(int i=0;i<rank;i++){
@@ -533,7 +540,7 @@ void PCACommand::output(string fnameRoot, vector<string> name_list, vector<vecto
                }
        }
        catch(exception& e) {
-               errorOut(e, "PCACommand", "output");
+               m->errorOut(e, "PCACommand", "output");
                exit(1);
        }
 }