created mothurOut class to handle logfiles

[mothur.git] / otuhierarchycommand.cpp

diff --git a/otuhierarchycommand.cpp b/otuhierarchycommand.cpp
index c39a638cf11375644a82e4d56c3c5659c56b35ee..a8a3531a67e97dd8669bbc24b83d2e930356e98c 100644 (file)
--- a/otuhierarchycommand.cpp
+++ b/otuhierarchycommand.cpp
@@ -10,9 +10,10 @@
 #include "otuhierarchycommand.h"
 
 //**********************************************************************************************************************
-OtuHierarchyCommand::OtuHierarchyCommand(string option){
+OtuHierarchyCommand::OtuHierarchyCommand(string option) {
        try {
                abort = false;
+               
                //allow user to run help
                if(option == "help") {  help(); abort = true; }
                
@@ -47,7 +48,7 @@ OtuHierarchyCommand::OtuHierarchyCommand(string option){
                        }
 
                        listFile = validParameter.validFile(parameters, "list", true);
-                       if (listFile == "not found") { mothurOut("list is a required parameter for the otu.hierarchy command."); mothurOutEndLine(); abort = true; }
+                       if (listFile == "not found") { m->mothurOut("list is a required parameter for the otu.hierarchy command."); m->mothurOutEndLine(); abort = true; }
                        else if (listFile == "not open") { abort = true; }      
                        
                        //if the user changes the output directory command factory will send this info to us in the output parameter 
@@ -59,20 +60,20 @@ OtuHierarchyCommand::OtuHierarchyCommand(string option){
                        //check for optional parameter and set defaults
                        // ...at some point should added some additional type checking...
                        label = validParameter.validFile(parameters, "label", false);                   
-                       if (label == "not found") { mothurOut("label is a required parameter for the otu.hierarchy command."); mothurOutEndLine(); abort = true; }
+                       if (label == "not found") { m->mothurOut("label is a required parameter for the otu.hierarchy command."); m->mothurOutEndLine(); abort = true; }
                        else { 
                                splitAtDash(label, labels);
-                               if (labels.size() != 2) { mothurOut("You must provide 2 labels."); mothurOutEndLine(); abort = true; }
+                               if (labels.size() != 2) { m->mothurOut("You must provide 2 labels."); m->mothurOutEndLine(); abort = true; }
                        }       
                        
                        output = validParameter.validFile(parameters, "output", false);                 if (output == "not found") { output = "name"; }
                        
-                       if ((output != "name") && (output != "number")) { mothurOut("output options are name and number. I will use name."); mothurOutEndLine(); output = "name"; }
+                       if ((output != "name") && (output != "number")) { m->mothurOut("output options are name and number. I will use name."); m->mothurOutEndLine(); output = "name"; }
                }
                
        }
        catch(exception& e) {
-               errorOut(e, "OtuHierarchyCommand", "OtuHierarchyCommand");
+               m->errorOut(e, "OtuHierarchyCommand", "OtuHierarchyCommand");
                exit(1);
        }                       
 }
@@ -80,17 +81,17 @@ OtuHierarchyCommand::OtuHierarchyCommand(string option){
 
 void OtuHierarchyCommand::help(){
        try {
-               mothurOut("The otu.hierarchy command is used to see how otus relate at two distances. \n");
-               mothurOut("The otu.hierarchy command parameters are list, label and output.  list and label parameters are required. \n");
-               mothurOut("The output parameter allows you to output the names of the sequence in the OTUs or the OTU numbers. Options are name and number, default is name. \n");
-               mothurOut("The otu.hierarchy command should be in the following format: \n");
-               mothurOut("otu.hierarchy(list=yourListFile, label=yourLabels).\n");
-               mothurOut("Example otu.hierarchy(list=amazon.fn.list, label=0.01-0.03).\n");
-               mothurOut("The otu.hierarchy command outputs a .otu.hierarchy file which is described on the wiki.\n");
-               mothurOut("Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListFile).\n\n");
+               m->mothurOut("The otu.hierarchy command is used to see how otus relate at two distances. \n");
+               m->mothurOut("The otu.hierarchy command parameters are list, label and output.  list and label parameters are required. \n");
+               m->mothurOut("The output parameter allows you to output the names of the sequence in the OTUs or the OTU numbers. Options are name and number, default is name. \n");
+               m->mothurOut("The otu.hierarchy command should be in the following format: \n");
+               m->mothurOut("otu.hierarchy(list=yourListFile, label=yourLabels).\n");
+               m->mothurOut("Example otu.hierarchy(list=amazon.fn.list, label=0.01-0.03).\n");
+               m->mothurOut("The otu.hierarchy command outputs a .otu.hierarchy file which is described on the wiki.\n");
+               m->mothurOut("Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListFile).\n\n");
        }
        catch(exception& e) {
-               errorOut(e, "OtuHierarchyCommand", "help");
+               m->errorOut(e, "OtuHierarchyCommand", "help");
                exit(1);
        }
 }
@@ -116,7 +117,7 @@ int OtuHierarchyCommand::execute(){
                                reverse(lists.begin(), lists.end());
                        }
                }else{
-                       mothurOut("error getting listvectors, unable to read 2 different vectors, check your label inputs."); mothurOutEndLine(); return 0;
+                       m->mothurOut("error getting listvectors, unable to read 2 different vectors, check your label inputs."); m->mothurOutEndLine(); return 0;
                }
                
                //map sequences to bin number in the "little" otu
@@ -173,10 +174,15 @@ int OtuHierarchyCommand::execute(){
                
                out.close();
                
+               m->mothurOutEndLine();
+               m->mothurOut("Output File Name: "); m->mothurOutEndLine();
+               m->mothurOut(outputFileName); m->mothurOutEndLine();    
+               m->mothurOutEndLine();
+               
                return 0;
        }
        catch(exception& e) {
-               errorOut(e, "OtuHierarchyCommand", "execute");
+               m->errorOut(e, "OtuHierarchyCommand", "execute");
                exit(1);
        }
 }
@@ -264,12 +270,12 @@ vector<ListVector> OtuHierarchyCommand::getListVectors() {
                set<string>::iterator it;
                bool needToRun = false;
                for (it = userLabels.begin(); it != userLabels.end(); it++) {  
-                       mothurOut("Your file does not include the label " + *it); 
+                       m->mothurOut("Your file does not include the label " + *it); 
                        if (processedLabels.count(lastLabel) != 1) {
-                               mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine();
+                               m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
                                needToRun = true;
                        }else {
-                               mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine();
+                               m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
                        }
                }
                
@@ -293,7 +299,7 @@ vector<ListVector> OtuHierarchyCommand::getListVectors() {
                return lists;
        }
        catch(exception& e) {
-               errorOut(e, "OtuHierarchyCommand", "getListVectors");
+               m->errorOut(e, "OtuHierarchyCommand", "getListVectors");
                exit(1);
        }
 }