created mothurOut class to handle logfiles

[mothur.git] / readtreecommand.cpp

diff --git a/readtreecommand.cpp b/readtreecommand.cpp
index a11465d669a55de0c5555f616c36f51caef74ea2..da66ee1eb0971362e8f19ff62155c26239da5615 100644 (file)
--- a/readtreecommand.cpp
+++ b/readtreecommand.cpp
@@ -10,11 +10,11 @@
 #include "readtreecommand.h"
 
 //**********************************************************************************************************************
-ReadTreeCommand::ReadTreeCommand(string option){
+ReadTreeCommand::ReadTreeCommand(string option)  {
        try {
                globaldata = GlobalData::getInstance();
                abort = false;
-               
+                               
                //allow user to run help
                if(option == "help") { help(); abort = true; }
                
@@ -71,12 +71,12 @@ ReadTreeCommand::ReadTreeCommand(string option){
                        //check for required parameters
                        treefile = validParameter.validFile(parameters, "tree", true);
                        if (treefile == "not open") { abort = true; }
-                       else if (treefile == "not found") { treefile = ""; mothurOut("tree is a required parameter for the read.tree command."); mothurOutEndLine(); abort = true;  }   
+                       else if (treefile == "not found") { treefile = ""; m->mothurOut("tree is a required parameter for the read.tree command."); m->mothurOutEndLine(); abort = true;  }     
                        else {  globaldata->setTreeFile(treefile);  globaldata->setFormat("tree");      }
                        
                        groupfile = validParameter.validFile(parameters, "group", true);
                        if (groupfile == "not open") { abort = true; }  
-                       else if (groupfile == "not found") { groupfile = ""; mothurOut("group is a required parameter for the read.tree command."); mothurOutEndLine(); abort = true;   }
+                       else if (groupfile == "not found") { groupfile = ""; m->mothurOut("group is a required parameter for the read.tree command."); m->mothurOutEndLine(); abort = true;     }
                        else {  
                                globaldata->setGroupFile(groupfile); 
                                //read in group map info.
@@ -98,7 +98,7 @@ ReadTreeCommand::ReadTreeCommand(string option){
                }
        }
        catch(exception& e) {
-               errorOut(e, "ReadTreeCommand", "ReadTreeCommand");              
+               m->errorOut(e, "ReadTreeCommand", "ReadTreeCommand");           
                exit(1);
        }
 }
@@ -106,14 +106,14 @@ ReadTreeCommand::ReadTreeCommand(string option){
 
 void ReadTreeCommand::help(){
        try {
-               mothurOut("The read.tree command must be run before you execute a unifrac.weighted, unifrac.unweighted. \n");
-               mothurOut("It also must be run before using the parsimony command, unless you are using the randomtree parameter.\n");
-               mothurOut("The read.tree command should be in the following format: read.tree(tree=yourTreeFile, group=yourGroupFile).\n");
-               mothurOut("The tree and group parameters are both required.\n");
-               mothurOut("Note: No spaces between parameter labels (i.e. tree), '=' and parameters (i.e.yourTreefile).\n\n");
+               m->mothurOut("The read.tree command must be run before you execute a unifrac.weighted, unifrac.unweighted. \n");
+               m->mothurOut("It also must be run before using the parsimony command, unless you are using the randomtree parameter.\n");
+               m->mothurOut("The read.tree command should be in the following format: read.tree(tree=yourTreeFile, group=yourGroupFile).\n");
+               m->mothurOut("The tree and group parameters are both required.\n");
+               m->mothurOut("Note: No spaces between parameter labels (i.e. tree), '=' and parameters (i.e.yourTreefile).\n\n");
        }
        catch(exception& e) {
-               errorOut(e, "ReadTreeCommand", "help"); 
+               m->errorOut(e, "ReadTreeCommand", "help");      
                exit(1);
        }
 }
@@ -135,7 +135,7 @@ int ReadTreeCommand::execute(){
                
                readOk = read->read(); 
                
-               if (readOk != 0) { mothurOut("Read Terminated."); mothurOutEndLine(); globaldata->gTree.clear(); delete globaldata->gTreemap; return 0; }
+               if (readOk != 0) { m->mothurOut("Read Terminated."); m->mothurOutEndLine(); globaldata->gTree.clear(); delete globaldata->gTreemap; return 0; }
                
                vector<Tree*> T = globaldata->gTree;
 
@@ -160,7 +160,7 @@ int ReadTreeCommand::execute(){
                                        map<string, string>::iterator it = nameMap.find(treeMap->namesOfSeqs[i]);
                                        
                                        if (it == nameMap.end()) {
-                                               mothurOut(treeMap->namesOfSeqs[i] + " is in your groupfile and not in your tree. It will be disregarded."); mothurOutEndLine();
+                                               m->mothurOut(treeMap->namesOfSeqs[i] + " is in your groupfile and not in your tree. It will be disregarded."); m->mothurOutEndLine();
                                                treeMap->removeSeq(treeMap->namesOfSeqs[i]);
                                                i--; //need this because removeSeq removes name from namesOfSeqs
                                        }
@@ -171,7 +171,7 @@ int ReadTreeCommand::execute(){
                return 0;
        }
        catch(exception& e) {
-               errorOut(e, "ReadTreeCommand", "execute");      
+               m->errorOut(e, "ReadTreeCommand", "execute");   
                exit(1);
        }
 }
@@ -198,14 +198,14 @@ int ReadTreeCommand::readNamesFile() {
                                splitAtComma(second, dupNames);
                                
                                for (int i = 0; i < dupNames.size(); i++) {     nameMap[dupNames[i]] = dupNames[i];  }
-                       }else {  mothurOut(first + " has already been seen in namefile, disregarding names file."); mothurOutEndLine(); in.close(); globaldata->names.clear(); return 1; }                      
+                       }else {  m->mothurOut(first + " has already been seen in namefile, disregarding names file."); m->mothurOutEndLine(); in.close(); globaldata->names.clear(); return 1; }                        
                }
                in.close();
                
                return 0;
        }
        catch(exception& e) {
-               errorOut(e, "ReadTreeCommand", "readNamesFile");
+               m->errorOut(e, "ReadTreeCommand", "readNamesFile");
                exit(1);
        }
 }