working on chimera.perseus. made removeConfidences function smarter. Fixed bug in...

[mothur.git] / mergegroupscommand.cpp

diff --git a/mergegroupscommand.cpp b/mergegroupscommand.cpp
index 74bf0dea86c84c093d7d84b9c807b92be74892c6..af2af96b4dc6ae122fd0b9383d9486b3c776234e 100644 (file)
--- a/mergegroupscommand.cpp
+++ b/mergegroupscommand.cpp
@@ -43,7 +43,7 @@ string MergeGroupsCommand::getHelpString(){
                helpString += "The merge.groups command should be in the following format: merge.groups(design=yourDesignFile, shared=yourSharedFile).\n";
                helpString += "Example merge.groups(design=temp.design, groups=A-B-C, shared=temp.shared).\n";
                helpString += "The default value for groups is all the groups in your sharedfile, and all labels in your inputfile will be used.\n";
-               helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n";
+               helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n";
                return helpString;
        }
        catch(exception& e) {
@@ -73,6 +73,7 @@ MergeGroupsCommand::MergeGroupsCommand(string option) {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();
@@ -125,7 +126,7 @@ MergeGroupsCommand::MergeGroupsCommand(string option) {
                                designfile = m->getDesignFile(); 
                                if (designfile != "") { m->mothurOut("Using " + designfile + " as input file for the design parameter."); m->mothurOutEndLine(); }
                                else {  m->mothurOut("You have no current designfile and the design parameter is required."); m->mothurOutEndLine(); abort = true; }
-                       }       
+                       }else { m->setDesignFile(designfile); } 
                        
                        //make sure the user has already run the read.otu command
                        sharedfile = validParameter.validFile(parameters, "shared", true);
@@ -135,7 +136,7 @@ MergeGroupsCommand::MergeGroupsCommand(string option) {
                                sharedfile = m->getSharedFile(); 
                                if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
                                else {  m->mothurOut("You have no current sharedfile and the shared parameter is required."); m->mothurOutEndLine(); abort = true; }
-                       }       
+                       }else { m->setSharedFile(sharedfile); } 
                        
                        //check for optional parameter and set defaults
                        // ...at some point should added some additional type checking...
@@ -149,7 +150,7 @@ MergeGroupsCommand::MergeGroupsCommand(string option) {
                        groups = validParameter.validFile(parameters, "groups", false);                 
                        if (groups == "not found") { groups = "all";  }
                        m->splitAtDash(groups, Groups);
-                       m->Groups = Groups;
+                       m->setGroups(Groups);
                }
                
        }
@@ -186,11 +187,13 @@ int MergeGroupsCommand::execute(){
                //as long as you are not at the end of the file or done wih the lines you want
                while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
                        
-                       if (m->control_pressed) {  out.close(); for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } m->Groups.clear();  delete designMap;  for (int i = 0; i < outputNames.size(); i++) {   remove(outputNames[i].c_str()); } return 0; }
+                       if (m->control_pressed) {  out.close(); for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } m->clearGroups();  delete designMap;  for (int i = 0; i < outputNames.size(); i++) {    m->mothurRemove(outputNames[i]); } return 0; }
                        
                        if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){                  
                                
                                m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+                               
+                               if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
                                process(lookup, out);
                                
                                processedLabels.insert(lookup[0]->getLabel());
@@ -204,6 +207,7 @@ int MergeGroupsCommand::execute(){
                                lookup = input.getSharedRAbundVectors(lastLabel);
                                m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
                                
+                               if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
                                process(lookup, out);
                                
                                processedLabels.insert(lookup[0]->getLabel());
@@ -217,13 +221,13 @@ int MergeGroupsCommand::execute(){
                        //prevent memory leak
                        for (int i = 0; i < lookup.size(); i++) {  delete lookup[i]; lookup[i] = NULL; }
                        
-                       if (m->control_pressed) {  out.close(); m->Groups.clear();   delete designMap;  for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); } return 0; }
+                       if (m->control_pressed) {  out.close(); m->clearGroups();   delete designMap;  for (int i = 0; i < outputNames.size(); i++) {   m->mothurRemove(outputNames[i]); } return 0; }
                        
                        //get next line to process
                        lookup = input.getSharedRAbundVectors();                                
                }
                
-               if (m->control_pressed) { out.close(); m->Groups.clear();  delete designMap;  for (int i = 0; i < outputNames.size(); i++) {    remove(outputNames[i].c_str()); }  return 0; }
+               if (m->control_pressed) { out.close(); m->clearGroups();  delete designMap;  for (int i = 0; i < outputNames.size(); i++) {     m->mothurRemove(outputNames[i]); }  return 0; }
                
                //output error messages about any remaining user labels
                set<string>::iterator it;
@@ -245,6 +249,7 @@ int MergeGroupsCommand::execute(){
                        
                        m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
                        
+                       if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
                        process(lookup, out);
                        
                        for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
@@ -252,10 +257,10 @@ int MergeGroupsCommand::execute(){
                
                out.close();
                //reset groups parameter
-               m->Groups.clear();  
+               m->clearGroups();  
                delete designMap;
                
-               if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str()); } return 0;}
+               if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]); } return 0;}
                
                
                //set shared file as new current sharedfile