1.21.0

[mothur.git] / unifracweightedcommand.cpp

diff --git a/unifracweightedcommand.cpp b/unifracweightedcommand.cpp
index 29cdf94091cebb65104e1b5691e5691e19a4e495..d6431a051b56f3144dcfc80d430e7d61351da30a 100644 (file)
--- a/unifracweightedcommand.cpp
+++ b/unifracweightedcommand.cpp
@@ -48,7 +48,7 @@ string UnifracWeightedCommand::getHelpString(){
                helpString += "Example unifrac.weighted(groups=A-B-C, iters=500).\n";
                helpString += "The default value for groups is all the groups in your groupfile, and iters is 1000.\n";
                helpString += "The unifrac.weighted command output two files: .weighted and .wsummary their descriptions are in the manual.\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) {
@@ -80,6 +80,7 @@ UnifracWeightedCommand::UnifracWeightedCommand(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();
@@ -133,6 +134,10 @@ UnifracWeightedCommand::UnifracWeightedCommand(string option) {
                        }
                        
                        m->runParse = true;
+                       m->Groups.clear();
+                       m->namesOfGroups.clear();
+                       m->Treenames.clear();
+                       m->names.clear();
                        
                        //check for required parameters
                        treefile = validParameter.validFile(parameters, "tree", true);
@@ -141,16 +146,18 @@ UnifracWeightedCommand::UnifracWeightedCommand(string option) {
                                treefile = m->getTreeFile(); 
                                if (treefile != "") { m->mothurOut("Using " + treefile + " as input file for the tree parameter."); m->mothurOutEndLine(); }
                                else {  m->mothurOut("You have no current tree file and the tree parameter is required."); m->mothurOutEndLine(); abort = true; }                                                               
-                       }       
+                       }else { m->setTreeFile(treefile); }     
                        
                        //check for required parameters
                        groupfile = validParameter.validFile(parameters, "group", true);
                        if (groupfile == "not open") { abort = true; }
                        else if (groupfile == "not found") { groupfile = ""; }
+                       else { m->setGroupFile(groupfile); }
                        
                        namefile = validParameter.validFile(parameters, "name", true);
                        if (namefile == "not open") { abort = true; }
                        else if (namefile == "not found") { namefile = ""; }
+                       else { m->setNameFile(namefile); }
                        
                        outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = ""; }
                        
@@ -200,6 +207,8 @@ int UnifracWeightedCommand::execute() {
        
                if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
+               m->setTreeFile(treefile);
+               
                if (groupfile != "") {
                        //read in group map info.
                        tmap = new TreeMap(groupfile);
@@ -243,7 +252,7 @@ int UnifracWeightedCommand::execute() {
                                
                                if (m->control_pressed) { 
                                        delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }
-                                       for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); } outputTypes.clear();
+                                       for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]); } outputTypes.clear();
                                        m->Groups.clear();
                                        return 0;
                                }
@@ -286,7 +295,7 @@ int UnifracWeightedCommand::execute() {
                for (int i = 0; i < T.size(); i++) {
                        
                        if (m->control_pressed) { delete tmap; delete weighted;
-                               for (int i = 0; i < T.size(); i++) { delete T[i]; } outSum.close(); for (int i = 0; i < outputNames.size(); i++) {      remove(outputNames[i].c_str());  } return 0; }
+                               for (int i = 0; i < T.size(); i++) { delete T[i]; } outSum.close(); for (int i = 0; i < outputNames.size(); i++) {      m->mothurRemove(outputNames[i]);  } return 0; }
 
                        counter = 0;
                        rScores.resize(numComp);  //data[0] = weightedscore AB, data[1] = weightedscore AC...
@@ -301,7 +310,7 @@ int UnifracWeightedCommand::execute() {
                        userData = weighted->getValues(T[i], processors, outputDir);  //userData[0] = weightedscore
                        
                        if (m->control_pressed) { delete tmap; delete weighted;
-                               for (int i = 0; i < T.size(); i++) { delete T[i]; } if (random) { delete output; } outSum.close(); for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str());  } return 0; }
+                               for (int i = 0; i < T.size(); i++) { delete T[i]; } if (random) { delete output; } outSum.close(); for (int i = 0; i < outputNames.size(); i++) {       m->mothurRemove(outputNames[i]);  } return 0; }
                        
                        //save users score
                        for (int s=0; s<numComp; s++) {
@@ -355,7 +364,7 @@ int UnifracWeightedCommand::execute() {
                                        #endif
                                        
                                        if (m->control_pressed) { delete tmap; delete weighted;
-                                               for (int i = 0; i < T.size(); i++) { delete T[i]; } delete output; outSum.close(); for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str());  } return 0; }
+                                               for (int i = 0; i < T.size(); i++) { delete T[i]; } delete output; outSum.close(); for (int i = 0; i < outputNames.size(); i++) {       m->mothurRemove(outputNames[i]);  } return 0; }
                                        
                                        //report progress
 //                                     m->mothurOut("Iter: " + toString(j+1)); m->mothurOutEndLine();          
@@ -393,7 +402,7 @@ int UnifracWeightedCommand::execute() {
                
                
                if (m->control_pressed) { delete tmap; delete weighted;
-                       for (int i = 0; i < T.size(); i++) { delete T[i]; } outSum.close(); for (int i = 0; i < outputNames.size(); i++) {      remove(outputNames[i].c_str());  } return 0;  }
+                       for (int i = 0; i < T.size(); i++) { delete T[i]; } outSum.close(); for (int i = 0; i < outputNames.size(); i++) {      m->mothurRemove(outputNames[i]);  } return 0;  }
                
                printWSummaryFile();
                
@@ -406,7 +415,7 @@ int UnifracWeightedCommand::execute() {
                
                
                if (m->control_pressed) { 
-                       for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  }
+                       for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);  }
                        return 0; 
                }
                
@@ -491,7 +500,7 @@ int UnifracWeightedCommand::createProcesses(Tree* t, vector< vector<string> > na
                        double tempScore;
                        for (int j = lines[(i+1)].start; j < (lines[(i+1)].start + lines[(i+1)].num); j++) { in >> tempScore; scores[j].push_back(tempScore); }
                        in.close();
-                       remove(s.c_str());
+                       m->mothurRemove(s);
                }
                
                return 0;