removed UWSig and WSig from output if user does not set random=T

[mothur.git] / parsimonycommand.cpp

diff --git a/parsimonycommand.cpp b/parsimonycommand.cpp
index a8c2d156be775455c729d9341386ecfb952323e4..ff1209287b4e17b2fcc58678703123aae2cadbc1 100644 (file)
--- a/parsimonycommand.cpp
+++ b/parsimonycommand.cpp
@@ -43,7 +43,7 @@ string ParsimonyCommand::getHelpString(){
                helpString += "Example parsimony(random=out, iters=500).\n";
                helpString += "The default value for random is "" (meaning you want to use the trees in your inputfile, randomtree=out means you just want the random distribution of trees outputted to out.rd_parsimony),\n";
                helpString += "and iters is 1000.  The parsimony command output two files: .parsimony and .psummary their descriptions are in the manual.\n";
-               helpString += "Note: No spaces between parameter labels (i.e. random), '=' and parameters (i.e.yourOutputFilename).\n\n";
+               helpString += "Note: No spaces between parameter labels (i.e. random), '=' and parameters (i.e.yourOutputFilename).\n";
                return helpString;
        }
        catch(exception& e) {
@@ -74,6 +74,7 @@ ParsimonyCommand::ParsimonyCommand(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();
@@ -125,6 +126,10 @@ ParsimonyCommand::ParsimonyCommand(string option)  {
                        }
                        
                        m->runParse = true;
+                       m->Groups.clear();
+                       m->namesOfGroups.clear();
+                       m->Treenames.clear();
+                       m->names.clear();
                        
                        outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = ""; }
                        
@@ -139,16 +144,18 @@ ParsimonyCommand::ParsimonyCommand(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); }
                        }
                        
                        //if the user changes the output directory command factory will send this info to us in the output parameter 
@@ -188,6 +195,9 @@ int ParsimonyCommand::execute() {
                //randomtree will tell us if user had their own treefile or if they just want the random distribution
                //user has entered their own tree
                if (randomtree == "") { 
+                       
+                       m->setTreeFile(treefile);
+                       
                        if (groupfile != "") {
                                //read in group map info.
                                tmap = new TreeMap(groupfile);
@@ -231,7 +241,7 @@ int ParsimonyCommand::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 +296,7 @@ int ParsimonyCommand::execute() {
                        delete reading; delete pars; delete output;
                        delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }
                        if (randomtree == "") {  outSum.close();  }
-                       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;
                }
@@ -311,7 +321,7 @@ int ParsimonyCommand::execute() {
                                        delete reading; delete pars; delete output;
                                        delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }
                                        if (randomtree == "") {  outSum.close();  }
-                                       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;
                                }
@@ -349,7 +359,7 @@ int ParsimonyCommand::execute() {
                                if (m->control_pressed) { 
                                        delete reading; delete pars; delete output; delete randT;
                                        if (randomtree == "") {  outSum.close();  }
-                                       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();
                                        delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }
                                        m->Groups.clear();
                                        return 0;
@@ -387,7 +397,7 @@ int ParsimonyCommand::execute() {
                                if (m->control_pressed) { 
                                        delete reading; delete pars; delete output; delete randT;
                                        delete tmap; 
-                                       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;
                                }
@@ -399,7 +409,7 @@ int ParsimonyCommand::execute() {
                                if (m->control_pressed) { 
                                        delete reading; delete pars;  delete output; delete randT;
                                        delete tmap; 
-                                       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;
                                }
@@ -456,7 +466,7 @@ int ParsimonyCommand::execute() {
                                delete reading; delete pars; delete output;
                                delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }
                                if (randomtree == "") {  outSum.close();  }
-                               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;
                }
@@ -475,7 +485,7 @@ int ParsimonyCommand::execute() {
                delete pars; delete output; 
                delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }
                
-               if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str()); } outputTypes.clear(); return 0;}
+               if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]); } outputTypes.clear(); return 0;}
                
                m->mothurOutEndLine();
                m->mothurOut("Output File Names: "); m->mothurOutEndLine();