rewrote metastats command in c++, added mothurRemove function to handle ~ error....

[mothur.git] / phylodiversitycommand.cpp

diff --git a/phylodiversitycommand.cpp b/phylodiversitycommand.cpp
index 0822582b2d16b4575f584fbefdd2fffefb39cf55..d273e1dd3f4aab843190aceb4888e547a8bd81f5 100644 (file)
--- a/phylodiversitycommand.cpp
+++ b/phylodiversitycommand.cpp
@@ -52,7 +52,7 @@ string PhyloDiversityCommand::getHelpString(){
                helpString += "The phylo.diversity command should be in the following format: phylo.diversity(groups=yourGroups, rarefy=yourRarefy, iters=yourIters).\n";
                helpString += "Example phylo.diversity(groups=A-B-C, rarefy=T, iters=500).\n";
                helpString += "The phylo.diversity command output two files: .phylo.diversity and if rarefy=T, .rarefaction.\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) {
@@ -84,6 +84,7 @@ PhyloDiversityCommand::PhyloDiversityCommand(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();;
@@ -136,6 +137,10 @@ PhyloDiversityCommand::PhyloDiversityCommand(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);
@@ -145,21 +150,18 @@ PhyloDiversityCommand::PhyloDiversityCommand(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") { 
-                               //if there is a current design file, use it
-                               groupfile = m->getGroupFile(); 
-                               if (groupfile != "") { m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine(); }
-                               else {  m->mothurOut("You have no current group file and the group parameter is required."); m->mothurOutEndLine(); abort = true; }                                                             
-                       }
+                       if (groupfile == "not open") { groupfile = ""; 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 = m->hasPath(treefile);       }
                        
@@ -210,9 +212,18 @@ int PhyloDiversityCommand::execute(){
                
                if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
-               //read in group map info.
-               tmap = new TreeMap(groupfile);
-               tmap->readMap();
+               m->setTreeFile(treefile);
+               
+               if (groupfile != "") {
+                       //read in group map info.
+                       tmap = new TreeMap(groupfile);
+                       tmap->readMap();
+               }else{ //fake out by putting everyone in one group
+                       Tree* tree = new Tree(treefile); delete tree;  //extracts names from tree to make faked out groupmap
+                       tmap = new TreeMap();
+                       
+                       for (int i = 0; i < m->Treenames.size(); i++) { tmap->addSeq(m->Treenames[i], "Group1"); }
+               }
                
                if (namefile != "") { readNamesFile(); }
                
@@ -246,7 +257,7 @@ int PhyloDiversityCommand::execute(){
                                
                                if (m->control_pressed) { 
                                        delete tmap; for (int i = 0; i < trees.size(); i++) { delete trees[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;
                                }
@@ -266,7 +277,7 @@ int PhyloDiversityCommand::execute(){
                }
                
                SharedUtil* util = new SharedUtil();
-               util->setGroups(m->Groups, tmap->namesOfGroups, "treegroup");   //sets the groups the user wants to analyze
+               util->setGroups(m->Groups, tmap->namesOfGroups, "phylo.diversity");     //sets the groups the user wants to analyze
                delete util;
                
                //incase the user had some mismatches between the tree and group files we don't want group xxx to be analyzed
@@ -277,7 +288,7 @@ int PhyloDiversityCommand::execute(){
                //for each of the users trees
                for(int i = 0; i < trees.size(); i++) {
                
-                       if (m->control_pressed) { delete tmap; for (int j = 0; j < trees.size(); j++) { delete trees[j]; } for (int j = 0; j < outputNames.size(); j++) {       remove(outputNames[j].c_str());         } return 0; }
+                       if (m->control_pressed) { delete tmap; for (int j = 0; j < trees.size(); j++) { delete trees[j]; } for (int j = 0; j < outputNames.size(); j++) {       m->mothurRemove(outputNames[j]);        } return 0; }
                        
                        ofstream outSum, outRare, outCollect;
                        string outSumFile = outputDir + m->getRootName(m->getSimpleName(treefile))  + toString(i+1) + ".phylodiv.summary";
@@ -366,7 +377,7 @@ int PhyloDiversityCommand::execute(){
                }
                
        
-               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; }
 
                m->mothurOutEndLine();
                m->mothurOut("Output File Names: "); m->mothurOutEndLine();
@@ -456,7 +467,7 @@ int PhyloDiversityCommand::createProcesses(vector<int>& procIters, Tree* t, map<
                        }
                                
                        in.close();
-                       remove(inTemp.c_str());
+                       m->mothurRemove(inTemp);
                }
                
 #endif