moved utilities out of mothur.h and into mothurOut class.

[mothur.git] / phylodiversitycommand.cpp

diff --git a/phylodiversitycommand.cpp b/phylodiversitycommand.cpp
index 5a2d33fd724d94949bb03adb617639a1ce28450c..619a7f7786cbe9852f87ea5953ff52459284f5b3 100644 (file)
--- a/phylodiversitycommand.cpp
+++ b/phylodiversitycommand.cpp
@@ -34,7 +34,7 @@ PhyloDiversityCommand::PhyloDiversityCommand(string option)  {
                        }
                        
                        //if the user changes the output directory command factory will send this info to us in the output parameter 
-                       outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = hasPath(globaldata->getTreeFile());         }
+                       outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(globaldata->getTreeFile());              }
                        
                        if (globaldata->gTree.size() == 0) {//no trees were read
                                m->mothurOut("You must execute the read.tree command, before you may execute the phylo.diversity command."); m->mothurOutEndLine(); abort = true;  }
@@ -47,22 +47,22 @@ PhyloDiversityCommand::PhyloDiversityCommand(string option)  {
                        convert(temp, iters); 
                        
                        temp = validParameter.validFile(parameters, "rarefy", false);                   if (temp == "not found") { temp = "F"; }
-                       rarefy = isTrue(temp);
+                       rarefy = m->isTrue(temp);
                        if (!rarefy) { iters = 1;  }
                        
                        temp = validParameter.validFile(parameters, "summary", false);                  if (temp == "not found") { temp = "T"; }
-                       summary = isTrue(temp);
+                       summary = m->isTrue(temp);
                        
                        temp = validParameter.validFile(parameters, "scale", false);                    if (temp == "not found") { temp = "F"; }
-                       scale = isTrue(temp);
+                       scale = m->isTrue(temp);
                        
                        temp = validParameter.validFile(parameters, "collect", false);                  if (temp == "not found") { temp = "F"; }
-                       collect = isTrue(temp);
+                       collect = m->isTrue(temp);
                        
                        groups = validParameter.validFile(parameters, "groups", false);                 
                        if (groups == "not found") { groups = ""; Groups = globaldata->gTreemap->namesOfGroups;  globaldata->Groups = Groups;  }
                        else { 
-                               splitAtDash(groups, Groups);
+                               m->splitAtDash(groups, Groups);
                                globaldata->Groups = Groups;
                        }
                        
@@ -124,20 +124,20 @@ int PhyloDiversityCommand::execute(){
                        if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());         } return 0; }
                        
                        ofstream outSum, outRare, outCollect;
-                       string outSumFile = outputDir + getRootName(getSimpleName(globaldata->getTreeFile()))  + toString(i+1) + ".phylodiv.summary";
-                       string outRareFile = outputDir + getRootName(getSimpleName(globaldata->getTreeFile()))  + toString(i+1) + ".phylodiv.rarefaction";
-                       string outCollectFile = outputDir + getRootName(getSimpleName(globaldata->getTreeFile()))  + toString(i+1) + ".phylodiv";
+                       string outSumFile = outputDir + m->getRootName(m->getSimpleName(globaldata->getTreeFile()))  + toString(i+1) + ".phylodiv.summary";
+                       string outRareFile = outputDir + m->getRootName(m->getSimpleName(globaldata->getTreeFile()))  + toString(i+1) + ".phylodiv.rarefaction";
+                       string outCollectFile = outputDir + m->getRootName(m->getSimpleName(globaldata->getTreeFile()))  + toString(i+1) + ".phylodiv";
                        
-                       if (summary)    { openOutputFile(outSumFile, outSum); outputNames.push_back(outSumFile);                                }
-                       if (rarefy)             { openOutputFile(outRareFile, outRare); outputNames.push_back(outRareFile);                             }
-                       if (collect)    { openOutputFile(outCollectFile, outCollect); outputNames.push_back(outCollectFile);    }
+                       if (summary)    { m->openOutputFile(outSumFile, outSum); outputNames.push_back(outSumFile);                             }
+                       if (rarefy)             { m->openOutputFile(outRareFile, outRare); outputNames.push_back(outRareFile);                          }
+                       if (collect)    { m->openOutputFile(outCollectFile, outCollect); outputNames.push_back(outCollectFile); }
                        
                        int numLeafNodes = trees[i]->getNumLeaves();
                        
                        //create a vector containing indexes of leaf nodes, randomize it, select nodes to send to calculator
                        vector<int> randomLeaf;
                        for (int j = 0; j < numLeafNodes; j++) {  
-                               if (inUsersGroups(trees[i]->tree[j].getGroup(), globaldata->Groups) == true) { //is this a node from the group the user selected.
+                               if (m->inUsersGroups(trees[i]->tree[j].getGroup(), globaldata->Groups) == true) { //is this a node from the group the user selected.
                                        randomLeaf.push_back(j); 
                                }
                        }