fixed phylo.diversity

[mothur.git] / readtreecommand.cpp

diff --git a/readtreecommand.cpp b/readtreecommand.cpp
index 0a86f36dfdced49cb6151205e82c0372556e1209..fdfdb050f22c4ccc281646d1d56c8a5aa6b33806 100644 (file)
--- a/readtreecommand.cpp
+++ b/readtreecommand.cpp
@@ -154,46 +154,47 @@ int ReadTreeCommand::execute(){
                }
 
                
-//             Sarah, isn't this checking already done when assigning the sequences to the groups?  it makes read.tree
-//             wicked slow...  For some reason my tree is coming in here eventhough the number of sequences in the tree
-//             agrees with the number of lines in the name file and the number of sequences represented by the name file
-//             agrees with the number of sequences in the group file
-
-               //output any names that are in group file but not in tree
+               //if you provide a namefile we will use the numNames in the namefile as long as the number of unique match the tree names size.
+               int numNamesInTree;
+               if (namefile != "")  {  
+                       if (numUniquesInName == globaldata->Treenames.size()) {  numNamesInTree = nameMap.size();  }
+                       else {   numNamesInTree = globaldata->Treenames.size();  }
+               }else {  numNamesInTree = globaldata->Treenames.size();  }
                
-//             if (globaldata->Treenames.size() < treeMap->getNumSeqs()) {
-//                     cout << "in here" << endl;
-//                     for (int i = 0; i < treeMap->namesOfSeqs.size(); i++) {
-//                             //is that name in the tree?
-//                             int count = 0;
-//                             for (int j = 0; j < globaldata->Treenames.size(); j++) {
-//                                     if (treeMap->namesOfSeqs[i] == globaldata->Treenames[j]) { break; } //found it
-//                                     count++;
-//                             }
-//                             
-//                             if (m->control_pressed) {  
-//                                     for (int i = 0; i < T.size(); i++) {  delete T[i];  }
-//                                     globaldata->gTree.clear();
-//                                     delete globaldata->gTreemap;
-//                                     return 0;
-//                             }
-//                             
-//                             //then you did not find it so report it 
-//                             if (count == globaldata->Treenames.size()) { 
-//                                     //if it is in your namefile then don't remove
-//                                     map<string, string>::iterator it = nameMap.find(treeMap->namesOfSeqs[i]);
-//                                     
-//                                     if (it == nameMap.end()) {
-//                                             m->mothurOut(treeMap->namesOfSeqs[i] + " is in your groupfile and not in your tree. It will be disregarded."); m->mothurOutEndLine();
-//                                             treeMap->removeSeq(treeMap->namesOfSeqs[i]);
-//                                             i--; //need this because removeSeq removes name from namesOfSeqs
-//                                     }
-//                             }
-//                     }
-//                     
-//                     globaldata->gTreemap = treeMap;
-//             }
                
+               //output any names that are in group file but not in tree
+               if (numNamesInTree < treeMap->getNumSeqs()) {
+                       for (int i = 0; i < treeMap->namesOfSeqs.size(); i++) {
+                               //is that name in the tree?
+                               int count = 0;
+                               for (int j = 0; j < globaldata->Treenames.size(); j++) {
+                                       if (treeMap->namesOfSeqs[i] == globaldata->Treenames[j]) { break; } //found it
+                                       count++;
+                               }
+                               
+                               if (m->control_pressed) {  
+                                       for (int i = 0; i < T.size(); i++) {  delete T[i];  }
+                                       globaldata->gTree.clear();
+                                       delete globaldata->gTreemap;
+                                       return 0;
+                               }
+                               
+                               //then you did not find it so report it 
+                               if (count == globaldata->Treenames.size()) { 
+                                       //if it is in your namefile then don't remove
+                                       map<string, string>::iterator it = nameMap.find(treeMap->namesOfSeqs[i]);
+                                       
+                                       if (it == nameMap.end()) {
+                                               m->mothurOut(treeMap->namesOfSeqs[i] + " is in your groupfile and not in your tree. It will be disregarded."); m->mothurOutEndLine();
+                                               treeMap->removeSeq(treeMap->namesOfSeqs[i]);
+                                               i--; //need this because removeSeq removes name from namesOfSeqs
+                                       }
+                               }
+                       }
+                       
+                       globaldata->gTreemap = treeMap;
+               }
+
                return 0;
        }
        catch(exception& e) {
@@ -205,6 +206,7 @@ int ReadTreeCommand::execute(){
 int ReadTreeCommand::readNamesFile() {
        try {
                globaldata->names.clear();
+               numUniquesInName = 0;
                
                ifstream in;
                m->openInputFile(namefile, in);
@@ -215,6 +217,8 @@ int ReadTreeCommand::readNamesFile() {
                while(!in.eof()) {
                        in >> first >> second; m->gobble(in);
                        
+                       numUniquesInName++;
+
                        itNames = globaldata->names.find(first);
                        if (itNames == globaldata->names.end()) {  
                                globaldata->names[first] = second; 
@@ -224,7 +228,7 @@ int ReadTreeCommand::readNamesFile() {
                                m->splitAtComma(second, dupNames);
                                
                                for (int i = 0; i < dupNames.size(); i++) {     nameMap[dupNames[i]] = dupNames[i];  }
-                       }else {  m->mothurOut(first + " has already been seen in namefile, disregarding names file."); m->mothurOutEndLine(); in.close(); globaldata->names.clear(); return 1; }                        
+                       }else {  m->mothurOut(first + " has already been seen in namefile, disregarding names file."); m->mothurOutEndLine(); in.close(); globaldata->names.clear(); namefile = ""; return 1; }                 
                }
                in.close();