added name option to read.tree for use in unifrac and parimony commands

[mothur.git] / readtreecommand.cpp

diff --git a/readtreecommand.cpp b/readtreecommand.cpp
index 5b371f51acc0eeec74e2b52c5c9a63319a74b892..09f899b947bf9bb4b455de86479d34ffa709d46f 100644 (file)
--- a/readtreecommand.cpp
+++ b/readtreecommand.cpp
@@ -20,7 +20,7 @@ ReadTreeCommand::ReadTreeCommand(string option){
                
                else {
                        //valid paramters for this command
-                       string Array[] =  {"tree","group","outputdir","inputdir"};
+                       string Array[] =  {"tree","group","name","outputdir","inputdir"};
                        vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                        
                        OptionParser parser(option);
@@ -56,6 +56,15 @@ ReadTreeCommand::ReadTreeCommand(string option){
                                        //if the user has not given a path then, add inputdir. else leave path alone.
                                        if (path == "") {       parameters["group"] = inputDir + it->second;            }
                                }
+                               
+                               it = parameters.find("name");
+                               //user has given a template file
+                               if(it != parameters.end()){ 
+                                       path = hasPath(it->second);
+                                       //if the user has not given a path then, add inputdir. else leave path alone.
+                                       if (path == "") {       parameters["name"] = inputDir + it->second;             }
+                               }
+
                        }
 
                        
@@ -76,6 +85,11 @@ ReadTreeCommand::ReadTreeCommand(string option){
                                globaldata->gTreemap = treeMap;
                        }
                        
+                       namefile = validParameter.validFile(parameters, "name", true);
+                       if (namefile == "not open") { abort = true; }
+                       else if (namefile == "not found") { treefile = ""; }
+                       else { readNamesFile(); }       
+                       
                        if (abort == false) {
                                filename = treefile;
                                read = new ReadNewickTree(filename);
@@ -130,7 +144,7 @@ int ReadTreeCommand::execute(){
                        T[i]->assembleTree();
                }
 
-               //output any names that are in names file but not in tree
+               //output any names that are in group file but not in tree
                if (globaldata->Treenames.size() < treeMap->getNumSeqs()) {
                        for (int i = 0; i < treeMap->namesOfSeqs.size(); i++) {
                                //is that name in the tree?
@@ -142,8 +156,13 @@ int ReadTreeCommand::execute(){
                                
                                //then you did not find it so report it 
                                if (count == globaldata->Treenames.size()) { 
-                                       mothurOut(treeMap->namesOfSeqs[i] + " is in your namefile and not in your tree. It will be disregarded."); mothurOutEndLine();
-                                       treeMap->removeSeq(treeMap->namesOfSeqs[i]);
+                                       //if it is in your namefile then don't remove
+                                       map<string, string>::iterator it = nameMap.find(treeMap->namesOfSeqs[i]);
+                                       
+                                       if (it == nameMap.end()) {
+                                               mothurOut(treeMap->namesOfSeqs[i] + " is in your groupfile and not in your tree. It will be disregarded."); mothurOutEndLine();
+                                               treeMap->removeSeq(treeMap->namesOfSeqs[i]);
+                                       }
                                }
                        }
                }
@@ -155,5 +174,39 @@ int ReadTreeCommand::execute(){
                exit(1);
        }
 }
+/*****************************************************************/
+int ReadTreeCommand::readNamesFile() {
+       try {
+               globaldata->names.clear();
+               
+               ifstream in;
+               openInputFile(namefile, in);
+               
+               string first, second;
+               map<string, string>::iterator itNames;
+               
+               while(!in.eof()) {
+                       in >> first >> second; gobble(in);
+                       
+                       itNames = globaldata->names.find(first);
+                       if (itNames == globaldata->names.end()) {  
+                               globaldata->names[first] = second; 
+                               
+                               //we need a list of names in your namefile to use above when removing extra seqs above so we don't remove them
+                               vector<string> dupNames;
+                               splitAtComma(second, dupNames);
+                               
+                               for (int i = 0; i < dupNames.size(); i++) {     nameMap[dupNames[i]] = dupNames[i];  }
+                       }else {  mothurOut(first + " has already been seen in namefile, disregarding names file."); mothurOutEndLine(); in.close(); globaldata->names.clear(); return 1; }                      
+               }
+               in.close();
+               
+               return 0;
+       }
+       catch(exception& e) {
+               errorOut(e, "ReadTreeCommand", "readNamesFile");
+               exit(1);
+       }
+}
 
 //**********************************************************************************************************************