X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=readtreecommand.cpp;h=89efc9abcf0057f68189ddad6975b5e1464fca09;hb=e03de8796670a0c747aed63483daa09c8b86aea0;hp=0a86f36dfdced49cb6151205e82c0372556e1209;hpb=0034e0e7f58987a1e6e0881f5495a4c542842645;p=mothur.git

diff --git a/readtreecommand.cpp b/readtreecommand.cpp
index 0a86f36..89efc9a 100644
--- a/readtreecommand.cpp
+++ b/readtreecommand.cpp
@@ -76,8 +76,20 @@ ReadTreeCommand::ReadTreeCommand(string option)  {
 			
 			groupfile = validParameter.validFile(parameters, "group", true);
 			if (groupfile == "not open") { abort = true; }	
-			else if (groupfile == "not found") { groupfile = ""; m->mothurOut("group is a required parameter for the read.tree command."); m->mothurOutEndLine(); abort = true;	}
-			else {  
+			else if (groupfile == "not found") { 
+				groupfile = ""; 
+				
+				m->mothurOut("You have not provided a group file. I am assumming all sequence are from the same group."); m->mothurOutEndLine(); 	
+				
+				if (treefile != "") {  Tree* tree = new Tree(treefile); delete tree;  } //extracts names from tree to make faked out groupmap
+				
+				globaldata->setGroupFile(groupfile); 
+				//read in group map info.
+				treeMap = new TreeMap();
+				for (int i = 0; i < globaldata->Treenames.size(); i++) { treeMap->addSeq(globaldata->Treenames[i], "Group1"); }
+				globaldata->gTreemap = treeMap;
+					
+			}else {  
 				globaldata->setGroupFile(groupfile); 
 				//read in group map info.
 				treeMap = new TreeMap(groupfile);
@@ -154,46 +166,47 @@ 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 +218,7 @@ int ReadTreeCommand::execute(){
 int ReadTreeCommand::readNamesFile() {
 	try {
 		globaldata->names.clear();
+		numUniquesInName = 0;
 		
 		ifstream in;
 		m->openInputFile(namefile, in);
@@ -215,6 +229,8 @@ 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; 
@@ -223,8 +239,8 @@ int ReadTreeCommand::readNamesFile() {
 				vector<string> dupNames;
 				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; }			
+				for (int i = 0; i < dupNames.size(); i++) {	nameMap[dupNames[i]] = dupNames[i];  if ((groupfile == "") && (i != 0)) { globaldata->gTreemap->addSeq(dupNames[i], "Group1"); }  }
+			}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();