From: pschloss <pschloss>
Date: Thu, 26 Aug 2010 20:48:56 +0000 (+0000)
Subject: changes to read.tree
X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=commitdiff_plain;h=0034e0e7f58987a1e6e0881f5495a4c542842645

changes to read.tree
---

diff --git a/readtreecommand.cpp b/readtreecommand.cpp
index deae495..0a86f36 100644
--- a/readtreecommand.cpp
+++ b/readtreecommand.cpp
@@ -153,38 +153,46 @@ int ReadTreeCommand::execute(){
 			T[i]->assembleTree();
 		}
 
+		
+//		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 (globaldata->Treenames.size() < 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;
-		}
+		
+//		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;
+//		}
 		
 		return 0;
 	}
diff --git a/tree.cpp b/tree.cpp
index 14d86e6..a104477 100644
--- a/tree.cpp
+++ b/tree.cpp
@@ -69,6 +69,9 @@ void Tree::addNamesToCounts() {
 
 				
 		//go through each leaf and update its pcounts and pgroups
+		
+		float A = clock();
+
 		for (int i = 0; i < numLeaves; i++) {
 
 			string name = tree[i].getName();
@@ -132,7 +135,11 @@ void Tree::addNamesToCounts() {
 				tree[i].setGroup(nodeGroups);
 				
 			}//end else
-		}//end for					
+		}//end for		
+		
+		float B = clock();
+		cout << "addNamesToCounts\t" << (B - A) / CLOCKS_PER_SEC << endl;	
+
 	}
 	catch(exception& e) {
 		m->errorOut(e, "Tree", "addNamesToCounts");
@@ -168,7 +175,8 @@ void Tree::setIndex(string searchName, int index) {
 /*****************************************************************/
 int Tree::assembleTree() {
 	try {
-	
+		float A = clock();
+
 		//if user has given a names file we want to include that info in the pgroups and pcount info.
 		if(globaldata->names.size() != 0) {  addNamesToCounts();  }
 		
@@ -179,7 +187,8 @@ int Tree::assembleTree() {
 			tree[i].pGroups = (mergeGroups(i));
 			tree[i].pcount = (mergeGcounts(i));
 		}
-		
+		float B = clock();
+		cout << "assembleTree\t" << (B-A) / CLOCKS_PER_SEC << endl;
 		return 0;
 	}
 	catch(exception& e) {