made read.tree not require a groupfile, if one is not given all seqs are assumed...

[mothur.git] / tree.cpp

diff --git a/tree.cpp b/tree.cpp
index a104477d0a90280a528d5cea4deb80ba2133ba09..3cb26113f8deb8acf3bf28f7040becf2bac7385f 100644 (file)
--- a/tree.cpp
+++ b/tree.cpp
@@ -9,7 +9,19 @@
 
 #include "tree.h"
 
-
+/*****************************************************************/
+Tree::Tree(string g) {
+       try {
+               globaldata = GlobalData::getInstance();
+               m = MothurOut::getInstance();
+               
+               parseTreeFile();  globaldata->runParse = false;  
+       }
+       catch(exception& e) {
+               m->errorOut(e, "Tree", "Tree - just parse");
+               exit(1);
+       }
+}
 /*****************************************************************/
 Tree::Tree() {
        try {
@@ -70,7 +82,7 @@ void Tree::addNamesToCounts() {
                                
                //go through each leaf and update its pcounts and pgroups
                
-               float A = clock();
+               //float A = clock();
 
                for (int i = 0; i < numLeaves; i++) {
 
@@ -137,8 +149,8 @@ void Tree::addNamesToCounts() {
                        }//end else
                }//end for              
                
-               float B = clock();
-               cout << "addNamesToCounts\t" << (B - A) / CLOCKS_PER_SEC << endl;       
+               //float B = clock();
+               //cout << "addNamesToCounts\t" << (B - A) / CLOCKS_PER_SEC << endl;     
 
        }
        catch(exception& e) {
@@ -175,7 +187,7 @@ void Tree::setIndex(string searchName, int index) {
 /*****************************************************************/
 int Tree::assembleTree() {
        try {
-               float A = clock();
+               //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();  }
@@ -187,8 +199,8 @@ 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;
+               //float B = clock();
+               //cout << "assembleTree\t" << (B-A) / CLOCKS_PER_SEC << endl;
                return 0;
        }
        catch(exception& e) {