added sort to heatmap to put shared otus at the top and updated some error checking

[mothur.git] / readtreecommand.cpp

diff --git a/readtreecommand.cpp b/readtreecommand.cpp
index 452c0ec7b2fb881d46884832906ebd5053a5e7ae..6af28ad7788a351e1a320aaf433c800c2c529f1b 100644 (file)
--- a/readtreecommand.cpp
+++ b/readtreecommand.cpp
@@ -18,6 +18,9 @@ ReadTreeCommand::ReadTreeCommand(){
                //read in group map info.
                treeMap = new TreeMap(globaldata->getGroupFile());
                treeMap->readMap();
+               
+               //memory leak prevention
+               //if (globaldata->gTreemap != NULL) { delete globaldata->gTreemap;  }
                globaldata->gTreemap = treeMap;
 
                read = new ReadNewickTree(filename);
@@ -43,12 +46,19 @@ ReadTreeCommand::~ReadTreeCommand(){
 
 int ReadTreeCommand::execute(){
        try {
-       
-               read->read(); 
+               int readOk;
+               
+               readOk = read->read(); 
+               
+               if (readOk != 0) { cout << "Read Terminated." << endl; globaldata->gTree.clear(); delete globaldata->gTreemap; return 0; }
                
-               Tree* T = globaldata->gTree;
-//             T->createNewickFile();
+               vector<Tree*> T = globaldata->gTree;
                
+               //assemble users trees
+               for (int i = 0; i < T.size(); i++) {
+                       T[i]->assembleTree();
+               }
+
                return 0;
        }
        catch(exception& e) {
@@ -60,4 +70,5 @@ int ReadTreeCommand::execute(){
                exit(1);
        }
 }
-//**********************************************************************************************************************
\ No newline at end of file
+
+//**********************************************************************************************************************