X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=tree.cpp;h=7da3cef3718502640d61377bccbaae0d8e4213d3;hb=aa9238c0a9e6e7aa0ed8b8b606b08ad4fd7dcfe3;hp=731eb64d93f95b485f8607308e3e88345138813c;hpb=5a1e62397b91f57d0d3aff635891df04b8999a88;p=mothur.git

diff --git a/tree.cpp b/tree.cpp
index 731eb64..7da3cef 100644
--- a/tree.cpp
+++ b/tree.cpp
@@ -14,6 +14,7 @@
 Tree::Tree() {
 	try {
 		globaldata = GlobalData::getInstance();
+		m = MothurOut::getInstance();
 		
 		if (globaldata->runParse == true) {  parseTreeFile();  globaldata->runParse = false;  }
 //for(int i = 0; i < 	globaldata->Treenames.size(); i++) { cout << i << '\t' << globaldata->Treenames[i] << endl;  }	
@@ -44,7 +45,7 @@ Tree::Tree() {
 		}
 	}
 	catch(exception& e) {
-		errorOut(e, "Tree", "Tree");
+		m->errorOut(e, "Tree", "Tree");
 		exit(1);
 	}
 }
@@ -73,7 +74,7 @@ void Tree::addNamesToCounts() {
 			
 			map<string, string>::iterator itNames = globaldata->names.find(name);
 			
-			if (itNames == globaldata->names.end()) { mothurOut(name + " is not in your name file, please correct."); mothurOutEndLine(); exit(1);  }
+			if (itNames == globaldata->names.end()) { m->mothurOut(name + " is not in your name file, please correct."); m->mothurOutEndLine(); exit(1);  }
 			else {
 				vector<string> dupNames;
 				splitAtComma(globaldata->names[name], dupNames);
@@ -134,7 +135,7 @@ void Tree::addNamesToCounts() {
 				
 	}
 	catch(exception& e) {
-		errorOut(e, "Tree", "addNamesToCounts");
+		m->errorOut(e, "Tree", "addNamesToCounts");
 		exit(1);
 	}
 }
@@ -148,7 +149,7 @@ int Tree::getIndex(string searchName) {
 		
 	}
 	catch(exception& e) {
-		errorOut(e, "Tree", "getIndex");
+		m->errorOut(e, "Tree", "getIndex");
 		exit(1);
 	}
 }
@@ -160,12 +161,12 @@ void Tree::setIndex(string searchName, int index) {
 		globaldata->gTreemap->setIndex(searchName, index);
 	}
 	catch(exception& e) {
-		errorOut(e, "Tree", "setIndex");
+		m->errorOut(e, "Tree", "setIndex");
 		exit(1);
 	}
 }
 /*****************************************************************/
-void Tree::assembleTree() {
+int Tree::assembleTree() {
 	try {
 	
 		//if user has given a names file we want to include that info in the pgroups and pcount info.
@@ -173,12 +174,16 @@ void Tree::assembleTree() {
 		
 		//build the pGroups in non leaf nodes to be used in the parsimony calcs.
 		for (int i = numLeaves; i < numNodes; i++) {
+			if (m->control_pressed) { return 1; }
+
 			tree[i].pGroups = (mergeGroups(i));
 			tree[i].pcount = (mergeGcounts(i));
 		}
+		
+		return 0;
 	}
 	catch(exception& e) {
-		errorOut(e, "Tree", "assembleTree");
+		m->errorOut(e, "Tree", "assembleTree");
 		exit(1);
 	}
 }
@@ -216,7 +221,7 @@ void Tree::getCopy(Tree* copy) {
 		
 	}
 	catch(exception& e) {
-		errorOut(e, "Tree", "getCopy");
+		m->errorOut(e, "Tree", "getCopy");
 		exit(1);
 	}
 }
@@ -269,7 +274,7 @@ map<string, int> Tree::mergeGroups(int i) {
 		return parsimony;
 	}
 	catch(exception& e) {
-		errorOut(e, "Tree", "mergeGroups");
+		m->errorOut(e, "Tree", "mergeGroups");
 		exit(1);
 	}
 }
@@ -335,7 +340,7 @@ map<string, int> Tree::mergeUserGroups(int i, vector<string> g) {
 		return parsimony;
 	}
 	catch(exception& e) {
-		errorOut(e, "Tree", "mergeUserGroups");
+		m->errorOut(e, "Tree", "mergeUserGroups");
 		exit(1);
 	}
 }
@@ -358,7 +363,7 @@ map<string,int> Tree::mergeGcounts(int position) {
 		return sum;
 	}
 	catch(exception& e) {
-		errorOut(e, "Tree", "mergeGcounts");
+		m->errorOut(e, "Tree", "mergeGcounts");
 		exit(1);
 	}
 }
@@ -400,7 +405,7 @@ void Tree::randomLabels(vector<string> g) {
 		}
 	}
 	catch(exception& e) {
-		errorOut(e, "Tree", "randomLabels");
+		m->errorOut(e, "Tree", "randomLabels");
 		exit(1);
 	}
 }
@@ -430,7 +435,7 @@ void Tree::randomLabels(string groupA, string groupB) {
 		}
 	}		
 	catch(exception& e) {
-		errorOut(e, "Tree", "randomLabels");
+		m->errorOut(e, "Tree", "randomLabels");
 		exit(1);
 	}
 }
@@ -446,7 +451,7 @@ void Tree::randomBlengths()  {
 		}
 	}
 	catch(exception& e) {
-		errorOut(e, "Tree", "randomBlengths");
+		m->errorOut(e, "Tree", "randomBlengths");
 		exit(1);
 	}
 }
@@ -503,7 +508,7 @@ void Tree::randomTopology() {
 		}
 	}
 	catch(exception& e) {
-		errorOut(e, "Tree", "randomTopology");
+		m->errorOut(e, "Tree", "randomTopology");
 		exit(1);
 	}
 }
@@ -515,7 +520,7 @@ void Tree::print(ostream& out) {
 		out << ";" << endl;
 	}
 	catch(exception& e) {
-		errorOut(e, "Tree", "print");
+		m->errorOut(e, "Tree", "print");
 		exit(1);
 	}
 }
@@ -527,7 +532,7 @@ void Tree::printForBoot(ostream& out) {
 		out << ";" << endl;
 	}
 	catch(exception& e) {
-		errorOut(e, "Tree", "printForBoot");
+		m->errorOut(e, "Tree", "printForBoot");
 		exit(1);
 	}
 }
@@ -549,7 +554,7 @@ void Tree::createNewickFile(string f) {
 		out.close();
 	}
 	catch(exception& e) {
-		errorOut(e, "Tree", "createNewickFile");
+		m->errorOut(e, "Tree", "createNewickFile");
 		exit(1);
 	}
 }
@@ -568,7 +573,7 @@ int Tree::findRoot() {
 		return -1;
 	}
 	catch(exception& e) {
-		errorOut(e, "Tree", "findRoot");
+		m->errorOut(e, "Tree", "findRoot");
 		exit(1);
 	}
 }
@@ -614,7 +619,7 @@ void Tree::printBranch(int node, ostream& out, string mode) {
 		
 	}
 	catch(exception& e) {
-		errorOut(e, "Tree", "printBranch");
+		m->errorOut(e, "Tree", "printBranch");
 		exit(1);
 	}
 }
@@ -710,7 +715,7 @@ void Tree::parseTreeFile() {
 		filehandle.close();
 	}
 	catch(exception& e) {
-		errorOut(e, "Tree", "parseTreeFile");
+		m->errorOut(e, "Tree", "parseTreeFile");
 		exit(1);
 	}
 }
@@ -774,7 +779,7 @@ int Tree::readTreeString(ifstream& filehandle)	{
 		return 0;
 	}
 	catch(exception& e) {
-		errorOut(e, "Tree", "readTreeString");
+		m->errorOut(e, "Tree", "readTreeString");
 		exit(1);
 	}
 }