From 5589a967aab6b83d826508f4c37a789fb6a2a26e Mon Sep 17 00:00:00 2001
From: westcott <westcott>
Date: Fri, 6 Mar 2009 15:29:54 +0000
Subject: [PATCH] fixed bug wit unifrac files

---
 fullmatrix.cpp               | 26 +++++++++++++++++++-------
 fullmatrix.h                 |  2 +-
 parsimonycommand.cpp         |  1 +
 unifracunweightedcommand.cpp |  1 +
 4 files changed, 22 insertions(+), 8 deletions(-)

diff --git a/fullmatrix.cpp b/fullmatrix.cpp
index 75cb0df..6ff9334 100644
--- a/fullmatrix.cpp
+++ b/fullmatrix.cpp
@@ -10,11 +10,23 @@
 #include "fullmatrix.h"
 
 
-/**************************************************************************
-FullMatrix::FullMatrix(ifstream& in) {
-
-}
-~FullMatrix::FullMatrix(){}
+/**************************************************************************/
+//This constructor reads a distance matrix file and stores the data in the matrix.
+FullMatrix::FullMatrix(ifstream& f) {
+	try{
+		f >> numSeqs;
+		
 	
-	int FullMatrix::getNumSeqs(){}
-*/
\ No newline at end of file
+	}
+	catch(exception& e) {
+		cout << "Standard Error: " << e.what() << " has occurred in the FullMatrix class Function FullMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the FullMatrix class function FullMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+}
+/**************************************************************************/	
+int FullMatrix::getNumSeqs(){ return numSeqs; }
+/**************************************************************************/
\ No newline at end of file
diff --git a/fullmatrix.h b/fullmatrix.h
index 4fe1145..389816a 100644
--- a/fullmatrix.h
+++ b/fullmatrix.h
@@ -17,7 +17,7 @@ class FullMatrix {
 public:
 	FullMatrix(){};
 	FullMatrix(ifstream&);
-	~FullMatrix();
+	~FullMatrix(){};
 	
 	int getNumSeqs();
 	
diff --git a/parsimonycommand.cpp b/parsimonycommand.cpp
index ee2125e..633ddad 100644
--- a/parsimonycommand.cpp
+++ b/parsimonycommand.cpp
@@ -340,6 +340,7 @@ void ParsimonyCommand::setGroups() {
 					allGroups = allGroups.substr(0, allGroups.length()-1);
 				}
 			}else{//user has enter "all" and wants the default groups
+				globaldata->Groups.clear();
 				for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
 					globaldata->Groups.push_back(tmap->namesOfGroups[i]);
 					numGroups++;
diff --git a/unifracunweightedcommand.cpp b/unifracunweightedcommand.cpp
index bebd43b..6e217c8 100644
--- a/unifracunweightedcommand.cpp
+++ b/unifracunweightedcommand.cpp
@@ -220,6 +220,7 @@ void UnifracUnweightedCommand::setGroups() {
 					allGroups = allGroups.substr(0, allGroups.length()-1);
 				}
 			}else{//user has enter "all" and wants the default groups
+				globaldata->Groups.clear();
 				for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
 					globaldata->Groups.push_back(tmap->namesOfGroups[i]);
 					numGroups++;
-- 
2.39.5