added distance command and filterseqs

[mothur.git] / readnexus.cpp

diff --git a/readnexus.cpp b/readnexus.cpp
index 25444d5093f637d6b0ff8a09bc8816463745299d..5dffa42ae7c8fe72105cebfe50d4187e08cc3957 100644 (file)
--- a/readnexus.cpp
+++ b/readnexus.cpp
@@ -12,11 +12,8 @@
 #include <fstream>
 
 /*******************************************************************************/
-ReadNexus::ReadNexus(string file) {
+ReadNexus::ReadNexus(string file) : ReadSeqs(file) {
        try {
-               openInputFile(file, filehandle);
-               nexusFile = file;
-               globaldata = GlobalData::getInstance();
        }
        catch(exception& e) {
                cout << "Standard Error: " << e.what() << " has occurred in the ReadTree class Function ReadTree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
@@ -56,7 +53,7 @@ void ReadNexus::read() {
                                sequencedb.add(newSeq);
                        } 
                        else 
-                               sequencedb.set(count, sequencedb.get(count).getAligned() + sequence);
+                               sequencedb.set(count, sequencedb.get(count).getUnaligned() + sequence);
                        
                        count++;
                        if(count == numSeqs) {