added distance command and filterseqs

[mothur.git] / readseqsphylip.cpp

diff --git a/readseqsphylip.cpp b/readseqsphylip.cpp
index 40f56a0c7efe29962418b4cb056ef51374517867..fbb99c9b0d44daddf431e1fc11be168bdcc69393 100644 (file)
--- a/readseqsphylip.cpp
+++ b/readseqsphylip.cpp
@@ -31,11 +31,8 @@ bool ReadPhylip::isSeq(string seq) {
 }
 
 /*******************************************************************************/
-ReadPhylip::ReadPhylip(string file) {
+ReadPhylip::ReadPhylip(string file) : ReadSeqs(file) {
        try {
-               openInputFile(file, filehandle);
-               phylipFile = 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";
@@ -107,7 +104,7 @@ void ReadPhylip::read() {
                                }
                        }
                        if(!(last && count == 0))
-                               sequencedb.set(count, sequencedb.get(count).getAligned() + sequence);
+                               sequencedb.set(count, sequencedb.get(count).getUnaligned() + sequence);
                        if(letterCount == numLetters && count == 0)
                                last = true;
                }