added distance command and filterseqs

[mothur.git] / readclustal.cpp

diff --git a/readclustal.cpp b/readclustal.cpp
index 2f31539623d91656f26740d803795752e156e177..f42b3597a12d5dbe25d07f6d6007bb24de416f61 100644 (file)
--- a/readclustal.cpp
+++ b/readclustal.cpp
@@ -12,11 +12,8 @@
 #include <fstream>
 
 /*******************************************************************************/
-ReadClustal::ReadClustal(string file) {
+ReadClustal::ReadClustal(string file) : ReadSeqs(file){
        try {
-               openInputFile(file, filehandle);
-               clustalFile = 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";
@@ -43,6 +40,7 @@ void ReadClustal::read() {
        
        int count = 0;
        int numSeqs = 0;
+       int lastSeqLength = 0;
        bool firstDone = false; 
        
        while(!filehandle.eof()) {
@@ -61,16 +59,20 @@ void ReadClustal::read() {
 
                if(name.find_first_of("*") == -1) {
                        filehandle >> sequence;
+                       lastSeqLength = sequence.length();
                        if(!firstDone) {
                                Sequence newSeq(name, sequence);
                                sequencedb.add(newSeq);
                        } 
                        else 
-                               sequencedb.set(count, sequencedb.get(count).getAligned() + sequence);
+                               sequencedb.set(count, sequencedb.get(count).getUnaligned() + sequence);
                                
                        count++;
                }
        }
+       if(count == 1)
+               sequencedb.set(0, sequencedb.get(0).getUnaligned().substr(0, sequencedb.get(0).getUnaligned().length() - lastSeqLength));
+               
        filehandle.close();
 }