filterseqscommand added

[mothur.git] / readseqscommand.cpp

diff --git a/readseqscommand.cpp b/readseqscommand.cpp
index 919855b26bba0a3d09c115c7f92dad2f81f6d47f..2ca75679b3a9ca5869e380ccfc4ff4328336f0a4 100644 (file)
--- a/readseqscommand.cpp
+++ b/readseqscommand.cpp
@@ -13,14 +13,34 @@
 ReadSeqsCommand::ReadSeqsCommand(){
        try {
                globaldata = GlobalData::getInstance();
-               
+               filename = globaldata->inputFileName;
+               if(globaldata->getFastaFile().compare("") != 0) {
+                       readFasta = new ReadFasta(filename);
+                       readFasta->read();
+                       globaldata->gSequenceDB = readFasta->getDB();
+               }
+               else if(globaldata->getNexusFile().compare("") != 0) {
+                       readNexus = new ReadNexus(filename);
+                       readNexus->read();
+                       globaldata->gSequenceDB = readNexus->getDB();
+               }
+               else if(globaldata->getClustalFile().compare("") != 0) {
+                       readClustal = new ReadClustal(filename);
+                       readClustal->read();
+                       globaldata->gSequenceDB = readClustal->getDB();
+               }
+               else if(globaldata->getPhylipFile().compare("") != 0) {
+                       readPhylip = new ReadPhylip(filename);
+                       readPhylip->read();
+                       globaldata->gSequenceDB = readPhylip->getDB();
+               }
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the ReadOtuCommand class Function ReadOtuCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               cout << "Standard Error: " << e.what() << " has occurred in the ReadSeqsCommand class Function ReadSeqsCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
                exit(1);
        }
        catch(...) {
-               cout << "An unknown error has occurred in the ReadOtuCommand class function ReadOtuCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               cout << "An unknown error has occurred in the ReadSeqsCommand class function ReadSeqsCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
                exit(1);
        }
 }
@@ -41,7 +61,7 @@ int ReadSeqsCommand::execute(){
                filebuf fb;
                
                //fb.open ("fasta.txt",ios::out);
-//             readFasta->read();
+               //readFasta->read();
 //             SequenceDB* db = readFasta->getDB();
                
                //fb.open("nexus.txt",ios::out);
@@ -59,7 +79,7 @@ int ReadSeqsCommand::execute(){
                
                
                //for(int i = 0; i < db->size(); i++) {
-//                     cout << db->get(i).getLength() << "\n" << db->get(i).getName() << ": " << db->get(i).getUnaligned() << "\n\n";
+//                     cout << db->get(i).getLength() << "\n" << db->get(i).getName() << ": " << db->get(i).getAligned() << "\n\n";
 //             }
 
                //ostream os(&fb);