removed readseqs, readfasta, readnexus, readclustal, readseqsphylip and updated seque...

[mothur.git] / distancecommand.cpp

diff --git a/distancecommand.cpp b/distancecommand.cpp
index fbec46c80fb35a1c97889d47ea61e8a4e9f5e686..6eb7d576833e0ba944d8f445ff662f2e1d86e661 100644 (file)
--- a/distancecommand.cpp
+++ b/distancecommand.cpp
@@ -24,6 +24,11 @@ DistanceCommand::DistanceCommand(){
                convert(globaldata->getProcessors(), processors);
                convert(globaldata->getCutOff(), cutoff);
                
+               //open file
+               string filename = globaldata->getFastaFile();
+               openInputFile(filename, in);
+
+               
                int i;
                if (isTrue(countends) == true) {
                        for (i=0; i<globaldata->Estimators.size(); i++) {
@@ -67,21 +72,10 @@ DistanceCommand::DistanceCommand(){
 int DistanceCommand::execute(){
        try {
                
-               //read file
-               string filename = globaldata->inputFileName;
-               
-               if(globaldata->getFastaFile() != "") {
-               readSeqs =  new ReadFasta(filename); }
-               else if(globaldata->getNexusFile() != "") {
-               readSeqs = new ReadNexus(filename); }
-               else if(globaldata->getClustalFile() != "") {
-               readSeqs = new ReadClustal(filename); }
-               else if(globaldata->getPhylipFile() != "") {
-               readSeqs = new ReadPhylip(filename); }
-               
-               readSeqs->read();
-               seqDB = readSeqs->getDB();
-               
+               //reads fasta file and fills sequenceDB
+               if(globaldata->getFastaFile() != "") {  seqDB = new SequenceDB(in);  }
+               else { cout << "Error no fasta file." << endl; return 0; }
+                               
                int numSeqs = seqDB->getNumSeqs();
                cutoff += 0.005;
                
@@ -279,11 +273,11 @@ int DistanceCommand::driver(Dist* distCalculator, SequenceDB* align, int startLi
                for(int i=startLine;i<endLine;i++){
                        
                        for(int j=0;j<i;j++){
-                               distCalculator->calcDist(align->get(i), align->get(j));
+                               distCalculator->calcDist(*(align->get(i)), *(align->get(j)));
                                double dist = distCalculator->getDist();
                                
                                if(dist <= cutoff){
-                                       distFile << align->get(i).getName() << ' ' << align->get(j).getName() << ' ' << dist << endl;
+                                       distFile << align->get(i)->getName() << ' ' << align->get(j)->getName() << ' ' << dist << endl;
                                }
                                
                        }