changed random forest output filename

[mothur.git] / clusterfragmentscommand.cpp

diff --git a/clusterfragmentscommand.cpp b/clusterfragmentscommand.cpp
index ef199ccdf0a11efba99eaf0299ff50413b70b89f..9c1408c9a112dcc3ad9ed579026e2528c334a102 100644 (file)
--- a/clusterfragmentscommand.cpp
+++ b/clusterfragmentscommand.cpp
@@ -181,7 +181,7 @@ ClusterFragmentsCommand::ClusterFragmentsCommand(string option) {
             countfile = validParameter.validFile(parameters, "count", true);
                        if (countfile == "not open") { abort = true; countfile = ""; }  
                        else if (countfile == "not found") { countfile = ""; }
-                       else { ct.readTable(countfile); m->setCountTableFile(countfile); }
+                       else { ct.readTable(countfile, true); m->setCountTableFile(countfile); }
                        
             if ((countfile != "") && (namefile != "")) { m->mothurOut("When executing a cluster.fragments command you must enter ONLY ONE of the following: count or name."); m->mothurOutEndLine(); abort = true; }
                        
@@ -262,10 +262,10 @@ int ClusterFragmentsCommand::execute(){
                                alignSeqs[i].active = 0;
                                
                        }//end if active i
-                       if(i % 100 == 0)        { m->mothurOut(toString(i) + "\t" + toString(numSeqs - count) + "\t" + toString(count)); m->mothurOutEndLine(); }
+                       if(i % 100 == 0)        { m->mothurOutJustToScreen(toString(i) + "\t" + toString(numSeqs - count) + "\t" + toString(count)+"\n");       }
                }
                
-               if(numSeqs % 100 != 0)  { m->mothurOut(toString(numSeqs) + "\t" + toString(numSeqs - count) + "\t" + toString(count)); m->mothurOutEndLine();   }
+               if(numSeqs % 100 != 0)  { m->mothurOutJustToScreen(toString(numSeqs) + "\t" + toString(numSeqs - count) + "\t" + toString(count)+"\n"); }
        
                
                string fileroot = outputDir + m->getRootName(m->getSimpleName(fastafile));