working on pam

[mothur.git] / classifyseqscommand.cpp

diff --git a/classifyseqscommand.cpp b/classifyseqscommand.cpp
index 147b3830dded524050b2b8cf96cfbbabde09e3c0..1b56433073d404e2c7f33513f7362f8306afcb42 100644 (file)
--- a/classifyseqscommand.cpp
+++ b/classifyseqscommand.cpp
@@ -258,7 +258,6 @@ ClassifySeqsCommand::ClassifySeqsCommand(string option)  {
 
                        namefile = validParameter.validFile(parameters, "name", false);
                        if (namefile == "not found") { namefile = "";  }
-
                        else { 
                                m->splitAtDash(namefile, namefileNames);
                                
@@ -813,7 +812,7 @@ int ClassifySeqsCommand::execute(){
                 PhyloSummary* taxaSum;
                 if (hasCount) { 
                     ct = new CountTable();
-                    ct->readTable(countfileNames[s]);
+                    ct->readTable(countfileNames[s], true, false);
                     taxaSum = new PhyloSummary(taxonomyFileName, ct);
                     taxaSum->summarize(tempTaxonomyFile);
                 }else {
@@ -1152,11 +1151,11 @@ int ClassifySeqsCommand::driver(linePair* filePos, string taxFName, string tempT
                        #endif
                        
                        //report progress
-                       if((count) % 100 == 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
+                       if((count) % 100 == 0){ m->mothurOutJustToScreen("Processing sequence: " + toString(count) +"\n");              }
                        
                }
                //report progress
-               if((count) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
+               if((count) % 100 != 0){ m->mothurOutJustToScreen("Processing sequence: " + toString(count)+"\n");               }
                        
                inFASTA.close();
                outTax.close();