X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=classifyseqscommand.cpp;h=1b56433073d404e2c7f33513f7362f8306afcb42;hp=147b3830dded524050b2b8cf96cfbbabde09e3c0;hb=cf9987b67aa49777a4c91c2d21f96e58bf17aa82;hpb=14cddf859d97118481161bf3e85a647976020758

diff --git a/classifyseqscommand.cpp b/classifyseqscommand.cpp
index 147b383..1b56433 100644
--- 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();