X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=classifyseqscommand.cpp;h=1b56433073d404e2c7f33513f7362f8306afcb42;hp=6ec2d3886a218405f8132a03fe1c59e0b8c29c20;hb=cf9987b67aa49777a4c91c2d21f96e58bf17aa82;hpb=8159f34321e2c771638059b59a986caca9f3ab60

diff --git a/classifyseqscommand.cpp b/classifyseqscommand.cpp
index 6ec2d38..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);
 				
@@ -782,7 +781,7 @@ int ClassifySeqsCommand::execute(){
 			}
 #endif
 			
-			if (!m->isBlank(newaccnosFile)) { m->mothurOutEndLine(); m->mothurOut("[WARNING]: mothur suspects some of your sequences may be reversed, please check " + newaccnosFile + " for the list of the sequences."); m->mothurOutEndLine(); 
+			if (!m->isBlank(newaccnosFile)) { m->mothurOutEndLine(); m->mothurOut("[WARNING]: mothur reversed some your sequences for a better classification.  If you would like to take a closer look, please check " + newaccnosFile + " for the list of the sequences."); m->mothurOutEndLine(); 
                 outputNames.push_back(newaccnosFile); outputTypes["accnos"].push_back(newaccnosFile);
             }else { m->mothurRemove(newaccnosFile); }
 
@@ -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 {
@@ -1044,6 +1043,9 @@ int ClassifySeqsCommand::createProcesses(string taxFileName, string tempTaxFile,
 		//Close all thread handles and free memory allocations.
 		for(int i=0; i < pDataArray.size(); i++){
 			num += pDataArray[i]->count;
+            if (pDataArray[i]->count != pDataArray[i]->end) {
+                m->mothurOut("[ERROR]: process " + toString(i) + " only processed " + toString(pDataArray[i]->count) + " of " + toString(pDataArray[i]->end) + " sequences assigned to it, quitting. \n"); m->control_pressed = true; 
+            }
 			CloseHandle(hThreadArray[i]);
 			delete pDataArray[i];
 		}
@@ -1149,11 +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();