X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=preclustercommand.cpp;h=fbbe4bb3a2fc5c99f77875292849e0a0e95f1043;hb=6b32d112bb60e9f7eb6d4407a4eed4c49b67bced;hp=c2564c1f769a835fd85559f10811672eb6a34e0d;hpb=b740fb182372143e152143c6cc5b9ac8591f09b7;p=mothur.git

diff --git a/preclustercommand.cpp b/preclustercommand.cpp
index c2564c1..fbbe4bb 100644
--- a/preclustercommand.cpp
+++ b/preclustercommand.cpp
@@ -192,7 +192,7 @@ PreClusterCommand::PreClusterCommand(string option) {
 			else if (countfile == "not open") { abort = true; countfile =  ""; }	
 			else {   
                 m->setCountTableFile(countfile); 
-                ct.readTable(countfile);
+                ct.readTable(countfile, true, false);
                 if (ct.hasGroupInfo()) { bygroup = true; }
                 else { bygroup = false;  }
             }
@@ -597,7 +597,7 @@ int PreClusterCommand::process(string newMapFile){
                     out << "ideal_seq_" << (i+1) << '\t' << alignSeqs[i].numIdentical << endl << chunk << endl;;
                     
                 }//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"); 	}
             }
         }else {
             map<int, string> mapFile;
@@ -632,7 +632,7 @@ int PreClusterCommand::process(string newMapFile){
                     }//end abundance check
                 }//end for loop j
                 
-                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"); 	}
             }
             
             for (int i = 0; i < numSeqs; i++) {
@@ -903,15 +903,9 @@ void PreClusterCommand::readNameFile(){
 		while (!in.eof()) {
 			in >> firstCol >> secondCol; m->gobble(in);
             
-            for (int i = 0; i < firstCol.length(); i++) {
-                if (firstCol[i] == ':') { firstCol[i] = '_'; m->changedSeqNames = true; }
-            }
-            
-            int size = 1;
-            for (int i = 0; i < secondCol.length(); i++) {
-                if (secondCol[i] == ':') { secondCol[i] = '_'; m->changedSeqNames = true; }
-                else if(secondCol[i] == ','){	size++;	}
-            }
+            m->checkName(firstCol);
+            m->checkName(secondCol);
+            int size = m->getNumNames(secondCol);
             
 			names[firstCol] = secondCol;
             sizes[firstCol] = size;