Adds tax space to list/get/remove.seqs

#265
mothur · 0755b8563f1b15df1bc5064fc961fc932550a776 · mothur-westcott committed Aug 24, 2016 · Aug 24, 2016 · 0755b85
1 parent 3caf426
commit 0755b8563f1b15df1bc5064fc961fc932550a776
Unified Split

Showing with 7 additions and 14 deletions.

+2 −4 source/commands/getseqscommand.cpp

+2 −5 source/commands/listseqscommand.cpp

+3 −5 source/commands/removeseqscommand.cpp
diff --git a/source/commands/getseqscommand.cpp b/source/commands/getseqscommand.cpp
@@ -1031,8 +1031,8 @@ int GetSeqsCommand::readTax(){
 
 			if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName);  return 0; }
 
-			in >> name;				//read from first column
-			in >> tax;			//read from second column
+            in >> name; m->gobble(in);
+            tax = m->getline(in); m->gobble(in);
             
             if (!dups) {//adjust name if needed
                 map<string, string>::iterator it = uniqueMap.find(name);
@@ -1053,8 +1053,6 @@ int GetSeqsCommand::readTax(){
                     m->mothurOut("[WARNING]: " + name + " is in your taxonomy file more than once.  Mothur requires sequence names to be unique. I will only add it once.\n");
                 }
 			}
-					
-			m->gobble(in);
 		}
 		in.close();
 		out.close();
diff --git a/source/commands/listseqscommand.cpp b/source/commands/listseqscommand.cpp
@@ -540,13 +540,10 @@ int ListSeqsCommand::readTax(){
 		
 			if (m->control_pressed) { in.close(); return 0; }
 
-			in >> firstCol;				
-			in >> secondCol;			
+            in >> firstCol; m->gobble(in);
+            secondCol = m->getline(in); m->gobble(in);
 			
 			names.push_back(firstCol);
-			
-			m->gobble(in);
-			
 		}
 		in.close();
 		
diff --git a/source/commands/removeseqscommand.cpp b/source/commands/removeseqscommand.cpp
@@ -959,9 +959,9 @@ int RemoveSeqsCommand::readTax(){
 		while(!in.eof()){
 			if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
 			
-			in >> name;	m->gobble(in);			//read from first column
-			in >> tax;			//read from second column
-			
+            in >> name; m->gobble(in);
+            tax = m->getline(in); m->gobble(in);
+            
             if (!dups) {//adjust name if needed
                 map<string, string>::iterator it = uniqueMap.find(name);
                 if (it != uniqueMap.end()) { name = it->second; }
@@ -978,8 +978,6 @@ int RemoveSeqsCommand::readTax(){
                     m->mothurOut("[WARNING]: " + name + " is in your taxonomy file more than once.  Mothur requires sequence names to be unique. I will only add it once.\n");
                 }
 			}else {  removedCount++;  }
-					
-			m->gobble(in);
 		}
 		in.close();
 		out.close();