added modify names parameter to set.dir

[mothur.git] / flowdata.cpp

diff --git a/flowdata.cpp b/flowdata.cpp
index d5adcf7163a14c27c4c783efd05359aa1494e1a7..66261e33b922f17be93e3f929582ca9ea7d9208f 100644 (file)
--- a/flowdata.cpp
+++ b/flowdata.cpp
@@ -68,9 +68,7 @@ string FlowData::getSequenceName(ifstream& flowFile) {
         flowFile >> name;
                
                if (name.length() != 0) { 
-            for (int i = 0; i < name.length(); i++) {
-                if (name[i] == ':') { name[i] = '_'; m->changedSeqNames = true; }
-            }
+            m->checkName(name);
         }else{ m->mothurOut("Error in reading your flowfile, at position " + toString(flowFile.tellg()) + ". Blank name."); m->mothurOutEndLine(); m->control_pressed = true;  }
         
                return name;
@@ -86,7 +84,7 @@ string FlowData::getSequenceName(ifstream& flowFile) {
 void FlowData::updateEndFlow(){
        try{
                
-        //if (baseFlow.length() > 4) { return; }
+        if (baseFlow.length() > 4) { return; }
         
                //int currLength = 0;
                float maxIntensity = (float) maxHomoP + 0.49;