working on pam

[mothur.git] / clustersplitcommand.cpp

diff --git a/clustersplitcommand.cpp b/clustersplitcommand.cpp
index 95693cc420a7e55d5c9a96a102e3d9e55ad0221c..874eb6d7b535e9e400cca8f22593280ecd959b42 100644 (file)
--- a/clustersplitcommand.cpp
+++ b/clustersplitcommand.cpp
@@ -833,8 +833,10 @@ int ClusterSplitCommand::mergeLists(vector<string> listNames, map<float, int> us
                m->openOutputFile(listFileName, outList);
         outputNames.push_back(listFileName); outputTypes["list"].push_back(listFileName);
                
-               
                map<float, int>::iterator itLabel;
+        
+        //clears out junk for autocompleting of list files above.  Perhaps there is a beter way to handle this from within the data structure?
+        m->printedListHeaders = false;
 
                //for each label needed
                for(itLabel = userLabels.begin(); itLabel != userLabels.end(); itLabel++) {
@@ -890,6 +892,8 @@ int ClusterSplitCommand::mergeLists(vector<string> listNames, map<float, int> us
                 rabund->print(outRabund);
             }
                        //outList << endl;
+            if (!m->printedListHeaders) { 
+                m->listBinLabelsInFile.clear(); completeList.printHeaders(outList); }
             completeList.print(outList);
                        
                        if (rabund != NULL) { delete rabund; }
@@ -1174,7 +1178,7 @@ string ClusterSplitCommand::clusterClassicFile(string thisDistFile, string thisN
             cluster->readPhylipFile(thisDistFile, nameMap);
                }else if (countfile != "") {
             ct = new CountTable();
-            ct->readTable(thisNamefile, false);
+            ct->readTable(thisNamefile, false, false);
             cluster->readPhylipFile(thisDistFile, ct);
         }
         tag = cluster->getTag();
@@ -1302,7 +1306,7 @@ string ClusterSplitCommand::clusterFile(string thisDistFile, string thisNamefile
             read->read(nameMap);
                }else if (countfile != "") {
             ct = new CountTable();
-            ct->readTable(thisNamefile, false);
+            ct->readTable(thisNamefile, false, false);
             read->read(ct);
         }else { read->read(nameMap); }