added otulabels to heatmap.bin. made OTUlabels “smarter” so OTU01 and OTU001 are...

[mothur.git] / removelineagecommand.cpp

diff --git a/removelineagecommand.cpp b/removelineagecommand.cpp
index 66bbc1779bc16055076d6b1b814233f69e077d6d..01f45ca97329fbbe383c2157f12880ca05671a10 100644 (file)
--- a/removelineagecommand.cpp
+++ b/removelineagecommand.cpp
@@ -665,7 +665,7 @@ int RemoveLineageCommand::readCount(){
         //check for groups that have been eliminated
         CountTable ct;
         if (ct.testGroups(outputFileName)) {
-            ct.readTable(outputFileName, true);
+            ct.readTable(outputFileName, true, false);
             ct.printTable(outputFileName);
         }
                
@@ -705,7 +705,7 @@ int RemoveLineageCommand::readConsList(){
             }
             otuLabel += sbinNumber;
             
-            if (names.count(otuLabel) == 0) {
+            if (names.count(m->getSimpleLabel(otuLabel)) == 0) {
                 newList.push_back(list->get(i));
             }else { removedCount++; }
         }
@@ -843,7 +843,7 @@ int RemoveLineageCommand::readShared(){
             if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) { delete newLookup[j]; } for (int j = 0; j < lookup.size(); j++) { delete lookup[j]; } return 0; }
             
             //is this otu on the list
-            if (names.count(m->currentBinLabels[i]) == 0) {
+            if (names.count(m->getSimpleLabel(m->currentBinLabels[i])) == 0) {
                 wroteSomething = true;
                 newLabels.push_back(m->currentBinLabels[i]);
                 for (int j = 0; j < newLookup.size(); j++) { //add this OTU to the new lookup
@@ -1242,7 +1242,7 @@ int RemoveLineageCommand::readConsTax(){
                                                //wroteSomething = true;
                                                //out << name << '\t' << tax << endl;
                                        }else{ //this sequence contains the taxon the user wants to remove
-                                               names.insert(otuLabel);
+                                               names.insert(m->getSimpleLabel(otuLabel));
                                                remove=true; break;
                                        }
                                        
@@ -1256,7 +1256,7 @@ int RemoveLineageCommand::readConsTax(){
                                                        //wroteSomething = true;
                                                        //out << name << '\t' << tax << endl;
                                                }else{ //this sequence contains the taxon the user wants to remove
-                                                       names.insert(otuLabel);
+                                                       names.insert(m->getSimpleLabel(otuLabel));
                                                        remove=true; break;
                                                }
                                        }else { //both have confidences so we want to make sure the users confidences are greater then or equal to the taxons
@@ -1309,7 +1309,7 @@ int RemoveLineageCommand::readConsTax(){
                                                        
                                                        //passed the test so remove you
                                                        if (remove) {
-                                                               names.insert(otuLabel);
+                                                               names.insert(m->getSimpleLabel(otuLabel));
                                                                remove=true; break;
                                                        }else {
                                                                //wroteSomething = true;