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

[mothur.git] / getlineagecommand.cpp

diff --git a/getlineagecommand.cpp b/getlineagecommand.cpp
index 005a89f2ebbee9e1b4c37567b6ce382979c90226..862aef7a0da6dde200bc387209bdd73d730015f5 100644 (file)
--- a/getlineagecommand.cpp
+++ b/getlineagecommand.cpp
@@ -514,7 +514,7 @@ int GetLineageCommand::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);
         }
 
@@ -628,7 +628,7 @@ int GetLineageCommand::readConsList(){
             }
             otuLabel += sbinNumber;
             
-            if (names.count(otuLabel) != 0) {
+            if (names.count(m->getSimpleLabel(otuLabel)) != 0) {
                                selectedCount++;
                 newList.push_back(list->get(i));
             }
@@ -767,7 +767,7 @@ int GetLineageCommand::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) {
                 numSelected++; wroteSomething = true;
                 newLabels.push_back(m->currentBinLabels[i]);
                 for (int j = 0; j < newLookup.size(); j++) { //add this OTU to the new lookup
@@ -1241,7 +1241,7 @@ int GetLineageCommand::readConsTax(){
                                        int pos = newtax.find(noConfidenceTaxons[j]);
                     
                                        if (pos != string::npos) { //this sequence contains the taxon the user wants
-                                               names.insert(otuLabel);
+                                               names.insert(m->getSimpleLabel(otuLabel));
                                                out << otuLabel << '\t' << numReps << '\t' << tax << endl;
                                                //since you belong to at least one of the taxons we want you are included so no need to search for other
                                                break;
@@ -1253,7 +1253,7 @@ int GetLineageCommand::readConsTax(){
                                                int pos = newtax.find(noConfidenceTaxons[j]);
                         
                                                if (pos != string::npos) { //this sequence contains the taxon the user wants
-                                                       names.insert(otuLabel);
+                                                       names.insert(m->getSimpleLabel(otuLabel));
                                                        out << otuLabel << '\t' << numReps << '\t' << tax << endl;
                                                        //since you belong to at least one of the taxons we want you are included so no need to search for other
                                                        break;
@@ -1309,7 +1309,7 @@ int GetLineageCommand::readConsTax(){
                             
                                                        //passed the test so add you
                                                        if (good) {
-                                                               names.insert(otuLabel);
+                                                               names.insert(m->getSimpleLabel(otuLabel));
                                                                out << otuLabel << '\t' << numReps << '\t' << tax << endl;
                                                                break;
                                                        }