added get.rabund and get.sabund command and fixed bug introduced by line by line...

[mothur.git] / venncommand.cpp

diff --git a/venncommand.cpp b/venncommand.cpp
index 519e6cbec1be64d87fbb1af2f54208df1e04e46f..bb3762cc54f741d1e7c0a1fd7bdf9bc6c35f38db 100644 (file)
--- a/venncommand.cpp
+++ b/venncommand.cpp
@@ -115,16 +115,18 @@ int VennCommand::execute(){
                //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
                set<string> processedLabels;
                set<string> userLabels = globaldata->labels;
+               set<int> userLines = globaldata->lines;
                
                if (format != "list") { 
                        
                        //as long as you are not at the end of the file or done wih the lines you want
-                       while((lookup[0] != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0))) {
+                       while((lookup[0] != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
                
                                if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(lookup[0]->getLabel()) == 1){                   
                                        cout << lookup[0]->getLabel() << '\t' << count << endl;
                                        processedLabels.insert(lookup[0]->getLabel());
                                        userLabels.erase(lookup[0]->getLabel());
+                                       userLines.erase(count);
                                        
                                        if (lookup.size() > 4) {
                                                cout << "Error: Too many groups chosen.  You may use up to 4 groups with the venn command.  I will use the first four groups in your groupfile." << endl;
@@ -184,7 +186,7 @@ int VennCommand::execute(){
                        
                }else{
                
-                       while((sabund != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0))) {
+                       while((sabund != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
                
                                if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(sabund->getLabel()) == 1){                      
        
@@ -193,6 +195,7 @@ int VennCommand::execute(){
                                        
                                        processedLabels.insert(sabund->getLabel());
                                        userLabels.erase(sabund->getLabel());
+                                       userLines.erase(count);
                                }
                                
                                if ((anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastSAbund->getLabel()) != 1)) {