added hcluster command and fixed some bugs, namely one with smart distancing.

[mothur.git] / screenseqscommand.cpp

diff --git a/screenseqscommand.cpp b/screenseqscommand.cpp
index 4b267b532ae1a19be791c380339b928212477edd..d5e917c204f1c2757cae52eb5dc8227929851ed1 100644 (file)
--- a/screenseqscommand.cpp
+++ b/screenseqscommand.cpp
@@ -206,6 +206,14 @@ void ScreenSeqsCommand::screenNameGroupFile(set<string> badSeqNames){
        goodNameOut.close();
        badNameOut.close();
        
+       //we were unable to remove some of the bad sequences
+       if (badSeqNames.size() != 0) {
+               for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {  
+                       mothurOut("Your namefile does not include the sequence " + *it + " please correct."); 
+                       mothurOutEndLine();
+               }
+       }
+
        if(groupfile != ""){
                
                ifstream inputGroups;
@@ -234,6 +242,14 @@ void ScreenSeqsCommand::screenNameGroupFile(set<string> badSeqNames){
                inputGroups.close();
                goodGroupOut.close();
                badGroupOut.close();
+               
+               //we were unable to remove some of the bad sequences
+               if (badSeqGroups.size() != 0) {
+                       for (it = badSeqGroups.begin(); it != badSeqGroups.end(); it++) {  
+                               mothurOut("Your namefile does not include the sequence " + *it + " please correct."); 
+                               mothurOutEndLine();
+                       }
+               }
        }
 }
 
@@ -265,6 +281,15 @@ void ScreenSeqsCommand::screenGroupFile(set<string> badSeqNames){
                }
                gobble(inputGroups);
        }
+       
+       //we were unable to remove some of the bad sequences
+       if (badSeqNames.size() != 0) {
+               for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {  
+                       mothurOut("Your groupfile does not include the sequence " + *it + " please correct."); 
+                       mothurOutEndLine();
+               }
+       }
+       
        inputGroups.close();
        goodGroupOut.close();
        badGroupOut.close();
@@ -312,6 +337,15 @@ void ScreenSeqsCommand::screenAlignReport(set<string> badSeqNames){
                }
                gobble(inputAlignReport);
        }
+       
+       //we were unable to remove some of the bad sequences
+       if (badSeqNames.size() != 0) {
+               for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {  
+                       mothurOut("Your file does not include the sequence " + *it + " please correct."); 
+                       mothurOutEndLine();
+               }
+       }
+
        inputAlignReport.close();
        goodAlignReportOut.close();
        badAlignReportOut.close();