finished adding the names option to trim.seqs

[mothur.git] / trimseqscommand.cpp

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index ed84cc0c60d404b0d7c12eb0c3751a2e2a601706..64522a5f157820e529b3261d0acaf898f32136b6 100644 (file)
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -432,8 +432,9 @@ int TrimSeqsCommand::execute(){
                //output group counts
                m->mothurOutEndLine();
                int total = 0;
+               if (groupCounts.size() != 0) {  m->mothurOut("Group count: \n");  }
                for (map<string, int>::iterator it = groupCounts.begin(); it != groupCounts.end(); it++) {
-                        total += it->second; m->mothurOut("Group " + it->first + " contains " + toString(it->second) + " sequences."); m->mothurOutEndLine(); 
+                        total += it->second; m->mothurOut(it->first + "\t" + toString(it->second)); m->mothurOutEndLine(); 
                }
                if (total != 0) { m->mothurOut("Total of all groups is " + toString(total)); m->mothurOutEndLine(); }
                
@@ -650,6 +651,17 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
                                                
                                                outGroupsFile << currSeq.getName() << '\t' << thisGroup << endl;
                                                
+                                               if (nameFile != "") {
+                                                       map<string, string>::iterator itName = nameMap.find(currSeq.getName());
+                                                       if (itName != nameMap.end()) { 
+                                                               vector<string> thisSeqsNames; 
+                                                               m->splitAtChar(itName->second, thisSeqsNames, ',');
+                                                               for (int k = 1; k < thisSeqsNames.size(); k++) { //start at 1 to skip self
+                                                                       outGroupsFile << thisSeqsNames[k] << '\t' << thisGroup << endl;
+                                                               }
+                                                       }else { m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your namefile, please correct."); m->mothurOutEndLine(); }                                                   
+                                               }
+                                               
                                                map<string, int>::iterator it = groupCounts.find(thisGroup);
                                                if (it == groupCounts.end()) {  groupCounts[thisGroup] = 1; }
                                                else { groupCounts[it->first]++; }