fixed some bugs and added mgcluster command

[mothur.git] / readdistcommand.cpp

diff --git a/readdistcommand.cpp b/readdistcommand.cpp
index f6b41951962b7ce6b85ae50a9958bc0408c13835..f6cf5db3948ea8da4557fad5b98da360019922e7 100644 (file)
--- a/readdistcommand.cpp
+++ b/readdistcommand.cpp
@@ -164,6 +164,34 @@ int ReadDistCommand::execute(){
                        openInputFile(distFileName, in);
                        matrix = new FullMatrix(in); //reads the matrix file
                        in.close();
+                       
+                       //if files don't match...
+                       if (matrix->getNumSeqs() < groupMap->getNumSeqs()) {  
+                               mothurOut("Your distance file contains " + toString(matrix->getNumSeqs()) + " sequences, and your group file contains " + toString(groupMap->getNumSeqs()) + " sequences.");  mothurOutEndLine();                               
+                               //create new group file
+                               string newGroupFile = getRootName(groupfile) + "editted.groups";
+                               ofstream outGroups;
+                               openOutputFile(newGroupFile, outGroups);
+                               
+                               for (int i = 0; i < matrix->getNumSeqs(); i++) {
+                                       Names temp = matrix->getRowInfo(i);
+                                       outGroups << temp.seqName << '\t' << temp.groupName << endl;
+                               }
+                               outGroups.close();
+                               
+                               mothurOut(newGroupFile + " is a new group file containing only the sequence that are in your distance file. I will read this file instead."); mothurOutEndLine();
+                               
+                               //read new groupfile
+                               delete groupMap; groupMap = NULL;
+                               groupfile = newGroupFile;
+                               globaldata->setGroupFile(groupfile); 
+                               
+                               groupMap = new GroupMap(groupfile);
+                               groupMap->readMap();
+                               
+                               globaldata->gGroupmap = groupMap;
+                       }
+                       
                        //memory leak prevention
                        if (globaldata->gMatrix != NULL) { delete globaldata->gMatrix;  }
                        globaldata->gMatrix = matrix; //save matrix for coverage commands