X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=readdistcommand.cpp;h=f6cf5db3948ea8da4557fad5b98da360019922e7;hb=c82900be3ceed3d9bc491bdc98b1819ef85c1af7;hp=c4756c3260db6a660526ef09b66f668b25de12ef;hpb=72ebb6fa35b45b149812d47c2b1cb8acaca64659;p=mothur.git

diff --git a/readdistcommand.cpp b/readdistcommand.cpp
index c4756c3..f6cf5db 100644
--- a/readdistcommand.cpp
+++ b/readdistcommand.cpp
@@ -72,7 +72,7 @@ ReadDistCommand::ReadDistCommand(string option){
 			if (columnfile != "") {
 				if (namefile == "") {  cout << "You need to provide a namefile if you are going to use the column format." << endl; abort = true; }
 			}
-		
+			
 			//check for optional parameter and set defaults
 			// ...at some point should added some additional type checking...
 			//get user cutoff and precision or use defaults
@@ -93,6 +93,7 @@ ReadDistCommand::ReadDistCommand(string option){
 				else if (format == "matrix") { 
 					groupMap = new GroupMap(groupfile);
 					groupMap->readMap();
+	
 					if (globaldata->gGroupmap != NULL) { delete globaldata->gGroupmap;  }
 					globaldata->gGroupmap = groupMap;
 				}
@@ -155,7 +156,7 @@ int ReadDistCommand::execute(){
 		
 		if (abort == true) {	return 0;	}
 
-		//time_t start = time(NULL);
+		time_t start = time(NULL);
 		size_t numDists = 0;
 		
 		if (format == "matrix") {
@@ -163,6 +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
@@ -203,7 +232,7 @@ int ReadDistCommand::execute(){
 		//	}
       //mothurOut(dist_string); mothurOutEndLine(); mothurOut(count_string); mothurOutEndLine();
 		}
-		//mothurOut("It took " + toString(time(NULL) - start) + " secs to read " + toString(numDists) + " distances (cutoff: " + toString(cutoff) + ")"); mothurOutEndLine();
+		mothurOut("It took " + toString(time(NULL) - start) + " secs to read "); mothurOutEndLine();
 		return 0;
 		
 	}