fixed some bugs and added mgcluster command

[mothur.git] / readdistcommand.cpp

diff --git a/readdistcommand.cpp b/readdistcommand.cpp
index c4756c3260db6a660526ef09b66f668b25de12ef..f6cf5db3948ea8da4557fad5b98da360019922e7 100644 (file)
--- 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;
                
        }