forced rarefaction.single to output ending line for all groups. added subsample...

[mothur.git] / treegroupscommand.cpp

diff --git a/treegroupscommand.cpp b/treegroupscommand.cpp
index 3eeeae292e674dbc7823522ce8e35d8d531ab70e..c26199d673088b5b64872b672ab8e64ca780e616 100644 (file)
--- a/treegroupscommand.cpp
+++ b/treegroupscommand.cpp
@@ -27,7 +27,7 @@ vector<string> TreeGroupCommand::setParameters(){
                CommandParameter pcalc("calc", "Multiple", "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-kstest-sharednseqs-ochiai-anderberg-kulczynski-kulczynskicody-lennon-morisitahorn-braycurtis-whittaker-odum-canberra-structeuclidean-structchord-hellinger-manhattan-structpearson-soergel-spearman-structkulczynski-speciesprofile-hamming-structchi2-gower-memchi2-memchord-memeuclidean-mempearson", "jclass-thetayc", "", "", "",true,false); parameters.push_back(pcalc);
                
         CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
-        CommandParameter poutput("output", "Multiple", "lt-square", "lt", "", "", "",false,false); parameters.push_back(poutput);
+//CommandParameter poutput("output", "Multiple", "lt-square", "lt", "", "", "",false,false); parameters.push_back(poutput);
                CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
                CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
                
@@ -570,13 +570,6 @@ vector< vector<double> > TreeGroupCommand::makeSimsDist() {
 int TreeGroupCommand::makeSimsShared() {
        try {
         
-        numGroups = lookup.size();
-               lines.resize(processors);
-               for (int i = 0; i < processors; i++) {
-                       lines[i].start = int (sqrt(float(i)/float(processors)) * numGroups);
-                       lines[i].end = int (sqrt(float(i+1)/float(processors)) * numGroups);
-               }       
-        
         if (subsample) { 
             if (subsampleSize == -1) { //user has not set size, set size = smallest samples size
                 subsampleSize = lookup[0]->getNumSeqs();
@@ -601,8 +594,17 @@ int TreeGroupCommand::makeSimsShared() {
                 lookup = temp;
                 m->setGroups(Groups);
             }
+            
+            if (lookup.size() < 2) { m->mothurOut("You have not provided enough valid groups.  I cannot run the command."); m->mothurOutEndLine(); m->control_pressed = true; return 0; }
         }
         
+        numGroups = lookup.size();
+               lines.resize(processors);
+               for (int i = 0; i < processors; i++) {
+                       lines[i].start = int (sqrt(float(i)/float(processors)) * numGroups);
+                       lines[i].end = int (sqrt(float(i+1)/float(processors)) * numGroups);
+               }       
+        
                set<string> processedLabels;
                set<string> userLabels = labels;