added otu.association command. added calcSpearman, calcKendall and calcPearson functi...

[mothur.git] / subsamplecommand.cpp

diff --git a/subsamplecommand.cpp b/subsamplecommand.cpp
index 49a821045e122b5097fde092a5845378e21afc60..c352feb099a83879bae9e1aca0f35d5bfe56e691 100644 (file)
--- a/subsamplecommand.cpp
+++ b/subsamplecommand.cpp
@@ -234,7 +234,7 @@ SubSampleCommand::SubSampleCommand(string option) {
                        }
                        
                        string temp = validParameter.validFile(parameters, "size", false);              if (temp == "not found"){       temp = "0";             }
-                       convert(temp, size);  
+                       m->mothurConvert(temp, size);  
                        
                        temp = validParameter.validFile(parameters, "persample", false);                if (temp == "not found"){       temp = "f";             }
                        persample = m->isTrue(temp);
@@ -255,6 +255,10 @@ SubSampleCommand::SubSampleCommand(string option) {
                        if ((groupfile != "") && ((fastafile != "") && (listfile != ""))) { 
                                m->mothurOut("A new group file can only be made from the subsample of a listfile or fastafile, not both. Please correct."); m->mothurOutEndLine(); abort = true; }
                        
+                       if ((fastafile != "") && (namefile == "")) {
+                               vector<string> files; files.push_back(fastafile);
+                               parser.getNameFile(files);
+                       }
                }
 
        }
@@ -426,6 +430,7 @@ int SubSampleCommand::getSubSampleFasta() {
                if (persample) {
                        //initialize counts
                        map<string, int> groupCounts;
+                       map<string, int>::iterator itGroupCounts;
                        for (int i = 0; i < Groups.size(); i++) { groupCounts[Groups[i]] = 0; }
                        
                        for (int j = 0; j < names.size(); j++) {
@@ -435,7 +440,10 @@ int SubSampleCommand::getSubSampleFasta() {
                                string group = groupMap->getGroup(names[j]);
                                if (group == "not found") { m->mothurOut("[ERROR]: " + names[j] + " is not in your groupfile. please correct."); m->mothurOutEndLine(); group = "NOTFOUND"; }
                                else{
-                                       if (groupCounts[group] < size) {        subset.insert(names[j]);        }
+                                       itGroupCounts = groupCounts.find(group);
+                                       if (itGroupCounts != groupCounts.end()) {
+                                               if (groupCounts[group] < size) {        subset.insert(names[j]);        groupCounts[group]++; }
+                                       }
                                }                               
                        }
                }else {
@@ -1025,6 +1033,7 @@ int SubSampleCommand::getSubSampleList() {
                if (persample) {
                        //initialize counts
                        map<string, int> groupCounts;
+                       map<string, int>::iterator itGroupCounts;
                        for (int i = 0; i < Groups.size(); i++) { groupCounts[Groups[i]] = 0; }
                        
                        for (int j = 0; j < names.size(); j++) {
@@ -1034,7 +1043,10 @@ int SubSampleCommand::getSubSampleList() {
                                string group = groupMap->getGroup(names[j]);
                                if (group == "not found") { m->mothurOut("[ERROR]: " + names[j] + " is not in your groupfile. please correct."); m->mothurOutEndLine(); group = "NOTFOUND"; }
                                else{
-                                       if (groupCounts[group] < size) {        subset.insert(names[j]);        }
+                                       itGroupCounts = groupCounts.find(group);
+                                       if (itGroupCounts != groupCounts.end()) {
+                                               if (groupCounts[group] < size) {        subset.insert(names[j]);        groupCounts[group]++; }
+                                       }
                                }                               
                        }
                }else{