added mothurgetpid function. fixed bug with align.seqs related to g++ 4.8 change...

[mothur.git] / treegroupscommand.h

diff --git a/treegroupscommand.h b/treegroupscommand.h
index b29670ae614205a7ee286116379ddda86f0e7cf9..3c26eb1088a4a7b53eb1458f166ea6aa282e9fe8 100644 (file)
--- a/treegroupscommand.h
+++ b/treegroupscommand.h
@@ -60,6 +60,8 @@
 #include "memchord.h"
 #include "memeuclidean.h"
 #include "mempearson.h"
+#include "sharedrjsd.h"
+#include "sharedjsd.h"
 
 
 
@@ -78,8 +80,9 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "tree.shared";                         }
        string getCommandCategory()             { return "OTU-Based Approaches";        }
-       string getOutputFileNameTag(string, string);
+       
        string getHelpString(); 
+    string getOutputPattern(string);   
        string getCitation() { return "http://www.mothur.org/wiki/Tree.shared"; }
        string getDescription()         { return "generate a tree file that describes the dissimilarity among groups"; }
 
@@ -138,6 +141,7 @@ struct treeSharedData {
        unsigned long long start;
        unsigned long long end;
        MothurOut* m;
+    int count;
        
        treeSharedData(){}
        treeSharedData(MothurOut* mout, unsigned long long st, unsigned long long en, vector<string> est, vector<SharedRAbundVector*> lu) {
@@ -146,6 +150,7 @@ struct treeSharedData {
                end = en;
         Estimators = est;
         thisLookup = lu;
+        count=0;
        }
 };
 /**************************************************************************************************/
@@ -248,6 +253,8 @@ static DWORD WINAPI MyTreeSharedThreadFunction(LPVOID lpParam){
                vector<SharedRAbundVector*> subset;
                for (int k = pDataArray->start; k < pDataArray->end; k++) { // pass cdd each set of groups to compare
                        
+            pDataArray->count++;
+            
                        for (int l = 0; l < k; l++) {
                                
                                if (k != l) { //we dont need to similiarity of a groups to itself