X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=parsimony.h;h=51c0496b1405c43793ba2c47c7557c6b0c43630f;hp=11d4cc859b2c35295a273780499485ac70e1c052;hb=cf9987b67aa49777a4c91c2d21f96e58bf17aa82;hpb=5a3592c6478d5d786ec20e4bee71854ad92fdb8c

diff --git a/parsimony.h b/parsimony.h
index 11d4cc8..51c0496 100644
--- a/parsimony.h
+++ b/parsimony.h
@@ -12,25 +12,117 @@
  */
 
 #include "treecalculator.h"
-#include "treemap.h"
-#include "globaldata.hpp"
+#include "counttable.h"
 
 /***********************************************************************/
 
 class Parsimony : public TreeCalculator  {
 	
 	public:
-		Parsimony(TreeMap* t) : tmap(t) {};
+		Parsimony() {};
 		~Parsimony() {};
-		EstOutput getValues(Tree*);
-		EstOutput getValues(Tree*, string, string) { return data; };
+		EstOutput getValues(Tree*, int, string);
 		
 	private:
-		GlobalData* globaldata;
+		struct linePair {
+			int start;
+			int num;
+			linePair(int i, int j) : start(i), num(j) {}
+		};
+		vector<linePair> lines;
+	
 		EstOutput data;
-		TreeMap* tmap;
-		map<string, int>::iterator it;
+		int processors;
+		string outputDir;
+	
+		EstOutput driver(Tree*, vector< vector<string> >, int, int, CountTable*); 
+		EstOutput createProcesses(Tree*, vector< vector<string> >, CountTable*);
 };
-
 /***********************************************************************/
-#endif
\ No newline at end of file
+struct parsData {
+    int start;
+	int num;
+	MothurOut* m;
+    EstOutput results;
+    vector< vector<string> > namesOfGroupCombos;
+    Tree* t;
+    CountTable* ct;
+    
+	parsData(){}
+	parsData(MothurOut* mout, int st, int en, vector< vector<string> > ngc, Tree* tree, CountTable* count) {
+        m = mout;
+		start = st;
+		num = en;
+        namesOfGroupCombos = ngc;
+        t = tree;
+        ct = count;
+	}
+};
+
+/**************************************************************************************************/
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+#else
+static DWORD WINAPI MyParsimonyThreadFunction(LPVOID lpParam){
+	parsData* pDataArray;
+	pDataArray = (parsData*)lpParam;
+	try {
+        
+        pDataArray->results.resize(pDataArray->num);
+		
+		Tree* copyTree = new Tree(pDataArray->ct);
+		int count = 0;
+		
+		for (int h = pDataArray->start; h < (pDataArray->start+pDataArray->num); h++) {
+            
+			if (pDataArray->m->control_pressed) { delete copyTree; return 0; }
+            
+			int score = 0;
+			
+			//groups in this combo
+			vector<string> groups = pDataArray->namesOfGroupCombos[h];
+			
+			//copy users tree so that you can redo pgroups
+			copyTree->getCopy(pDataArray->t);
+			
+			//create pgroups that reflect the groups the user want to use
+			for(int i=copyTree->getNumLeaves();i<copyTree->getNumNodes();i++){
+				copyTree->tree[i].pGroups = (copyTree->mergeUserGroups(i, groups));
+			}
+			
+			for(int i=copyTree->getNumLeaves();i<copyTree->getNumNodes();i++){
+				
+				if (pDataArray->m->control_pressed) { return 0; }
+				
+				int lc = copyTree->tree[i].getLChild();
+				int rc = copyTree->tree[i].getRChild();
+				
+				int iSize = copyTree->tree[i].pGroups.size();
+				int rcSize = copyTree->tree[rc].pGroups.size();
+				int lcSize = copyTree->tree[lc].pGroups.size();
+				
+				//if isize are 0 then that branch is to be ignored
+				if (iSize == 0) { }
+				else if ((rcSize == 0) || (lcSize == 0)) { }
+				//if you have more groups than either of your kids then theres been a change.
+				else if(iSize > rcSize || iSize > lcSize){
+					score++;
+				}
+			}
+			
+			pDataArray->results[count] = score;
+			count++;
+		}
+        
+		delete copyTree;
+        
+        return 0;
+        
+    }
+	catch(exception& e) {
+		pDataArray->m->errorOut(e, "Parsimony", "MyParsimonyThreadFunction");
+		exit(1);
+	}
+}
+#endif
+
+#endif