X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=shhhseqscommand.h;h=ffd72b9ebdc161291f9705333f018cb56c09559c;hp=5aceca8888e959c4ac4e511b15f954e7564c40c5;hb=615301e57c25e241356a9c2380648d117709458d;hpb=e0dc0bcef2a0f7e1f63abb531dbb1ad533da98ca

diff --git a/shhhseqscommand.h b/shhhseqscommand.h
index 5aceca8..ffd72b9 100644
--- a/shhhseqscommand.h
+++ b/shhhseqscommand.h
@@ -29,8 +29,10 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "shhh.seqs";	}
 	string getCommandCategory()		{ return "Sequence Processing";		}
+	
 	string getHelpString();	
-	string getCitation() { return "http://www.mothur.org/wiki/Shhh.seqs"; }
+    string getOutputPattern(string);	
+	string getCitation() { return "Schloss PD, Gevers D, Westcott SL (2011).  Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies.  PLoS ONE.  6:e27310.\nQuince C, Lanzen A, Davenport RJ, Turnbaugh PJ (2011).  Removing noise from pyrosequenced amplicons.  BMC Bioinformatics  12:38.\nhttp://www.mothur.org/wiki/Shhh.seqs"; }
 	string getDescription()		{ return "shhh.seqs"; }
 	
 	
@@ -55,8 +57,8 @@ private:
 	int loadData(correctDist*, seqNoise&, vector<string>&, vector<string>&, vector<string>&, vector<int>&, map<string, string>&, vector<Sequence>&);
 
 	int driver(seqNoise&, vector<string>&, vector<string>&, vector<string>&, vector<int>&, string, string, string, string);
-	int driverGroups(SequenceParser&, string, string, string, int, int, vector<string>);
-	int createProcessesGroups(SequenceParser&, string, string, string, vector<string>);
+	vector<string> driverGroups(SequenceParser&, string, string, string, int, int, vector<string>);
+	vector<string> createProcessesGroups(SequenceParser&, string, string, string, vector<string>);
 	int deconvoluteResults(string, string);
 
 
@@ -75,8 +77,9 @@ struct shhhseqsData {
 	MothurOut* m;
 	int start;
 	int end;
-	int sigma, threadID;
+	int sigma, threadID, count;
 	vector<string> groups;
+	vector<string> mapfileNames;
 	
 	shhhseqsData(){}
 	shhhseqsData(string f, string n, string g, string nff,  string nnf, string nmf, vector<string> gr, MothurOut* mout, int st, int en, int s, int tid) {
@@ -85,18 +88,19 @@ struct shhhseqsData {
 		groupfile = g;
 		newFName = nff;
 		newNName = nnf;
-		newNName = nmf;
+		newMName = nmf;
 		m = mout;
 		start = st;
 		end = en;
 		sigma = s;
 		threadID = tid;
 		groups = gr;
+        count=0;
 	}
 };
 
 /**************************************************************************************************/
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 #else
 static DWORD WINAPI MyShhhSeqsThreadFunction(LPVOID lpParam){ 
 	shhhseqsData* pDataArray;
@@ -110,12 +114,14 @@ static DWORD WINAPI MyShhhSeqsThreadFunction(LPVOID lpParam){
 		//precluster each group
 		for (int k = pDataArray->start; k < pDataArray->end; k++) {
 			
+            pDataArray->count++;
+            
 			int start = time(NULL);
 			
 			if (pDataArray->m->control_pressed) {  return 0; }
 			
 			pDataArray->m->mothurOutEndLine(); pDataArray->m->mothurOut("Processing group " + pDataArray->groups[k] + ":"); pDataArray->m->mothurOutEndLine();
-			
+
 			map<string, string> thisNameMap;
 			thisNameMap = parser.getNameMap(pDataArray->groups[k]); 
 			vector<Sequence> thisSeqs = parser.getSeqs(pDataArray->groups[k]);
@@ -311,10 +317,9 @@ static DWORD WINAPI MyShhhSeqsThreadFunction(LPVOID lpParam){
 			
 			pDataArray->m->appendFiles(pDataArray->newFName+pDataArray->groups[k], pDataArray->newFName); pDataArray->m->mothurRemove(pDataArray->newFName+pDataArray->groups[k]);
 			pDataArray->m->appendFiles(pDataArray->newNName+pDataArray->groups[k], pDataArray->newNName); pDataArray->m->mothurRemove(pDataArray->newNName+pDataArray->groups[k]);
+			pDataArray->mapfileNames.push_back(pDataArray->newMName+pDataArray->groups[k]+".map");
 			
 			pDataArray->m->mothurOut("It took " + toString(time(NULL) - start) + " secs to process group " + pDataArray->groups[k] + "."); pDataArray->m->mothurOutEndLine(); 
-			
-							
 		}
 		
 		return 0;
@@ -322,7 +327,7 @@ static DWORD WINAPI MyShhhSeqsThreadFunction(LPVOID lpParam){
 		
 	}
 	catch(exception& e) {
-		pDataArray->m->errorOut(e, "PreClusterCommand", "MyPreclusterThreadFunction");
+		pDataArray->m->errorOut(e, "ShhhSeqsCommand", "MyShhhSeqsThreadFunction");
 		exit(1);
 	}
 }