X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=countseqscommand.h;h=a5326d401e870c1878b5d8e7f4c2708bc0c48f04;hp=54982c11939e82fae8de341f74c1aa3a01e4f609;hb=615301e57c25e241356a9c2380648d117709458d;hpb=49d2b7459c5027557564b21e9487dadafbbbdc96

diff --git a/countseqscommand.h b/countseqscommand.h
index 54982c1..a5326d4 100644
--- a/countseqscommand.h
+++ b/countseqscommand.h
@@ -11,6 +11,7 @@
  */
 
 #include "command.hpp"
+#include "groupmap.h"
 
 class CountSeqsCommand : public Command {
 	
@@ -23,8 +24,9 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "count.seqs";				}
 	string getCommandCategory()		{ return "Sequence Processing";		}
-	string getOutputFileNameTag(string, string);
+	
 	string getHelpString();	
+    string getOutputPattern(string);	
 	string getCitation() { return "http://www.mothur.org/wiki/Count.seqs"; }
 	string getDescription()		{ return "counts the number of sequences represented by each unique sequence in a namesfile"; }
 
@@ -33,11 +35,137 @@ public:
 	
 	
 private:
+    
+    struct linePair {
+		unsigned long long start;
+		unsigned long long end;
+		linePair(unsigned long long i, unsigned long long j) : start(i), end(j) {}
+	};
+    
 	string namefile, groupfile, outputDir, groups;
-	bool abort;
-	vector<string> Groups;
+	bool abort, large;
+	vector<string> Groups, outputNames;
+    int processors;
+    
+    int processSmall(string);
+    int processLarge(string);
+    map<int, string> processNameFile(string);
+    map<int, string> getGroupNames(string, set<string>&);
+    
+    int createProcesses(GroupMap*&, string);
+    int driver(unsigned long long, unsigned long long, string, GroupMap*&);
+    
+};
+
+/***********************************************************************/
+struct countData {
+    unsigned long long start;
+	unsigned long long end;
+	MothurOut* m;
+    string outputFileName, namefile, groupfile;
+    GroupMap* groupMap;
+    int total;
+    vector<string> Groups;
+    
+	countData(){}
+	countData(string fn, GroupMap* g, MothurOut* mout, unsigned long long st, unsigned long long en, string gfn, string nfn, vector<string> gr) {
+        m = mout;
+		start = st;
+		end = en;
+        groupMap = g;
+        groupfile = gfn;
+        namefile = nfn;
+        outputFileName = fn;
+        Groups = gr;
+        total = 0;
+	}
 };
 
+/**************************************************************************************************/
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+#else
+static DWORD WINAPI MyCountThreadFunction(LPVOID lpParam){
+	countData* pDataArray;
+	pDataArray = (countData*)lpParam;
+	try {
+        ofstream out;
+        pDataArray->m->openOutputFile(pDataArray->outputFileName, out);
+        
+        ifstream in;
+		pDataArray->m->openInputFile(pDataArray->namefile, in);
+		in.seekg(pDataArray->start);
+        
+        //print header if you are process 0
+		if ((pDataArray->start == 0) || (pDataArray->start == 1)) {
+			in.seekg(0);
+		}else { //this accounts for the difference in line endings.
+			in.seekg(pDataArray->start-1); pDataArray->m->gobble(in);
+		}
+        
+        pDataArray->total = 0;
+		for(int i = 0; i < pDataArray->end; i++){ //end is the number of sequences to process
+            
+			if (pDataArray->m->control_pressed) { break; }
+			
+			string firstCol, secondCol;
+			in >> firstCol; pDataArray->m->gobble(in); in >> secondCol; pDataArray->m->gobble(in);
+            //cout << firstCol << '\t' << secondCol << endl;
+            pDataArray->m->checkName(firstCol);
+            pDataArray->m->checkName(secondCol);
+            
+			vector<string> names;
+			pDataArray->m->splitAtChar(secondCol, names, ',');
+			
+			if (pDataArray->groupfile != "") {
+				//set to 0
+				map<string, int> groupCounts;
+				int total = 0;
+				for (int i = 0; i < pDataArray->Groups.size(); i++) { groupCounts[pDataArray->Groups[i]] = 0; }
+				
+				//get counts for each of the users groups
+				for (int i = 0; i < names.size(); i++) {
+					string group = pDataArray->groupMap->getGroup(names[i]);
+					
+					if (group == "not found") { pDataArray->m->mothurOut("[ERROR]: " + names[i] + " is not in your groupfile, please correct."); pDataArray->m->mothurOutEndLine(); }
+					else {
+						map<string, int>::iterator it = groupCounts.find(group);
+						
+						//if not found, then this sequence is not from a group we care about
+						if (it != groupCounts.end()) {
+							it->second++;
+							total++;
+						}
+					}
+				}
+				
+				if (total != 0) {
+					out << firstCol << '\t' << total << '\t';
+					for (map<string, int>::iterator it = groupCounts.begin(); it != groupCounts.end(); it++) {
+						out << it->second << '\t';
+					}
+					out << endl;
+				}
+			}else {
+				out << firstCol << '\t' << names.size() << endl;
+			}
+			
+			pDataArray->total += names.size();
+		}
+		in.close();
+        out.close();
+
+                
+        return 0;
+    }
+	catch(exception& e) {
+		pDataArray->m->errorOut(e, "CountSeqsCommand", "MyCountThreadFunction");
+		exit(1);
+	}
+}
+#endif
+
+
+
 #endif