From 4418e128575c1d667720090d7b45d9b48de81a3a Mon Sep 17 00:00:00 2001
From: Sarah Westcott <mothur.westcott@gmail.com>
Date: Tue, 1 May 2012 08:17:42 -0400
Subject: [PATCH] fixed bug in rarefaction.single creating the groups file.
 working on cooccurrence command

---
 cooccurrencecommand.cpp | 10 +++++++---
 rarefactcommand.cpp     | 18 ++++++++++--------
 trialswap2.h            |  2 +-
 3 files changed, 18 insertions(+), 12 deletions(-)

diff --git a/cooccurrencecommand.cpp b/cooccurrencecommand.cpp
index b4965f5..45bc0f5 100644
--- a/cooccurrencecommand.cpp
+++ b/cooccurrencecommand.cpp
@@ -318,7 +318,7 @@ int CooccurrenceCommand::getCooccurrence(vector<SharedRAbundVector*>& thisLookUp
             }
         }
         //don't need a prob matrix because we just shuffle the rows, may use this in the future
-//        else if (matrix == "sim2") {
+        else if (matrix == "sim2") { }
 //            for(int i=0;i<nrows;i++) {
 //                start = 0.0;
 //                for(int j=0;j<ncols;j++) {
@@ -412,7 +412,7 @@ int CooccurrenceCommand::getCooccurrence(vector<SharedRAbundVector*>& thisLookUp
         }
 
         //populate null matrix from probability matrix, do this a lot.
-        for(int i=0;i<runs;i++){
+        for(int h=0;h<runs;h++){
             nullmatrix.clear();
             //zero-fill the null matrix
             nullmatrix.assign(nrows, vector<int>(ncols, 0));
@@ -420,6 +420,7 @@ int CooccurrenceCommand::getCooccurrence(vector<SharedRAbundVector*>& thisLookUp
             if(matrix == "sim1" || matrix == "sim6" || matrix == "sim8" || matrix == "sim7") {
                 count = 0;
                 while(count < n) {
+                    if (m->control_pressed) { return 0; }
                 nextnum2:
                     previous = 0.0;
                     randnum = rand() / double(RAND_MAX);
@@ -453,10 +454,12 @@ int CooccurrenceCommand::getCooccurrence(vector<SharedRAbundVector*>& thisLookUp
                     previous = 0.0;
                     count = 0;
                     while(count < rowtotal[i]) {
+                        previous = 0.0;
+                        if (m->control_pressed) { return 0; }
                         randnum = rand() / double(RAND_MAX);
                         for(int j=0;j<ncols;j++) {
                             current = probabilityMatrix[ncols * i + j];
-                            if(randnum <= current && randnum > previous && nullmatrix[i][j] != 1) {
+                            if((randnum <= current && randnum > previous && nullmatrix[i][j] != 1) || (previous==current)){
                                 nullmatrix[i][j] = 1;
                                 count++;
                                 previous = 0.0;
@@ -473,6 +476,7 @@ int CooccurrenceCommand::getCooccurrence(vector<SharedRAbundVector*>& thisLookUp
                 for(int j=0;j<ncols;j++) {
                     count = 0;
                     while(count < columntotal[j]) {
+                        if (m->control_pressed) { return 0; }
                         randnum = rand() / double(RAND_MAX);
                         for(int i=0;i<nrows;i++) {
                             current = probabilityMatrix[ncols * i + j];
diff --git a/rarefactcommand.cpp b/rarefactcommand.cpp
index dabcef4..82ff7fa 100644
--- a/rarefactcommand.cpp
+++ b/rarefactcommand.cpp
@@ -474,7 +474,6 @@ vector<string> RareFactCommand::createGroupFile(vector<string>& outputNames, map
 		
 		//find different types of files
 		map<string, map<string, string> > typesFiles;
-        map<string, string> temp; 
 		for (int i = 0; i < outputNames.size(); i++) {
 			string extension = m->getExtension(outputNames[i]);
 			
@@ -485,9 +484,15 @@ vector<string> RareFactCommand::createGroupFile(vector<string>& outputNames, map
 			string newLine = labels.substr(0, labels.find_first_of('\t'));
 			
 			newLine += "\tGroup" + labels.substr(labels.find_first_of('\t'));
-			
-            temp[outputNames[i]] = file2Group[i];
-			typesFiles[extension] = temp;
+            
+            map<string, map<string, string> >::iterator itfind = typesFiles.find(extension);
+            if (itfind != typesFiles.end()) {
+                (itfind->second)[outputNames[i]] = file2Group[i];
+            }else {
+                map<string, string> temp;  
+                temp[outputNames[i]] = file2Group[i];
+                typesFiles[extension] = temp;
+            }
 			
 			string combineFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "groups" + extension;
 			
@@ -507,7 +512,6 @@ vector<string> RareFactCommand::createGroupFile(vector<string>& outputNames, map
 			string combineFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "groups" + it->first;
 			m->openOutputFileAppend(combineFileName, out);
 			newFileNames.push_back(combineFileName);
-			
 			map<string, string> thisTypesFiles = it->second;
 		
 			//open each type summary file
@@ -518,7 +522,7 @@ vector<string> RareFactCommand::createGroupFile(vector<string>& outputNames, map
                 
                 string thisfilename = itFileNameGroup->first;
                 string group = itFileNameGroup->second;
-                
+               
 				ifstream temp;
 				m->openInputFile(thisfilename, temp);
 				
@@ -541,7 +545,6 @@ vector<string> RareFactCommand::createGroupFile(vector<string>& outputNames, map
 					count++;
 									
 					thisFilesLines.push_back(thisLine);
-					
 					m->gobble(temp);
 				}
 				
@@ -562,7 +565,6 @@ vector<string> RareFactCommand::createGroupFile(vector<string>& outputNames, map
 				for (map<string, string>::iterator itFileNameGroup = thisTypesFiles.begin(); itFileNameGroup != thisTypesFiles.end(); itFileNameGroup++) {
                     
 					string thisfilename = itFileNameGroup->first;
-                    
 					map<int, int>::iterator itLine = lineToNumber.find(k);
 					if (itLine != lineToNumber.end()) {
 						string output = toString(itLine->second);
diff --git a/trialswap2.h b/trialswap2.h
index 2bd6939..4c03278 100644
--- a/trialswap2.h
+++ b/trialswap2.h
@@ -21,7 +21,7 @@ public:
     
     double calc_pvalue_lessthan (vector<double>, double);
     double calc_pvalue_greaterthan (vector<double>, double);
-    void swap_checkerboards (vector<vector<int> > &, vector<int>, vector<int>, int, int);
+    int swap_checkerboards (vector<vector<int> > &, vector<int>, vector<int>, int, int);
     int calc_combo (int, int, vector<vector<int> > &);
     double calc_vratio (int, int, vector<int>, vector<int>);
     int calc_checker (vector<vector<int> > &, vector<int>, int, int);
-- 
2.39.2