fixed bug in rarefaction.single creating the groups file. working on cooccurrence...

diff --git a/cooccurrencecommand.cpp b/cooccurrencecommand.cpp
index b4965f5a91a2d12e4101aadc3b7258741de4945f..45bc0f58dd9cbf5fbcb32a7038fde29fb749551d 100644 (file)
--- 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 dabcef486ee7541c183fc594f10da9a9f6624561..82ff7faef0d8886d21fc6b642f34c88c1b143ea1 100644 (file)
--- 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 2bd6939482e962ac02332154ce459fac68c644ed..4c03278917e9bda274c5693b328bf9cbe58b6104 100644 (file)
--- 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);