added pcr.seqs command. fixed bug in rarefacftion.single that caused parsing error...

[mothur.git] / rarefactcommand.cpp

diff --git a/rarefactcommand.cpp b/rarefactcommand.cpp
index 47d55a0f07459c4128ed737f420c102ae42ea791..dabcef486ee7541c183fc594f10da9a9f6624561 100644 (file)
--- a/rarefactcommand.cpp
+++ b/rarefactcommand.cpp
@@ -351,7 +351,7 @@ int RareFactCommand::execute(){
                                                rDisplays.push_back(new RareDisplay(new NSeqs(), new ThreeColumnFile(fileNameRoot+"r_nseqs")));
                                                outputNames.push_back(fileNameRoot+"r_nseqs"); outputTypes["r_nseqs"].push_back(fileNameRoot+"r_nseqs");
                                        }
-                    file2Group[outputNames.size()-1] = groups[p];
+                    if (inputFileNames.size() > 1) { file2Group[outputNames.size()-1] = groups[p]; }
                                }
                        }
                        
@@ -473,7 +473,8 @@ vector<string> RareFactCommand::createGroupFile(vector<string>& outputNames, map
                vector<string> newFileNames;
                
                //find different types of files
-               map<string, vector<string> > typesFiles;
+               map<string, map<string, string> > typesFiles;
+        map<string, string> temp; 
                for (int i = 0; i < outputNames.size(); i++) {
                        string extension = m->getExtension(outputNames[i]);
                        
@@ -485,7 +486,8 @@ vector<string> RareFactCommand::createGroupFile(vector<string>& outputNames, map
                        
                        newLine += "\tGroup" + labels.substr(labels.find_first_of('\t'));
                        
-                       typesFiles[extension].push_back(outputNames[i]+"_"+file2Group[i]);
+            temp[outputNames[i]] = file2Group[i];
+                       typesFiles[extension] = temp;
                        
                        string combineFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "groups" + extension;
                        
@@ -499,23 +501,23 @@ vector<string> RareFactCommand::createGroupFile(vector<string>& outputNames, map
                
                //for each type create a combo file
                map<int, int> lineToNumber; 
-               for (map<string, vector<string> >::iterator it = typesFiles.begin(); it != typesFiles.end(); it++) {
+               for (map<string, map<string, string> >::iterator it = typesFiles.begin(); it != typesFiles.end(); it++) {
                        
                        ofstream out;
                        string combineFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "groups" + it->first;
                        m->openOutputFileAppend(combineFileName, out);
                        newFileNames.push_back(combineFileName);
                        
-                       vector<string> thisTypesFiles = it->second;
+                       map<string, string> thisTypesFiles = it->second;
                
                        //open each type summary file
                        map<string, vector<string> > files; //maps file name to lines in file
                        int maxLines = 0;
                        int numColumns = 0;
-                       for (int i=0; i<thisTypesFiles.size(); i++) {
+                       for (map<string, string>::iterator itFileNameGroup = thisTypesFiles.begin(); itFileNameGroup != thisTypesFiles.end(); itFileNameGroup++) {
                 
-                string thisfilename = thisTypesFiles[i].substr(0, thisTypesFiles[i].find_last_of('_'));
-                string group = thisTypesFiles[i].substr(thisTypesFiles[i].find_last_of('_')+1);
+                string thisfilename = itFileNameGroup->first;
+                string group = itFileNameGroup->second;
                 
                                ifstream temp;
                                m->openInputFile(thisfilename, temp);
@@ -524,15 +526,6 @@ vector<string> RareFactCommand::createGroupFile(vector<string>& outputNames, map
                                m->getline(temp);       m->gobble(temp);
                                
                                vector<string> thisFilesLines;
-                               //string fileNameRoot = m->getRootName(thisTypesFiles[i]);
-                               //map<string, string>::iterator itName = nameMap.find(fileNameRoot);
-                               //string group = "";
-                               //if (itName != nameMap.end()) {
-                               //      group = itName->second;
-                               //}else {
-                               //      group = "not found" + i;
-                               //      m->mothurOut("[ERROR]: can't parse filename."); m->mothurOutEndLine();
-                               //}
                                
                                thisFilesLines.push_back(group);
                                int count = 1;
@@ -552,7 +545,7 @@ vector<string> RareFactCommand::createGroupFile(vector<string>& outputNames, map
                                        m->gobble(temp);
                                }
                                
-                               files[thisTypesFiles[i]] = thisFilesLines;
+                               files[thisfilename] = thisFilesLines;
                                
                                //save longest file for below
                                if (maxLines < thisFilesLines.size()) { maxLines = thisFilesLines.size(); }
@@ -566,17 +559,19 @@ vector<string> RareFactCommand::createGroupFile(vector<string>& outputNames, map
                        for (int k = 1; k < maxLines; k++) {
                                
                                //grab data for each group
-                               for (int i=0; i<thisTypesFiles.size(); i++) {
-                                       
+                               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);
-                                               if (k < files[thisTypesFiles[i]].size()) {
-                                                       string line = files[thisTypesFiles[i]][k];
+                                               if (k < files[thisfilename].size()) {
+                                                       string line = files[thisfilename][k];
                                                        output = line.substr(0, line.find_first_of('\t'));
-                                                       output += '\t' + files[thisTypesFiles[i]][0] + '\t' + line.substr(line.find_first_of('\t'));
+                                                       output += '\t' + files[thisfilename][0] + '\t' + line.substr(line.find_first_of('\t'));
                                                }else{
-                                                       output += '\t' + files[thisTypesFiles[i]][0] + '\t';
+                                                       output += '\t' + files[thisfilename][0] + '\t';
                                                        for (int h = 0; h < numColumns; h++) {
                                                                output += "NA\t";
                                                        }