added unix to ifdefs. minor changes while testing 1.24.0.

[mothur.git] / rarefactcommand.cpp

diff --git a/rarefactcommand.cpp b/rarefactcommand.cpp
index b8c1c6f1a6420f8a139eb5c71b0320b87277035e..47d55a0f07459c4128ed737f420c102ae42ea791 100644 (file)
--- a/rarefactcommand.cpp
+++ b/rarefactcommand.cpp
@@ -287,7 +287,7 @@ int RareFactCommand::execute(){
                                
                if (m->control_pressed) { return 0; }
                
-               map<string, string> nameMap;
+               map<int, string> file2Group; //index in outputNames[i] -> group
                for (int p = 0; p < inputFileNames.size(); p++) {
                        
                        string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p]));
@@ -296,7 +296,6 @@ int RareFactCommand::execute(){
                        
                        if (inputFileNames.size() > 1) {
                                m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[p]); m->mothurOutEndLine(); m->mothurOutEndLine();
-                               nameMap[fileNameRoot] = groups[p];
                        }
                        int i;
                        ValidCalculators validCalculator;
@@ -352,6 +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];
                                }
                        }
                        
@@ -450,7 +450,7 @@ int RareFactCommand::execute(){
                if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       m->mothurRemove(outputNames[i]); } return 0; }
 
                //create summary file containing all the groups data for each label - this function just combines the info from the files already created.
-               if ((sharedfile != "") && (groupMode)) {   outputNames = createGroupFile(outputNames, nameMap);  }
+               if ((sharedfile != "") && (groupMode)) {   outputNames = createGroupFile(outputNames, file2Group);  }
 
                if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       m->mothurRemove(outputNames[i]); } return 0; }
 
@@ -467,7 +467,7 @@ int RareFactCommand::execute(){
        }
 }
 //**********************************************************************************************************************
-vector<string> RareFactCommand::createGroupFile(vector<string>& outputNames, map<string, string> nameMap) {
+vector<string> RareFactCommand::createGroupFile(vector<string>& outputNames, map<int, string> file2Group) {
        try {
                
                vector<string> newFileNames;
@@ -485,7 +485,7 @@ vector<string> RareFactCommand::createGroupFile(vector<string>& outputNames, map
                        
                        newLine += "\tGroup" + labels.substr(labels.find_first_of('\t'));
                        
-                       typesFiles[extension].push_back(outputNames[i]);
+                       typesFiles[extension].push_back(outputNames[i]+"_"+file2Group[i]);
                        
                        string combineFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "groups" + extension;
                        
@@ -513,23 +513,26 @@ vector<string> RareFactCommand::createGroupFile(vector<string>& outputNames, map
                        int maxLines = 0;
                        int numColumns = 0;
                        for (int i=0; i<thisTypesFiles.size(); i++) {
-                                                               
+                
+                string thisfilename = thisTypesFiles[i].substr(0, thisTypesFiles[i].find_last_of('_'));
+                string group = thisTypesFiles[i].substr(thisTypesFiles[i].find_last_of('_')+1);
+                
                                ifstream temp;
-                               m->openInputFile(thisTypesFiles[i], temp);
+                               m->openInputFile(thisfilename, temp);
                                
                                //read through first line - labels
                                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();
-                               }
+                               //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;
@@ -555,7 +558,7 @@ vector<string> RareFactCommand::createGroupFile(vector<string>& outputNames, map
                                if (maxLines < thisFilesLines.size()) { maxLines = thisFilesLines.size(); }
                                
                                temp.close();
-                               m->mothurRemove(thisTypesFiles[i]);
+                               m->mothurRemove(thisfilename);
                        }