fixes while testing 1.33.0

[mothur.git] / parselistscommand.cpp

diff --git a/parselistscommand.cpp b/parselistscommand.cpp
index 5a568f3511d38f56601362d860a9643e702c9a1b..cfd1b6b9705ccb131e050ce132547192892d12ea 100644 (file)
--- a/parselistscommand.cpp
+++ b/parselistscommand.cpp
@@ -53,7 +53,7 @@ string ParseListCommand::getOutputPattern(string type) {
     try {
         string pattern = "";
         
-        if (type == "list") {  pattern = "[filename],[group],list"; } 
+        if (type == "list") {  pattern = "[filename],[group],[distance],list"; } 
         else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
         
         return pattern;
@@ -169,7 +169,7 @@ ParseListCommand::ParseListCommand(string option)  {
                        else if (countfile == "not open") { abort = true; countfile =  ""; }    
                        else {   
                 m->setCountTableFile(countfile); 
-                ct.readTable(countfile, true);
+                ct.readTable(countfile, true, false);
                 if (!ct.hasGroupInfo()) { 
                     abort = true;
                     m->mothurOut("[ERROR]: The parse.list command requires group info to be present in your countfile, quitting."); m->mothurOutEndLine();
@@ -205,27 +205,6 @@ int ParseListCommand::execute(){
        
                if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
-               //set fileroot
-               map<string, string> variables; 
-        variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(listfile));
-               
-               //fill filehandles with neccessary ofstreams
-               int i;
-               ofstream* temp;
-               vector<string> gGroups;
-        if (groupfile != "") { gGroups = groupMap->getNamesOfGroups(); }
-        else { gGroups = ct.getNamesOfGroups(); }
-        
-               for (i=0; i<gGroups.size(); i++) {
-                       temp = new ofstream;
-                       filehandles[gGroups[i]] = temp;
-                       
-            variables["[group]"] = gGroups[i];
-                       string filename = getOutputFileName("list",variables);
-                       outputNames.push_back(filename); outputTypes["list"].push_back(filename);
-                       m->openOutputFile(filename, *temp);
-               }
-               
                //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
                set<string> processedLabels;
                set<string> userLabels = labels;        
@@ -236,16 +215,13 @@ int ParseListCommand::execute(){
                
                if (m->control_pressed) { 
                        delete list; if (groupfile != "") { delete groupMap; }
-                       for (i=0; i<gGroups.size(); i++) {  (*(filehandles[gGroups[i]])).close();  delete filehandles[gGroups[i]]; } 
-                       for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]); } outputTypes.clear();
-                       return 0;
+                       for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]); } outputTypes.clear(); return 0;
                }
                
                while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
                
                        if (m->control_pressed) { 
                                delete list; if (groupfile != "") { delete groupMap; }
-                               for (i=0; i<gGroups.size(); i++) {  (*(filehandles[gGroups[i]])).close();  delete filehandles[gGroups[i]]; } 
                                for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]); } outputTypes.clear();
                                return 0;
                        }
@@ -283,7 +259,6 @@ int ParseListCommand::execute(){
                
                if (m->control_pressed) { 
                        if (groupfile != "") { delete groupMap; }
-                       for (i=0; i<gGroups.size(); i++) {  (*(filehandles[gGroups[i]])).close();  delete filehandles[gGroups[i]]; } 
                        for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]); } outputTypes.clear();
                        return 0;
                }
@@ -304,7 +279,6 @@ int ParseListCommand::execute(){
                
                if (m->control_pressed) { 
                        if (groupfile != "") { delete groupMap; }
-                       for (i=0; i<gGroups.size(); i++) {  (*(filehandles[gGroups[i]])).close();  delete filehandles[gGroups[i]]; } 
                        for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]); } outputTypes.clear();
                        return 0;
                }
@@ -320,11 +294,6 @@ int ParseListCommand::execute(){
                        delete list;
                }
                
-               for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
-                       (*(filehandles[it3->first])).close();
-                       delete it3->second;
-               }
-               
                if (groupfile != "") { delete groupMap; }
                
                if (m->control_pressed) { 
@@ -354,8 +323,33 @@ int ParseListCommand::execute(){
 /**********************************************************************************************************************/
 int ParseListCommand::parse(ListVector* thisList) {
        try {
+        map<string, ofstream*> filehandles;
+        map<string, ofstream*>::iterator it3;
+        
+        //set fileroot
+               map<string, string> variables;
+        variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(listfile));
+        variables["[distance]"] = thisList->getLabel();
+               
+               //fill filehandles with neccessary ofstreams
+               ofstream* temp;
+               vector<string> gGroups;
+        if (groupfile != "") { gGroups = groupMap->getNamesOfGroups(); }
+        else { gGroups = ct.getNamesOfGroups(); }
+        
+               for (int i=0; i<gGroups.size(); i++) {
+                       temp = new ofstream;
+                       filehandles[gGroups[i]] = temp;
+                       
+            variables["[group]"] = gGroups[i];
+                       string filename = getOutputFileName("list",variables);
+                       m->openOutputFile(filename, *temp);
+            outputNames.push_back(filename); outputTypes["list"].push_back(filename);
+               }
+
        
                map<string, string> groupVector;
+        map<string, string> groupLabels;
                map<string, string>::iterator itGroup;
                map<string, int> groupNumBins;
                
@@ -363,11 +357,12 @@ int ParseListCommand::parse(ListVector* thisList) {
                for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
                        groupNumBins[it3->first] = 0;
                        groupVector[it3->first] = "";
+            groupLabels[it3->first] = "label\tnumOtus\t";
                }
 
-               
+               vector<string> binLabels = thisList->getLabels();
                for (int i = 0; i < thisList->getNumBins(); i++) {
-                       if (m->control_pressed) { return 0; }
+                       if (m->control_pressed) { break; }
                        
                        map<string, string> groupBins;
                        string bin = list->get(i); 
@@ -408,14 +403,26 @@ int ParseListCommand::parse(ListVector* thisList) {
                        
                        //print parsed bin info to files
                        for (itGroup = groupBins.begin(); itGroup != groupBins.end(); itGroup++) {
-                               groupVector[itGroup->first] +=  itGroup->second + '\t'; 
+                               groupVector[itGroup->first] +=  itGroup->second + '\t';
+                groupLabels[itGroup->first] +=  binLabels[i] + '\t';
                        }
                
                }
                
+        if (m->control_pressed) {
+            for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
+                (*(filehandles[it3->first])).close();
+                delete it3->second;
+            }
+            return 0;
+        }
+        
                //end list vector
                for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
+            (*(filehandles[it3->first])) << groupLabels[it3->first] << endl;
                        (*(filehandles[it3->first])) << thisList->getLabel() << '\t' << groupNumBins[it3->first] << '\t' << groupVector[it3->first] << endl;  // label numBins  listvector for that group
+            (*(filehandles[it3->first])).close();
+            delete it3->second;
                }
                
                return 0;