added smart distance feature and optimized all commands using line by line processing

[mothur.git] / parselistcommand.cpp

diff --git a/parselistcommand.cpp b/parselistcommand.cpp
index f1447980cd918a6f712447a928621cb689f35efe..20f92f73b3e8107bd47a1e99f253779e67d2a423 100644 (file)
--- a/parselistcommand.cpp
+++ b/parselistcommand.cpp
@@ -17,7 +17,8 @@ ParseListCommand::ParseListCommand(){
                //read in group map info.
                groupMap = new GroupMap(globaldata->getGroupFile());
                groupMap->readMap();
-                       
+
+               
                //fill filehandles with neccessary ofstreams
                int i;
                ofstream* temp;
@@ -44,7 +45,7 @@ ParseListCommand::ParseListCommand(){
        }
 }
 /***********************************************************************/
-void ParseListCommand::parse(int index) {
+void ParseListCommand::parse(int index, SharedListVector* list) {
        try {
                string prefix, suffix, groupsName;
                suffix = list->get(index);
@@ -93,49 +94,71 @@ int ParseListCommand::execute(){
                        read->read(&*globaldata); 
                        input = globaldata->ginput;
                        list = globaldata->gSharedList;
+                       SharedListVector* lastList = list;
+               
+                       //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 = globaldata->labels;
 
                        //read in group map info.
                        groupMap = new GroupMap(globaldata->getGroupFile());
                        groupMap->readMap();
                        
-                       string seq, label;
-                       int i;
                        //create new list vectors to fill with parsed data
-                       for (i=0; i<groupMap->getNumGroups(); i++) {
+                       for (int i=0; i<groupMap->getNumGroups(); i++) {
                                groupOfLists[groupMap->namesOfGroups[i]] = new SharedListVector();
                        }
                        
+                                               
                        //parses and sets each groups listvector
-                       while(list != NULL){
-                               label = list->getLabel();
-                               
-                               if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(label) == 1){
-                               
-                                       for(i=0; i<list->size(); i++) {
-                                               parse(i); //parses data[i] list of sequence names
-                                               for (it=listGroups.begin(); it != listGroups.end(); it++) {  //loop through map and set new list vectors
-                                                       seq = it->second;
-                                                       seq = seq.substr(1, seq.length()); //rips off extra comma
-                                                       groupOfLists[it->first]->push_back(seq); //sets new listvector for each group
-                                               }
-                                               listGroups.clear();
-                                       }
-                                       //prints each new list file
-                                       for (i=0; i<groupMap->getNumGroups(); i++) {
-                                               groupOfLists[groupMap->namesOfGroups[i]]->setLabel(label);
-                                               groupOfLists[groupMap->namesOfGroups[i]]->print(*(filehandles[groupMap->namesOfGroups[i]]));
-                                               groupOfLists[groupMap->namesOfGroups[i]]->clear();
-                                       }
+                       //as long as you are not at the end of the file or done wih the lines you want
+                       while((list != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0))) {
+                                                               
+                               if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(list->getLabel()) == 1){
+                                       cout << list->getLabel() << '\t' << count << endl;
+                                       process(list);
                                        
-                                       cout << label << '\t' << count << endl;
+                                       processedLabels.insert(list->getLabel());
+                                       userLabels.erase(list->getLabel());
                                }
                                
+                               if ((anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastList->getLabel()) != 1)) {
+                                       cout << lastList->getLabel() << '\t' << count << endl;
+                                       process(lastList);
+                                       
+                                       processedLabels.insert(lastList->getLabel());
+                                       userLabels.erase(lastList->getLabel());
+                               }
+
+                               if (count != 1) { delete lastList; }
+                               lastList = list;                        
+
                                list = input->getSharedListVector();
                                count++;
                        }
                        
+                       //output error messages about any remaining user labels
+                       set<string>::iterator it;
+                       bool needToRun = false;
+                       for (it = userLabels.begin(); it != userLabels.end(); it++) {  
+                               cout << "Your file does not include the label "<< *it; 
+                               if (processedLabels.count(lastList->getLabel()) != 1) {
+                                       cout << ". I will use " << lastList->getLabel() << "." << endl;
+                                       needToRun = true;
+                               }else {
+                                       cout << ". Please refer to " << lastList->getLabel() << "." << endl;
+                               }
+                       }
+               
+                       //run last line if you need to
+                       if (needToRun == true)  {
+                               cout << lastList->getLabel() << '\t' << count << endl;
+                               process(lastList);
+                       }
+                       delete lastList;
+
                        //set groupmap for .shared commands
-                       //if (globaldata->gGroupmap != NULL) { delete globaldata->gGroupmap; }
+                       if (globaldata->gGroupmap != NULL) { delete globaldata->gGroupmap; }
                        globaldata->gGroupmap = groupMap; 
                        
                        return 0;
@@ -158,3 +181,33 @@ ParseListCommand::~ParseListCommand(){
        delete read;    
 }
 //**********************************************************************************************************************
+void ParseListCommand::process(SharedListVector* thisList) {
+       try {
+                       string seq;
+
+                       for(int i=0; i<thisList->size(); i++) {
+                               parse(i, thisList); //parses data[i] list of sequence names
+                               for (it=listGroups.begin(); it != listGroups.end(); it++) {  //loop through map and set new list vectors
+                                       seq = it->second;
+                                       seq = seq.substr(1, seq.length()); //rips off extra comma
+                                       groupOfLists[it->first]->push_back(seq); //sets new listvector for each group
+                               }
+                               listGroups.clear();
+                       }
+                       //prints each new list file
+                       for (int i=0; i<groupMap->getNumGroups(); i++) {
+                               groupOfLists[groupMap->namesOfGroups[i]]->setLabel(thisList->getLabel());
+                               groupOfLists[groupMap->namesOfGroups[i]]->print(*(filehandles[groupMap->namesOfGroups[i]]));
+                               groupOfLists[groupMap->namesOfGroups[i]]->clear();
+                       }
+
+       }
+       catch(exception& e) {
+               cout << "Standard Error: " << e.what() << " has occurred in the ParseListCommand class Function process. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the ParseListCommand class function process. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+}
\ No newline at end of file