added load.logfile command. changed summary.single output for subsample=t.

[mothur.git] / binsequencecommand.cpp

diff --git a/binsequencecommand.cpp b/binsequencecommand.cpp
index 34965f624cc789e830783302f4ccd36993e28ea4..7569a4be3113144a96048f5a4d624d271c15b9f4 100644 (file)
--- a/binsequencecommand.cpp
+++ b/binsequencecommand.cpp
@@ -50,6 +50,26 @@ string BinSeqCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
+string BinSeqCommand::getOutputFileNameTag(string type, string inputName=""){  
+       try {
+        string outputFileName = "";
+               map<string, vector<string> >::iterator it;
+        
+        //is this a type this command creates
+        it = outputTypes.find(type);
+        if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+        else {
+            if (type == "fasta") {  outputFileName =  "fasta"; }
+            else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
+        }
+        return outputFileName;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "BinSeqCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
 BinSeqCommand::BinSeqCommand(){        
        try {
                abort = true; calledHelp = true; 
@@ -71,6 +91,7 @@ BinSeqCommand::BinSeqCommand(string option) {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();
@@ -137,6 +158,7 @@ BinSeqCommand::BinSeqCommand(string option) {
                                else {  m->mothurOut("You have no current fasta file and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
                        }
                        else if (fastafile == "not open") { abort = true; }     
+                       else { m->setFastaFile(fastafile); }
                        
                        listfile = validParameter.validFile(parameters, "list", true);
                        if (listfile == "not found") {                  
@@ -145,6 +167,7 @@ BinSeqCommand::BinSeqCommand(string option) {
                                else {  m->mothurOut("You have no current list file and the list parameter is required."); m->mothurOutEndLine(); abort = true; }
                        }
                        else if (listfile == "not open") { listfile = ""; abort = true; }       
+                       else { m->setListFile(listfile); }
                        
                        //if the user changes the output directory command factory will send this info to us in the output parameter 
                        outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  
@@ -164,12 +187,19 @@ BinSeqCommand::BinSeqCommand(string option) {
                        }
                        
                        namesfile = validParameter.validFile(parameters, "name", true);
-                       if (namesfile == "not open") { abort = true; }  
+                       if (namesfile == "not open") { namesfile = ""; abort = true; }  
                        else if (namesfile == "not found") { namesfile = ""; }
+                       else {  m->setNameFile(namesfile); }
 
                        groupfile = validParameter.validFile(parameters, "group", true);
                        if (groupfile == "not open") { abort = true; }
                        else if (groupfile == "not found") { groupfile = ""; }
+                       else { m->setGroupFile(groupfile); }
+                       
+                       if (namesfile == ""){
+                               vector<string> files; files.push_back(fastafile); 
+                               parser.getNameFile(files);
+                       }
                        
                }
        }
@@ -216,12 +246,12 @@ int BinSeqCommand::execute(){
                                
                while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
                        
-                       if(m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str());         } delete input;  delete fasta; if (groupfile != "") {  delete groupMap;   } return 0; } 
+                       if(m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]);                } delete input;  delete fasta; if (groupfile != "") {  delete groupMap;   } return 0; } 
                        
                        if(allLines == 1 || labels.count(list->getLabel()) == 1){
                                
                                error = process(list);  
-                               if (error == 1) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());         } delete input;  delete fasta; if (groupfile != "") {  delete groupMap;   } return 0; } 
+                               if (error == 1) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);                } delete input;  delete fasta; if (groupfile != "") {  delete groupMap;   } return 0; } 
                                                        
                                processedLabels.insert(list->getLabel());
                                userLabels.erase(list->getLabel());
@@ -234,7 +264,7 @@ int BinSeqCommand::execute(){
                                list = input->getListVector(lastLabel);
                                
                                error = process(list);  
-                               if (error == 1) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());         } delete input;  delete fasta; if (groupfile != "") {  delete groupMap;   } return 0; }
+                               if (error == 1) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);                } delete input;  delete fasta; if (groupfile != "") {  delete groupMap;   } return 0; }
                                                                                                        
                                processedLabels.insert(list->getLabel());
                                userLabels.erase(list->getLabel());
@@ -249,7 +279,7 @@ int BinSeqCommand::execute(){
                        list = input->getListVector();
                }
                
-               if(m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str());         } delete input;  delete fasta; if (groupfile != "") {  delete groupMap;   } return 0; } 
+               if(m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]);                } delete input;  delete fasta; if (groupfile != "") {  delete groupMap;   } return 0; } 
 
                //output error messages about any remaining user labels
                set<string>::iterator it;
@@ -270,7 +300,7 @@ int BinSeqCommand::execute(){
                        list = input->getListVector(lastLabel);
                                
                        error = process(list);  
-                       if (error == 1) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());         } delete input;  delete fasta; if (groupfile != "") {  delete groupMap;   } return 0; }
+                       if (error == 1) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);                } delete input;  delete fasta; if (groupfile != "") {  delete groupMap;   } return 0; }
                        
                        delete list;  
                }
@@ -279,7 +309,7 @@ int BinSeqCommand::execute(){
                delete fasta; 
                if (groupfile != "") {  delete groupMap;   } 
                
-               if(m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str());         }  return 0; }  
+               if(m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]);                }  return 0; }  
                
                m->mothurOutEndLine();
                m->mothurOut("Output File Names: "); m->mothurOutEndLine();
@@ -334,8 +364,8 @@ int BinSeqCommand::process(ListVector* list) {
        try {
                                string binnames, name, sequence;
                                
-                               string outputFileName = outputDir + m->getRootName(m->getSimpleName(listfile)) + list->getLabel() + ".fasta";
-                               m->openOutputFile(outputFileName, out);
+        string outputFileName = outputDir + m->getRootName(m->getSimpleName(listfile)) + list->getLabel() + getOutputFileNameTag("fasta");
+        m->openOutputFile(outputFileName, out);
                                
                                //save to output list of output file names
                                outputNames.push_back(outputFileName);  outputTypes["fasta"].push_back(outputFileName);