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

[mothur.git] / getsharedotucommand.cpp

diff --git a/getsharedotucommand.cpp b/getsharedotucommand.cpp
index 02461365b505bdea22cc977594fc1341ca7bac46..9beca6aa96f75a58891b5326b5cbd94209701656 100644 (file)
--- a/getsharedotucommand.cpp
+++ b/getsharedotucommand.cpp
@@ -46,8 +46,8 @@ string GetSharedOTUCommand::getHelpString(){
                helpString += "The output parameter allows you to output the list of names without the group and bin number added. \n";
                helpString += "With this option you can use the names file as an input in get.seqs and remove.seqs commands. To do this enter output=accnos. \n";
                helpString += "The get.sharedseqs command outputs a .names file for each distance level containing a list of sequences in the OTUs shared by the groups specified.\n";
-               helpString += "The get.sharedseqs command should be in the following format: get.sharedseqs(label=yourLabels, groups=yourGroups, fasta=yourFastafile, output=yourOutput).\n";
-               helpString += "Example get.sharedseqs(list=amazon.fn.list, label=unique-0.01, group=forest-pasture, fasta=amazon.fasta, output=accnos).\n";
+               helpString += "The get.sharedseqs command should be in the following format: get.sharedseqs(list=yourListFile, group=yourGroupFile, label=yourLabels, unique=yourGroups, fasta=yourFastafile, output=yourOutput).\n";
+               helpString += "Example get.sharedseqs(list=amazon.fn.list, label=unique-0.01, group= amazon.groups, unique=forest-pasture, fasta=amazon.fasta, output=accnos).\n";
                helpString += "The output to the screen is the distance and the number of otus at that distance for the groups you specified.\n";
                helpString += "The default value for label is all labels in your inputfile. The default for groups is all groups in your file.\n";
                helpString += "Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabel).\n";
@@ -58,6 +58,29 @@ string GetSharedOTUCommand::getHelpString(){
                exit(1);
        }
 }
+//**********************************************************************************************************************
+string GetSharedOTUCommand::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 =  "shared.fasta";   }
+            else if (type == "accnos")      {   outputFileName =  "accnos";         }
+            else if (type == "sharedseqs")  {   outputFileName =  "shared.seqs";    }
+            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, "GetSharedOTUCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
+
 //**********************************************************************************************************************
 GetSharedOTUCommand::GetSharedOTUCommand(){    
        try {
@@ -182,7 +205,7 @@ GetSharedOTUCommand::GetSharedOTUCommand(string option)  {
                        else { 
                                userGroups = "unique." + groups;
                                m->splitAtDash(groups, Groups);
-                               m->Groups = Groups;
+                               m->setGroups(Groups);
                                
                        }
                        
@@ -191,7 +214,7 @@ GetSharedOTUCommand::GetSharedOTUCommand(string option)  {
                        else { 
                                userGroups = groups;
                                m->splitAtDash(groups, Groups);
-                               m->Groups = Groups;
+                               m->setGroups(Groups);
                                unique = false;
                        }
                        
@@ -221,7 +244,7 @@ int GetSharedOTUCommand::execute(){
                if (m->control_pressed) { delete groupMap; return 0; }
                
                if (Groups.size() == 0) {
-                       Groups = groupMap->namesOfGroups;
+                       Groups = groupMap->getNamesOfGroups();
                        
                        //make string for outputfile name
                        userGroups = "unique.";
@@ -230,7 +253,9 @@ int GetSharedOTUCommand::execute(){
                }else{
                        //sanity check for group names
                        SharedUtil util;
-                       util.setGroups(Groups, groupMap->namesOfGroups);
+                       vector<string> namesOfGroups = groupMap->getNamesOfGroups(); 
+                       util.setGroups(Groups, namesOfGroups);
+                       groupMap->setNamesOfGroups(namesOfGroups);
                }
        
                //put groups in map to find easier
@@ -325,7 +350,7 @@ int GetSharedOTUCommand::execute(){
                
 
                //reset groups parameter
-               m->Groups.clear();  
+               m->clearGroups();  
                
                if (lastlist != NULL) {         delete lastlist;        }
                
@@ -370,9 +395,9 @@ int GetSharedOTUCommand::process(ListVector* shared) {
                
                if (outputDir == "") { outputDir += m->hasPath(listfile); }
                if (output != "accnos") {
-                       outputFileNames = outputDir + m->getRootName(m->getSimpleName(listfile)) + shared->getLabel() + userGroups + ".shared.seqs";
+                       outputFileNames = outputDir + m->getRootName(m->getSimpleName(listfile)) + shared->getLabel() + userGroups + "." + getOutputFileNameTag("sharedseqs");
                }else {
-                       outputFileNames = outputDir + m->getRootName(m->getSimpleName(listfile)) + shared->getLabel() + userGroups + ".accnos";
+                       outputFileNames = outputDir + m->getRootName(m->getSimpleName(listfile)) + shared->getLabel() + userGroups + "." + getOutputFileNameTag("accnos");
                }
                m->openOutputFile(outputFileNames, outNames);
                
@@ -479,7 +504,7 @@ int GetSharedOTUCommand::process(ListVector* shared) {
                //if fasta file provided output new fasta file
                if ((fastafile != "") && wroteSomething) {
                        if (outputDir == "") { outputDir += m->hasPath(fastafile); }
-                       string outputFileFasta = outputDir + m->getRootName(m->getSimpleName(fastafile)) + shared->getLabel() + userGroups + ".shared.fasta";
+                       string outputFileFasta = outputDir + m->getRootName(m->getSimpleName(fastafile)) + shared->getLabel() + userGroups + "." + getOutputFileNameTag("fasta");
                        ofstream outFasta;
                        m->openOutputFile(outputFileFasta, outFasta);
                        outputNames.push_back(outputFileFasta); outputTypes["fasta"].push_back(outputFileFasta);