added modify names parameter to set.dir

[mothur.git] / countgroupscommand.cpp

diff --git a/countgroupscommand.cpp b/countgroupscommand.cpp
index 716dc90693969140d3af32403d3818c04224d7f9..83c2d315d0b8f781caa02c04c4fed5e1cb6b6a0d 100644 (file)
--- a/countgroupscommand.cpp
+++ b/countgroupscommand.cpp
@@ -14,13 +14,13 @@
 //**********************************************************************************************************************
 vector<string> CountGroupsCommand::setParameters(){    
        try {
-               CommandParameter pshared("shared", "InputTypes", "", "", "sharedGroup", "sharedGroup", "none",false,false); parameters.push_back(pshared);
-               CommandParameter pgroup("group", "InputTypes", "", "", "sharedGroup", "sharedGroup", "none",false,false); parameters.push_back(pgroup);
-        CommandParameter pcount("count", "InputTypes", "", "", "sharedGroup", "sharedGroup", "none",false,false); parameters.push_back(pcount);
-               CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(paccnos);
-               CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
-               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+               CommandParameter pshared("shared", "InputTypes", "", "", "sharedGroup", "sharedGroup", "none","summary",false,false,true); parameters.push_back(pshared);
+               CommandParameter pgroup("group", "InputTypes", "", "", "sharedGroup", "sharedGroup", "none","summary",false,false,true); parameters.push_back(pgroup);
+        CommandParameter pcount("count", "InputTypes", "", "", "sharedGroup", "sharedGroup", "none","summary",false,false,true); parameters.push_back(pcount);
+               CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(paccnos);
+               CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
                
                vector<string> myArray;
                for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
@@ -32,6 +32,21 @@ vector<string> CountGroupsCommand::setParameters(){
        }
 }
 //**********************************************************************************************************************
+string CountGroupsCommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
+        
+        if (type == "summary") {  pattern = "[filename],count.summary"; }
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "PrimerDesignCommand", "getOutputPattern");
+        exit(1);
+    }
+}
+//**********************************************************************************************************************
 string CountGroupsCommand::getHelpString(){    
        try {
                string helpString = "";
@@ -55,6 +70,8 @@ CountGroupsCommand::CountGroupsCommand(){
        try {
                abort = true; calledHelp = true;
                setParameters();
+        vector<string> tempOutNames;
+               outputTypes["summary"] = tempOutNames;
        }
        catch(exception& e) {
                m->errorOut(e, "CountGroupsCommand", "CountGroupsCommand");
@@ -125,6 +142,8 @@ CountGroupsCommand::CountGroupsCommand(string option)  {
                                }
                        }
                        
+            vector<string> tempOutNames;
+            outputTypes["summary"] = tempOutNames;
                        
                        //check for required parameters
                        accnosfile = validParameter.validFile(parameters, "accnos", true);
@@ -200,6 +219,15 @@ int CountGroupsCommand::execute(){
                if (accnosfile != "") { m->readAccnos(accnosfile, Groups); m->setGroups(Groups); }
                
                if (groupfile != "") {
+            map<string, string> variables; 
+            string thisOutputDir = outputDir;
+            if (outputDir == "") {  thisOutputDir += m->hasPath(groupfile);  }
+            variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(groupfile));
+            string outputFileName = getOutputFileName("summary", variables);
+            outputNames.push_back(outputFileName); outputTypes["summary"].push_back(outputFileName);
+            ofstream out;
+            m->openOutputFile(outputFileName, out);
+            
                        GroupMap groupMap(groupfile);
                        groupMap.readMap();
                        
@@ -214,16 +242,26 @@ int CountGroupsCommand::execute(){
                 int num = groupMap.getNumSeqs(Groups[i]);
                 total += num;
                                m->mothurOut(Groups[i] + " contains " + toString(num) + "."); m->mothurOutEndLine();
+                out << Groups[i] << '\t' << num << endl;
                        }
-            
+            out.close();
             m->mothurOut("\nTotal seqs: " + toString(total) + "."); m->mothurOutEndLine();
                }
         
         if (m->control_pressed) { return 0; }
         
         if (countfile != "") {
+            map<string, string> variables; 
+            string thisOutputDir = outputDir;
+            if (outputDir == "") {  thisOutputDir += m->hasPath(countfile);  }
+            variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(countfile));
+            string outputFileName = getOutputFileName("summary", variables);
+            outputNames.push_back(outputFileName); outputTypes["summary"].push_back(outputFileName);
+            ofstream out;
+            m->openOutputFile(outputFileName, out);
+            
                        CountTable ct;
-                       ct.readTable(countfile);
+                       ct.readTable(countfile, true);
             
                        //make sure groups are valid
                        //takes care of user setting groupNames that are invalid or setting groups=all
@@ -236,7 +274,9 @@ int CountGroupsCommand::execute(){
                 int num = ct.getGroupCount(Groups[i]);
                 total += num;
                                m->mothurOut(Groups[i] + " contains " + toString(num) + "."); m->mothurOutEndLine();
+                out << Groups[i] << '\t' << num << endl;
                        }
+            out.close();
             
             m->mothurOut("\nTotal seqs: " + toString(total) + "."); m->mothurOutEndLine();
                }
@@ -247,17 +287,33 @@ int CountGroupsCommand::execute(){
                        InputData input(sharedfile, "sharedfile");
                        vector<SharedRAbundVector*> lookup = input.getSharedRAbundVectors();
                        
+            map<string, string> variables; 
+            string thisOutputDir = outputDir;
+            if (outputDir == "") {  thisOutputDir += m->hasPath(countfile);  }
+            variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(countfile));
+            string outputFileName = getOutputFileName("summary", variables);
+            outputNames.push_back(outputFileName); outputTypes["summary"].push_back(outputFileName);
+            ofstream out;
+            m->openOutputFile(outputFileName, out);
+            
             int total = 0;
                        for (int i = 0; i < lookup.size(); i++) {
                 int num = lookup[i]->getNumSeqs();
                 total += num;
                                m->mothurOut(lookup[i]->getGroup() + " contains " + toString(num) + "."); m->mothurOutEndLine();
                                delete lookup[i];
+                out << lookup[i]->getGroup() << '\t' << num << endl;
                        }
+            out.close();
                        
             m->mothurOut("\nTotal seqs: " + toString(total) + "."); m->mothurOutEndLine();
                }
-                               
+                       
+        m->mothurOutEndLine();
+               m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+               for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }       
+               m->mothurOutEndLine();
+        
                return 0;               
        }