sffinfo bug with flow grams right index when clipQualRight=0

[mothur.git] / summarytaxcommand.cpp

diff --git a/summarytaxcommand.cpp b/summarytaxcommand.cpp
index e932eee49c2477de737caf62d143a5140aea4340..c76f175b047ef9ee46eff28911c1a21cd6310a97 100644 (file)
--- a/summarytaxcommand.cpp
+++ b/summarytaxcommand.cpp
@@ -13,13 +13,13 @@
 //**********************************************************************************************************************
 vector<string> SummaryTaxCommand::setParameters(){     
        try {
-               CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptaxonomy);
-        CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none",false,false); parameters.push_back(pname);
-        CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none",false,false); parameters.push_back(pcount);
-               CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none",false,false); parameters.push_back(pgroup);
-               CommandParameter preftaxonomy("reftaxonomy", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(preftaxonomy);
-               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+               CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "none","summary",false,true,true); parameters.push_back(ptaxonomy);
+        CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none","",false,false,true); parameters.push_back(pname);
+        CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none","",false,false,true); parameters.push_back(pcount);
+               CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none","",false,false,true); parameters.push_back(pgroup);
+               CommandParameter preftaxonomy("reftaxonomy", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(preftaxonomy);
+               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);          }
@@ -51,24 +51,19 @@ string SummaryTaxCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
-string SummaryTaxCommand::getOutputFileNameTag(string type, string inputName=""){      
-       try {
-        string outputFileName = "";
-               map<string, vector<string> >::iterator it;
+string SummaryTaxCommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
         
-        //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 == "summary")            {   outputFileName =  "tax.summary";   }
-            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, "SummaryTaxCommand", "getOutputFileNameTag");
-               exit(1);
-       }
+        if (type == "summary") {  pattern = "[filename],tax.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, "SummaryTaxCommand", "getOutputPattern");
+        exit(1);
+    }
 }
 //**********************************************************************************************************************
 SummaryTaxCommand::SummaryTaxCommand(){        
@@ -277,13 +272,15 @@ int SummaryTaxCommand::execute(){
                                }
                        }
                        in.close();
-               }
+               }else { numSeqs = taxaSum->summarize(taxfile);  }
                
                if (m->control_pressed) {  if (groupMap != NULL) { delete groupMap; } if (ct != NULL) { delete ct; } delete taxaSum; return 0; }
                
                //print summary file
                ofstream outTaxTree;
-               string summaryFile = outputDir + m->getRootName(m->getSimpleName(taxfile)) + getOutputFileNameTag("summary");
+        map<string, string> variables; 
+               variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(taxfile));
+               string summaryFile = getOutputFileName("summary",variables);
                m->openOutputFile(summaryFile, outTaxTree);
                taxaSum->print(outTaxTree);
                outTaxTree.close();
@@ -296,7 +293,7 @@ int SummaryTaxCommand::execute(){
                m->mothurOutEndLine();
                m->mothurOut("It took " + toString(time(NULL) - start) + " secs to create the summary file for " + toString(numSeqs) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
                m->mothurOutEndLine();
-               m->mothurOut("Output File Name: "); m->mothurOutEndLine();
+               m->mothurOut("Output File Names: "); m->mothurOutEndLine();
                m->mothurOut(summaryFile); m->mothurOutEndLine();       outputNames.push_back(summaryFile); outputTypes["summary"].push_back(summaryFile);
                m->mothurOutEndLine();