fixed bug in phylo.diversity rooting. added filename patterns and create filename...

[mothur.git] / listotulabelscommand.cpp

diff --git a/listotulabelscommand.cpp b/listotulabelscommand.cpp
index 4a12197b9f21534173c92f6d99c389a3aabb907f..e50196bec8bdb8e22004561df9537648d529514d 100644 (file)
--- a/listotulabelscommand.cpp
+++ b/listotulabelscommand.cpp
@@ -12,13 +12,13 @@
 //**********************************************************************************************************************
 vector<string> ListOtuLabelsCommand::setParameters(){  
        try {
-        CommandParameter pshared("shared", "InputTypes", "", "", "SharedRel", "SharedRel", "none",false,false); parameters.push_back(pshared);
-               CommandParameter prelabund("relabund", "InputTypes", "", "", "SharedRel", "SharedRel", "none",false,false); parameters.push_back(prelabund);
-        CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
-               CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
+        CommandParameter pshared("shared", "InputTypes", "", "", "SharedRel", "SharedRel", "none","otulabels",false,false,true); parameters.push_back(pshared);
+               CommandParameter prelabund("relabund", "InputTypes", "", "", "SharedRel", "SharedRel", "none","otulabels",false,false); parameters.push_back(prelabund);
+        CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+               CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
         //every command must have inputdir and outputdir.  This allows mothur users to redirect input and output files.
-               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+               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);          }
@@ -47,26 +47,20 @@ string ListOtuLabelsCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
-string ListOtuLabelsCommand::getOutputFileNameTag(string type, string inputName=""){   
-       try {
-        string outputFileName = "";
-               map<string, vector<string> >::iterator it;
+string ListOtuLabelsCommand::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 == "otulabels")             {   outputFileName =  "otulabels";       }
-            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, "ListOtuLabelsCommand", "getOutputFileNameTag");
-               exit(1);
-       }
+        if (type == "otulabels") {  pattern = "[filename],[distance],otulabels"; } 
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "ListOtuLabelsCommand", "getOutputPattern");
+        exit(1);
+    }
 }
-
 //**********************************************************************************************************************
 ListOtuLabelsCommand::ListOtuLabelsCommand(){  
        try {
@@ -365,7 +359,10 @@ int ListOtuLabelsCommand::execute(){
 int ListOtuLabelsCommand::createList(vector<SharedRAbundVector*>& lookup){
        try {
         
-        string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputFileName)) + lookup[0]->getLabel() + "." + getOutputFileNameTag("otulabels");
+        map<string, string> variables; 
+        variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputFileName));
+        variables["[distance]"] = lookup[0]->getLabel();
+        string outputFileName = getOutputFileName("otulabels",variables);
         outputNames.push_back(outputFileName);  outputTypes["otulabels"].push_back(outputFileName);
                ofstream out;
                m->openOutputFile(outputFileName, out);
@@ -386,8 +383,10 @@ int ListOtuLabelsCommand::createList(vector<SharedRAbundVector*>& lookup){
 
 int ListOtuLabelsCommand::createList(vector<SharedRAbundFloatVector*>& lookup){
        try {
-        
-        string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputFileName)) + lookup[0]->getLabel() + "." + getOutputFileNameTag("otulabels");
+        map<string, string> variables; 
+        variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputFileName));
+        variables["[distance]"] = lookup[0]->getLabel();
+        string outputFileName = getOutputFileName("otulabels",variables);
         outputNames.push_back(outputFileName);  outputTypes["accnos"].push_back(outputFileName);
                ofstream out;
                m->openOutputFile(outputFileName, out);