fixes while testing

[mothur.git] / readotucommand.cpp

diff --git a/readotucommand.cpp b/readotucommand.cpp
index 5b9cde8c84b10e0d4f6dd938dbf68191000930f4..8683fc3fa80154729ea5228fcaa38fb03726603a 100644 (file)
--- a/readotucommand.cpp
+++ b/readotucommand.cpp
@@ -9,6 +9,55 @@
 
 #include "readotucommand.h"
 
+//**********************************************************************************************************************
+vector<string> ReadOtuCommand::getValidParameters(){   
+       try {
+               string Array[] =  {"list","order","shared","relabund","label","group","sabund", "rabund","groups","ordergroup","outputdir","inputdir"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ReadOtuCommand", "getValidParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+ReadOtuCommand::ReadOtuCommand(){      
+       try {
+               abort = true;
+               //initialize outputTypes
+               vector<string> tempOutNames;
+               outputTypes["rabund"] = tempOutNames;
+               outputTypes["shared"] = tempOutNames;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ReadOtuCommand", "ReadOtuCommand");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> ReadOtuCommand::getRequiredParameters(){        
+       try {
+               string Array[] =  {"list","shared","relabund","sabund","rabund","or"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ChopSeqsCommand", "getRequiredParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> ReadOtuCommand::getRequiredFiles(){     
+       try {
+               vector<string> myArray;
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ReadOtuCommand", "getRequiredFiles");
+               exit(1);
+       }
+}
 //**********************************************************************************************************************
 ReadOtuCommand::ReadOtuCommand(string option)  {
        try {
@@ -34,7 +83,12 @@ ReadOtuCommand::ReadOtuCommand(string option)  {
                        for (it = parameters.begin(); it != parameters.end(); it++) { 
                                if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
                        }
-       
+                       
+                       //initialize outputTypes
+                       vector<string> tempOutNames;
+                       outputTypes["rabund"] = tempOutNames;
+                       outputTypes["shared"] = tempOutNames;
+                       
                        globaldata->newRead();
                        
                        //if the user changes the input directory command factory will send this info to us in the output parameter 
@@ -45,7 +99,7 @@ ReadOtuCommand::ReadOtuCommand(string option)  {
                                it = parameters.find("list");
                                //user has given a template file
                                if(it != parameters.end()){ 
-                                       path = hasPath(it->second);
+                                       path = m->hasPath(it->second);
                                        //if the user has not given a path then, add inputdir. else leave path alone.
                                        if (path == "") {       parameters["list"] = inputDir + it->second;             }
                                }
@@ -53,7 +107,7 @@ ReadOtuCommand::ReadOtuCommand(string option)  {
                                it = parameters.find("order");
                                //user has given a template file
                                if(it != parameters.end()){ 
-                                       path = hasPath(it->second);
+                                       path = m->hasPath(it->second);
                                        //if the user has not given a path then, add inputdir. else leave path alone.
                                        if (path == "") {       parameters["order"] = inputDir + it->second;            }
                                }
@@ -61,7 +115,7 @@ ReadOtuCommand::ReadOtuCommand(string option)  {
                                it = parameters.find("shared");
                                //user has given a template file
                                if(it != parameters.end()){ 
-                                       path = hasPath(it->second);
+                                       path = m->hasPath(it->second);
                                        //if the user has not given a path then, add inputdir. else leave path alone.
                                        if (path == "") {       parameters["shared"] = inputDir + it->second;           }
                                }
@@ -69,7 +123,7 @@ ReadOtuCommand::ReadOtuCommand(string option)  {
                                it = parameters.find("group");
                                //user has given a template file
                                if(it != parameters.end()){ 
-                                       path = hasPath(it->second);
+                                       path = m->hasPath(it->second);
                                        //if the user has not given a path then, add inputdir. else leave path alone.
                                        if (path == "") {       parameters["group"] = inputDir + it->second;            }
                                }
@@ -77,7 +131,7 @@ ReadOtuCommand::ReadOtuCommand(string option)  {
                                it = parameters.find("sabund");
                                //user has given a template file
                                if(it != parameters.end()){ 
-                                       path = hasPath(it->second);
+                                       path = m->hasPath(it->second);
                                        //if the user has not given a path then, add inputdir. else leave path alone.
                                        if (path == "") {       parameters["sabund"] = inputDir + it->second;           }
                                }
@@ -85,7 +139,7 @@ ReadOtuCommand::ReadOtuCommand(string option)  {
                                it = parameters.find("rabund");
                                //user has given a template file
                                if(it != parameters.end()){ 
-                                       path = hasPath(it->second);
+                                       path = m->hasPath(it->second);
                                        //if the user has not given a path then, add inputdir. else leave path alone.
                                        if (path == "") {       parameters["rabund"] = inputDir + it->second;           }
                                }
@@ -93,7 +147,7 @@ ReadOtuCommand::ReadOtuCommand(string option)  {
                                it = parameters.find("ordergroup");
                                //user has given a template file
                                if(it != parameters.end()){ 
-                                       path = hasPath(it->second);
+                                       path = m->hasPath(it->second);
                                        //if the user has not given a path then, add inputdir. else leave path alone.
                                        if (path == "") {       parameters["ordergroup"] = inputDir + it->second;               }
                                }
@@ -101,7 +155,7 @@ ReadOtuCommand::ReadOtuCommand(string option)  {
                                it = parameters.find("relabund");
                                //user has given a template file
                                if(it != parameters.end()){ 
-                                       path = hasPath(it->second);
+                                       path = m->hasPath(it->second);
                                        //if the user has not given a path then, add inputdir. else leave path alone.
                                        if (path == "") {       parameters["relabund"] = inputDir + it->second;         }
                                }
@@ -159,7 +213,7 @@ ReadOtuCommand::ReadOtuCommand(string option)  {
                        groups = validParameter.validFile(parameters, "groups", false);                 
                        if (groups == "not found") { groups = ""; }
                        else { 
-                               splitAtDash(groups, Groups);
+                               m->splitAtDash(groups, Groups);
                                globaldata->Groups = Groups;
                        }
 
@@ -176,7 +230,7 @@ ReadOtuCommand::ReadOtuCommand(string option)  {
                        label = validParameter.validFile(parameters, "label", false);                   
                        if (label == "not found") { label = ""; }
                        else { 
-                               if(label != "all") {  splitAtDash(label, labels);  allLines = 0;  }
+                               if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
                                else { allLines = 1;  }
                                globaldata->labels = labels;
                        }
@@ -255,6 +309,8 @@ int ReadOtuCommand::execute(){
                                //m->mothurOutEndLine();
                        }
                        
+                       outputTypes = shared->getOutputFiles();
+                       
                        delete shared;
                }
                return 0;