fixed parameter issues

diff --git a/errorchecking.cpp b/errorchecking.cpp
index 35ea56cabca2e1beefdf2d77bde419a4d7220d0a..7d63e9b5a53b77afcb277963f31418ac8bdfccd9 100644 (file)
--- a/errorchecking.cpp
+++ b/errorchecking.cpp
@@ -241,12 +241,12 @@ bool ErrorCheck::checkInput(string input) {
                }
                
                if ((commandName == "collect.single") || (commandName == "rarefaction.single") || (commandName == "summary.single") ){ 
-                       if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "")) { cout << "You must read a listfile, sabundfile or rabundfile before you can use the collect.single, rarefaction.single or summary.single commands." << endl; return false; }
+                       if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "")) { cout << "You must read a list, sabund or rabund before you can use the collect.single, rarefaction.single or summary.single commands." << endl; return false; }
                }
                
                if ((commandName == "collect.shared") || (commandName == "rarefaction.shared") || (commandName == "summary.shared") ){ 
-                       if (globaldata->getListFile() == "") { cout << "You must read a listfile and a groupfile before you can use the collect.shared, rarefaction.shared or summary.shared commands." << endl; return false; }
-                       else if (globaldata->getGroupFile() == "") { cout << "You must read a listfile and a groupfile before you can use the collect.shared, rarefaction.shared or summary.shared commands." << endl; return false; }
+                       if (globaldata->getListFile() == "") { cout << "You must read a list and a group before you can use the collect.shared, rarefaction.shared or summary.shared commands." << endl; return false; }
+                       else if (globaldata->getGroupFile() == "") { cout << "You must read a list and a group before you can use the collect.shared, rarefaction.shared or summary.shared commands." << endl; return false; }
                }
  
                
@@ -329,12 +329,12 @@ void ErrorCheck::validateReadDist() {
                ifstream filehandle;
                int ableToOpen;
                
-               if ((phylipfile == "") && (columnfile == "")) { cout << "When executing a read.dist you must enter a phylipfile or a columnfile." << endl; errorFree = false; }
-               else if ((phylipfile != "") && (columnfile != "")) { cout << "When executing a read.dist you must enter ONLY ONE of the following: phylipfile or columnfile." << endl; errorFree = false; }
+               if ((phylipfile == "") && (columnfile == "")) { cout << "When executing a read.dist you must enter a phylip or a column." << endl; errorFree = false; }
+               else if ((phylipfile != "") && (columnfile != "")) { cout << "When executing a read.dist you must enter ONLY ONE of the following: phylip or column." << endl; errorFree = false; }
                
                if (columnfile != "") {
                        if (namefile == "") {
-                               cout << "You need to provide a namefile name if you are going to use the column format." << endl;
+                               cout << "You need to provide a namefile if you are going to use the column format." << endl;
                                errorFree = false; 
                        }else {
                                ableToOpen = openInputFile(namefile, filehandle);
@@ -365,8 +365,8 @@ void ErrorCheck::validateParseFiles() {
                
                //checks for valid files
        
-               if (listfile == "") { cout << "When executing a read.list you must enter a listfile and a groupfile." << endl; errorFree = false; }
-               else if (groupfile == "") { cout << "When executing a read.list you must enter a listfile and a groupfile." << endl; errorFree = false; }
+               if (listfile == "") { cout << "When executing a read.otu for groups you must enter a list and a group." << endl; errorFree = false; }
+               else if (groupfile == "") { cout << "When executing a read.otu for groups you must enter a list and a group." << endl; errorFree = false; }
        
                //checks parameters on the read command
                if (listfile != "") {
@@ -447,15 +447,15 @@ void ErrorCheck::validateReadPhil() {
                //checks to make sure only one file type is given
                if (listfile != "") { 
                        if ((rabundfile != "") || (sabundfile != "")) { 
-                               cout << "When executing a read.otu you must enter ONLY ONE of the following: listfile, rabundfile or sabundfile." << endl; errorFree = false; }
+                               cout << "When executing a read.otu you must enter ONLY ONE of the following: list, rabund or sabund." << endl; errorFree = false; }
                }else if (rabundfile != "") { 
                        if ((listfile != "") || (sabundfile != "")) { 
-                               cout << "When executing a read.otu you must enter ONLY ONE of the following: listfile, rabundfile or sabundfile." << endl; errorFree = false; }
+                               cout << "When executing a read.otu you must enter ONLY ONE of the following: list, rabund or sabund." << endl; errorFree = false; }
                }else if (sabundfile != "") { 
                        if ((listfile != "") || (rabundfile != "")) { 
-                               cout << "When executing a read.otu you must enter ONLY ONE of the following: listfile, rabundfile or sabundfile." << endl; errorFree = false; }
+                               cout << "When executing a read.otu you must enter ONLY ONE of the following: list, rabund or sabund." << endl; errorFree = false; }
                }else if ((listfile == "") && (rabundfile == "") && (sabundfile == "")) {
-                           cout << "When executing a read.otu you must enter one of the following: listfile, rabundfile or sabundfile." << endl; errorFree = false; 
+                           cout << "When executing a read.otu you must enter one of the following: list, rabund or sabund." << endl; errorFree = false; 
                }
                
                //checks parameters on the read command

diff --git a/validparameter.cpp b/validparameter.cpp
index 10dad74017fd33627fa9df4375b8cffc32170b8b..70287c907b0d92e92c43780299603b3a05b09f02 100644 (file)
--- a/validparameter.cpp
+++ b/validparameter.cpp
@@ -14,15 +14,15 @@
 ValidParameters::ValidParameters() {
        try {
        
-               parameters["phylip"]                    = "phylip";
-               parameters["columnfile"]                = "columnfile";
-               parameters["listfile"]                  = "listfile"; 
-               parameters["rabundfile"]                = "rabundfile"; 
-               parameters["sabundfile"]                = "sabundfile"; 
-               parameters["namefile"]                  = "namefile"; 
-               parameters["groupfile"]                 = "groupfile"; 
-               parameters["orderfile"]                 = "orderfile"; 
-               parameters["fastafile"]                 = "fastafile"; 
+               parameters["phylip"]            = "phylip";
+               parameters["column"]            = "column";
+               parameters["list"]                      = "list"; 
+               parameters["rabund"]            = "rabund"; 
+               parameters["sabund"]            = "sabund"; 
+               parameters["name"]                      = "name"; 
+               parameters["group"]                     = "group"; 
+               parameters["order"]                     = "order"; 
+               parameters["fasta"]                     = "fasta"; 
                parameters["treefile"]                  = "treefile";
                parameters["fileroot"]                  = "fileroot";
                parameters["cutoff"]                    = "cutoff";