I've changed the listfile, sabundfile, etc. option handles to not need the "file...

diff --git a/errorchecking.cpp b/errorchecking.cpp
index 121a0120a17fb1410901a219a95d0361911d7187..6ec145b7e97341178f3821e0be1dfb6cc7e360c6 100644 (file)
--- a/errorchecking.cpp
+++ b/errorchecking.cpp
@@ -72,16 +72,16 @@ bool ErrorCheck::checkInput(string input) {
                                //is it a valid parameter
                                if (validParameter->isValidParameter(parameter) != true) { return false; }
                                
-                               if (parameter == "phylipfile" )         { phylipfile = value; }
-                               if (parameter == "columnfile" )         { columnfile = value; }
-                               if (parameter == "listfile" )           { listfile = value; }
-                               if (parameter == "rabundfile" )         { rabundfile = value; }
-                               if (parameter == "sabundfile" )         { sabundfile = value; }
-                               if (parameter == "namefile" )           { namefile = value; }
-                               if (parameter == "orderfile" )          { orderfile = value; }
-                               if (parameter == "fastafile" )          { fastafile = value; }
+                               if (parameter == "phylip" )             { phylipfile = value; }
+                               if (parameter == "column" )             { columnfile = value; }
+                               if (parameter == "list" )               { listfile = value; }
+                               if (parameter == "rabund" )             { rabundfile = value; }
+                               if (parameter == "sabund" )             { sabundfile = value; }
+                               if (parameter == "name" )               { namefile = value; }
+                               if (parameter == "order" )              { orderfile = value; }
+                               if (parameter == "fasta" )              { fastafile = value; }
                                if (parameter == "treefile" )           { treefile = value; }
-                               if (parameter == "groupfile" )          { groupfile = value; }
+                               if (parameter == "group" )              { groupfile = value; }
                                if (parameter == "cutoff" )                     { cutoff = value; }
                                if (parameter == "precision" )          { precision = value; }
                                if (parameter == "iters" )                      { iters = value; }
@@ -141,15 +141,15 @@ bool ErrorCheck::checkInput(string input) {
                                //is it a valid parameter
                                if (validParameter->isValidParameter(parameter) != true) { return false; }
                                
-                               if (parameter == "phylipfile" )         { phylipfile = value; }
-                               if (parameter == "columnfile" )         { columnfile = value; }                         
-                               if (parameter == "listfile" )           { listfile = value; }
-                               if (parameter == "rabundfile" )         { rabundfile = value; }
-                               if (parameter == "sabundfile" )         { sabundfile = value; }
-                               if (parameter == "namefile" )           { namefile = value; }
-                               if (parameter == "orderfile" )          { orderfile = value; }
-                               if (parameter == "groupfile" )          { groupfile = value; }
-                               if (parameter == "fastafile" )          { fastafile = value; }
+                               if (parameter == "phylip" )             { phylipfile = value; }
+                               if (parameter == "column" )             { columnfile = value; }                         
+                               if (parameter == "list" )               { listfile = value; }
+                               if (parameter == "rabund" )             { rabundfile = value; }
+                               if (parameter == "sabund" )             { sabundfile = value; }
+                               if (parameter == "name" )               { namefile = value; }
+                               if (parameter == "order" )              { orderfile = value; }
+                               if (parameter == "group" )              { groupfile = value; }
+                               if (parameter == "fasta" )              { fastafile = value; }
                                if (parameter == "treefile" )           { treefile = value; }
                                if (parameter == "cutoff" )                     { cutoff = value; }
                                if (parameter == "precision" )          { precision = value; }

diff --git a/globaldata.cpp b/globaldata.cpp
index 87f1ccae776b9e435c00189ed63317e1595cc374..713ae9af7346dbcdffe38e3f38f9f93b1129984d 100644 (file)
--- a/globaldata.cpp
+++ b/globaldata.cpp
@@ -97,16 +97,16 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                                splitAtComma(value, optionText);
                                splitAtEquals(key, value);
                                
-                               if (key == "phylipfile" )       { phylipfile = value; inputFileName = value; fileroot = value; format = "phylip";       }
-                               if (key == "columnfile" )       { columnfile = value; inputFileName = value; fileroot = value; format = "column";       }
-                               if (key == "listfile" )         { listfile = value; inputFileName = value; fileroot = value; format = "list";           }
-                               if (key == "rabundfile" )       { rabundfile = value; inputFileName = value; fileroot = value; format = "rabund";       }
-                               if (key == "sabundfile" )       { sabundfile = value; inputFileName = value; fileroot = value; format = "sabund";       } 
-                               if (key == "fastafile" )        { fastafile = value; inputFileName = value; fileroot = value; format = "fasta";         } 
+                               if (key == "phylip" )   { phylipfile = value; inputFileName = value; fileroot = value; format = "phylip";       }
+                               if (key == "column" )   { columnfile = value; inputFileName = value; fileroot = value; format = "column";       }
+                               if (key == "list" )             { listfile = value; inputFileName = value; fileroot = value; format = "list";           }
+                               if (key == "rabund" )   { rabundfile = value; inputFileName = value; fileroot = value; format = "rabund";       }
+                               if (key == "sabund" )   { sabundfile = value; inputFileName = value; fileroot = value; format = "sabund";       } 
+                               if (key == "fasta" )    { fastafile = value; inputFileName = value; fileroot = value; format = "fasta";         } 
                                if (key == "treefile" )         { treefile = value; inputFileName = value; fileroot = value; format = "tree";           }
-                               if (key == "namefile" )         { namefile = value;             }
-                               if (key == "orderfile" )        { orderfile = value;    }
-                               if (key == "groupfile" )        { groupfile = value;    }
+                               if (key == "name" )             { namefile = value;             }
+                               if (key == "order" )    { orderfile = value;    }
+                               if (key == "group" )    { groupfile = value;    }
                                if (key == "cutoff" )           { cutoff = value;               }
                                if (key == "precision" )        { precision = value;    }
                                if (key == "iters" )            { iters = value;                }
@@ -162,16 +162,16 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                        //saves the last parameter
                        value = optionText;
                        splitAtEquals(key, value);
-                       if (key == "phylipfile" )       { phylipfile = value; inputFileName = value; fileroot = value; format = "phylip";       }
-                       if (key == "columnfile" )       { columnfile = value; inputFileName = value; fileroot = value; format = "column";       }
-                       if (key == "listfile" )         { listfile = value; inputFileName = value; fileroot = value; format = "list";           }
-                       if (key == "rabundfile" )       { rabundfile = value; inputFileName = value; fileroot = value; format = "rabund";       }
-                       if (key == "sabundfile" )       { sabundfile = value; inputFileName = value; fileroot = value; format = "sabund";       }
-                       if (key == "fastafile" )        { fastafile = value; inputFileName = value; fileroot = value; format = "fasta";         }
+                       if (key == "phylip" )   { phylipfile = value; inputFileName = value; fileroot = value; format = "phylip";       }
+                       if (key == "column" )   { columnfile = value; inputFileName = value; fileroot = value; format = "column";       }
+                       if (key == "list" )             { listfile = value; inputFileName = value; fileroot = value; format = "list";           }
+                       if (key == "rabund" )   { rabundfile = value; inputFileName = value; fileroot = value; format = "rabund";       }
+                       if (key == "sabund" )   { sabundfile = value; inputFileName = value; fileroot = value; format = "sabund";       }
+                       if (key == "fasta" )    { fastafile = value; inputFileName = value; fileroot = value; format = "fasta";         }
                        if (key == "treefile" )         { treefile = value; inputFileName = value; fileroot = value; format = "tree";           }  
-                       if (key == "namefile" )         { namefile = value;             }
-                       if (key == "orderfile" )        { orderfile = value;    }
-                       if (key == "groupfile" )        { groupfile = value;    }
+                       if (key == "name" )             { namefile = value;             }
+                       if (key == "order" )    { orderfile = value;    }
+                       if (key == "group" )    { groupfile = value;    }
                        if (key == "cutoff" )           { cutoff = value;               }
                        if (key == "precision" )        { precision = value;    }
                        if (key == "iters" )            { iters = value;                }

diff --git a/helpcommand.cpp b/helpcommand.cpp
index 565d742a0fda164d559be4315b0e114a01050211..0d9bdcd177c52fb5f971a44c2a9b16f04abed8a2 100644 (file)
--- a/helpcommand.cpp
+++ b/helpcommand.cpp
@@ -24,12 +24,12 @@ int HelpCommand::execute(){
        globaldata = GlobalData::getInstance();
        
        if (globaldata->helpRequest == "read.dist") {
-               cout << "The read.dist command parameter options are phylipfile or columnfile, namefile, cutoff and precision" << "\n";
+               cout << "The read.dist command parameter options are phylip or column, name, cutoff and precision" << "\n";
                cout << "The read.dist command should be in the following format: " << "\n";
-               cout << "read.dist(phylipfile=yourDistFile, namefile=yourNameFile, cutoff=yourCutoff, precision=yourPrecision) " << "\n";
-               cout << "The phylipfile or columnfile parameter is required, but only one may be used.  If you use a columnfile the namefile is required. " << "\n";
+               cout << "read.dist(phylip=yourDistFile, name=yourNameFile, cutoff=yourCutoff, precision=yourPrecision) " << "\n";
+               cout << "The phylip or column parameter is required, but only one may be used.  If you use a column file the name filename is required. " << "\n";
                cout << "If you do not provide a cutoff value 10.00 is assumed. If you do not provide a precision value then 100 is assumed." << "\n";
-               cout << "Note: No spaces between parameter labels (i.e. distfile), '=' and parameters (i.e.yourDistfile)." << "\n" << "\n";
+               cout << "Note: No spaces between parameter labels (i.e. dist), '=' and parameters (i.e.yourDistfile)." << "\n" << "\n";
        }else if (globaldata->helpRequest == "read.otu") {
                cout << "The read.otu command parameter options are listfile, rabundfile, sabundfile or orderfile." << "\n";
                cout << "The read.otu command should be in the following format: " << "\n";

diff --git a/validparameter.cpp b/validparameter.cpp
index 13976a4eb8955347cf42db74dc957fd8b329bf1e..10dad74017fd33627fa9df4375b8cffc32170b8b 100644 (file)
--- a/validparameter.cpp
+++ b/validparameter.cpp
@@ -14,7 +14,7 @@
 ValidParameters::ValidParameters() {
        try {
        
-               parameters["phylipfile"]                = "phylipfile";
+               parameters["phylip"]                    = "phylip";
                parameters["columnfile"]                = "columnfile";
                parameters["listfile"]                  = "listfile"; 
                parameters["rabundfile"]                = "rabundfile";