finishing the container classes, combining read.otu and read.list commands. some...

[mothur.git] / globaldata.cpp

diff --git a/globaldata.cpp b/globaldata.cpp
index 6d67d0da0fd41c2978a073a5f377746331b0d9a6..f09ea358b61c3e30b6880937a9f606969bfca63b 100644 (file)
--- a/globaldata.cpp
+++ b/globaldata.cpp
@@ -96,22 +96,22 @@ 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 == "namefile" )         { namefile = value; }
-                               if (key == "orderfile" )        { orderfile = value; }
-                               if (key == "groupfile" )        { groupfile = value; }
-                               if (key == "cutoff" )           { cutoff = value; }
-                               if (key == "precision" )        { precision = value; }
-                               if (key == "iters" )            { iters = value; }
-                               if (key == "jumble" )           { jumble = value; }
-                               if (key == "freq" )                     { freq = value; }
-                               if (key == "method" )           { method = value; }
-                               if (key == "fileroot" )         { fileroot = 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 == "namefile" )         { namefile = value;             }
+                               if (key == "orderfile" )        { orderfile = value;    }
+                               if (key == "groupfile" )        { groupfile = value;    }
+                               if (key == "cutoff" )           { cutoff = value;               }
+                               if (key == "precision" )        { precision = value;    }
+                               if (key == "iters" )            { iters = value;                }
+                               if (key == "jumble" )           { jumble = value;               }
+                               if (key == "freq" )                     { freq = value;                 }
+                               if (key == "method" )           { method = value;               }
+                               if (key == "fileroot" )         { fileroot = value;             }
                                
                                if (key == "single") {//stores estimators in a vector
                                        singleEstimators.clear(); //clears out old values
@@ -160,22 +160,22 @@ 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 == "namefile" )         { namefile = value; }
-                       if (key == "orderfile" )        { orderfile = value; }
-                       if (key == "groupfile" )        { groupfile = value; }
-                       if (key == "cutoff" )           { cutoff = value; }
-                       if (key == "precision" )        { precision = value; }
-                       if (key == "iters" )            { iters = value; }
-                       if (key == "jumble" )           { jumble = value; }
-                       if (key == "freq" )                     { freq = value; }
-                       if (key == "method" )           { method = value; }
-                       if (key == "fileroot" )         { fileroot = 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 == "namefile" )         { namefile = value;             }
+                       if (key == "orderfile" )        { orderfile = value;    }
+                       if (key == "groupfile" )        { groupfile = value;    }
+                       if (key == "cutoff" )           { cutoff = value;               }
+                       if (key == "precision" )        { precision = value;    }
+                       if (key == "iters" )            { iters = value;                }
+                       if (key == "jumble" )           { jumble = value;               }
+                       if (key == "freq" )                     { freq = value;                 }
+                       if (key == "method" )           { method = value;               }
+                       if (key == "fileroot" )         { fileroot = value;             }
 
                        if (key == "single") {//stores estimators in a vector
                                singleEstimators.clear(); //clears out old values
@@ -222,6 +222,8 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                        }
                }
                
+               //set format for shared
+               if ((listfile != "") && (groupfile != "")) { format = "shared"; }
                                
                //input defaults
                if (commandString == "collect.single") {
@@ -322,8 +324,8 @@ void GlobalData::clear() {
        fileroot                =       "";
        single                  =       "sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson-rarefraction";
        rarefaction             =       "rarefaction";
-       shared                  =       "sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN";
-       sharedsummary   =   "sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN";
+       shared                  =       "sharedSobs-sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN";
+       sharedsummary   =   "sharedSobs-sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN";
        summary                 =       "summary-chao-ace-jack-bootstrap-shannon-npshannon-simpson";
        sharedrarefaction = "sharedobserved";
 }