removed line option

[mothur.git] / readotucommand.cpp

diff --git a/readotucommand.cpp b/readotucommand.cpp
index 999d8de95ecdda62b411e3d5fab11092d3105636..2e2bbc90baf0fbcfe9abb79b049c1cf2589edfe0 100644 (file)
--- a/readotucommand.cpp
+++ b/readotucommand.cpp
@@ -21,7 +21,7 @@ ReadOtuCommand::ReadOtuCommand(string option){
                
                else {
                        //valid paramters for this command
-                       string Array[] =  {"list","order","shared", "line", "label","group","sabund", "rabund"};
+                       string Array[] =  {"list","order","shared", "label","group","sabund", "rabund"};
                        vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                        
                        OptionParser parser(option);
@@ -77,14 +77,6 @@ ReadOtuCommand::ReadOtuCommand(string option){
                
                        //check for optional parameter and set defaults
                        // ...at some point should added some additional type checking...
-                       line = validParameter.validFile(parameters, "line", false);                             
-                       if (line == "not found") { line = ""; }
-                       else { 
-                               if(line != "all") {  splitAtDash(line, lines);  allLines = 0;  }
-                               else { allLines = 1;  }
-                               globaldata->lines = lines;
-                       }
-                       
                        label = validParameter.validFile(parameters, "label", false);                   
                        if (label == "not found") { label = ""; }
                        else { 
@@ -95,9 +87,6 @@ ReadOtuCommand::ReadOtuCommand(string option){
                        
                        globaldata->allLines = allLines;
                        
-                       //make sure user did not use both the line and label parameters
-                       if ((line != "") && (label != "")) { mothurOut("You cannot use both the line and label parameters at the same time. "); mothurOutEndLine(); abort = true; }
-                       
                        orderfile = validParameter.validFile(parameters, "order", true);
                        if (orderfile == "not open") { abort = true; }  
                        else if (orderfile == "not found") { orderfile = ""; }
@@ -123,16 +112,15 @@ void ReadOtuCommand::help(){
        try {
                mothurOut("The read.otu command must be run before you execute a collect.single, rarefaction.single, summary.single, \n");
                mothurOut("collect.shared, rarefaction.shared or summary.shared command.   Mothur will generate a .list, .rabund and .sabund upon completion of the cluster command \n");
-               mothurOut("or you may use your own. The read.otu command parameter options are list, rabund, sabund, shared, group, order, line and label.\n");
+               mothurOut("or you may use your own. The read.otu command parameter options are list, rabund, sabund, shared, group, order and label.\n");
                mothurOut("The read.otu command can be used in two ways.  The first is to read a list, rabund or sabund and run the collect.single, rarefaction.single or summary.single.\n");
                mothurOut("For this use the read.otu command should be in the following format: read.otu(list=yourListFile, order=yourOrderFile, label=yourLabels).\n");
                mothurOut("The list, rabund or sabund parameter is required, but you may only use one of them.\n");
-               mothurOut("The line and label parameters are optional but you may not use both the line and label parameters at the same time.\n");
-               mothurOut("The label and line parameters are used to read specific lines in your input.\n");
+               mothurOut("The label parameter is used to read specific labels in your input.\n");
                mothurOut("The second way to use the read.otu command is to read a list and a group, or a shared so you can use the collect.shared, rarefaction.shared or summary.shared commands.\n");
-               mothurOut("In this case the read.otu command should be in the following format: read.otu(list=yourListFile, group=yourGroupFile, line=yourLines) or read.otu(shared=yourSharedFile).  \n");
+               mothurOut("In this case the read.otu command should be in the following format: read.otu(list=yourListFile, group=yourGroupFile) or read.otu(shared=yourSharedFile).  \n");
                mothurOut("The list parameter and group paramaters or the shared paremeter is required. When using the command the second way with a list and group file read.otu command parses the .list file\n");
-               mothurOut("and separates it into groups.  It outputs a .shared file containing the OTU information for each group. The read.otu command also outputs a .list file for each group. \n");
+               mothurOut("and separates it into groups.  It outputs a .shared file containing the OTU information for each group. The read.otu command also outputs a .rabund file for each group. \n");
                mothurOut("Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListfile).\n\n");
 
        }